Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold20
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 119540
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Found at i:3982 original size:9 final size:9
Alignment explanation
Indices: 3875--3981 Score: 151
Period size: 9 Copynumber: 11.9 Consensus size: 9
3865 CTCGACCTTT
*
3875 TCCTTCTTT
1 TCCTTCTTG
3884 TCCTTCTTG
1 TCCTTCTTG
* *
3893 TCTTTCTTT
1 TCCTTCTTG
*
3902 TCCTTCTTC
1 TCCTTCTTG
*
3911 TCCTTCTTT
1 TCCTTCTTG
3920 TCCTTCTTG
1 TCCTTCTTG
3929 TCCTTCTTG
1 TCCTTCTTG
3938 TCCTTCTTG
1 TCCTTCTTG
3947 TCCTTCTTG
1 TCCTTCTTG
*
3956 TCCTTCTTC
1 TCCTTCTTG
*
3965 TCCTTCTTC
1 TCCTTCTTG
3974 TCCTTCTT
1 TCCTTCTT
3982 CACCCGCTTC
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 90 1.00
ACGTcount: A:0.00, C:0.36, G:0.05, T:0.60
Consensus pattern (9 bp):
TCCTTCTTG
Left flanking sequence: Indices 3375 -- 3874
ATCTTTTGATCTGGTCGTCCTTGGACACACCACCGTAAACGGCGACACACTCAATAGAGGTGCCC
TGGGTGAGGGTGACAAGGTTGTCGTAAATTTGCATGGCCAACTCACGCGTGGGGGAGATAGCCAT
CACCAGCAAACCCTTCTTCTTCAGCTCCAAAATGGCGTTGATGGCGGGGACACCAAAGGCGAAGG
TTTTACCCGACCCAGTCTCAGCAACACCAATGACGTCCTTACCGGCCAACAAGTAGGGCCAGGCA
ACAGCCTGAATGGGAGTGGGCTTGCTGAACCGCTTAAGGGCATCGGAAACCTTAGGGTTGAGGGT
CACCTGCGAGAACGACAAAAGCGGTCTCAACTTGGTCTGGGTGTCGTCAACGCTAACCTCGTTCT
CCTTGAGGAAAGCGTCAATATCCAGCTGGGGCAACGCAGCCAATTCAGCCAGCTCGACGTAACCC
AGCGCCAGGCTCAGGGTGTGTTCAGGCTCGGAGTGCTCGACCTTT
Right flanking sequence: Indices 3982 -- 4481
CACCCGCTTCTCATCCTTAGATTCTTCTCTATCGCGTTTACCCATCTTTACCTGGTTTGTATGGT
CGTTAGATGCGCATCCTTGACATGTTGAAAAATTCCTATGCAGGCTCGCGATGAGCACAACGGGG
ACTCGAGCCAAATTGCATGAGCATGAGTGAGGGTACGGGTAACTACCAAAACTTGAAATTTTAGG
GGCCAACTAAGAGAAGAAGACGGGGACTACTAAATACCACAAAGTCAAAGTATACTGAGACGTAA
AATTTCAAACCTTCATTACGATGAAGCCTTCGACTAGCATTTCTATGGCCTGGAGGATACCTTGT
GGTCGCTTATCGAAGTCCAAGTTTTCAACACTCAAGCGAGATCACGGGTGCCAGTCTCAACGCAA
TCAAACAGAGCTTTGAAACGGTAGAAAGTTACAAATACAGCCGGGAACTCGTCTCTTTGGACCTC
TCACCAGCTGACTTTAAGTCAGGTTTTGACGATATGACCACATAT
Found at i:16825 original size:24 final size:24
Alignment explanation
Indices: 16795--17062 Score: 218
Period size: 24 Copynumber: 11.3 Consensus size: 24
16785 TTGCGGGGCC
*
16795 CCAAACGAGGGCTGAGGAGCCTGG
1 CCAAACGACGGCTGAGGAGCCTGG
* *
16819 CCAAACGACGGTTGCGGAGCCTGG
1 CCAAACGACGGCTGAGGAGCCTGG
* * *
16843 CCAAAGGAAGGCTGGGGAGCCTGG
1 CCAAACGACGGCTGAGGAGCCTGG
* *
16867 CCAAATGACGGCTGGGGAGCCTGG
1 CCAAACGACGGCTGAGGAGCCTGG
* *
16891 CCAAACGACGGCTGGGGAGCCTGT
1 CCAAACGACGGCTGAGGAGCCTGG
* * *
16915 CCGAACGACGGCTGAGGGGCCTGC
1 CCAAACGACGGCTGAGGAGCCTGG
* * *
16939 CCAAACGAGGGTTGAGGAGCCTGT
1 CCAAACGACGGCTGAGGAGCCTGG
* * * * *
16963 CCGAACGACGGCTGCGGCGCTTGA
1 CCAAACGACGGCTGAGGAGCCTGG
* ** *** **
16987 CCAAAC--TGGCCAAACTGCC-CA
1 CCAAACGACGGCTGAGGAGCCTGG
*
17008 CCAAACGACGGCTGGGGAGCCTGG
1 CCAAACGACGGCTGAGGAGCCTGG
* * *
17032 CCAAACGACGGTTGCGGGGCCTGG
1 CCAAACGACGGCTGAGGAGCCTGG
17056 CCAAACG
1 CCAAACG
17063 GCTGCTGACC
Statistics
Matches: 192, Mismatches: 49, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
21 7 0.04
22 5 0.03
23 6 0.03
24 174 0.91
ACGTcount: A:0.22, C:0.29, G:0.38, T:0.11
Consensus pattern (24 bp):
CCAAACGACGGCTGAGGAGCCTGG
Left flanking sequence: Indices 16295 -- 16794
TGCGATGAGATGTGCTATTTTCCAGGGCGGGTACCTGCTCCCTGTGTGGTGGACACGAACTGCGT
GGTGCGGCTAGTGGACCAGGTGATCTGAGGGTCTAAAGCGGTCCGCCATTCGGTAAAGCGGTCTA
GTCGTGCTTCTCAACGTAAATGTGTCCCTATACCACTTCAACTACGCCGACCGCTCTCTTGCCCA
ATGCACTATCCCACTTTTTTGCTGTCCCCACCACCGTAAAATCCATCTGTCTGATTCGGTGCATT
AGTGGTGCTTATCATTGAGTGTCGTATTTCTATAATCGCTTCACAGCTATGCGGATCCTAAACTA
GAAACCAAACGGGTTGTCTGGGGTGGCTGCCGCCAAGTTGGCTCGGCTGGCCCCGGTCTGTTGCA
GTTGCATGGGCGAGTTACCGAATCCCAACCCGGTGGGCTGCGATTGGAGAGGAGCTCCACCTCCA
AACCCTTCAAACGAGGGCTGGCCACCAAAGGTGGTTTGCGGGGCC
Right flanking sequence: Indices 17063 -- 17562
GCTGCTGACCGAATGGCTGGTCCTGGCCACCGAGCGACGTCTGGCCAAACTGGTTCGTCATCTGG
TTCATCTGGGCGTTGAACGGCTGCCCGGGCTGCTGGCCGGTTTGCAACGAGTTGGGCGAGTTCAT
GAAGCCGCCCGTGATCTGCTTACCAAACGACAGCTGCGGCACGAACGCGTTGCCAATGCCACCCG
TGGTCGACGCCTGCATGGGCTGGGTCTGGTTTTGCTGGCCCTGCTGGTTCTGGCCCGTTCCGTTC
AGGCCCTGGCCCATCTGCGCCATCTGCTGCTGAGACGCGGGCTGCCACGGCATCACCGGGTTGCC
GGTGGACTGGCCCACCTGGCCCGTGCCAAACTGCGGCATCTGGGGCATCTGGGCGGGACCAGTGC
CAAACTGCGGCATCTGACCGGTGCCAAACTGAGGCATCAGGCCCCCGGTAGGCTGGCCTCCGGTC
CGCTGGGTCGGCACCAACGGACCCGTCTTCTGCAACGACAACCCC
Found at i:16871 original size:72 final size:72
Alignment explanation
Indices: 16794--17062 Score: 251
Period size: 72 Copynumber: 3.8 Consensus size: 72
16784 TTTGCGGGGC
* *
16794 CCCAAACGAGGGCTGAGGAGCCTGGCCAAACGACGGTTGCGGAGCCTGGCCAAAGGAAGGCTG-G
1 CCCAAACGAGGGCTGAGGAGCCTGGCCAAACGACGGCTGCGGAGCCTGGCCAAACGAAGGCTGAG
16858 GGAGCCTG
66 GG-GCCTG
* * * * * * * *
16866 GCCAAATGACGGCTGGGGAGCCTGGCCAAACGACGGCTGGGGAGCCTGTCCGAACGACGGCTGAG
1 CCCAAACGAGGGCTGAGGAGCCTGGCCAAACGACGGCTGCGGAGCCTGGCCAAACGAAGGCTGAG
16931 GGGCCTG
66 GGGCCTG
* * * * * * * ** *
16938 CCCAAACGAGGGTTGAGGAGCCTGTCCGAACGACGGCTGCGGCGCTTGACCAAAC--TGGCCAAA
1 CCCAAACGAGGGCTGAGGAGCCTGGCCAAACGACGGCTGCGGAGCCTGGCCAAACGAAGGCTGAG
**
17001 CTGCC--
66 GGGCCTG
* * * *
17006 CACCAAACGACGGCTGGGGAGCCTGGCCAAACGACGGTTGCGGGGCCTGGCCAAACG
1 C-CCAAACGAGGGCTGAGGAGCCTGGCCAAACGACGGCTGCGGAGCCTGGCCAAACG
17063 GCTGCTGACC
Statistics
Matches: 157, Mismatches: 37, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
68 1 0.01
69 45 0.29
70 7 0.04
72 101 0.64
73 3 0.02
ACGTcount: A:0.22, C:0.29, G:0.38, T:0.11
Consensus pattern (72 bp):
CCCAAACGAGGGCTGAGGAGCCTGGCCAAACGACGGCTGCGGAGCCTGGCCAAACGAAGGCTGAG
GGGCCTG
Left flanking sequence: Indices 16294 -- 16793
TTGCGATGAGATGTGCTATTTTCCAGGGCGGGTACCTGCTCCCTGTGTGGTGGACACGAACTGCG
TGGTGCGGCTAGTGGACCAGGTGATCTGAGGGTCTAAAGCGGTCCGCCATTCGGTAAAGCGGTCT
AGTCGTGCTTCTCAACGTAAATGTGTCCCTATACCACTTCAACTACGCCGACCGCTCTCTTGCCC
AATGCACTATCCCACTTTTTTGCTGTCCCCACCACCGTAAAATCCATCTGTCTGATTCGGTGCAT
TAGTGGTGCTTATCATTGAGTGTCGTATTTCTATAATCGCTTCACAGCTATGCGGATCCTAAACT
AGAAACCAAACGGGTTGTCTGGGGTGGCTGCCGCCAAGTTGGCTCGGCTGGCCCCGGTCTGTTGC
AGTTGCATGGGCGAGTTACCGAATCCCAACCCGGTGGGCTGCGATTGGAGAGGAGCTCCACCTCC
AAACCCTTCAAACGAGGGCTGGCCACCAAAGGTGGTTTGCGGGGC
Right flanking sequence: Indices 17063 -- 17562
GCTGCTGACCGAATGGCTGGTCCTGGCCACCGAGCGACGTCTGGCCAAACTGGTTCGTCATCTGG
TTCATCTGGGCGTTGAACGGCTGCCCGGGCTGCTGGCCGGTTTGCAACGAGTTGGGCGAGTTCAT
GAAGCCGCCCGTGATCTGCTTACCAAACGACAGCTGCGGCACGAACGCGTTGCCAATGCCACCCG
TGGTCGACGCCTGCATGGGCTGGGTCTGGTTTTGCTGGCCCTGCTGGTTCTGGCCCGTTCCGTTC
AGGCCCTGGCCCATCTGCGCCATCTGCTGCTGAGACGCGGGCTGCCACGGCATCACCGGGTTGCC
GGTGGACTGGCCCACCTGGCCCGTGCCAAACTGCGGCATCTGGGGCATCTGGGCGGGACCAGTGC
CAAACTGCGGCATCTGACCGGTGCCAAACTGAGGCATCAGGCCCCCGGTAGGCTGGCCTCCGGTC
CGCTGGGTCGGCACCAACGGACCCGTCTTCTGCAACGACAACCCC
Found at i:17476 original size:24 final size:24
Alignment explanation
Indices: 17444--17490 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
17434 ATCTGGGCGG
*
17444 GACCAGTGCCAAACTGCGGCATCT
1 GACCAGTGCCAAACTGAGGCATCT
*
17468 GACCGGTGCCAAACTGAGGCATC
1 GACCAGTGCCAAACTGAGGCATC
17491 AGGCCCCCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.15
Consensus pattern (24 bp):
GACCAGTGCCAAACTGAGGCATCT
Left flanking sequence: Indices 16944 -- 17443
CGAGGGTTGAGGAGCCTGTCCGAACGACGGCTGCGGCGCTTGACCAAACTGGCCAAACTGCCCAC
CAAACGACGGCTGGGGAGCCTGGCCAAACGACGGTTGCGGGGCCTGGCCAAACGGCTGCTGACCG
AATGGCTGGTCCTGGCCACCGAGCGACGTCTGGCCAAACTGGTTCGTCATCTGGTTCATCTGGGC
GTTGAACGGCTGCCCGGGCTGCTGGCCGGTTTGCAACGAGTTGGGCGAGTTCATGAAGCCGCCCG
TGATCTGCTTACCAAACGACAGCTGCGGCACGAACGCGTTGCCAATGCCACCCGTGGTCGACGCC
TGCATGGGCTGGGTCTGGTTTTGCTGGCCCTGCTGGTTCTGGCCCGTTCCGTTCAGGCCCTGGCC
CATCTGCGCCATCTGCTGCTGAGACGCGGGCTGCCACGGCATCACCGGGTTGCCGGTGGACTGGC
CCACCTGGCCCGTGCCAAACTGCGGCATCTGGGGCATCTGGGCGG
Right flanking sequence: Indices 17491 -- 17990
AGGCCCCCGGTAGGCTGGCCTCCGGTCCGCTGGGTCGGCACCAACGGACCCGTCTTCTGCAACGA
CAACCCCTGGCCAAACAGCGTGGTGGGCATCGTCATCTGGCCCTGCTGGAGCACGGGAGCCACGC
CCCCGAACGAGGTGGCCGGCATCCCGGTAGCCATCCCGCCCGTGGGCATGCCTCCGGTGGTGGCC
ATCACCATCACCAGCTGGCCCGTGGGCTGGATCGCCATGAACCCCGTGGGCTGGATCGCCACAAA
ACCCGTGGGCTGGATGGCCATGAACCCGGTGGGCTGCGCAGGAACAAGCCCGCCCGTGCGCACCG
GCACCAACTCGCCGGTCTTCTGGGCACTGACCGGCGCAAACTGCGGCGGAGGCACCGCGGGCCGC
GCCGGAGCAGGCGGCTGGGCCGTCTTGGTGGGCTGGAGCGCTGGCTGCAGCGGCGCCGCGTCGGA
CACACTGGCGGGAGGCTTGGCGTTGGCGTCGTAGGGTTTGATGTT
Found at i:17731 original size:24 final size:24
Alignment explanation
Indices: 17704--17786 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
17694 CACCAGCTGG
17704 CCCGTGGGCTGGATCGCCATGAAC
1 CCCGTGGGCTGGATCGCCATGAAC
** *
17728 CCCGTGGGCTGGATCGCCACAAAA
1 CCCGTGGGCTGGATCGCCATGAAC
*
17752 CCCGTGGGCTGGATGGCCATGAAC
1 CCCGTGGGCTGGATCGCCATGAAC
*
17776 CCGGTGGGCTG
1 CCCGTGGGCTG
17787 CGCAGGAACA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.17, C:0.31, G:0.36, T:0.16
Consensus pattern (24 bp):
CCCGTGGGCTGGATCGCCATGAAC
Left flanking sequence: Indices 17204 -- 17703
TGATCTGCTTACCAAACGACAGCTGCGGCACGAACGCGTTGCCAATGCCACCCGTGGTCGACGCC
TGCATGGGCTGGGTCTGGTTTTGCTGGCCCTGCTGGTTCTGGCCCGTTCCGTTCAGGCCCTGGCC
CATCTGCGCCATCTGCTGCTGAGACGCGGGCTGCCACGGCATCACCGGGTTGCCGGTGGACTGGC
CCACCTGGCCCGTGCCAAACTGCGGCATCTGGGGCATCTGGGCGGGACCAGTGCCAAACTGCGGC
ATCTGACCGGTGCCAAACTGAGGCATCAGGCCCCCGGTAGGCTGGCCTCCGGTCCGCTGGGTCGG
CACCAACGGACCCGTCTTCTGCAACGACAACCCCTGGCCAAACAGCGTGGTGGGCATCGTCATCT
GGCCCTGCTGGAGCACGGGAGCCACGCCCCCGAACGAGGTGGCCGGCATCCCGGTAGCCATCCCG
CCCGTGGGCATGCCTCCGGTGGTGGCCATCACCATCACCAGCTGG
Right flanking sequence: Indices 17787 -- 18286
CGCAGGAACAAGCCCGCCCGTGCGCACCGGCACCAACTCGCCGGTCTTCTGGGCACTGACCGGCG
CAAACTGCGGCGGAGGCACCGCGGGCCGCGCCGGAGCAGGCGGCTGGGCCGTCTTGGTGGGCTGG
AGCGCTGGCTGCAGCGGCGCCGCGTCGGACACACTGGCGGGAGGCTTGGCGTTGGCGTCGTAGGG
TTTGATGTTGACCAAGTCCTGCAACGAGCCCGTGTACTGCGGGGTCTGGGGCGCCGGCAGCGGCG
ACGGCTTCGTCAAGTCCTCGGTGGAGCGGGCCGCGGGCCGGGCCACCCACGCGTCGTCGTCGGGC
GCCTTCACCGGCAGCGGCAACGCGCCTGCGTCCACCGGCGGCGGGGCTGCCACCGCGGAGTTGTT
CTTGAGCGACCCGTCCTGCCCGGTGAACAACGGCTGCGGCGGCTGCGGCTCCTCGCTGCGCTTGC
GGTCGAACTTGGTGTCCAAGAACTTCATCACCCGGATAATGTCTC
Found at i:18681 original size:21 final size:20
Alignment explanation
Indices: 18648--18686 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
18638 CGAGGTCCTC
18648 CACCGAGAGCTTGGACGCCTG
1 CACCGAGAGCTT-GACGCCTG
* *
18669 CACCGCGATCTTGACGCC
1 CACCGAGAGCTTGACGCC
18687 GTTGGTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.15
Consensus pattern (20 bp):
CACCGAGAGCTTGACGCCTG
Left flanking sequence: Indices 18148 -- 18647
GGCGGCGGGGCTGCCACCGCGGAGTTGTTCTTGAGCGACCCGTCCTGCCCGGTGAACAACGGCTG
CGGCGGCTGCGGCTCCTCGCTGCGCTTGCGGTCGAACTTGGTGTCCAAGAACTTCATCACCCGGA
TAATGTCTCCCTCACGCAACCCCAACGTGCGCAAGAGCGGCGGCGAGATGTCCTCGAGCACCGCG
TCGTCCATGCGCTCGCGCGAGAAGTTCAACAGGTACCGCTGGCAGTTGCCGATGTCGACGCCGCA
CCCGAGGAAGAACTCAAACCAGTCGTAGTCGGACTCGGCCGCGCCCTGGCTCGCCACCTGGCCCA
GCGGCGGCCGCAGCCCGCTCAGCGAGCGGCCGACGTCGTTGATGGCGGCGGTGGCCAGCCGCTCG
CGGTGGGAGTCCAGCCGGCGCGCCGTGCGCTTCAGGTTGGCCCGTGCCACCTCCTCCTTCTGCGC
CTCCAACAGCTTGCCCGTGACCTTCTCCACGTACTCGAGGTCCTC
Right flanking sequence: Indices 18687 -- 19186
GTTGGTCTTGTGCAAGTGGATCTTGCCGTCGACAAACCCCAAGAACTCCGCCTCCACCTTGAACA
GGCCCAGCAGGTCGATCCACGTGCGCACGCGGTGGTAGTTGGGCATGCTCTTGTCGGCGTCGGCC
GCGCCCTTCTTCTTGTCGCGCTGGGCACGGTCGCGCTCGCGGATCTTGTCGCGCTCGTTGCGGTC
GCGGTGGCGGCTCTTCTTCTCCACCACCCGGCCCTTCAGGTGCTTTTGCTTGCGGGCGCCGTCCG
TCAACCGGTCCAAGTTGGTGGTGGCCACCACCTCGATGTACGACGCGGGCACCACCCCCAGCCGC
TTGGTCTGGGTGTGCTGGCACATCCACCACTCCTTGCTCTTGACGTCGTTGATCACGTACACCTC
GTCGCCCTCGCGGCACCCGAGCTCGTCGGGCAGCTGCGCCTGGAAGTCGAACATGAGCCGCCCGA
TCTTGCGGTTGTCGGAACCGGTGGTGGCCACCAGGGCACGTGCCA
Found at i:19580 original size:12 final size:12
Alignment explanation
Indices: 19563--19605 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
19553 GCTGGTCGTG
19563 GTCGCGCTGGGA
1 GTCGCGCTGGGA
19575 GTCGCGCTGGGA
1 GTCGCGCTGGGA
19587 GTCGCGCTGGGA
1 GTCGCGCTGGGA
19599 GTCGCGC
1 GTCGCGC
19606 AGGTCGTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.07, C:0.28, G:0.49, T:0.16
Consensus pattern (12 bp):
GTCGCGCTGGGA
Left flanking sequence: Indices 19063 -- 19562
ATCACGTACACCTCGTCGCCCTCGCGGCACCCGAGCTCGTCGGGCAGCTGCGCCTGGAAGTCGAA
CATGAGCCGCCCGATCTTGCGGTTGTCGGAACCGGTGGTGGCCACCAGGGCACGTGCCACTTCGC
CGAGGCCGCGGCCCAGGTCGGCGGCCTTGAAGTCCTGGATCACCGAGCAGATGGCCTCGGCGACG
TCTTTCAGCCCCGCGTGGAGCTCCACCAGCGCCTGCGGGTGCTTGAGCTCCAAGAACACGTGCTT
TTTCTCGTTGGTGCACTCCTTGAGGTCCTTCATCCGCCACTCGTTGTCGAGCGACGACGCGCCGC
CACGCAACTTCGAGAGCTTCTTGACGTTGGGCGCGAGCTTGACGGTGCGCGGGACGACGCTGAGG
ACCACCGGCCGCTTCTTGCGCCCGTCGATCTCGTCGATGTACCACGTGAAGTACTCGCCGTCGAA
CCCGTGCTGCGGCAGGTCGTCGCCGACGCTCACGGGCTGGTCGTG
Right flanking sequence: Indices 19606 -- 20105
AGGTCGTAGTGGTCGCGCTCGTCGCCCTGGCTCGCCGCCGAGGTGGCGGTGTTGCCTCGAGGCCG
GGTGGGCATCGGAGGAGCCTCCTCCTCCTCCTCTTCCTCGCCCGTTACCGGCGCCGGTTGCGCTT
CCGGCGTGGCCCGGTCCTTGTGCACGGGCGGAGGGGCAAAGTTGATGGGCGGGAGCGCTGCGGCC
GACACCCCCTGTGCCGTGGCCGGGGTGGCTGCGGTGGTGGGCTGGGACTCGCTGGGCAACGGCGG
CAACGGCTGCTCGCTCGAGCCAAACAACTTGTCGGCCACCTGGACGTAGTTGGCCGGGACAAACC
CGTACACCTTGCCTGCGGTGTCCCCCGCAAGCAACCAGTCGGGGTCCTTGTTGTCGTAGATGTTG
AAGCGGTCGCCCTCCTTGAACAGCAACTCCTCGTCGGTTTGCTTGTCGTAGTCGTACAACGCAGA
GCACTGCTGCACTATCGGAGCAGGCTCAATGTAGTTCAGGGGCAC
Found at i:47730 original size:9 final size:9
Alignment explanation
Indices: 47715--47747 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
47705 CTTCGTCAGA
47715 GTCCAACTC
1 GTCCAACTC
*
47724 TTCCAACTC
1 GTCCAACTC
47733 GTCCAACTC
1 GTCCAACTC
47742 GTCCAA
1 GTCCAA
47748 TTCACCCCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.42, G:0.09, T:0.24
Consensus pattern (9 bp):
GTCCAACTC
Left flanking sequence: Indices 47215 -- 47714
CTGTAGCCACTAAGTTTTTACGGAACTTTAGTAATATACCCTAGGACTTTATTTTTTCCAGTAAT
TATAGCGTGTGAACGGTGCTTCCTGTGACGTTCACTTATGTTCGCTTATATACGATTCATCGCGC
CCCTTGCATGACGTATGTACCCTGTCGCCTCATTTGGTAACGGTTGTCTACAAACAGACAAGGCG
TGTTTACGTGCGCGCTGGAGCGAACGCTGCCCTGTAGTTACACAAACCGAACGGCGCGTAGTTAA
ATTCAACTAGGACACAGTAGCAGACCGTGATAATACGCCGTTAGCCATGGTGGACCTCTTTTTAC
TATATAATTACTATTACTTGATATGAGTGCCAGCCAACTCGTCGGCAATCTCGTCGACCGCCTTG
TCGGGCTGTTCGGCGGTGCCCGCGAGGTCCTTCTCCAAAACCTCCAAGTCCAAGTCCTCCTCCAA
CTCATCAGCACCCTCGTCGTCATCGTCTTCATCTTCTTCGTCAGA
Right flanking sequence: Indices 47748 -- 48247
TTCACCCCCCTGTGCTTCCAAGGCTTCCTTGAGAGCCTCGGCATGGTCCAACTCCTCCTCAAATT
GGTTCCCGTTCAACTCGACGATGGCCAACTGGGGCAATTTGCCGTCCTTAACCGCCGCAGCCAAC
TCCTCAACGGCGTCGGCCCGCAACTCGTTGTATTGCAATTTGAGCGTGGTCACCAGCTTGGGCAA
CGCCTTCACCACGGCAAGAGCACCCTTGGGCTTCAAAAGCGCGTCGTTCAAGTTCAACTCGGTAA
TCTCGGTCCACGAGTTGGTCAAGGCCTCGGCAAGCGCCAACCCACCCCGCGCGGTGACGGTGTTG
TCTTGCAAATCCAACACACGCAACTTGTGCAACCGGTTAGCCAAGCCGACAATCAACTTGGTAGC
GCCAGCCGGACGAATACCGTTCTGGTACAAGCGGACCTCGGCCAAGTCCGGGTGGTTGCCCAACC
CGACGGCCAAGTGGTTGACGGACCCGTTCTCCAAACGGTTGCGAC
Found at i:55165 original size:39 final size:39
Alignment explanation
Indices: 55055--55157 Score: 161
Period size: 39 Copynumber: 2.6 Consensus size: 39
55045 TCGTTTACTC
* *
55055 CACCTCCAATGTCGCAGCTGTCTACCACCACGTTCACCG
1 CACCTCCAATGTCGCAGCTGTCGACCACGACGTTCACCG
* *
55094 CACCTCCATTGTCGCAACTGTCGACCACGACGTTCACCG
1 CACCTCCAATGTCGCAGCTGTCGACCACGACGTTCACCG
*
55133 CACCGCCAATGTCGCAGCTGTCGAC
1 CACCTCCAATGTCGCAGCTGTCGAC
55158 ATTGACGTCG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.20, C:0.42, G:0.18, T:0.19
Consensus pattern (39 bp):
CACCTCCAATGTCGCAGCTGTCGACCACGACGTTCACCG
Left flanking sequence: Indices 54555 -- 55054
CAACCGCGGTGTCATGGACAAGCGCCAGATTTACGCCAACCCGTTGTTGCACTCGACCACCACCG
AGTTCCGCCATGTGGTGCACCACGACAACGAAAAGCTCCAGCAAATCTCCGAAGACAGCTACTCT
GTCCTGCTGTTTGAGGAGGAGATCAAGCCGTTGGACATGACCCAGATCCCGGTGCCCCAGCGCGC
GGGCTCGTTGAGCTCGTTGTCGTACACCCGTCCCATCAACCCGCACAGCTCGCAAACGGACTTGC
TGCGTCGCAAACCTCCCCCCGACTTTGATCCTATTCGCAACGTCGTGCGGCTGAACCCGCCTCAG
CAACGCCCGTTCAGCCCTCCGGCAACGCGTACGTTCACTGCTCCTCTGGTGGCTGCTAATGTGGG
ACCATCTATGTCTCAGCTGTCTACGGGCACGTTTACCCAACCGTTCCCGCCTCCGCAGCTGGACA
GCTATGCTCCTCCGCCTTCGCAGCCGTCGGCCACTTCGTTTACTC
Right flanking sequence: Indices 55158 -- 55657
ATTGACGTCGATGTCGAACCAGCCTACGGGCCAACGCGGGTTCACCAGACTCCAGTCCGAGCCGG
TGCCCACCTACGACCCTGACCAACAGTACTATGGCGGCTACCCTGGATCCTCCACCGAGTACTAC
AGACCCGACCACCTGTACCCTGCTCCACCCGCCCCCACCTATAACAACCCCCTGCATGCCGGATC
GTTGACGTCTTTAACTGATCTGGCCTCCGGCTCGCCCCCCTCGGACGATGCCTTCACTCCCTACC
CTGTAAGAGGGGTTTCGATGTACGGTGATGATGTTAGCCGGTCCAACTCATACACCTACCCACAG
CATTAGCCTTTCGGCAAGAGAATAAATCAAGAATACATCATAAATGCACGCGAATTCATTGACAA
GAAGCCAACTAGAGTGGTACTGTAGTCATGCAGCTGTATGAAGTAGAAGAACTTTGCAGAACTGC
CTCAGAGAACAGCCTTGTTGAACAGTGAAGACAATCTTGTTATGC
Found at i:61404 original size:54 final size:54
Alignment explanation
Indices: 61321--61539 Score: 341
Period size: 54 Copynumber: 4.1 Consensus size: 54
61311 CGTCGTCACC
* * * *
61321 AGAAGAGGCTGGTTTCGAA-GAACCACCGGATGTGGAGCCTCTTGAAGCGGAGGA
1 AGAAGAGGCTGG-TTCCAATGAGCCGCCGGATGTGGAGCCTCTCGAAGCGGAGGA
* *
61375 AGAAGAGGTTGGTTCCAATGAGCCGCCGGATGTGGAGCCTCTCGAAGCCGAGGA
1 AGAAGAGGCTGGTTCCAATGAGCCGCCGGATGTGGAGCCTCTCGAAGCGGAGGA
*
61429 AGAAGAGGCTGGTTCCAACGAGCCGCCGGATGTGGAGCCTCTCGAAGCGGAGGA
1 AGAAGAGGCTGGTTCCAATGAGCCGCCGGATGTGGAGCCTCTCGAAGCGGAGGA
* *
61483 AGAAGAGGCTGGTTCCAATGAACCGCCGGATGTGGAGCCTCTCGAAGCGGAGAA
1 AGAAGAGGCTGGTTCCAATGAGCCGCCGGATGTGGAGCCTCTCGAAGCGGAGGA
61537 AGA
1 AGA
61540 TGTGGAGCCT
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
53 5 0.03
54 147 0.97
ACGTcount: A:0.26, C:0.21, G:0.37, T:0.15
Consensus pattern (54 bp):
AGAAGAGGCTGGTTCCAATGAGCCGCCGGATGTGGAGCCTCTCGAAGCGGAGGA
Left flanking sequence: Indices 60821 -- 61320
GCTCCCATAAACGACGCCTACGACGAGCCTACCAAGGAGCCTCGTGTTAGTGGTATTAAGCCAGG
GTCGTCCCGTCTGAGACTGTCCCGACTGAGAGGTGCGCCAAAGCTGTCAGACAAATCACTGCGTC
CTCAGTCGAAGTCCAAGCGGGGCAGGGCACCAAGGTCAGCACCGAAAGACCTGAATGACCAGTAC
TGGAACAAGAAGCCCGACCTGAGTTTGTTCGACGAGCTCATTGGTGCTGGAGCTCCGCTGGGTCC
CAACACAGCCAATCACAGCTCTCCGGTCAAACAAGCACCTCAACCTGGGTTCATGCTGCTCTCTT
CGGGTCATATTGACGTTGGGCTTGACTACGACGACTATGAGGCTGACTACGACGACTCTCCGCAG
AAACGGCGCTTGAAGGTACCTATCGAAGCTTCTTCTCCGATCCAGAAACCAGCAGCGACTCCTAA
TATTCCGCTGTCGCCCTCCACAAATGGGAATGCCCCGTCGTCACC
Right flanking sequence: Indices 61540 -- 62039
TGTGGAGCCTCCAAAGTCAGAAAATGAGGGCGTGCAAGAAACTCCTGGTGAGAAAGATGAGGTCG
AGGTATCGTCTCCGAAGGCTTCGGACCAACCAACAACAGTCGTGAAGTCCCCAGTTCCCAGCGCT
CATCTGAGCGAGGACGAGCTTGAACAGAGTCAGTCCCAGAAGCTGGTAGACCTGCCTGAAGTTGG
TGGTAAAAGTGCAATGACTGATAAGCTGACTCCGCGAGAGAGTGTGCACGATGCGCTGGATATAT
CGGAGGTTGCAGAGGAATCCACCAACGAAGCCACGCCCGCTGGTCGGGTCGCAGAACCGGTGGTG
CTGGGAAACAGCCTGATCGGTGACATCGAGAGTATTGAGGCTAGTACCCAGGATGCTGAAGAAAG
TGTAGATACAAAGGAAAAGAGTCAAGGCGAGCGCGAGGCACACCCGTTGGAGGTTGATTCGGGTT
CCGACTCAACCTCTGACGCCCCGCCGGCTGTACGAACCCGTCGTA
Found at i:78575 original size:21 final size:21
Alignment explanation
Indices: 78549--78590 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
78539 CTAGCGTTAC
78549 CTCATTAAAGCCCCACATTGT
1 CTCATTAAAGCCCCACATTGT
*
78570 CTCATTAAAGCCCCACGTTGT
1 CTCATTAAAGCCCCACATTGT
78591 TGTCATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.29
Consensus pattern (21 bp):
CTCATTAAAGCCCCACATTGT
Left flanking sequence: Indices 78049 -- 78548
GGGGTGGGGGTCTATGGGGAAAACTGCCGAGGGGGCGCCTTTTGTGGTTGCTCGGGTGTTTGCAC
GGGGTTTTGTGGAGGTGGCCGTGGTGCTCGTATAGGTGCAGGTAGTCTGTGGCTACAACTCGGGT
TGGTTACGGGCGATACGAGCTCCTTACGACTCGGTTGGGGCGGCATTGTGTGCGTGGCGAGAGGA
TGGGCTGAGCATGGAGGTACGGTAGTGTGACGAGAGACCACCCAAGTAACCAGGGGGCGAATGCA
ACGCGTTTACCGCTGTGAGTCATCTTCTGCCCAAGTAGGCATTGGTCGAGATAACCACTCGTCAT
ATTTCGCTTACGTTAGCGGTAAACGTAGTCCAATCCACCTTCCCTGCCGCTCACTCAATCAAAAT
ATGCCCCTTACCATCTGCCCCTTACGATCCCCATTTTTCTACTTTTACAAATATTTTGCATTTCT
ACAATCCGCTCCTGTCTCTACATTTATTCATTAGTCTAGCGTTAC
Right flanking sequence: Indices 78591 -- 79090
TGTCATAGAAGAAGTTAGGCAAAGTATCCATCTGGAAAAAGTTGGTTGGGTCCGGGTTGAAACTG
TCGGTCAAAAAGTCTCCCCGGAGAATGCCACTGTAGTGGGTCTGGCTGCCGTTGGTCGACGACTG
CTGGACCCCCACCGCGTGGTCTGGGTACCCGTCGTAGGCAGTGGGCCCGTCCAAGATGTTGTTGA
TGGCCGGGTTCATGCTGGGACTCCACGCCTCGGTGGGCCGCAGCGACGGCCCGTGGTGCGCAGCG
GCCGCCCCCAGGTTGGGGGTGGTGCTGTGCGACAGCGTGCGCTCGGGATTGGTGGCGCTGTTGGG
GTTCAGGTGGCTATTTACAAATGGCAGATCACCGGTGATCCCCTGGAGTTTGACGGCGAGCTCGT
TCAGGTTGAGGAAGAGCTCGGGGTAGGCGACCCGCGCGTTTTCAAAGTGCTGTTGCAACGGGGGG
TTGTTCGAAAACAACTTCAGGTCGTTGCGCAACTCGTAAATCACC
Found at i:84316 original size:14 final size:14
Alignment explanation
Indices: 84282--84363 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 14
84272 GAAGTGTAGG
*
84282 ATGGTGGGTGGAGA
1 ATGGTGGGTAGAGA
* *
84296 GTAGTGGGTAGAGA
1 ATGGTGGGTAGAGA
*
84310 ATGGTGGCTAG-GA
1 ATGGTGGGTAGAGA
84323 ATGGTGGGTAGAGA
1 ATGGTGGGTAGAGA
* * *
84337 ATAGTGAGGGAGAAA
1 ATGGTG-GGTAGAGA
*
84352 ATGGTGTGTAGA
1 ATGGTGGGTAGA
84364 AATTTGGTGA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
13 12 0.23
14 30 0.57
15 11 0.21
ACGTcount: A:0.29, C:0.01, G:0.48, T:0.22
Consensus pattern (14 bp):
ATGGTGGGTAGAGA
Left flanking sequence: Indices 83782 -- 84281
GCCGACGTGTACTTTGACCTCCAACAGCTCCAGCCCACCGCGGCAGACGACGCCAAGAACAAGAA
GGCCAAGAAGCCGGCCAAGACGAGCAAGAAGCTCACCAAGATGCGCAACGAGTGGGCGGCCAAGG
TTGAGCTGGTCAAGGACGACGCCGACCCGTTAGGGGCGCAGGCGCTTGCCGATGCCTTGGCGCTG
GACTTGATGGAGCAGTTGTTTGTGGTGGCTAAGCCGTTGGCGGAGCAGGCCAAGGACTTTGAGGC
AACGTGGCGGGTGTTGTTCCGGGTGTACGTGGCCCAGGGCAAGTACGTGTTGGCGTTGCAGGCGA
TCAAGCAGTTGGCGCGGTTGCACTACCCGGTAGCGGACGCGGTGGCCGAATTGAAGCAGACGATG
GAGGGGGACGAGCAGGCCAACGCCGCCATCAAGCAGGTGGTGGCCAAGGGCATCGAGGCCGCGTT
CCCCGATTTATAGAGCTATAAACGATAGAGAACGAGAAGTGTAGG
Right flanking sequence: Indices 84364 -- 84863
AATTTGGTGAAGGAGAGTTTGTTGAAAAGATACTGGTATGCAATGAGAAGAACAAAATGAAAAGA
GTGATTGAATTATCCGGGTCTCAATCTCTGAGTCACATTGGCTACATACTCTCTCAGTTTCCTGT
ATTACCTATCATAAATCATGAGTTCATCCACCCCTCCACCTGCGACCGGGCCACGCTCGAGGCCA
AATTAAGCGACTGGGTGCCAAACGGGAAGTAGCTCACGGTGTACCACAACGCCGCAAGCAACTGG
ATCACCGCAAAAATCAACGAGAGAATCGTCGACCGCAAGCTCAACGCACTCACCAACGTCATGAT
GATCAGGGTGAAAAACGCCACCGTAAACAAAATCCGGGTGCTGCTAAACAAGTGGGTCACGTACG
CCTGTGCCCCCTGCAACACCCCAAACGATATCAAAAAGAACACCAGCCCGAGCGACCACAAGATG
GCAAATTTTCGGGGCTTGAGCGACAACACGGGGAACAAGAAAATG
Found at i:84329 original size:41 final size:41
Alignment explanation
Indices: 84278--84357 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
84268 ACGAGAAGTG
* * * *
84278 TAGGATGGTGGGTGGAGAGTAGTG-GGTAGAGAATGGTGGC
1 TAGGATGGTGGGTAGAGAATAGTGAGGGAGAAAATGGTGGC
84318 TAGGAATGGTGGGTAGAGAATAGTGAGGGAGAAAATGGTG
1 TAGG-ATGGTGGGTAGAGAATAGTGAGGGAGAAAATGGTG
84358 TGTAGAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.12
41 18 0.53
42 12 0.35
ACGTcount: A:0.29, C:0.01, G:0.49, T:0.21
Consensus pattern (41 bp):
TAGGATGGTGGGTAGAGAATAGTGAGGGAGAAAATGGTGGC
Left flanking sequence: Indices 83778 -- 84277
CCTCGCCGACGTGTACTTTGACCTCCAACAGCTCCAGCCCACCGCGGCAGACGACGCCAAGAACA
AGAAGGCCAAGAAGCCGGCCAAGACGAGCAAGAAGCTCACCAAGATGCGCAACGAGTGGGCGGCC
AAGGTTGAGCTGGTCAAGGACGACGCCGACCCGTTAGGGGCGCAGGCGCTTGCCGATGCCTTGGC
GCTGGACTTGATGGAGCAGTTGTTTGTGGTGGCTAAGCCGTTGGCGGAGCAGGCCAAGGACTTTG
AGGCAACGTGGCGGGTGTTGTTCCGGGTGTACGTGGCCCAGGGCAAGTACGTGTTGGCGTTGCAG
GCGATCAAGCAGTTGGCGCGGTTGCACTACCCGGTAGCGGACGCGGTGGCCGAATTGAAGCAGAC
GATGGAGGGGGACGAGCAGGCCAACGCCGCCATCAAGCAGGTGGTGGCCAAGGGCATCGAGGCCG
CGTTCCCCGATTTATAGAGCTATAAACGATAGAGAACGAGAAGTG
Right flanking sequence: Indices 84358 -- 84857
TGTAGAAATTTGGTGAAGGAGAGTTTGTTGAAAAGATACTGGTATGCAATGAGAAGAACAAAATG
AAAAGAGTGATTGAATTATCCGGGTCTCAATCTCTGAGTCACATTGGCTACATACTCTCTCAGTT
TCCTGTATTACCTATCATAAATCATGAGTTCATCCACCCCTCCACCTGCGACCGGGCCACGCTCG
AGGCCAAATTAAGCGACTGGGTGCCAAACGGGAAGTAGCTCACGGTGTACCACAACGCCGCAAGC
AACTGGATCACCGCAAAAATCAACGAGAGAATCGTCGACCGCAAGCTCAACGCACTCACCAACGT
CATGATGATCAGGGTGAAAAACGCCACCGTAAACAAAATCCGGGTGCTGCTAAACAAGTGGGTCA
CGTACGCCTGTGCCCCCTGCAACACCCCAAACGATATCAAAAAGAACACCAGCCCGAGCGACCAC
AAGATGGCAAATTTTCGGGGCTTGAGCGACAACACGGGGAACAAG
Found at i:87837 original size:32 final size:32
Alignment explanation
Indices: 87797--87874 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
87787 GCGAGTGTAG
* *
87797 AGCTAGCAACACCTCTATAGGGCGACATCTCT
1 AGCTAGCAACACCTCTAGAGGGCAACATCTCT
* **
87829 AGCTAGCAACATCTCTAGCTGGCAACATCTCT
1 AGCTAGCAACACCTCTAGAGGGCAACATCTCT
87861 AGCTAGCAACACCT
1 AGCTAGCAACACCT
87875 ATAGCAACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (32 bp):
AGCTAGCAACACCTCTAGAGGGCAACATCTCT
Left flanking sequence: Indices 87297 -- 87796
CCGGTGCCTTGAAGTGCTACGCCTGCGGTAAGGCTGGCCACATCTCCAAGGACTGCCGTTCGGCT
GCTGGTGGCGACAACGTCGGTGCCAAGGCCTGCTACAACTGTGGCAAGCCCGGCCACATCTCCAA
GGAGTGCCCCGAGTAAGCGGAGTAGGGTGCAGATGCGAATAAGGAGTGGCGACAAGGGAGGGAGT
GTCGAATGTGACATGTGTTTGTGTTTTCCGGTTTTATATTTTCTTTTACCTCACTCTCCTTATTT
ATAGTTTGTAATTTTATGGTACCAAGGGTTCGAGTAGGAGGTAGATGGGGGGATTCGACCCTTAG
CAGTGGAGGTGCCGGGGGCAACACCAGGAGCTGAGGGGTGAATCCAGGACGCTACGCTGTAGGCG
CGCTGGACAGCAACAGTGCAGTGTGCGAGTGAACAGTCACTCACCATCAACAATCAAGCTGGCAA
AGTCTAGCTAGTTTCTAGCAACAAGAGATAAGCGAGCGAGTGTAG
Right flanking sequence: Indices 87875 -- 88374
ATAGCAACACCTCGGGCTGGCAACCTCCGGTCAGGTCTCTAGTTCGAGCACCATCACTACCTCGC
ACCACGGGTCACCGTTTCACCGACTGGGAGTAGTCCACGTGGACGTTCTTCCCATCGATAATACA
CTTGTGGTTCGTAAACTGGCTCACGGCCGCGTCCGCGTCCATCGCCTCGTCAAACTCCACAAACG
CAAACCGGCCCCCCTTGTCGTTCTCCTTGATCACGCACTGGGACACGGGACCGAACCGCCCAAAC
ACAATTTCGAGCAGCTGGGCCGTGGTCTCCTCGCCGAGCCGAGCCACAAACACCACCAGCGGCGA
CGGCTGGATGCGGAAGTCGGGCAAATCCCCCAACGCCTCGAGCGCCAACGCGTTGGCCCGGCTCT
TGGCACTGATCTTGTAGTCAAACGTCACCTCGTCCCGCACGCTGAACGGGTTGTGGAGCACCACC
ACCGACACCACCACCACCGGCACGGGCGATGCCTCGATATTAGCC
Found at i:87879 original size:16 final size:16
Alignment explanation
Indices: 87821--87871 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
87811 CTATAGGGCG
87821 ACATCTCTAGCTAGCA
1 ACATCTCTAGCTAGCA
*
87837 ACATCTCTAGCTGGCA
1 ACATCTCTAGCTAGCA
87853 ACATCTCTAGCTAGCA
1 ACATCTCTAGCTAGCA
87869 ACA
1 ACA
87872 CCTATAGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (16 bp):
ACATCTCTAGCTAGCA
Left flanking sequence: Indices 87321 -- 87820
GCGGTAAGGCTGGCCACATCTCCAAGGACTGCCGTTCGGCTGCTGGTGGCGACAACGTCGGTGCC
AAGGCCTGCTACAACTGTGGCAAGCCCGGCCACATCTCCAAGGAGTGCCCCGAGTAAGCGGAGTA
GGGTGCAGATGCGAATAAGGAGTGGCGACAAGGGAGGGAGTGTCGAATGTGACATGTGTTTGTGT
TTTCCGGTTTTATATTTTCTTTTACCTCACTCTCCTTATTTATAGTTTGTAATTTTATGGTACCA
AGGGTTCGAGTAGGAGGTAGATGGGGGGATTCGACCCTTAGCAGTGGAGGTGCCGGGGGCAACAC
CAGGAGCTGAGGGGTGAATCCAGGACGCTACGCTGTAGGCGCGCTGGACAGCAACAGTGCAGTGT
GCGAGTGAACAGTCACTCACCATCAACAATCAAGCTGGCAAAGTCTAGCTAGTTTCTAGCAACAA
GAGATAAGCGAGCGAGTGTAGAGCTAGCAACACCTCTATAGGGCG
Right flanking sequence: Indices 87872 -- 88371
CCTATAGCAACACCTCGGGCTGGCAACCTCCGGTCAGGTCTCTAGTTCGAGCACCATCACTACCT
CGCACCACGGGTCACCGTTTCACCGACTGGGAGTAGTCCACGTGGACGTTCTTCCCATCGATAAT
ACACTTGTGGTTCGTAAACTGGCTCACGGCCGCGTCCGCGTCCATCGCCTCGTCAAACTCCACAA
ACGCAAACCGGCCCCCCTTGTCGTTCTCCTTGATCACGCACTGGGACACGGGACCGAACCGCCCA
AACACAATTTCGAGCAGCTGGGCCGTGGTCTCCTCGCCGAGCCGAGCCACAAACACCACCAGCGG
CGACGGCTGGATGCGGAAGTCGGGCAAATCCCCCAACGCCTCGAGCGCCAACGCGTTGGCCCGGC
TCTTGGCACTGATCTTGTAGTCAAACGTCACCTCGTCCCGCACGCTGAACGGGTTGTGGAGCACC
ACCACCGACACCACCACCACCGGCACGGGCGATGCCTCGATATTA
Found at i:92280 original size:16 final size:16
Alignment explanation
Indices: 92241--92311 Score: 108
Period size: 16 Copynumber: 4.4 Consensus size: 16
92231 GTTGGTAGGA
92241 GTGTGGA-AATCTAGTG
1 GTGTGGAGAA-CTAGTG
92257 GATGTGGAGAACTAGTG
1 G-TGTGGAGAACTAGTG
92274 GTGTGGAGAACTAGTG
1 GTGTGGAGAACTAGTG
*
92290 GTGTGGGGAACTAGTG
1 GTGTGGAGAACTAGTG
92306 GTGTGG
1 GTGTGG
92312 TGCCTGAAGC
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
16 37 0.71
17 13 0.25
18 2 0.04
ACGTcount: A:0.23, C:0.06, G:0.45, T:0.27
Consensus pattern (16 bp):
GTGTGGAGAACTAGTG
Left flanking sequence: Indices 91741 -- 92240
TGAAGTTCAACAACACCGAGCGCGCGGTGACGCTGCGGATGTCGCAATTGCACAGCCGCCAGGAG
GACTTGCTTCCCAACGCGGCCTACGTGGCGGTGGCGGCGCTCGCCGGCACCATTGCTGGGCGCAA
GCACGGCTTTTTGGCCCGGGCGACGTTGCCGGTGGTGTTTGGTACGGCTGCCTTCCGCTACTTCC
TTCCCCAGACGTTTGCCAACACCACCAGCTTCCTCTGGGACGTGGAGCAGCAGAAGATGCCCGAG
GTGGCGCTCAAGCAGCAGGAGTTGGTGACGCTGACGGAGAACTTTGTCCGGGACATGGGCAAGAC
CACCGAGGAGCTGAGACAGTTTTTGCTGGAGCAGGCTGAGGGGTTGAGACGCAAGGTGGCCAGCA
TCACGGGGCTCAACGTCGAGGAGGACGTGTCGAAGAAGTAGTGGAGTACGTAGTATATAGAGAAC
GCATTAAGAAGAGAGTGTAGGGAATGGGTGGAAGGGTTGGTAGGA
Right flanking sequence: Indices 92312 -- 92811
TGCCTGAAGCCAGAGGATCATTGTGTCGTGTGAAAATCTACCATTCTTGTCACCACTACTATTAC
CACTACTACAATAAACATACAATCCTAACATACTAGTATTTGACAATGCGCAAAGCACGGCTGCA
AAACTCTCAAGCCATGAACATACACCGCCCGTTCGGGAAACCCCAGCACCGCCCGTCTCCTCTGC
CAGAAGCCTCCAGCTTCCTCCACCACAAACCACAAACACCCGCCTCCGCTATATATATGCTGTGT
CTATCGTCTATACTCTAACTATTTACATGGCGTTTTCCCACTCGAAACCCCGCGTACCCTACCGC
CACACCACCCCGTCGCCCACCAGCCTGTTCGCCCTGCCCAAGCTGTTGTTCCCCACCCCGGAGGA
CCTGGTGGTCAACCCGTTCATGCACAAGCCCCGCCGGTGGCCGTTTGGCCGCACCAGCGAGGGCA
GCCGCGAGCCGCTGCTGGAGCCCCCGTTGATCGACTCCCTCAAGC
Found at i:95032 original size:16 final size:16
Alignment explanation
Indices: 95013--95056 Score: 79
Period size: 16 Copynumber: 2.7 Consensus size: 16
95003 GGCTGGAGCG
95013 GGTGGCGGAAGTGGCA
1 GGTGGCGGAAGTGGCA
95029 GGTGGCGGAAGTGGCA
1 GGTGGCGGAAGTGGCA
95045 GGTGGCAGGAAG
1 GGTGGC-GGAAG
95057 GCAGGAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.20, C:0.11, G:0.57, T:0.11
Consensus pattern (16 bp):
GGTGGCGGAAGTGGCA
Left flanking sequence: Indices 94513 -- 95012
CACCAACAGGCCCAGACAGGCACTGACCATCTTCTGCCAAAACGAGATGTCGGACAGCATCGGTG
GGGTATTTTTCACGGTGCTGTGCCTAGTGTCTTTGCAGCCCGATTGACAATGCTGCACTCCTGTA
TGCGGGTGCGCCACCTAGTCCGATACGGGGTAGCGTTAGCGAGGTCGCTCGGCCGCCGGAAGCGG
TAGCGAGCGGTTACGGGGGTAGAGGCGGTGGGACGAGCACGGTGGTTGTTTTTGTGTAGACGGGA
GAAACTGCCTATTTGGTGGGCGGGCCGGTTGCGGTTGCCTGCCCCACTTTTTGGTTGCGATGCGA
TCGGGTCAGGCACAGACCACCGGTGATTCGCGGGTGCGTGGTAGACGAGATACTCGAGGCCGGGG
AGGGTTCTCTGTGCATCCGGGCGAGGTGGTTTGCACCGTTGAACGAACGCGACACGGAAGTGGTT
CCGCGACATTTAGTGAGATGATGAGGGCGGCAGGTGGCTGGAGCG
Right flanking sequence: Indices 95057 -- 95556
GCAGGAGAGGCGGCAGGAAAGGGAGAGGCAAGTGGCGGGGTTGGTACGAATGGTCGAAAGTAGGA
GAAAGCTGGGTGACTACTAGCAGGTTAGTGGTGTGAGCACGCAGTGGTAGACGTAGTATTGGCCC
GGGTAGTATATGCCCTACCTCAGCTGTCAGTGAGTCCAGCCAATTGTCAGAGCACACGACCGAGC
CTGTATCAACCTACCCCGTCCGCAATTTATAATCAAGCCACTTCTCCACTCTGCTTCTATTCTCT
TGCAACCAGATCACGCACGGTGCCTGGGGCGTGTTACATCGACCCGGCGAGCACGAGGCGGCGCC
CCAGTTTCATCTAGACGAGCAATGCCTCTAGCTCATCGCGATGACATGACTAAATCCGTTTGGAG
TGGCCCCATCCCACACCGTTGGCACCCAGGACCACTCAGGGCACGTAACACGGGGTTATCCAACC
TTATCCATTGTTTACATTAAATTGGGTGCGTTGCACGGTGCAGTG
Found at i:96453 original size:9 final size:9
Alignment explanation
Indices: 96441--96474 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
96431 CCGGTGGCCG
*
96441 CGGTGGAGA
1 CGGTGGAAA
96450 CGGTGGAAA
1 CGGTGGAAA
96459 CGGTGGAAA
1 CGGTGGAAA
96468 CGGTGGA
1 CGGTGGA
96475 GCCAGCGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.50, T:0.12
Consensus pattern (9 bp):
CGGTGGAAA
Left flanking sequence: Indices 95941 -- 96440
ACTGAACCTATTTCCCTCGATGATCCGTCGCACCATTTCGTTAGCGGAGGGCGAGACCATCGATC
TTGGCCGCAGCCTGTCCCAACGCGGGGAGGCCACCGCCACCAATTTGCGGTTTGACGAGAAGCGG
CTCTCGCGGCAGCACGCGCACATCCGCAAGCACCACGGCCAGTGGCAGGTGTCCGATGCCGACTC
CAAGTTTGGCACGTTTTTGGGCGACGCCTTTGTCCCCCCAGGCGAGTGGGTCGACTTGCATCTGG
GCGACCGGTTGGGGTTTGTGTTGAAGCACAGCTTGAAGCCTTTGAAGGAGCGCACGGGGTTGGCC
CACCTCGGCTACACCCCCGATGACGTGTCGTTGTGGTTCGACGTGGCGGTTGACGACTCCCTTAT
CCTCAGTGCGGTTAGCAGCCCGGCGCCCCGCGACGACCCCTTGACGGGCACCACGGAGGACAACG
GTGGCACCGAGGGGTCGGAGGACGTAGACAACGAGCCGGTGGCCG
Right flanking sequence: Indices 96475 -- 96974
GCCAGCGCAAGCGGTGGAAACCGTGGAAACCGTCACCGTGTTGGAGCCGCCGGTGGAGTGGGACG
GCGACACCGAGGGGCTCGAGGTGTTGCAGCCCACCGAGTTGGGCTCGGAGTCGGAGGTGGAGATT
GTAGACATGTCCACCGCGGTGCACCAGCCGTCCGAACTGCTTCTCAGCCCGGCCAAGCCCATCAA
TATCCCCATTTTCGAGCCCAAGTCGTCGGACGACGAGCTGGCGGAGTCGGACGAGCCGGCCCCGC
TTGCGTACGCGTTTGACGACTCGGACGTGCCCGCGGACTCCGACGTGGGCGAGTACCCGCTTTTT
GAGTGCGACCCCGAGAGCGACGAGCACCCGCTGGACGGGGTGTCGTCGGGCGACTTTGTGGTGGG
GCCCATCGAGTTGGAGGCGGTGGAGGTGGCGGGCGAGACTCCCGACGAGCTGTTTGTCCGCGACC
CGCGCATCGCCGTGGGCCCCCGCAAGCGCTCGTGGTGCGAGGTGG
Found at i:99631 original size:24 final size:23
Alignment explanation
Indices: 99599--99660 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
99589 TAGCAGGCAC
99599 AGCTCAAGCTTGGCCAGAGTGCAG
1 AGCTCAAGCTTGGCCAGAGT-CAG
* *
99623 AGCTCAAGCTTGACCAGAGTCGG
1 AGCTCAAGCTTGGCCAGAGTCAG
*
99646 ACACTCAAGCTTGGC
1 A-GCTCAAGCTTGGC
99661 TCTTCAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 3 0.09
24 30 0.91
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (23 bp):
AGCTCAAGCTTGGCCAGAGTCAG
Left flanking sequence: Indices 99099 -- 99598
CTAGCGTGGTGATTGGCAAACAACAGCCAAAATGCAAAGCTCCAAACGACAGTGGAGGGAGTGGG
GACCACGAGTATGCGACCGTTCGGGAGAACTGGGTTGGTTTGTAGCTTGTCGCACGCGCTCCCGA
AATTTTGGATTTAGATCTTTGCAGCAGCCACGGCTGAGCCAGAGGGAAGTGCAAGCGCGGAGGCG
TGGCGGCGGTGGCGTGGGCGGGTAGGGGTTTGCGGGGGTTTGTTGTCTGCTGTGCGCCGGTATTG
TGTGTCCTGCTGTGTATTGATCCGGACAATAGTCCCGATGACTGCGTAGTGAACGCGCAGTAGTT
AGTGAGTGTGTAGTGAGTATATAGCGAGTGCATTAGATAGACCAGCGGGCGTCTGACGCGTTGGT
TGTCATTAGGTGAGTGAGTATGCTTGATGTCTGGCTGAGCAGGTTTCGAGGCACGGGCAAGCGGG
TTTGAGGGCATGAGTAGTAGCAGGTTGGCCATATCTAGCAGGCAC
Right flanking sequence: Indices 99661 -- 100160
TCTTCAAGCAGTAGTCCAACAACTTGAACAACTTGGCGCGGTCCTTCTCGTTAAACACCCACAAC
CCGTAGATCTCGCCCAAGAGGTTCTTGACGATGATCAAGTTGTCGTTGAGCTCAACGTCCATCTC
GGTGATGCCGTTGTTGTTGACCCCGTGCGGGAACGCCGTTTTGGTGATCTTGTTGGGCACCAAAC
CGATGGAGAAGCACTCGGGGTTACTCCGGTTCAACAAAATGAGCCCGTAGCAAAAGAGCCGCTGC
AAGTCCTGGTAGCTGTGGCACGGGCCCTGGGGTAGCTGGAAGTCACGCAAGTAGAACGCCAAAGT
GCCCTGGAAGTCGGTCTTGACCCACGTCTCGTCCTCAAACTTGTAGATGACGCAGTGCGAGGTGA
AGTACACCAACTGCTTGATGGCAGGGTCGTAGCGGCTGATAACGTTGAAGTTGAGGGTATTGCGG
TAAAGTTTCAACGCATCTTGTGTCGAGATCTCCTCCTGCTGCGGT
Found at i:103011 original size:21 final size:21
Alignment explanation
Indices: 102986--103029 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
102976 TGCGTTCAAG
102986 GACGCGAAGAAGAAGGAGAGA
1 GACGCGAAGAAGAAGGAGAGA
* **
103007 GACGCTAAGAAGTGGGAGAGA
1 GACGCGAAGAAGAAGGAGAGA
103028 GA
1 GA
103030 GGCCGGTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.43, T:0.05
Consensus pattern (21 bp):
GACGCGAAGAAGAAGGAGAGA
Left flanking sequence: Indices 102486 -- 102985
AGGTGTTGAAGCACCACCCCGACAAGAAGTCCGCCTCTGGTGGTCTTGAGCAGGACGGTTTCTTC
AAGATTATCCAGAAGGCGTTCGAGACCATGTTGGACCCCGTTACCCGTAAGCAGTTTGACTCTGT
TGACGAGGGTGCCGACGTGTTGCCTCCTCCCGCCAAGTCCGAGTACGACTTCTACGAGGCCTGGG
GCCCCGTGTTCGAGGCCGAGTCCCGGTTCTCCAAGAAGGGTGCCTTGCCCAAGTTGGGTGACGCT
TCCACTCCCAAGGAGGAGGTTGACGCCTTCTACTCCGCCTGGGGTAAGTTCGACTCGTGGAAGTC
GTTCGAGTTCAAGGACGAGGATGTCCCTGATGACACTGCCAACCGTGACCACAAGCGTTACATCG
AGCGCAAGAACATTTCTAACCGTAAGAAGTTGAAGCAGGAGGACAACAAGCGATTGATCGACCTT
GTGGAGCGTGCCTACTCCGAGGACCCCCGTATCCGTGCGTTCAAG
Right flanking sequence: Indices 103030 -- 103529
GGCCGGTATCCGTGCTGCCGCTGAGAAGAAGGCTGCTGAGGAGGCCGCTGCCAAGAAGGCTGCCG
AGGCTGCTGCTGCTAAGAAGGCTGCCGAGGCCAACATGACCCCCGAGGAGAGAAAGAAGGCTAAG
GAGGCCGCCAAGAACGCCAAGAAGAAGGCTAAGCGTGCCATCCGTGGTGCCGCCGGTGAGGTTGA
GGGCGACGCTACCGCCATCGAGGCCGACATTGAGGCCATCGTTGCCAAGTTGGACGACACTGAGT
TGACTGACTTCGCTGCCGAGGTTGGCGACAAGAAGGGCGACGACGCCAAGAAGGCGTTCACCGAC
AAGGCCGCCGCCGTTGGCGTTGCTTCGTCGATGAAGGTGTTCAAGTAAATACTTAGGTAGTTGAA
CTACGTATCTTTGCTTCAAAAGAGGGGAACAAACTCCGACTACAACTCCGACGAGGCGTCATAGG
AGGGGAGTGAACAATCGCTCCGTTTTGTGTTTGAGTCAACTGGCT
Found at i:103125 original size:27 final size:27
Alignment explanation
Indices: 103046--103125 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 27
103036 TATCCGTGCT
** * *
103046 GCCGCTGAGAAGAAGGCTGCTGAGGAG
1 GCCGCTGCCAAGAAGGCTGCCGAGGCG
*
103073 GCCGCTGCCAAGAAGGCTGCCGAGGCT
1 GCCGCTGCCAAGAAGGCTGCCGAGGCG
* *
103100 GCTGCTGCTAAGAAGGCTGCCGAGGC
1 GCCGCTGCCAAGAAGGCTGCCGAGGC
103126 CAACATGACC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.21, C:0.26, G:0.40, T:0.12
Consensus pattern (27 bp):
GCCGCTGCCAAGAAGGCTGCCGAGGCG
Left flanking sequence: Indices 102546 -- 103045
TCTTCAAGATTATCCAGAAGGCGTTCGAGACCATGTTGGACCCCGTTACCCGTAAGCAGTTTGAC
TCTGTTGACGAGGGTGCCGACGTGTTGCCTCCTCCCGCCAAGTCCGAGTACGACTTCTACGAGGC
CTGGGGCCCCGTGTTCGAGGCCGAGTCCCGGTTCTCCAAGAAGGGTGCCTTGCCCAAGTTGGGTG
ACGCTTCCACTCCCAAGGAGGAGGTTGACGCCTTCTACTCCGCCTGGGGTAAGTTCGACTCGTGG
AAGTCGTTCGAGTTCAAGGACGAGGATGTCCCTGATGACACTGCCAACCGTGACCACAAGCGTTA
CATCGAGCGCAAGAACATTTCTAACCGTAAGAAGTTGAAGCAGGAGGACAACAAGCGATTGATCG
ACCTTGTGGAGCGTGCCTACTCCGAGGACCCCCGTATCCGTGCGTTCAAGGACGCGAAGAAGAAG
GAGAGAGACGCTAAGAAGTGGGAGAGAGAGGCCGGTATCCGTGCT
Right flanking sequence: Indices 103126 -- 103625
CAACATGACCCCCGAGGAGAGAAAGAAGGCTAAGGAGGCCGCCAAGAACGCCAAGAAGAAGGCTA
AGCGTGCCATCCGTGGTGCCGCCGGTGAGGTTGAGGGCGACGCTACCGCCATCGAGGCCGACATT
GAGGCCATCGTTGCCAAGTTGGACGACACTGAGTTGACTGACTTCGCTGCCGAGGTTGGCGACAA
GAAGGGCGACGACGCCAAGAAGGCGTTCACCGACAAGGCCGCCGCCGTTGGCGTTGCTTCGTCGA
TGAAGGTGTTCAAGTAAATACTTAGGTAGTTGAACTACGTATCTTTGCTTCAAAAGAGGGGAACA
AACTCCGACTACAACTCCGACGAGGCGTCATAGGAGGGGAGTGAACAATCGCTCCGTTTTGTGTT
TGAGTCAACTGGCTCAGGGGCTGTATATTTCCGGAATCCCGAAGACCGGGATCCCGTTATCGCCC
GGAGGCGGGCCCATATCTCTATTGTCTCCGGGGACCTAAATTAAA
Done.