Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold55
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: 18981
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.23
Found at i:3549 original size:10 final size:10
Alignment explanation
Indices: 3534--3575 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
3524 ATACATACCT
3534 ACACCCGCAC
1 ACACCCGCAC
*
3544 ACACCCACAC
1 ACACCCGCAC
3554 ACA-CC-CAC
1 ACACCCGCAC
*
3562 ACACACGCAC
1 ACACCCGCAC
3572 ACAC
1 ACAC
3576 TAAACTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.21
9 3 0.11
10 19 0.68
ACGTcount: A:0.38, C:0.57, G:0.05, T:0.00
Consensus pattern (10 bp):
ACACCCGCAC
Left flanking sequence: Indices 3034 -- 3533
AAATCTGATTGTTTCGCCGAGAGCAACCAGTGCCGCTAAGAGAGCCCGTGAAGCAAAGGACTCGG
TCCAAAGGCGCACCTAACGCACCCAGGTCAATACTATTGTTAAGTTTACGAGGTATCTACGTAGA
AGAGCCCATTAGTGGCATCTTTGTCCATTGTACCCCTTTCGATCAATAAAAGTGTGGCTCACGCT
TATCGCAAATCGTCGGAAGAATGGGCCTATAAGCGGGAGGACGGGCTCCGGGGCTGTGCGACGAC
CTGTCCTCGCAACCTGTGGCTCGTGGCCATGCCTATTCAAGGTTGCAACACGCGATCAGGAGGGT
CTTCGACGTCATACACAATAGATCGACGTAATCACGCTGGATAAGATTTAGGTTATGATACCAAG
ATAACCGGGTAACGAACGAAACATCTCTTCAAGGTGTTCAAACAAATTACGTTTTATCGATAGGA
TATCTCTTCCAATGAATCAGGCTGATCAATGGCTAATACATACCT
Right flanking sequence: Indices 3576 -- 4075
TAAACTCTATTAGCTTACTATTTACAAGCTTCTACCTACTCCGCCTTGGCTGCCTCCTTGGTCAA
CCCCGCCACACACTTCCACATCAACGCGAGCTCGTCGTCCAGCGCGTACCCCAGCGTCGCCCACC
GGATACGGCCCTCGTGGTCCAACAAGTACACGTAGCCCAGACACATGTTGTCGCACTTGAGCTTT
TCCCGAATGTCGTAAGGGAACACATGCTCGGGAAGCACAAAGTAGCGGTCCCAGCGGTCGTGGGG
CAAAGTACGTCGGATGTGGCCCTTGCTCATGTTGATGATGAACCCCTTCAACCAGTTCTGGGGGA
TGTTGATGTCAATCACCTGAGCCTCGGGGTACTGCTCCTTGAACTTGTTGTGGTAGTTTTCGCCC
TCCAAGAAGTCCTTGAACCAGGTGTTGACACAGTTTTCACCGGACACCGTCAGGTACACACGCAC
AATGTTGACGGGCCCCAACACGTCAAACAAGCTGGTGGGCCCCAC
Found at i:3559 original size:20 final size:20
Alignment explanation
Indices: 3534--3575 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3524 ATACATACCT
*
3534 ACACCCGCACACACCCACAC
1 ACACCCACACACACCCACAC
*
3554 ACACCCACACACACGCACAC
1 ACACCCACACACACCCACAC
3574 AC
1 AC
3576 TAAACTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.57, G:0.05, T:0.00
Consensus pattern (20 bp):
ACACCCACACACACCCACAC
Left flanking sequence: Indices 3034 -- 3533
AAATCTGATTGTTTCGCCGAGAGCAACCAGTGCCGCTAAGAGAGCCCGTGAAGCAAAGGACTCGG
TCCAAAGGCGCACCTAACGCACCCAGGTCAATACTATTGTTAAGTTTACGAGGTATCTACGTAGA
AGAGCCCATTAGTGGCATCTTTGTCCATTGTACCCCTTTCGATCAATAAAAGTGTGGCTCACGCT
TATCGCAAATCGTCGGAAGAATGGGCCTATAAGCGGGAGGACGGGCTCCGGGGCTGTGCGACGAC
CTGTCCTCGCAACCTGTGGCTCGTGGCCATGCCTATTCAAGGTTGCAACACGCGATCAGGAGGGT
CTTCGACGTCATACACAATAGATCGACGTAATCACGCTGGATAAGATTTAGGTTATGATACCAAG
ATAACCGGGTAACGAACGAAACATCTCTTCAAGGTGTTCAAACAAATTACGTTTTATCGATAGGA
TATCTCTTCCAATGAATCAGGCTGATCAATGGCTAATACATACCT
Right flanking sequence: Indices 3576 -- 4075
TAAACTCTATTAGCTTACTATTTACAAGCTTCTACCTACTCCGCCTTGGCTGCCTCCTTGGTCAA
CCCCGCCACACACTTCCACATCAACGCGAGCTCGTCGTCCAGCGCGTACCCCAGCGTCGCCCACC
GGATACGGCCCTCGTGGTCCAACAAGTACACGTAGCCCAGACACATGTTGTCGCACTTGAGCTTT
TCCCGAATGTCGTAAGGGAACACATGCTCGGGAAGCACAAAGTAGCGGTCCCAGCGGTCGTGGGG
CAAAGTACGTCGGATGTGGCCCTTGCTCATGTTGATGATGAACCCCTTCAACCAGTTCTGGGGGA
TGTTGATGTCAATCACCTGAGCCTCGGGGTACTGCTCCTTGAACTTGTTGTGGTAGTTTTCGCCC
TCCAAGAAGTCCTTGAACCAGGTGTTGACACAGTTTTCACCGGACACCGTCAGGTACACACGCAC
AATGTTGACGGGCCCCAACACGTCAAACAAGCTGGTGGGCCCCAC
Found at i:4792 original size:11 final size:11
Alignment explanation
Indices: 4776--4844 Score: 68
Period size: 11 Copynumber: 5.9 Consensus size: 11
4766 AATTCCCCAA
4776 CCACCACCCGT
1 CCACCACCCGT
4787 CCACCACCACCCGT
1 ---CCACCACCCGT
4801 CCACACCACCCGT
1 -C-CACCACCCGT
4814 CCACCACCCGT
1 CCACCACCCGT
**
4825 CCACCGGCCG-
1 CCACCACCCGT
4835 CCACCACCCG
1 CCACCACCCG
4845 CTCCTGCACA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
10 8 0.16
11 18 0.37
12 2 0.04
13 10 0.20
14 11 0.22
ACGTcount: A:0.19, C:0.64, G:0.12, T:0.06
Consensus pattern (11 bp):
CCACCACCCGT
Left flanking sequence: Indices 4276 -- 4775
GCGAGTATGTGTGGGACACCTTGCGGTTGAGGAGCACCGGGGTGTCTAGGCCAAACGGGCGGGTG
ATGGCCATGGGCTTTTCGAGCGGGGGCTTGGACGCCTCCTTGAGGGTGGTCACAAACCGTGGCAG
CTTGTGGAGCGGCGCCAGCGTGGCGAACCGCGCGATGGCAAGACGGTTCATGGTGAGTCGCACCG
GAATGGTGAGCGAAGAGAAGGGTGGTGGGGTTACGTAGAGAGAGGCAGAACTGGGCCAGGAAAAA
ACTCAAGAATGGAACCGGAAGCCAGCCACTACAGACAGAAGAAGATCATAGTGTGTTATTGTCCC
GACATTGGCTGATACTGATAATTGACTCATGTTGCAATTACATTGCGAGCGCGGTTATTTCCTCC
GGTGTATCAAGACGTGAAAAGCAGCAAACCGAACACTACACACCAACTTCCACAAACGGCCATCC
TTACCAACACAGCACACCACAACTGTCAGCGCCACAATTCCCCAA
Right flanking sequence: Indices 4845 -- 5344
CTCCTGCACACACCCTCACTTTTTTTTGACCGACGTTAAACCTCTCCACCAGAACCCCATCCATA
TGTCGATCCCCCTCCTCAACGGGCTAGCCCACCAGCTGGTGGACCACGTGATGGAGGATCTTCTT
GTGCGCTTTGTCGTCAACTGCCCCGACGAAGACCTTCTGCTGATCGAACGCGTTTTTTTCCAGGT
GGAGGAGGCCCAGTGGTTCTACACAGACTTTGTCCGGTTGTTGGACCCCAAGTTGCCCCCGATGA
AAATGAAGCAGTTTGCGGGCAAGATGTTGGAAAAGGCCCCGCTCATCTGGAAGTGGGGCGATCCG
GGCGACGCCCTCGCCCGTTTTGGCCACTACAAGCTGACGATCCCCGTGCGCGGGGTGGCGTGCTT
CAATCCCGATTTCTCGAAGGTGCTTCTTGTCAAGGGCACCGACTCCAACCTGTGGTCGTTTCCCC
GAGGCAAAATCTCCAAGGGCGAGCTGGATATCGAGTGTGCGGTCC
Found at i:4792 original size:14 final size:14
Alignment explanation
Indices: 4775--4821 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
4765 CAATTCCCCA
4775 ACCACCACCCGTCC
1 ACCACCACCCGTCC
4789 ACCACCACCCGTCC
1 ACCACCACCCGTCC
4803 A-CACCACCCGTCC
1 ACCACCACCCGTCC
4816 ACCACC
1 ACCACC
4822 CGTCCACCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.41
14 19 0.59
ACGTcount: A:0.23, C:0.64, G:0.06, T:0.06
Consensus pattern (14 bp):
ACCACCACCCGTCC
Left flanking sequence: Indices 4275 -- 4774
AGCGAGTATGTGTGGGACACCTTGCGGTTGAGGAGCACCGGGGTGTCTAGGCCAAACGGGCGGGT
GATGGCCATGGGCTTTTCGAGCGGGGGCTTGGACGCCTCCTTGAGGGTGGTCACAAACCGTGGCA
GCTTGTGGAGCGGCGCCAGCGTGGCGAACCGCGCGATGGCAAGACGGTTCATGGTGAGTCGCACC
GGAATGGTGAGCGAAGAGAAGGGTGGTGGGGTTACGTAGAGAGAGGCAGAACTGGGCCAGGAAAA
AACTCAAGAATGGAACCGGAAGCCAGCCACTACAGACAGAAGAAGATCATAGTGTGTTATTGTCC
CGACATTGGCTGATACTGATAATTGACTCATGTTGCAATTACATTGCGAGCGCGGTTATTTCCTC
CGGTGTATCAAGACGTGAAAAGCAGCAAACCGAACACTACACACCAACTTCCACAAACGGCCATC
CTTACCAACACAGCACACCACAACTGTCAGCGCCACAATTCCCCA
Right flanking sequence: Indices 4822 -- 5321
CGTCCACCGGCCGCCACCACCCGCTCCTGCACACACCCTCACTTTTTTTTGACCGACGTTAAACC
TCTCCACCAGAACCCCATCCATATGTCGATCCCCCTCCTCAACGGGCTAGCCCACCAGCTGGTGG
ACCACGTGATGGAGGATCTTCTTGTGCGCTTTGTCGTCAACTGCCCCGACGAAGACCTTCTGCTG
ATCGAACGCGTTTTTTTCCAGGTGGAGGAGGCCCAGTGGTTCTACACAGACTTTGTCCGGTTGTT
GGACCCCAAGTTGCCCCCGATGAAAATGAAGCAGTTTGCGGGCAAGATGTTGGAAAAGGCCCCGC
TCATCTGGAAGTGGGGCGATCCGGGCGACGCCCTCGCCCGTTTTGGCCACTACAAGCTGACGATC
CCCGTGCGCGGGGTGGCGTGCTTCAATCCCGATTTCTCGAAGGTGCTTCTTGTCAAGGGCACCGA
CTCCAACCTGTGGTCGTTTCCCCGAGGCAAAATCTCCAAGGGCGA
Found at i:6182 original size:18 final size:18
Alignment explanation
Indices: 6155--6192 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6145 GCCACCGGCT
*
6155 CTGCGGGCGGGTCGGTGG
1 CTGCGAGCGGGTCGGTGG
6173 CTGCGAGCGGGTCGGTGG
1 CTGCGAGCGGGTCGGTGG
6191 CT
1 CT
6193 CCGCAGCCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.24, G:0.55, T:0.18
Consensus pattern (18 bp):
CTGCGAGCGGGTCGGTGG
Left flanking sequence: Indices 5655 -- 6154
GGAAATGGCCCTCAAGGAGTTGTTGGGGCTCACGAAGCCGTTGGAGAAGACCGACGACGCAGGCC
GCGAGTTGTTGAACATCTTGCAGGGCCCGCAGACCGGCCACGCCCAGACGCAGCCCCAGCCGCAC
CCGGGCCAGCCCGGCCCGCCTCCGATGATCCAGATCCCCCACTACGTGTACCAGCCGGTCCAGCA
GTTTTTGCCCGGCCCGATGCCGTTCCCGCCCATGCCCATGCAGTTTGCGCCGCCGCAACAGCCCC
CGAACCCGCAGCTGTTGCAGAAACCGACGATGAAGCCCGAGCTGAAGGAGTTGTTGCTGATCTTG
AACTCGCTGGGCACGCCCAAACGGTCGCGCGACGCCACGCCCACCGCTGGCCGCGACGCCAACCG
CCTGAAGGCCGACGAGCTCTTGCTGTTGTTCAAAAAGCCGTCGAAAAACCCTGTAGAAACGTCGC
CCGCGCCGCTGGTGGCGCTGGTGCCGCTGGTGGGAGCCACCGGCT
Right flanking sequence: Indices 6193 -- 6692
CCGCAGCCGCTGACACAGCCGCGCGACGGCCCTGCTGGCGACTTGTTGTCGATTTTGCACCGCAA
GGGCCAGCTGCCCGCGCCGTTTGAGCCGCTGAACGAGTTGGAGGGGTCGATGCGCGGGTCCCAGC
CGGGCCCGAAGAAGGTGACGGTGTTGAAGCGGCTGGAGAACAAGAACGCCAACGACTTGTTGTCG
TTGTTGAAGCCGAAGAAGGAGGACGAGCAGTCTGGTGGAGAGGCCCAGGCTAAGGAGGTCCAGGC
TAAGGAGGTCCAGGCTAAGGAGGCCCAGCCCAGGGAGGCCCAGCCCAAGGAGTCTCCGTCGCAGG
AGCTTTTGGGGATGTTGAGAGGCAAGCCAGACACTCCTGCTCAGGGCGAGGCGGCTCATCCTCAG
GCTCAGGCTCAGGCTCAGCCTGGTCAGGGTCATTTTCAGTCTCAGGCCCAGGCTCAGCCTCAGTC
TCAGGCTCAATCCCATCCTGTCCAGTCCCAGTCTCAACCTGTCCA
Found at i:6450 original size:15 final size:15
Alignment explanation
Indices: 6427--6495 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
6417 GTCTGGTGGA
6427 GAGGCCCAGGCTAAG
1 GAGGCCCAGGCTAAG
*
6442 GAGGTCCAGGCTAAG
1 GAGGCCCAGGCTAAG
*
6457 GAGGTCCAGGCTAAG
1 GAGGCCCAGGCTAAG
* * *
6472 GAGGCCCAGCCCAGG
1 GAGGCCCAGGCTAAG
6487 GAGGCCCAG
1 GAGGCCCAG
6496 CCCAAGGAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.25, C:0.28, G:0.41, T:0.07
Consensus pattern (15 bp):
GAGGCCCAGGCTAAG
Left flanking sequence: Indices 5927 -- 6426
TGTTGCAGAAACCGACGATGAAGCCCGAGCTGAAGGAGTTGTTGCTGATCTTGAACTCGCTGGGC
ACGCCCAAACGGTCGCGCGACGCCACGCCCACCGCTGGCCGCGACGCCAACCGCCTGAAGGCCGA
CGAGCTCTTGCTGTTGTTCAAAAAGCCGTCGAAAAACCCTGTAGAAACGTCGCCCGCGCCGCTGG
TGGCGCTGGTGCCGCTGGTGGGAGCCACCGGCTCTGCGGGCGGGTCGGTGGCTGCGAGCGGGTCG
GTGGCTCCGCAGCCGCTGACACAGCCGCGCGACGGCCCTGCTGGCGACTTGTTGTCGATTTTGCA
CCGCAAGGGCCAGCTGCCCGCGCCGTTTGAGCCGCTGAACGAGTTGGAGGGGTCGATGCGCGGGT
CCCAGCCGGGCCCGAAGAAGGTGACGGTGTTGAAGCGGCTGGAGAACAAGAACGCCAACGACTTG
TTGTCGTTGTTGAAGCCGAAGAAGGAGGACGAGCAGTCTGGTGGA
Right flanking sequence: Indices 6496 -- 6995
CCCAAGGAGTCTCCGTCGCAGGAGCTTTTGGGGATGTTGAGAGGCAAGCCAGACACTCCTGCTCA
GGGCGAGGCGGCTCATCCTCAGGCTCAGGCTCAGGCTCAGCCTGGTCAGGGTCATTTTCAGTCTC
AGGCCCAGGCTCAGCCTCAGTCTCAGGCTCAATCCCATCCTGTCCAGTCCCAGTCTCAACCTGTC
CAGTCTCAGTCTCAGTTTGCCCTGTCTCACCAGTCACCTACCCAGCCCGCTCAGCCCGCTCCCCA
GACTCTGAACCCCCTCCTTGACATGTTGCATAACCCACGCGAGCAGAAACTGGCGTCCAACGAAC
TCTTGGGCATGCTCCACAAGTCCCAGCTGGGCACACCCGCGTCGGGCTCGCCTGCTCCGAGCAAG
AACCCCGCGTCACAAGACCTTTTGAACCTTTTGAAGCCCAAGGAAAAGCCCGAACCCGCGCCGCA
GCCGCAGGAAACCCCGGAGTTCGAAGACTTCGAGGACTTCGAGGA
Found at i:6490 original size:30 final size:30
Alignment explanation
Indices: 6427--6504 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
6417 GTCTGGTGGA
* * *
6427 GAGGCCCAGGCTAAGGAGGTCCAGGCTAAG
1 GAGGCCCAGGCTAAGGAGGCCCAGCCCAAG
* *
6457 GAGGTCCAGGCTAAGGAGGCCCAGCCCAGG
1 GAGGCCCAGGCTAAGGAGGCCCAGCCCAAG
* *
6487 GAGGCCCAGCCCAAGGAG
1 GAGGCCCAGGCTAAGGAG
6505 TCTCCGTCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.28, G:0.40, T:0.06
Consensus pattern (30 bp):
GAGGCCCAGGCTAAGGAGGCCCAGCCCAAG
Left flanking sequence: Indices 5927 -- 6426
TGTTGCAGAAACCGACGATGAAGCCCGAGCTGAAGGAGTTGTTGCTGATCTTGAACTCGCTGGGC
ACGCCCAAACGGTCGCGCGACGCCACGCCCACCGCTGGCCGCGACGCCAACCGCCTGAAGGCCGA
CGAGCTCTTGCTGTTGTTCAAAAAGCCGTCGAAAAACCCTGTAGAAACGTCGCCCGCGCCGCTGG
TGGCGCTGGTGCCGCTGGTGGGAGCCACCGGCTCTGCGGGCGGGTCGGTGGCTGCGAGCGGGTCG
GTGGCTCCGCAGCCGCTGACACAGCCGCGCGACGGCCCTGCTGGCGACTTGTTGTCGATTTTGCA
CCGCAAGGGCCAGCTGCCCGCGCCGTTTGAGCCGCTGAACGAGTTGGAGGGGTCGATGCGCGGGT
CCCAGCCGGGCCCGAAGAAGGTGACGGTGTTGAAGCGGCTGGAGAACAAGAACGCCAACGACTTG
TTGTCGTTGTTGAAGCCGAAGAAGGAGGACGAGCAGTCTGGTGGA
Right flanking sequence: Indices 6505 -- 7004
TCTCCGTCGCAGGAGCTTTTGGGGATGTTGAGAGGCAAGCCAGACACTCCTGCTCAGGGCGAGGC
GGCTCATCCTCAGGCTCAGGCTCAGGCTCAGCCTGGTCAGGGTCATTTTCAGTCTCAGGCCCAGG
CTCAGCCTCAGTCTCAGGCTCAATCCCATCCTGTCCAGTCCCAGTCTCAACCTGTCCAGTCTCAG
TCTCAGTTTGCCCTGTCTCACCAGTCACCTACCCAGCCCGCTCAGCCCGCTCCCCAGACTCTGAA
CCCCCTCCTTGACATGTTGCATAACCCACGCGAGCAGAAACTGGCGTCCAACGAACTCTTGGGCA
TGCTCCACAAGTCCCAGCTGGGCACACCCGCGTCGGGCTCGCCTGCTCCGAGCAAGAACCCCGCG
TCACAAGACCTTTTGAACCTTTTGAAGCCCAAGGAAAAGCCCGAACCCGCGCCGCAGCCGCAGGA
AACCCCGGAGTTCGAAGACTTCGAGGACTTCGAGGACTTTGGCGA
Found at i:6496 original size:15 final size:15
Alignment explanation
Indices: 6427--6504 Score: 75
Period size: 15 Copynumber: 5.2 Consensus size: 15
6417 GTCTGGTGGA
* *
6427 GAGGCCCAGGCTAAG
1 GAGGCCCAGCCCAAG
* * *
6442 GAGGTCCAGGCTAAG
1 GAGGCCCAGCCCAAG
* * *
6457 GAGGTCCAGGCTAAG
1 GAGGCCCAGCCCAAG
*
6472 GAGGCCCAGCCCAGG
1 GAGGCCCAGCCCAAG
6487 GAGGCCCAGCCCAAG
1 GAGGCCCAGCCCAAG
6502 GAG
1 GAG
6505 TCTCCGTCGC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.26, C:0.28, G:0.40, T:0.06
Consensus pattern (15 bp):
GAGGCCCAGCCCAAG
Left flanking sequence: Indices 5927 -- 6426
TGTTGCAGAAACCGACGATGAAGCCCGAGCTGAAGGAGTTGTTGCTGATCTTGAACTCGCTGGGC
ACGCCCAAACGGTCGCGCGACGCCACGCCCACCGCTGGCCGCGACGCCAACCGCCTGAAGGCCGA
CGAGCTCTTGCTGTTGTTCAAAAAGCCGTCGAAAAACCCTGTAGAAACGTCGCCCGCGCCGCTGG
TGGCGCTGGTGCCGCTGGTGGGAGCCACCGGCTCTGCGGGCGGGTCGGTGGCTGCGAGCGGGTCG
GTGGCTCCGCAGCCGCTGACACAGCCGCGCGACGGCCCTGCTGGCGACTTGTTGTCGATTTTGCA
CCGCAAGGGCCAGCTGCCCGCGCCGTTTGAGCCGCTGAACGAGTTGGAGGGGTCGATGCGCGGGT
CCCAGCCGGGCCCGAAGAAGGTGACGGTGTTGAAGCGGCTGGAGAACAAGAACGCCAACGACTTG
TTGTCGTTGTTGAAGCCGAAGAAGGAGGACGAGCAGTCTGGTGGA
Right flanking sequence: Indices 6505 -- 7004
TCTCCGTCGCAGGAGCTTTTGGGGATGTTGAGAGGCAAGCCAGACACTCCTGCTCAGGGCGAGGC
GGCTCATCCTCAGGCTCAGGCTCAGGCTCAGCCTGGTCAGGGTCATTTTCAGTCTCAGGCCCAGG
CTCAGCCTCAGTCTCAGGCTCAATCCCATCCTGTCCAGTCCCAGTCTCAACCTGTCCAGTCTCAG
TCTCAGTTTGCCCTGTCTCACCAGTCACCTACCCAGCCCGCTCAGCCCGCTCCCCAGACTCTGAA
CCCCCTCCTTGACATGTTGCATAACCCACGCGAGCAGAAACTGGCGTCCAACGAACTCTTGGGCA
TGCTCCACAAGTCCCAGCTGGGCACACCCGCGTCGGGCTCGCCTGCTCCGAGCAAGAACCCCGCG
TCACAAGACCTTTTGAACCTTTTGAAGCCCAAGGAAAAGCCCGAACCCGCGCCGCAGCCGCAGGA
AACCCCGGAGTTCGAAGACTTCGAGGACTTCGAGGACTTTGGCGA
Found at i:6587 original size:6 final size:6
Alignment explanation
Indices: 6578--6656 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
6568 GCGGCTCATC
* * ** * *
6578 CTCAGG CTCAGG CTCAGG CTCA-G C-CTGG -TCAGG GTCATT TTCAGT
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG
* * *
6623 CTCAGG CCCAGG CTCAGC CTCAGT CTCAGG CTCA
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCA
6657 ATCCCATCCT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
4 1 0.02
5 6 0.11
6 50 0.88
ACGTcount: A:0.16, C:0.34, G:0.27, T:0.23
Consensus pattern (6 bp):
CTCAGG
Left flanking sequence: Indices 6078 -- 6577
AAAGCCGTCGAAAAACCCTGTAGAAACGTCGCCCGCGCCGCTGGTGGCGCTGGTGCCGCTGGTGG
GAGCCACCGGCTCTGCGGGCGGGTCGGTGGCTGCGAGCGGGTCGGTGGCTCCGCAGCCGCTGACA
CAGCCGCGCGACGGCCCTGCTGGCGACTTGTTGTCGATTTTGCACCGCAAGGGCCAGCTGCCCGC
GCCGTTTGAGCCGCTGAACGAGTTGGAGGGGTCGATGCGCGGGTCCCAGCCGGGCCCGAAGAAGG
TGACGGTGTTGAAGCGGCTGGAGAACAAGAACGCCAACGACTTGTTGTCGTTGTTGAAGCCGAAG
AAGGAGGACGAGCAGTCTGGTGGAGAGGCCCAGGCTAAGGAGGTCCAGGCTAAGGAGGTCCAGGC
TAAGGAGGCCCAGCCCAGGGAGGCCCAGCCCAAGGAGTCTCCGTCGCAGGAGCTTTTGGGGATGT
TGAGAGGCAAGCCAGACACTCCTGCTCAGGGCGAGGCGGCTCATC
Right flanking sequence: Indices 6657 -- 7156
ATCCCATCCTGTCCAGTCCCAGTCTCAACCTGTCCAGTCTCAGTCTCAGTTTGCCCTGTCTCACC
AGTCACCTACCCAGCCCGCTCAGCCCGCTCCCCAGACTCTGAACCCCCTCCTTGACATGTTGCAT
AACCCACGCGAGCAGAAACTGGCGTCCAACGAACTCTTGGGCATGCTCCACAAGTCCCAGCTGGG
CACACCCGCGTCGGGCTCGCCTGCTCCGAGCAAGAACCCCGCGTCACAAGACCTTTTGAACCTTT
TGAAGCCCAAGGAAAAGCCCGAACCCGCGCCGCAGCCGCAGGAAACCCCGGAGTTCGAAGACTTC
GAGGACTTCGAGGACTTTGGCGACCTCGACCACCAGTTCTCCCGCACGTTCCACAACTTCGACAT
CGAGCTGGACGAAGAAGACGTAGACCACCTCTTGGAAAACAACAAACCCATTGACTTTTTCAAGC
AGCAAGCCAGCCCGGACAAGATCCAGATCGCCAAGCCCGGGAGCT
Found at i:6587 original size:12 final size:12
Alignment explanation
Indices: 6570--6603 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6560 AGGGCGAGGC
*
6570 GGCTCATCCTCA
1 GGCTCAGCCTCA
*
6582 GGCTCAGGCTCA
1 GGCTCAGCCTCA
6594 GGCTCAGCCT
1 GGCTCAGCCT
6604 GGTCAGGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (12 bp):
GGCTCAGCCTCA
Left flanking sequence: Indices 6070 -- 6569
TTGTTCAAAAAGCCGTCGAAAAACCCTGTAGAAACGTCGCCCGCGCCGCTGGTGGCGCTGGTGCC
GCTGGTGGGAGCCACCGGCTCTGCGGGCGGGTCGGTGGCTGCGAGCGGGTCGGTGGCTCCGCAGC
CGCTGACACAGCCGCGCGACGGCCCTGCTGGCGACTTGTTGTCGATTTTGCACCGCAAGGGCCAG
CTGCCCGCGCCGTTTGAGCCGCTGAACGAGTTGGAGGGGTCGATGCGCGGGTCCCAGCCGGGCCC
GAAGAAGGTGACGGTGTTGAAGCGGCTGGAGAACAAGAACGCCAACGACTTGTTGTCGTTGTTGA
AGCCGAAGAAGGAGGACGAGCAGTCTGGTGGAGAGGCCCAGGCTAAGGAGGTCCAGGCTAAGGAG
GTCCAGGCTAAGGAGGCCCAGCCCAGGGAGGCCCAGCCCAAGGAGTCTCCGTCGCAGGAGCTTTT
GGGGATGTTGAGAGGCAAGCCAGACACTCCTGCTCAGGGCGAGGC
Right flanking sequence: Indices 6604 -- 7103
GGTCAGGGTCATTTTCAGTCTCAGGCCCAGGCTCAGCCTCAGTCTCAGGCTCAATCCCATCCTGT
CCAGTCCCAGTCTCAACCTGTCCAGTCTCAGTCTCAGTTTGCCCTGTCTCACCAGTCACCTACCC
AGCCCGCTCAGCCCGCTCCCCAGACTCTGAACCCCCTCCTTGACATGTTGCATAACCCACGCGAG
CAGAAACTGGCGTCCAACGAACTCTTGGGCATGCTCCACAAGTCCCAGCTGGGCACACCCGCGTC
GGGCTCGCCTGCTCCGAGCAAGAACCCCGCGTCACAAGACCTTTTGAACCTTTTGAAGCCCAAGG
AAAAGCCCGAACCCGCGCCGCAGCCGCAGGAAACCCCGGAGTTCGAAGACTTCGAGGACTTCGAG
GACTTTGGCGACCTCGACCACCAGTTCTCCCGCACGTTCCACAACTTCGACATCGAGCTGGACGA
AGAAGACGTAGACCACCTCTTGGAAAACAACAAACCCATTGACTT
Found at i:6690 original size:21 final size:21
Alignment explanation
Indices: 6664--6704 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6654 TCAATCCCAT
6664 CCTGTCCAGTCCCAGTCTCAA
1 CCTGTCCAGTCCCAGTCTCAA
*
6685 CCTGTCCAGTCTCAGTCTCA
1 CCTGTCCAGTCCCAGTCTCA
6705 GTTTGCCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.41, G:0.15, T:0.27
Consensus pattern (21 bp):
CCTGTCCAGTCCCAGTCTCAA
Left flanking sequence: Indices 6164 -- 6663
GGTCGGTGGCTGCGAGCGGGTCGGTGGCTCCGCAGCCGCTGACACAGCCGCGCGACGGCCCTGCT
GGCGACTTGTTGTCGATTTTGCACCGCAAGGGCCAGCTGCCCGCGCCGTTTGAGCCGCTGAACGA
GTTGGAGGGGTCGATGCGCGGGTCCCAGCCGGGCCCGAAGAAGGTGACGGTGTTGAAGCGGCTGG
AGAACAAGAACGCCAACGACTTGTTGTCGTTGTTGAAGCCGAAGAAGGAGGACGAGCAGTCTGGT
GGAGAGGCCCAGGCTAAGGAGGTCCAGGCTAAGGAGGTCCAGGCTAAGGAGGCCCAGCCCAGGGA
GGCCCAGCCCAAGGAGTCTCCGTCGCAGGAGCTTTTGGGGATGTTGAGAGGCAAGCCAGACACTC
CTGCTCAGGGCGAGGCGGCTCATCCTCAGGCTCAGGCTCAGGCTCAGCCTGGTCAGGGTCATTTT
CAGTCTCAGGCCCAGGCTCAGCCTCAGTCTCAGGCTCAATCCCAT
Right flanking sequence: Indices 6705 -- 7204
GTTTGCCCTGTCTCACCAGTCACCTACCCAGCCCGCTCAGCCCGCTCCCCAGACTCTGAACCCCC
TCCTTGACATGTTGCATAACCCACGCGAGCAGAAACTGGCGTCCAACGAACTCTTGGGCATGCTC
CACAAGTCCCAGCTGGGCACACCCGCGTCGGGCTCGCCTGCTCCGAGCAAGAACCCCGCGTCACA
AGACCTTTTGAACCTTTTGAAGCCCAAGGAAAAGCCCGAACCCGCGCCGCAGCCGCAGGAAACCC
CGGAGTTCGAAGACTTCGAGGACTTCGAGGACTTTGGCGACCTCGACCACCAGTTCTCCCGCACG
TTCCACAACTTCGACATCGAGCTGGACGAAGAAGACGTAGACCACCTCTTGGAAAACAACAAACC
CATTGACTTTTTCAAGCAGCAAGCCAGCCCGGACAAGATCCAGATCGCCAAGCCCGGGAGCTTGG
CGAGCCCGCAGCCGCACTACCAGCCGCAGTTCCCCCAGCAGGTGT
Found at i:11020 original size:20 final size:21
Alignment explanation
Indices: 10995--11034 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
10985 ACACTGTCTT
10995 ATTCTCTACTTCAAT-CCTTC
1 ATTCTCTACTTCAATACCTTC
11015 ATTCTCTACTTCAATACCTT
1 ATTCTCTACTTCAATACCTT
11035 GCCGTCGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTCTCTACTTCAATACCTTC
Left flanking sequence: Indices 10495 -- 10994
CGAGACACGTAGGGGTTAACGAAAGGTGGTCCCTGATCATACGGAAACTGTCGCGTGCTGCAACT
AGCAATTGATGACGAGGGCCACTGGGGGCTCGCTTAAGCATACGCAATGGGTTTTTGGTGGTATG
GTACGATACCAAGCCAAATCCGCGGGTGTCAACACACTACGGGAGGGTAGCAGGGGGTGGTTAGG
CACTATGGGGTGATGAAGCATTGTGGGGTGGTCCGAGAAAACAAAGTAACCAAGGAGTACACTCT
AACCAACCCACTCATCCCCTTTAGTGTTTCTTCTAGACTACCATTAAATCTCCCCTTCAACCAAG
GACCACTCTCAAATCTAAAGGAAGGACACCCAGGGGCGTAAAACTACGGTACTTCATACACCAAG
GAACGCTTGGACACTACGATGCACCCACTCACAAATCACCGATATACTACCTTCACGCTTCCACT
CTGTAAACGTCCTGAAAGCAGCTCAATCAGCTCACACACTGTCTT
Right flanking sequence: Indices 11035 -- 11534
GCCGTCGGCAATCTCAACCGACTTCCCGTCAACCACCACCGGCTTGTCCCACGCCATCATGTTCT
CAAAAAAGTCCTTGTCCTCCTCCTTCGAGGGGTCCAAAGGCTTGTAGTCGTACGACTCCCAGTCA
GGAGCAACGTCGAAAGCAGGCGCAAACTCCTTGCCACGCACAATGAACGCACCCACAATCCCGTT
GTTGTTGTTCTCCCCGTAGACAACCATGCACCCAAACATGTACTTGGTGGACGCGGACAACCGGT
TGAAGAACCCACCAACCAAGTTGTTGGACATAAAGGTGAGCGTCAACTCGTCGTTGTACTTGTAG
TCCACACGCCACATCGACCACTCGTCCGGGTTCCAGAAGTTCTTCCAGAACCAGGGGAGCGCCAC
CTCGCGCGTCTCCTCGTTGGAGTAGAATCTCTTCCACTCGTCAATGGGGGTGGAAGGCTTGCCGA
GCGCCTCAAGCGGGTGCTTGGGCTTGGGAGCCTGCTGGGGAGTCT
Found at i:12470 original size:9 final size:9
Alignment explanation
Indices: 12453--12487 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
12443 TATTGTGTTT
*
12453 GTTTAGTGG
1 GTTTCGTGG
12462 GTTTCGTGG
1 GTTTCGTGG
12471 GTTTCGTGG
1 GTTTCGTGG
12480 GTTT-GTGG
1 GTTTCGTGG
12488 TGTTCGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.03, C:0.06, G:0.46, T:0.46
Consensus pattern (9 bp):
GTTTCGTGG
Left flanking sequence: Indices 11953 -- 12452
CCCGTCGCCAGTCAACGGCTTGAACGCATGGGCAGCACAGAGGAGCACCTCCGAGTTGACCAACG
ACATCCACATATCAATCAAGGCGAACTCCAAAGTGTTTTTCCCAAGCAATTTGGAGTCCGGGTCC
GCCAACCGGATGAAGTAGAACACAAGAGCCGTAGTCTCGTGCATCTTGACTCCCTTGTTGGTGAT
GAAAACGGGCACTTTCTCACGAGGGAACGCCTTTTTGAACTCAGGGTGACCCTCATACGAGTCGT
ACACGGTGAGGTCAATCTTGTAGTGGTCGATAAACGCCTTGACCGCCAACGGGCGGGTTCTGGGG
CCTAAGATGATGGTGCCTTGGGACATGATTGGAGAATTACGCACCCCGCAACTTTTCAGAAATGG
TTGCTGTGGACGACAGAAGCGGGTGGGTGTAGGAATAGGGGAGTGTTGAGTGGTGCTGTCGGGTG
ATGGAAATGTAGTATGTATCTAGGTAGAGGTATTGTATTGTGTTT
Right flanking sequence: Indices 12488 -- 12987
TGTTCGCTTAACTCCGAACCACCCAAGAGGTGGTGACGAAGGCAGTAAATAATGGGGTGGAAAGG
TACGGAGCAATTCGGAGGAGAACTAACGGTTGAGGGTGCTGAATAACGCGCAATTGACTTTCTAG
CTCTCCTGGTGTCTGCGCTGTGAGGCCCTCTACATTGTATTATAGAAGCTCGTTACTGGAACGTG
TGAACTACAGTAGGTGAAGTTGCTTCACGGGTATAGCCCTTGAAAATACATCCACAGCTACACTC
ATGATACTCTTCACTATTCGACTTCAGACGTGTGGCAATTGCAATTCGTTGCCGTGATCGATAAG
GCACTTTAGATGAGGCTCAAAAGCAATCTCGTTAGCCATAAGAGACGTCGCATGATTCGCATACC
CACCCATTAAAACTACTCAGGCTCAGTTGTTATCAATCGCCCTCCAAACCGATGACGCTCTTGCC
AATTCCTCTCTGTATTGATCATTTCACGTTACATCACCCAACTAG
Done.