Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold73
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: 140288
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Found at i:5223 original size:9 final size:9
Alignment explanation
Indices: 5211--5244 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
5201 AAAATATTAG
5211 GTTTTGTGA
1 GTTTTGTGA
5220 GTTTTGTGA
1 GTTTTGTGA
5229 GTTTTGTGA
1 GTTTTGTGA
5238 GTTTTGT
1 GTTTTGT
5245 TAGTATTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.32, T:0.59
Consensus pattern (9 bp):
GTTTTGTGA
Left flanking sequence: Indices 4711 -- 5210
AATTGAGAGAAAAAATATCCACGGTGCTCTGCACGAATGCGGAAACTTCTATACAAGTACATCGC
AACTAATGTGCCAATAGATGTACCTCCGCATATTATGCTTCAACTGACGATTATTTACCATCAGG
TCGATTGTAACTCTTCTCTATTTCCCTGCTACATTTCATTACATGTACGAAGAAGTGTATCCATG
CAGACTTACGGCCCAGACAGCAGTGAATGACTTTTTCAGTAGACGAATCTCCGGCTTGAAAGTTG
AGGAAAAGTATCACTATGTGATCCGCAGCTTAGACTTCACTAGTGGAATGTTGTGCTAGTATCGG
AATGCGGAGTCGGGTGTGTAAAAATATTTTTGAGCTCATCCTTTTCTGAGCAAGCCACTTTCGCG
ACAATTACGGCATCATAAGAACTCACACACGCCTTTTTTGTGGTTACGCAAGTGCTCGCGCTAGA
GTGATGTCGAGAAATCAGACGCGCATCAAATCAACAAAATATTAG
Right flanking sequence: Indices 5245 -- 5744
TAGTATTGGTAACATTTAGAGCAAACAAATCCAACAGAGCCGAGTACCGCAAATACACATGGTGC
ATGTAGGAAATATGGAAAATAGATGGAAACTATACAAAGCGAATATTGAAAAGTTTAAATTGACT
ACTTCGTGTGTTACGTCATCAAGCCACAAGCCTGAATTAGGTTTGAGGACATCAAAATGCAATAA
ATTAGGTAATAAAAATTTGCCGAAATTCCGTGGCTTATTGTTTGCACTTCGGACGATCGGCGCAG
ACATGGTGAGTAAGCCTAGTGAAATAGTCGATTCACTATCAAATTCCACTCTCATAGATATACAT
GTCCCAAAGTAACGAGCATATTGCACAGATGCGTAGAAAATTTAATAGCTGCATATTTTGCCGCC
AACGCACCAACGCACCAACCAACGCACGGCGGAGCTAGCCGACGAATTGTTTATTTATCGAGTCA
ACCTGAAACATGGAAGTCAGGAAATTCTACTTCTGTGAGACCAGC
Found at i:6043 original size:13 final size:13
Alignment explanation
Indices: 6002--6027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5992 CCTCTTTTTC
6002 CTTTTTTTTCACT
1 CTTTTTTTTCACT
6015 CTTTTTTTTCACT
1 CTTTTTTTTCACT
6028 TTTCCTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTTTTTTCACT
Left flanking sequence: Indices 5502 -- 6001
CAGACATGGTGAGTAAGCCTAGTGAAATAGTCGATTCACTATCAAATTCCACTCTCATAGATATA
CATGTCCCAAAGTAACGAGCATATTGCACAGATGCGTAGAAAATTTAATAGCTGCATATTTTGCC
GCCAACGCACCAACGCACCAACCAACGCACGGCGGAGCTAGCCGACGAATTGTTTATTTATCGAG
TCAACCTGAAACATGGAAGTCAGGAAATTCTACTTCTGTGAGACCAGCTACTACAGGCGGTCGCA
TTCGTAAGAAGAAAATTCCTGCAAGCACTCTTTTGAATGGGTCATGAGAAACGTCCGGTGCTCGG
AATCGCCCTTCTTGCGAACCTTCGAAACAAAACAGATTCATGATAAGCACAATTTGAGTAACACC
CATAGATTTTTCCAGACTCAAAAAATTCTCCCGAACCGAGAATCGAACTCGGATCTCCCGCGTGA
CAAGCGGAGATACTAACCGTTATACTATCCGGGAACCTCTTTTTC
Right flanking sequence: Indices 6028 -- 6527
TTTCCTCCTTTTTTTTTCTTCACTTTTCCTGAACATTAACTAGATACTTAGAAAATTAACGGCAT
GCGTCTTGTATGGGGAACCGTTGATTGGAGAAAAACCCATTGCATTTGTCATGACATGTGTGTCA
TGGTATTTGGTTGGCTTATGTTTTACAGTCAGATCTTACGTATCTAAGTACGTAGTTAGCAAATT
ATATGGGAAAAAAAAAAATGTCAGCTTCAAGGCAGGGGTTTAGCGAGTTCCCCCCTAACCGCTTG
ACCCAAGATGTTCTTTTCGAGATGGCCCGGTTTCTCCGCGCCGTCTTCCTCTTACGGAAAGAGAC
ACGACTTTCAAACAGCGCCCCCTAGCCCGTCACTGAAGGCCATTTGAAAGAGTAGATTAAGAACA
AATTGGAATACATCAAGACGGGTAGAGGCATGGCATGATCGATGATTTGAGACCAAAAAACGAAA
AAATCAAAAAAATCGAAAAACCCAAATTAAACAATTCGAATTTCA
Found at i:68309 original size:15 final size:16
Alignment explanation
Indices: 68289--68373 Score: 117
Period size: 15 Copynumber: 5.6 Consensus size: 16
68279 TGTTGCACTT
68289 TCCTTGG-CAGCCTTC
1 TCCTTGGCCAGCCTTC
*
68304 TCCTTGGTC-GCCTTC
1 TCCTTGGCCAGCCTTC
68319 TCCTTGG-CAGCCTTC
1 TCCTTGGCCAGCCTTC
*
68334 TCCTCGGCCA-CCTTC
1 TCCTTGGCCAGCCTTC
68349 TCCTTGGCCA-CCTTC
1 TCCTTGGCCAGCCTTC
68364 TCCTTGGCCA
1 TCCTTGGCCA
68374 CTCTGATCAT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
14 1 0.02
15 61 0.94
16 3 0.05
ACGTcount: A:0.06, C:0.44, G:0.18, T:0.33
Consensus pattern (16 bp):
TCCTTGGCCAGCCTTC
Left flanking sequence: Indices 67789 -- 68288
TTTTACTCATGGGATTGATTTCTCTTTGGTGGGGGATGCTTTTCATGACCAATGTATACTTCCAC
TCAATCCTTGAAAAGTTTGTTGGTTTGGTGTTTGGTTTTGCGGCCATCATACCCATCTACATACT
CCCACGTTGGCTTCAGCCCCCAGTTGAGCCTGAAAGGCAAAAGCAAGCATAGAATGGCTCAAAAA
TCATGTAATCGAGATGTATATACTAATTAATGATGAACTATAGATTTTCGGCAACTGGTTCTTCA
ACTGCAGGTCTATTCTCAGTAGCCTTTGATGAGATACGAAGCTTTTCTAATCGCTTCTCTAAGTC
GGCCTCGCTAATTTGTGTTTCAGATGAGCCGGTGTCTTCGGTCATACCTCCTCTATGCAGATCAT
TGGTTACGGGTTCCTTCGTACTTCGCTCAGCCTCTTCTTTCTTTGCACGTTCATCAAGACTGTAC
TCCGTAGTCGCATTTTCCTTGGCCATCATAGCTTGTGTTGCACTT
Right flanking sequence: Indices 68374 -- 68873
CTCTGATCATTGTCTCTTCTCGGAGCATTCGATCAAATTCGTCATCGACTTCAGCCTCAGCGGCT
TCGTCAATGTTGACCTCCGCAAGACGAGCCCCTACTTCATCAATCTTGGACATCTCCTCCACAAT
GCTATCCTTGACTGCATCGACATCATCGGTATTCAATCGGTCGTTGTAGTACTTCATGGCTTCAG
CTGCGTCTTGCATCGCGTCCATCACCACCACATTCAGCTGACTCTCGTCTAGTTTCATCATCACC
AGGCGTAGTTGAGATTCCGAGGACATGCCCTGGTCAAGCAGCTGTAAAACACGCTTTTTGAGTCG
CAACAAATGCTTGATTCGAGCTTCAGGGGCTTTTGTTTTCACTAAATCACGAGTCTTCTTCTCTA
ACCGGCTCAATTCGGCTGCGAGTCCCTCATTCCTCTTGGTAGTCGCCTGGCATGCGTTCTTAACA
TCAATAAAAGTCTTTTCGCTATCGGTGATCTCCAGGGAGTTAAGC
Found at i:68323 original size:30 final size:30
Alignment explanation
Indices: 68289--68374 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
68279 TGTTGCACTT
* *
68289 TCCTTGGCAGCCTTCTCCTTGGTCGCCTTC
1 TCCTTGGCAGCCTTCTCCTTGGCCACCTTC
*
68319 TCCTTGGCAGCCTTCTCCTCGGCCACCTTC
1 TCCTTGGCAGCCTTCTCCTTGGCCACCTTC
68349 TCCTTGGCCA-CCTTCTCCTTGGCCAC
1 TCCTTGG-CAGCCTTCTCCTTGGCCAC
68375 TCTGATCATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 49 0.96
31 2 0.04
ACGTcount: A:0.06, C:0.44, G:0.17, T:0.33
Consensus pattern (30 bp):
TCCTTGGCAGCCTTCTCCTTGGCCACCTTC
Left flanking sequence: Indices 67789 -- 68288
TTTTACTCATGGGATTGATTTCTCTTTGGTGGGGGATGCTTTTCATGACCAATGTATACTTCCAC
TCAATCCTTGAAAAGTTTGTTGGTTTGGTGTTTGGTTTTGCGGCCATCATACCCATCTACATACT
CCCACGTTGGCTTCAGCCCCCAGTTGAGCCTGAAAGGCAAAAGCAAGCATAGAATGGCTCAAAAA
TCATGTAATCGAGATGTATATACTAATTAATGATGAACTATAGATTTTCGGCAACTGGTTCTTCA
ACTGCAGGTCTATTCTCAGTAGCCTTTGATGAGATACGAAGCTTTTCTAATCGCTTCTCTAAGTC
GGCCTCGCTAATTTGTGTTTCAGATGAGCCGGTGTCTTCGGTCATACCTCCTCTATGCAGATCAT
TGGTTACGGGTTCCTTCGTACTTCGCTCAGCCTCTTCTTTCTTTGCACGTTCATCAAGACTGTAC
TCCGTAGTCGCATTTTCCTTGGCCATCATAGCTTGTGTTGCACTT
Right flanking sequence: Indices 68375 -- 68874
TCTGATCATTGTCTCTTCTCGGAGCATTCGATCAAATTCGTCATCGACTTCAGCCTCAGCGGCTT
CGTCAATGTTGACCTCCGCAAGACGAGCCCCTACTTCATCAATCTTGGACATCTCCTCCACAATG
CTATCCTTGACTGCATCGACATCATCGGTATTCAATCGGTCGTTGTAGTACTTCATGGCTTCAGC
TGCGTCTTGCATCGCGTCCATCACCACCACATTCAGCTGACTCTCGTCTAGTTTCATCATCACCA
GGCGTAGTTGAGATTCCGAGGACATGCCCTGGTCAAGCAGCTGTAAAACACGCTTTTTGAGTCGC
AACAAATGCTTGATTCGAGCTTCAGGGGCTTTTGTTTTCACTAAATCACGAGTCTTCTTCTCTAA
CCGGCTCAATTCGGCTGCGAGTCCCTCATTCCTCTTGGTAGTCGCCTGGCATGCGTTCTTAACAT
CAATAAAAGTCTTTTCGCTATCGGTGATCTCCAGGGAGTTAAGCT
Found at i:77428 original size:15 final size:12
Alignment explanation
Indices: 77392--77435 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
77382 GTGTTCTGAC
77392 GAGCTGGATGAT
1 GAGCTGGATGAT
77404 GAGCTGGATGAT
1 GAGCTGGATGAT
77416 GAGCTGGATGAT
1 GAGCTGGATGAT
77428 GAGCTGGA
1 GAGCTGGA
77436 GGAACTGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.43, T:0.23
Consensus pattern (12 bp):
GAGCTGGATGAT
Left flanking sequence: Indices 76892 -- 77391
CTACTATCCCAGACCTGCGGATTGCGCGTATTGAGGGTTTGTTGGACTTTGGAGAAAGAGAGTTT
GGCATTCCTCAGTTGGTAGACATCACCGACTTTCGAAAGGATGTGCCTGATGAAAAGTGTTTGTT
GCCCTACATTTTGGAGCTACATCGCCAATTTGCTAGCGAGAACGTTTTAATTCCCAAAAGTGCAA
AACCTGGGTTGCCTTTGGGCCACGAGGTTAAAGTTAACGACAAGGAGACGACAAACCTTTCCAAG
AATCAGGGACATCTGATGGTTCAAGAGTTGGTTCGCAAATTGTCCGCAGGCTCGCTGGTAGAGCT
TGAGACTAACACGACAACTGAAACGATGAACACTAAACACGAACCAGGCGTTGAGTCATTCTCCG
GTGATGCTCCGCCGGAGACACCCAACAATAATGCTCCGCGTAAAGAGGATAATCAAAGTATACTT
GGGCATCTGGATGATGCGGGTAATTTGGAGCTGGGGTGTTCTGAC
Right flanking sequence: Indices 77436 -- 77935
GGAACTGGGAGATGATCTGGACCATCTGGACGGTCTGGATTGTGATCTGGAAAAGCCTGTCAAAA
TAAATTCAACTCAGAAGTGCCCAGCACATGGGCAACTACTCAATGGGCCACACACCCCAAGAACG
GACCGAAGTAAAAAAGTTGTGTCTTTTGCCTCGCCCGAGCACGATAGTGATGCGTCTAGTGAGGG
CTCTGCCGAGCTGTCCGAGGACGATGCCACATCTAGTTCGGAGTCTGGGTCAGAAACCCTGACAC
TTGGCGACAGCGCCGAACCGATCGGTGACGACAATAGCACACTTGCAAGTCTGGTTACTAGTCAA
GCCCCTAAACTCACATTCAAGCAACGTATGGGGATGGTCTTCAAAAAGAGAAGCAAATCAACAAT
CCCCTCTGAATCAGAAGAATCTGAGCTCGATCTGAAGTACGTGCAAGCTTCTCCTGTTGAACCAA
TCACTTACGACTTCAACACCACTAATGATCTCGTCTACGTGTTAG
Found at i:77443 original size:21 final size:23
Alignment explanation
Indices: 77395--77456 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
77385 TTCTGACGAG
*
77395 CTGGATGATGAGCTGGATGATGAG
1 CTGGATGATGAGCTGGATGA-GAA
77419 CTGGATGATGAGCTGGA-G-GAA
1 CTGGATGATGAGCTGGATGAGAA
*
77440 CTGGGA-GATGATCTGGA
1 CT-GGATGATGAGCTGGA
77457 CCATCTGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.40
22 3 0.09
23 1 0.03
24 17 0.49
ACGTcount: A:0.26, C:0.10, G:0.42, T:0.23
Consensus pattern (23 bp):
CTGGATGATGAGCTGGATGAGAA
Left flanking sequence: Indices 76895 -- 77394
CTATCCCAGACCTGCGGATTGCGCGTATTGAGGGTTTGTTGGACTTTGGAGAAAGAGAGTTTGGC
ATTCCTCAGTTGGTAGACATCACCGACTTTCGAAAGGATGTGCCTGATGAAAAGTGTTTGTTGCC
CTACATTTTGGAGCTACATCGCCAATTTGCTAGCGAGAACGTTTTAATTCCCAAAAGTGCAAAAC
CTGGGTTGCCTTTGGGCCACGAGGTTAAAGTTAACGACAAGGAGACGACAAACCTTTCCAAGAAT
CAGGGACATCTGATGGTTCAAGAGTTGGTTCGCAAATTGTCCGCAGGCTCGCTGGTAGAGCTTGA
GACTAACACGACAACTGAAACGATGAACACTAAACACGAACCAGGCGTTGAGTCATTCTCCGGTG
ATGCTCCGCCGGAGACACCCAACAATAATGCTCCGCGTAAAGAGGATAATCAAAGTATACTTGGG
CATCTGGATGATGCGGGTAATTTGGAGCTGGGGTGTTCTGACGAG
Right flanking sequence: Indices 77457 -- 77956
CCATCTGGACGGTCTGGATTGTGATCTGGAAAAGCCTGTCAAAATAAATTCAACTCAGAAGTGCC
CAGCACATGGGCAACTACTCAATGGGCCACACACCCCAAGAACGGACCGAAGTAAAAAAGTTGTG
TCTTTTGCCTCGCCCGAGCACGATAGTGATGCGTCTAGTGAGGGCTCTGCCGAGCTGTCCGAGGA
CGATGCCACATCTAGTTCGGAGTCTGGGTCAGAAACCCTGACACTTGGCGACAGCGCCGAACCGA
TCGGTGACGACAATAGCACACTTGCAAGTCTGGTTACTAGTCAAGCCCCTAAACTCACATTCAAG
CAACGTATGGGGATGGTCTTCAAAAAGAGAAGCAAATCAACAATCCCCTCTGAATCAGAAGAATC
TGAGCTCGATCTGAAGTACGTGCAAGCTTCTCCTGTTGAACCAATCACTTACGACTTCAACACCA
CTAATGATCTCGTCTACGTGTTAGTGGCGACCCGCAACCTTCGTG
Found at i:104660 original size:12 final size:12
Alignment explanation
Indices: 104643--104671 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
104633 GGACGAGGAG
104643 GAAGAGGAAGAC
1 GAAGAGGAAGAC
104655 GAAGAGGAAGAC
1 GAAGAGGAAGAC
104667 GAAGA
1 GAAGA
104672 AGAGGAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.41, T:0.00
Consensus pattern (12 bp):
GAAGAGGAAGAC
Left flanking sequence: Indices 104143 -- 104642
TTCGGAAGATTTCAACGTATTTTAGTTGTTGGTTTTGAGCCCATAACCAAACCCGCGATGCCTAC
GCAGTCTACCTCATCACTTACCTAACCAGACTCGTTATCTCCCACATCCAAATTATGGCTAAGAA
GAGCGCAAAAGGGGATGATCTCCTTTTGACCATCGACAGTGATGACGAACAAAATGTCTACGAGA
AGGTGAATCTGGATAGTGAGTCCGAGACTGAGGCTCCAGTCCCCAAAAAGGCCAAGAAGAGTAAG
AAGGGCAAAAAGGCGGCTCAGCCTGAGCCAGAGGCCGAAGACAAAGAGGCAGCTGACTTGAACCC
CGACTTTCAATTCATTGTGGAGGGTGGCATGGCCTCTTCTCGTTTCGATGGTTGGGATTTTGCTG
GCGATGAGAAGACTGGCCGGAAGGACGTTGATTTGGATGGCATCTTGCGTCGGAAAGGTGGTTTG
GTAAACCAAATGACTGGTGAAGAGGAGGCTCCTCAGGACGAGGAG
Right flanking sequence: Indices 104672 -- 105171
AGAGGAGGAGGAGGACGACGACGAAGCCGAGGAAGACGACGACGACGAAGCCGAAGAGGCCAACG
GCGAGGACGAAGACGACCTTGCCATGGACGGCTTTGGTATGGGTGTTCAGGCTGAGGCAGAGGAA
GCCGAGGAGGATGAGGAGGCCGAAGCTGAGGAGGAGCAAGCCTCCGAAGACGAAGCCCCCGTTGA
GGCTGACATGGATGAGGAGCATGGAGACGACGAGGAGAAGGAGGATGTTGAGGACCTGGCCGAGG
CTATCAAAGAGTTTTACGACACCGAGGAGCCTGCTACCAAGCAGAAGCACACTCTGTTTAACTCA
TTGCAGTTGTCCCGTCCCGTGCTCAAGGGGTTGGCGCAGCTTGGATACACGAAGCCGCTGCCGAT
TCAGAGTGCCGCCATCCCGATTGGTTTGCTTGGTAAAGACATCGTCGCGGGTGCCCAGACTGGTT
CCGGTAAGACCGCAGCATTCATGATTCCCATTATCGAGCGGTTGG
Found at i:104703 original size:24 final size:24
Alignment explanation
Indices: 104658--104730 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
104648 GGAAGACGAA
* * **
104658 GAGGAAGACGAAGAAGAGGAGGAG
1 GAGGACGACGACGAAGCCGAGGAG
*
104682 GAGGACGACGACGAAGCCGAGGAA
1 GAGGACGACGACGAAGCCGAGGAG
* *
104706 GACGACGACGACGAAGCCGAAGAG
1 GAGGACGACGACGAAGCCGAGGAG
104730 G
1 G
104731 CCAACGGCGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.44, T:0.00
Consensus pattern (24 bp):
GAGGACGACGACGAAGCCGAGGAG
Left flanking sequence: Indices 104158 -- 104657
CGTATTTTAGTTGTTGGTTTTGAGCCCATAACCAAACCCGCGATGCCTACGCAGTCTACCTCATC
ACTTACCTAACCAGACTCGTTATCTCCCACATCCAAATTATGGCTAAGAAGAGCGCAAAAGGGGA
TGATCTCCTTTTGACCATCGACAGTGATGACGAACAAAATGTCTACGAGAAGGTGAATCTGGATA
GTGAGTCCGAGACTGAGGCTCCAGTCCCCAAAAAGGCCAAGAAGAGTAAGAAGGGCAAAAAGGCG
GCTCAGCCTGAGCCAGAGGCCGAAGACAAAGAGGCAGCTGACTTGAACCCCGACTTTCAATTCAT
TGTGGAGGGTGGCATGGCCTCTTCTCGTTTCGATGGTTGGGATTTTGCTGGCGATGAGAAGACTG
GCCGGAAGGACGTTGATTTGGATGGCATCTTGCGTCGGAAAGGTGGTTTGGTAAACCAAATGACT
GGTGAAGAGGAGGCTCCTCAGGACGAGGAGGAAGAGGAAGACGAA
Right flanking sequence: Indices 104731 -- 105230
CCAACGGCGAGGACGAAGACGACCTTGCCATGGACGGCTTTGGTATGGGTGTTCAGGCTGAGGCA
GAGGAAGCCGAGGAGGATGAGGAGGCCGAAGCTGAGGAGGAGCAAGCCTCCGAAGACGAAGCCCC
CGTTGAGGCTGACATGGATGAGGAGCATGGAGACGACGAGGAGAAGGAGGATGTTGAGGACCTGG
CCGAGGCTATCAAAGAGTTTTACGACACCGAGGAGCCTGCTACCAAGCAGAAGCACACTCTGTTT
AACTCATTGCAGTTGTCCCGTCCCGTGCTCAAGGGGTTGGCGCAGCTTGGATACACGAAGCCGCT
GCCGATTCAGAGTGCCGCCATCCCGATTGGTTTGCTTGGTAAAGACATCGTCGCGGGTGCCCAGA
CTGGTTCCGGTAAGACCGCAGCATTCATGATTCCCATTATCGAGCGGTTGGTATTCAAGCCGGCA
AAGGGGGCTCTGACCCGAGTGATCATCTTGACCCCTACTCGTGAG
Found at i:110853 original size:18 final size:18
Alignment explanation
Indices: 110826--110864 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
110816 TCAAAAGGGC
*
110826 CAGGGGCAGC-AGCCTCAG
1 CAGGGACAGCAAG-CTCAG
110844 CAGGGACAGCAAGCTCAG
1 CAGGGACAGCAAGCTCAG
110862 CAG
1 CAG
110865 CCGAAGTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.28, C:0.31, G:0.36, T:0.05
Consensus pattern (18 bp):
CAGGGACAGCAAGCTCAG
Left flanking sequence: Indices 110326 -- 110825
AGCTGCAGCTGCTTACCAAGTACCTGTACCAGGCGATCGAGAAGTTCTTCCAGTCGTACCCCGAC
CCGTCGGTGGCCAACAAGGACGTCAAGGGGGTGCCGCGCGAGGCGGTGCTTGACCCTCGCCAGCT
GTACCAGTTGTTGTCGCTGCAGCGGTTTGCCTTGGGCGACCGTGTGATCTATGTGCACGACCTGG
GCAAGGTTCCGATGTTGTCCAAGGGCACAGTAGCGCTGATCATCACTCTTGGTGCTAAGACGCTG
TTGGGGGTGATCTTCGATAAGGAGTTGTTGAACGGCAGCACCATGCACGGCAAGCTTGCCACCAA
GCGCGGCATGCTGATCGACTCGCTGTTGGTGTTGAACTTGAGCAACCGCCAGTTCGTGTACCACT
CGAAGGCGCTGAAGAACCAGAAGGCTCGGGTGGCCCAGAGCGTCAACCAGACCTATGGCAAGCCC
CAGAAGGCTCCCCAGCGGGCTCTGACTCCCAAGGGTCAAAAGGGC
Right flanking sequence: Indices 110865 -- 111364
CCGAAGTCTCAGCAGAAGCCCAAGCCCAAGGGCAAGGGCAAAACCCCGCCTCCCCAACCTCAGAA
CGGTAACACCAAGCCTCAGAGCGAAGTCAACGCGAAGCAATCGCACGAGCTTCTTCTGATTCTTA
AGGGTCTGTCCAAGGACTCGAAGGACTCCAAGGACTCCAACGCAAAGGAGGAGCCACAGGAGGAG
CCGTCGAGCCAACAGAACCCTGCAGTGGCCAACCCGAACGCCATCAAGCTGATCTACGGGCAGAT
TTACTCCAACGTGATGAGTGAGGGCCAGATGCCGGTGCCGCAGATGTACATGCCCCCTCCCGGGC
AGTTCCCGCCGCAGATGATGCCGATGGTGCCTGGAGTCCCTGTGCCTCCGCAGTTCTACCAGCAG
CCTCCTCCGGGCCAGTTCTACCAGCCGTACGGCCAGCCCCCGCAGCAGCCTCAGCAGCCACAACA
GCCGCAACAACCCCACCCTCAGCAGCAGCAGCAGTCCCAGCAGCG
Found at i:111020 original size:9 final size:9
Alignment explanation
Indices: 111003--111034 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
110993 TAAGGGTCTG
111003 TCCAAGGAC
1 TCCAAGGAC
*
111012 TCGAAGGAC
1 TCCAAGGAC
111021 TCCAAGGAC
1 TCCAAGGAC
111030 TCCAA
1 TCCAA
111035 CGCAAAGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.12
Consensus pattern (9 bp):
TCCAAGGAC
Left flanking sequence: Indices 110503 -- 111002
TCTATGTGCACGACCTGGGCAAGGTTCCGATGTTGTCCAAGGGCACAGTAGCGCTGATCATCACT
CTTGGTGCTAAGACGCTGTTGGGGGTGATCTTCGATAAGGAGTTGTTGAACGGCAGCACCATGCA
CGGCAAGCTTGCCACCAAGCGCGGCATGCTGATCGACTCGCTGTTGGTGTTGAACTTGAGCAACC
GCCAGTTCGTGTACCACTCGAAGGCGCTGAAGAACCAGAAGGCTCGGGTGGCCCAGAGCGTCAAC
CAGACCTATGGCAAGCCCCAGAAGGCTCCCCAGCGGGCTCTGACTCCCAAGGGTCAAAAGGGCCA
GGGGCAGCAGCCTCAGCAGGGACAGCAAGCTCAGCAGCCGAAGTCTCAGCAGAAGCCCAAGCCCA
AGGGCAAGGGCAAAACCCCGCCTCCCCAACCTCAGAACGGTAACACCAAGCCTCAGAGCGAAGTC
AACGCGAAGCAATCGCACGAGCTTCTTCTGATTCTTAAGGGTCTG
Right flanking sequence: Indices 111035 -- 111534
CGCAAAGGAGGAGCCACAGGAGGAGCCGTCGAGCCAACAGAACCCTGCAGTGGCCAACCCGAACG
CCATCAAGCTGATCTACGGGCAGATTTACTCCAACGTGATGAGTGAGGGCCAGATGCCGGTGCCG
CAGATGTACATGCCCCCTCCCGGGCAGTTCCCGCCGCAGATGATGCCGATGGTGCCTGGAGTCCC
TGTGCCTCCGCAGTTCTACCAGCAGCCTCCTCCGGGCCAGTTCTACCAGCCGTACGGCCAGCCCC
CGCAGCAGCCTCAGCAGCCACAACAGCCGCAACAACCCCACCCTCAGCAGCAGCAGCAGTCCCAG
CAGCGGCCTTCTGAAAACGGCCGTGGCAGAGGTGGTGCTCGCGGGCGCGGTGGTGCTCGGGGACG
TGGCAGCAACCGCGGTCGTGGTGGTCGTCGGGGATCTCCTGCTCCCAAGCCGGCCCCTGCTTCTG
CGCAATGACCGTGTACGATTCTTACATTGTAATTATATTTCACCC
Found at i:127972 original size:31 final size:31
Alignment explanation
Indices: 127910--127972 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
127900 CAACCTCAAT
*
127910 TGAAGAGGCACCGTTGAAGGCACCCGCCATC
1 TGAAGAGGCACCGTTGAAGGCACCCACCATC
*
127941 TGAAGAGGCACCGTTGAAGGCACCCATCATC
1 TGAAGAGGCACCGTTGAAGGCACCCACCATC
127972 T
1 T
127973 ATCATCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
TGAAGAGGCACCGTTGAAGGCACCCACCATC
Left flanking sequence: Indices 127410 -- 127909
TCAGCTAACAAAACCGCCGATTATCATTTCAGGAGGAAGGTTCTCTGGTAATTATGCTTCTCCTT
CGCCTTAGTGGGGTACATGATTCCCTAAGTCGCATCATGTCGTTAGCCCAGCAAAAGAAAAATGT
GCCAAGAAGCCCATGTCGGCCTATGAAAGCAATCACGTTACGCGTGTCTAGGCAATAGATGCTGA
GAAATCATTTATTGTTTGAACGTTCCCTGAGGTTCTTTGTTGGTATTAGCAGTGCTCATAATGTT
CGAGCGATTTCCACGGTCAGTCATGCAAACACGTGACTTGAAACGTAGATTATTGCGATAAACAA
ACTTGTAGGACGTTGAATGAAGGCATTCTATCGAAGCATTTGGGACTTGGTATGACTTGAAAGTT
CAGTTTGGTGCTGGGTAACGAAATAGTTGTTGTCATGCCCACAGAACAGATGAATGTATTTCCAT
CTACAACGACTTGCGGGGCGGTCATCAAAGTCAGCCAACCTCAAT
Right flanking sequence: Indices 127973 -- 128472
ATCATCTGTTGACAATTGATCGCGAGATATATGATGGTCAGGAGCCCTGTCACAAGTTTAAATAT
CAGTGTAAACAAAAGATCGACCCTTATGAGTCTGTTACTGAAGGAGATTGAGCGGAAAGAACGCA
TGTTGGCGCAAGTCAAAAGGATGGCAGAAGATACGGAGACCTTCGTGAACGACCTAGACGCTGTC
GGGAGTAGGTTGGACTTGATGGGATCCAGCACAGAACAGATGAACCTTTTACTAGCAAATTGGAA
AATGACCACACGGGCCATGTACCTTGGGAGTGCTGCACAGGGGCGACATACAGAGGCTGATTTTG
AAGCTGGTAGAGCTCTCCCCGAGCAATTGGTGCGAATTCCCTTGGGCACAGAGCAGGAAGTTGGC
GACGACGAAAAAGCCGATGAGGGGTCAGGGGACGCGGTGGGGGACGAGTCTATTGAAGAAACAGC
TAGTAAATTAGCTGAGGTAGGTGAGTCTGAAAGCATTGCAAGTGA
Done.