Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ900993
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: 161386
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Found at i:31945 original size:22 final size:23
Alignment explanation
Indices: 31906--31951 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
31896 CTTTGAGACT
**
31906 TTCTTCTCTTTGCTAGAAT-CGC
1 TTCTTCTCTTTGAAAGAATGCGC
31928 TTCTTCTCTTTGAAAGAATGCGC
1 TTCTTCTCTTTGAAAGAATGCGC
31951 T
1 T
31952 GTGATCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (23 bp):
TTCTTCTCTTTGAAAGAATGCGC
Left flanking sequence: Indices 31406 -- 31905
CGGAAAGGAATGGAATTTCTTTAAGCTTCACTCCGCTATCAGACTAGTTGCGAAGCGTTGGGATA
ACTAAAGTGGAATATGCCTCAACTAGTTGCCCAGGATGAGGCCATTGCAGCCACTAGCACGGCCA
AGTCACCAACCTATGGCTCCGGGGAAGCCGGCAGGGAGGAAGGATGATAATCCAACCAAAGGAAT
TAGCCACTCGTTCTATCAATAGGCGCCGTGGGCCTATGAGCTTCTGGGCCTGTACGATTTCCTGT
CCTCAACAGTTCAAAACGCTTGACACTGAGAGCTTTGGTGAATATTTTGCCTTTTGGTTATGGAG
TCTTTCCTTCCTTCCAAGCCGCTTTCAAAGCAGTAGGCAGTCTCTTCTTTCTTCTTATATGGTAG
CCAGTCTTTTTTAGAATGGTTGAATAGAGCCTCCCTTCTGTCTCCCAGTCTGTCTTATAAGAAGA
TAGTAGTAAGTCAGTTGTAGGTTTACGAATGGCTTCTTTGAGACT
Right flanking sequence: Indices 31952 -- 32451
GTGATCTTTTCAAGTTCATCCTAGCTATCATCTCAATCATTCTTCATTCACTTCGAGCCCTCGGG
TAGTTTTCTCATCCAGGAGAGTAGTCTTAGAGGCGGTCTCCTCCCTGTCCTTCTTAGATGGTATC
CTCTCTGTCCTTCCCCTTTCCCGGACTCGAGAACCCCTGAAGCGCACTGGAAGCATCTCAAGGAA
AAGAGAGAAGTCAAATATCGTAGGCTTTAGATAAGATTCCCTAGTAGATAGCTAAGCTAAGAGAG
TGCTCCGGAAGAGCTAATATTAAAAATTCTTTCCCTTTCTTTCACCGAGGAGGCTAACTAGATAG
ATGGTGGGTCTAAGGAAGAGAAGAATATGAGCTATATTTTCATCCCCTTTCAGTTCCTTTCCTTA
TCCTTAGAACAGTAGGGTTTGAAGCTGGCAAAGTCAATCAATCCAGCAGTCAAAGGGGCAAGTGC
AGTCACTCAACCAACGCCTTTCAAGCAATATCTTAAGTAGGGGTA
Found at i:48582 original size:39 final size:39
Alignment explanation
Indices: 48527--48605 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
48517 CCCATCCTTC
*
48527 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
*
48566 AATATCATGATCGGGTCGACCAGGTCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
48605 A
1 A
48606 TAGAAAATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (39 bp):
AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 48027 -- 48526
CTCTCAGCGATTCTTTTCTCCGCTAATAACCCCTTCCCAACCAGCCCGCCCGATCGATTTTGTAA
GATCGGCTAATTCAAAGGGGTTAATCTGGTCCGAAGTTGTCGGAACGAATCGTTTGCTTTATCGA
ACAAAGCTTTCTTAGGGGGTCTTGGTTGGCCCCCTATTTTCAACCATTACAGCTGGCGTCGACCA
GCTTTGCGATACGGACGGACACGAAGAAGAACGCAGGCAGCGGAAATGCAAAAGAGAAGAGCAAA
GATTCCCGACTCAGAGCATGTTATTGACTCCACCATAAATCTGTTGAATGAAGGTAGCTTGCTTA
CTCTCAGCCACTAGTTAGAAGCAAATCCCTTGACTTCGTTTATGCCCTTATGCAGTAAAGAAAGC
AAGTGAGGCGGGCTAAGATTCCATTCGAAGTAACGTAAGAGGATTCGATGTTGCACCATCTTCAA
CTCTTCTCGGGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 48606 -- 49105
TAGAAAATCTAAAACGTACATAGCTGTTCCAGCGGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTTGAAATTGATTCTAAA
AGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTGGCTACATTTA
TGTTAAGTCTGGTCGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTTG
GTCTAGTAATTAGGAGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGC
Found at i:76845 original size:18 final size:19
Alignment explanation
Indices: 76822--76862 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
76812 TTCTTTCATC
76822 GGGAAAGAGA-AA-ATCAAG
1 GGGAAA-AGACAAGATCAAG
76840 GGGAAAAGACAAGATCAAG
1 GGGAAAAGACAAGATCAAG
76859 GGGA
1 GGGA
76863 CTGAACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 10 0.48
ACGTcount: A:0.51, C:0.07, G:0.37, T:0.05
Consensus pattern (19 bp):
GGGAAAAGACAAGATCAAG
Left flanking sequence: Indices 76322 -- 76821
TATCTGAACTCAAGCTTATTAGCCGGATTCCTATTCAACTACCCCGCTTCAAGCCCTGACCCTCA
TATAAGATAATTATGAAACCCAAGAAAAAGACCTACATACCTTTTCCTTCTTTGTGCTTTCTTTC
TAGTCCCTGTGTCCAAAGAAAAAGAAGTCCTTCTCCTTCTTCCTTTCTTTATGCTGCTGGCCTTT
TCTAGCCTGATAGTGAATGAAAGTTCAAGCAAGGTATGTCGAATTCCGCTCTTGCTTTGAGGACT
ATAGTCAGTACTTTACCTTTTGCTCTTCTCTTGGAGTTCCTTGGAATTCATAATCAATAGCGGGA
TCTCTCTCTCGACTGAGGTAGGTAACTCACATCTGGGCAGACACGCACTACGGGAATTCACTAGA
GACAGAGCCTTCTCCTAGCCATCTCCTTCACTAAATCAAGGGAAGAAACTCGAGAAAGAGCCCTA
TCTGTATCTGTATATACGCCTTCTATGGCTCACACTTCTTTCATC
Right flanking sequence: Indices 76863 -- 77362
CTGAACTATATCTTTAGTCGTCTCTACGACTATATCTCTAGCCGGAGCAACCACTGGAAGGAAGC
CTTCCGACCCGGACCGGAAGAGGCCTATTCCGCTGGTTCGGATTGGGAAAGAGCAGCCCTAGACT
CTGGTTCTTAGGAATGATTCATCCCTATGCTATGTATGATTCATCGGATTATTATTATGCGTCTT
CGGTGGGTGATTTAACGTATTCGGCGTCTGAAACAATGTACTCGCATGCTTACTTATCTATTCCC
ATCCACCACCCTTTCTCGGGATTTGAGAAACTACTAACTGTGAAAACGTTCGTGCCTTCTCCCAG
CTGAGAATGTAGATCAGTTGGCATCTGTAATAGAAAGAGACTCGCAGGCATTAGCTTTCCAGCTG
TCCATGCTTTCGATTCTCTCTCTCATTCCAAGGTAGGGAGGGTTGCTCGTTGTGGTTGCCCGTAC
CATGATTGGTTGATGGAAATTCTCCGTCGTTTACCGACCGATGGT
Found at i:149337 original size:14 final size:14
Alignment explanation
Indices: 149318--149347 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
149308 TTACTTAATC
149318 TTAATAGAGAGAGT
1 TTAATAGAGAGAGT
149332 TTAATAGAGAGAGT
1 TTAATAGAGAGAGT
149346 TT
1 TT
149348 CTCTTCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (14 bp):
TTAATAGAGAGAGT
Left flanking sequence: Indices 148818 -- 149317
TCAAGAGATTCCCCTTAAAGTCTATAGCAGCAACGGACCATTGTGTCCGTAAAAAAAGGTGAAAG
CGGAATAAGTGGTTACCCCATCACCCAAAACCCCTTGGCATTCGGTCTTGAGGAGCGTAAAGTCT
TCCCTTTTATGACTGGACTGATCATGAGATATCTCGAGCCAATTCAGGCTTCAGCAAGACCGACA
AGGGGACCGTCTGATGTTCACCCTTGGACAACATTCTTCGGTCCCCTTCAAATCCAATAGAAAGG
AATTCTTTTTTTTCCCTAAATCAATATTAACTAATATAACCCTGAATAGGACCCAGGGCTCCTTT
ACAGTCGAGCATCTTTGTTTGTGTTTGAATAGGGATTCATACATCCAAGGTCTAAAACGTCGGTT
TTTCGCAACTGCTACTTTCACAGAATCTCTTCGTAAAGCGGAATCTGGGTTAGATTTGAAGCCTT
GGTGGCGTATTGGTGGCTATAAAGCTAAGTGGAGCTTACTTAATC
Right flanking sequence: Indices 149348 -- 149847
CTCTTCTTGCAGAGAGATTTTGAAAGAATCGCTTCTTAGCGGCACCCGCTAGTTCGGAGGGATGT
TTGAAGAAGCCTAAGGGACTACTAATATGGATTCCCTTGCCGCGTATTAGTTTCCACAGGTTGGC
TTCCTTCAATGAGAGAACCCTCTGGATCCATTCATATACAACCATTCATATACAACAAATAGAAT
CCAATGCTGGTGGAAGGTGTCGAAGGGGTGAATCCCATAATGGCATCGAATGCAAGGCGCCAAAC
AAGCGCTAAGCGCGAGTCAAGCCGCCCTCTTTTAGACTCTATTTCCTCGTGTTGACTTGCAAGGA
ACCGCGACTTTCAAGATGTCGATGAGCCCGGAATGGGATTTGCTTTTTATAGATGAATTTCCCCA
CCCGGATTTGAGCCCCCTATTCTTGTAGTAATTGGAGTTAGAGCTTGGGACTTTCCCACTAAACA
AGGGTTCTCCGCCTCTTACTAATAGGACAGGACTATAGAATCAAG
Found at i:149524 original size:14 final size:14
Alignment explanation
Indices: 149505--149533 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
149495 CCCTCTGGAT
149505 CCATTCATATACAA
1 CCATTCATATACAA
149519 CCATTCATATACAA
1 CCATTCATATACAA
149533 C
1 C
149534 AAATAGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (14 bp):
CCATTCATATACAA
Left flanking sequence: Indices 149005 -- 149504
GACCGACAAGGGGACCGTCTGATGTTCACCCTTGGACAACATTCTTCGGTCCCCTTCAAATCCAA
TAGAAAGGAATTCTTTTTTTTCCCTAAATCAATATTAACTAATATAACCCTGAATAGGACCCAGG
GCTCCTTTACAGTCGAGCATCTTTGTTTGTGTTTGAATAGGGATTCATACATCCAAGGTCTAAAA
CGTCGGTTTTTCGCAACTGCTACTTTCACAGAATCTCTTCGTAAAGCGGAATCTGGGTTAGATTT
GAAGCCTTGGTGGCGTATTGGTGGCTATAAAGCTAAGTGGAGCTTACTTAATCTTAATAGAGAGA
GTTTAATAGAGAGAGTTTCTCTTCTTGCAGAGAGATTTTGAAAGAATCGCTTCTTAGCGGCACCC
GCTAGTTCGGAGGGATGTTTGAAGAAGCCTAAGGGACTACTAATATGGATTCCCTTGCCGCGTAT
TAGTTTCCACAGGTTGGCTTCCTTCAATGAGAGAACCCTCTGGAT
Right flanking sequence: Indices 149534 -- 150033
AAATAGAATCCAATGCTGGTGGAAGGTGTCGAAGGGGTGAATCCCATAATGGCATCGAATGCAAG
GCGCCAAACAAGCGCTAAGCGCGAGTCAAGCCGCCCTCTTTTAGACTCTATTTCCTCGTGTTGAC
TTGCAAGGAACCGCGACTTTCAAGATGTCGATGAGCCCGGAATGGGATTTGCTTTTTATAGATGA
ATTTCCCCACCCGGATTTGAGCCCCCTATTCTTGTAGTAATTGGAGTTAGAGCTTGGGACTTTCC
CACTAAACAAGGGTTCTCCGCCTCTTACTAATAGGACAGGACTATAGAATCAAGGCGCCCAAGGA
CAGAGGACCGGGCAGTTGATATCGATCGAAATTCCAGATTCTGATCTCTGAACTTAAAGCTTCAA
GTTCAAGTCAAAAAAAAGTCAGACAATTGAATGAGATGGTATGGGACTGCTTTCGAATTCCCGGG
AATAAGCCCTGCTAGTCTGGCTCCGAAGCTTTCTAAGACTCCCTT
Found at i:153273 original size:13 final size:13
Alignment explanation
Indices: 153241--153273 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
153231 GCATAAATAA
153241 ATATATATTTATT
1 ATATATATTTATT
153254 -TATTATATTTATT
1 ATA-TATATTTATT
153267 ATATATA
1 ATATATA
153274 ATAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.11
13 14 0.78
14 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATATATTTATT
Left flanking sequence: Indices 152741 -- 153240
TGCCCTTAGAACAGGCTTGAGGGAAGTTCCTTTTTCGAGATAGAAGACCAATAAAGGTATAACTG
CCCCCTTCTTGCCTGGAAGAAAGTAGATCACGGGTGGAAACTTACTCAAGGAAAGGGAACCAAGA
AAAGAACGAGCCGGATAAACGGGGACTTCTACTCACTGGAGGAATTCCCAATCATAGATAGAGGA
AAGGTTGAATGCTGCCCCCTTCCTCTGACTCCGAATCATTCTTTCAACCTTCGGCCAGGCGCCTA
ACTAACCTAACTAAGAGGAAGCTAGCATCTTACCGAAATCGGATTTCCTTTTCGTGCCATATGCG
CTTAGACTTTCTTTTTTGCCCCTCTTCCCGGTCCAATATTAGTTCTCGAAAGTCTTCGTTTCCGT
GTAGAAGCAAACTCTTCAAATTGTTGACCAACCCGGTTCAGAACGAGCGTAGAATTAAATAACCT
CTTAAAATCAGGATATCATCCCGATCTGCGGGCTTGCATAAATAA
Right flanking sequence: Indices 153274 -- 153773
ATAATAAGATTTTATATCGTATCGGAGATAATCAACTATGATTCCCTTCAAATAGGGATTGATCG
GTTTTTCCCCGACCAATCCACCACTCAATAGGTAGTTGACGTGACCCGGATGGTTTTCCAATAGC
CACACGAAGTCTTTCCCAACGCTTAGATTGAGTCGACATCATGCGAGATCGTACCCTGTATCCTG
CCCCTCCAAGACGAAACATAACATTACAAGAAGTCAGATTGGATTTAGTCTTGAGTTGACATAGA
CCAATGGTAGACCGACACATTAGAAGAGCTTGCATAGAGATAGGCGAGATGTCCACTTGGGCATT
CTTTGTCCAAAATCTCTTAGCAAACTCGAGAGTCCCATTATCAGATATTAGAGATTTAGATAGTG
AAATGGAAACTCCCATTCTATCTAATAACAGCCGGTATTGGAGAGCCACCTGCTCATCTGCAATG
ACGACATCGTCACCCAGAATGGCATAGCGCCTGAAAGGTCTTTTC
Found at i:158822 original size:17 final size:17
Alignment explanation
Indices: 158800--158833 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
158790 CATAATTGTT
158800 CTAGTGAATAACTAAAG
1 CTAGTGAATAACTAAAG
158817 CTAGTGAATAACTAAAG
1 CTAGTGAATAACTAAAG
158834 AAAATAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
CTAGTGAATAACTAAAG
Left flanking sequence: Indices 158300 -- 158799
AACAGTTCTCTGGAAAGAACTAATCAAAAAATTTCATTATATCCCTTCTAAGATCGTTTTTTTTT
TTATTTCGTCCGGTATTTCGTAGGAATAACCGATACACAACACAGATAGAGTAGAGAATCGATTT
TTTTTTTCTTCTATTAAAACTAATACTAATAAAAGAGGCCTTCGAATGACTAAATATAAAAACTG
GAATGTCTCTTAGTTTATTAGTTTAGTACTGACTAATGACTGCTCGCGCCATTTGGAATAGAATT
AATTTTGAATAATAAAGTAATAAATAAGAAAAATGTTCTATGTAAGACATAAAGTAGTTCCATTT
AGGAACTTATAATTGAGATATGAATATACTGAGTTGCACAAAAAAATAGTTTTTGCGTCAATTCA
AAGACTCGAAAAGGTTTTATAATCTTATAAAAGTGTCCGTTGAGCGCCTAGTAGCTATGTCATAA
TAGATCTGAACACTTGCCCGGATCAACTTCCATATCATAATTGTT
Right flanking sequence: Indices 158834 -- 159333
AAAATAGATAGATGGGAGATAGCAGAGGAAGAACTAAGTATAAACATCTCTCATAGGTTCACTAA
TTATTTAACTGTTGGCGGGTCTCTTTGTACGTGTTGTCCGGAAAGAGGAGGACTCAATGATTATT
CGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCCCATAAAAACTTCTTTCGAGCA
ATGGGCCAGACCCGGTCATTTCTCAAGAACAATAGCTAAAGGGCCTGATACTACTACTTGGATTT
GGAACCTACATGCTGATGCTCACGATTTTGATAGCCATACTAGTGATTTGGAGGAGATATCTCGA
AAAGTATTTAGTGCCCATTTCGGACAACTTTCCATCATCTTTCTTTGGCTGAGTGGCATGTATTT
CCACGGTGCTCGTTTTTCCAATTATGAAGCATGGTTAAGTGATCCTACTCACATTGGACCTAGTG
CCCAGGTGGTTTGGCCAATAGTGGGCCAAGAAATATTGAATGGTG
Done.