Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_062590
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: 277672
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Found at i:71305 original size:17 final size:17
Alignment explanation
Indices: 71278--71310 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
71268 ACTTGTGTCA
71278 GGGTAAAGCCCCCTTTAT
1 GGGTAAAG-CCCCTTTAT
71296 GGGT-AAGCCCCTTTA
1 GGGTAAAGCCCCTTTA
71311 GAGATAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (17 bp):
GGGTAAAGCCCCTTTAT
Left flanking sequence: Indices 70778 -- 71277
ATCGATCCTTAGTAATCGCGGGCCCCTAGTTGTTCACATAGATTTTTGCAGGCTCGAATAGGTAG
TTGGCTGCTGCGTCGTCGGAAGGGTCTTTTCCTTTGCTTGCGTAAGTTACCCTGCTTGCTATTCT
ATCACCCCTCGCCCGGCCTTTACTTGATTGATAGGGCTCCTTCACCAGGATCAATAGCCCAGCTA
CACTACCACTACCCGTAAGATAGAAGTAGGGCACTTCACTCACCTCAGAGAATGCACTACCTATC
TGTAATCAGTTCAGCTTAGAGTTGTTTGCTGACACACGCTACTATCACGCTGGTTGCTGCTTTCA
CTCGGATTCTCCTCGGGCGGATCAAGGGATATTGGCTTGGCTTGCGAAAGAACTTATAGTTGCAG
GATGGTTGGTTGACAGGTGTCTGGCTAGCAAAGAACCAGACAAAAAAAAACAAGTACAGTAGCGC
TATAGGCTATTTGATATAGTATAGCCGCGGAGACTACTTGTGTCA
Right flanking sequence: Indices 71311 -- 71810
GAGATAGGAAAACGGCCTAGCTGCTTTATTGAGGCAACATTGAGAATTTAAAAAAGAATTTGCTG
CTATTTCAGTGGTTGAAGTGCCGGTCGGCATTGCCTAAGTAACGTCCGACACTGTTTGCGCGCTT
CTCTCCTCTTCATTCAATGCAAAGACAACCGCCTGAGCGTCGCGTCTGACTCCAGCATCAGAGAA
GAAAGGCCCATATCTAATGCTTGCTTCAACCCGCACGAGATTGCCAAAATCTCAACGAGAGGAAA
CTCCGGCGCCCATACCTTTTGGTCTACACACCAAATCCTAATTAGCAAGATGGATCTTCCTCTTA
TATTTTTACCAAAAAAAGTTTTTCTGTTTAGCTTGTCAAGCCTAGAGCACACAGAAATAAGCAAC
TTGCCTATCGATATTAGGAGAACATAAGATATTCTATTTCTCAAAGCGCCTTGAAACCATGCAAA
AATCATCCAAACACTTTCTCTCAGCTTGAGAGCCTCAGAGAAACT
Found at i:198754 original size:39 final size:39
Alignment explanation
Indices: 198697--198775 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
198687 CCCATCCTTC
* *
198697 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
198736 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
198775 A
1 A
198776 TAGAAAATCG
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:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 198197 -- 198696
CACTGGAGAAGGTCATTTTTGGAGGGGTCGGAAGAACGGGTTTAAAAGAAATATATATATATTAT
ATTAGTTTGGTTTTTATGCAAAAAAGACAAAACGGGATTGGATTTCCACTCAGAAGGAAGGAAGG
TTAAATACCTTTGACAGGGTTGTATTTTTGGGATGGTGTTCAAACTCCCGAAATGAACCATTACA
GCTGGCGTCGACCAGCTTTGCGATACGTACGGACACGAAGAAGAACGCAGGCAGCGGAAATGCAA
AAGAGAAGAGCAAAGATTCCCGACCCTTATTGACTCAACCACAAATCTGTTGAATGAAGGTAGCT
TGCTTACTCTCAGCCACTAGTTAGAAGGAAATCCCTTTACTTTCTTTCAGAACCTTATGCAGTAC
AGAAAGCAAGTGAGGCGGGCTAAGATTCCATTCGAAGTAAGGTAACAAGATTCGATGTTGCACCA
CCTTCAACTCGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 198776 -- 199275
TAGAAAATCGAAAACGTACATAGCTGTTCCAGCCGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGAGCGTTCGGATTGTTACAACCTCTAGCGGATGGTTTGAAATTGATTCTAAA
AGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTGACTACATTTA
TGTTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATTCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTTG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATAGG
TTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGC
Found at i:244357 original size:11 final size:12
Alignment explanation
Indices: 244331--244356 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
244321 CTGAAATTTC
244331 TTTCTTTTTTAT
1 TTTCTTTTTTAT
244343 TTTCTTTTTTAT
1 TTTCTTTTTTAT
244355 TT
1 TT
244357 CACCGGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTAT
Left flanking sequence: Indices 243831 -- 244330
ACCTATAGAAAAGATCATCAGAGAGGAGACACCCCATTTTTGATTCCAGCCGAGAAGACTAGTAA
AAGGAAGGATCAAGAATGTCATATATTTCAGGAGCTAGATCAGTTGCCGATGAACAAGTAAGAAT
TGCCTCAACAAAAATTGATGGAATTGGACCTAAAAAAGCCATTCAGGTTCGTTATCGATTAGGTA
TCAGTGGGAACATAAAGATAAAAGAGTTAACTAAGTATCAGATCGACCAAATTGAACAAATGATA
GGTCAAGATCATGTTGTTCATTGGGAATTGAAGAGGGGAGAACGAGCAGACATCGAACGATTAAT
TTCTATTTCTTGTTATCGTGGAATTCGTCATCAAGATGGATTGCCCTTACGCGGTCAACGAACTC
ATACTAATGCAAGGACTTTTCGCAAGCTAATTCGGAAATGAAAGAAGTCTACCGAAAGCCCTTGG
TACTTGTCTGATCAATCACACTGTTCAATAGTTCACTGAAATTTC
Right flanking sequence: Indices 244357 -- 244856
CACCGGTTACTAATCCAGTATACGTATAGTAGGCCTCCTTCGCCACTCCACTAGTGGCTCGGCTT
GGTCTCGCTTCCTTCGCCCGACTATCGGCTCGGCTTCGTCCTAGAAGCTACTGCTTCCGCCTCTC
TAGGCTTCGCTATCGCTCATGACTGGTATAGTATATGGATCTCTCTATGTAGCGGTCGGCCTTCT
ATAAGCTTCGCCAGAAGCGACTAGTAGCTTCCCGAATGCCTCTTTACTTTAGTATGGTCTAGTCT
TTCCAATGCCTCCTTCCTTGCCGCCAACGTACGCTACTAGGAGAGTAAGCAAGCTACCTTGCTTG
CATTCTAGAAACGGTAGCTTCCGCGCCCTTCCTGCCTGCTGAAATTGATGTGAATGATCGTGACA
GCTCTTCAAATCCTATTCAGTCTGATTAGATATGTCACTGAAACAATCCGTTCTGTCTCTGTTTT
ATTTTAGGATTCCGAGAACGAGCCGGCCGATCCTAACATCATTTA
Found at i:258555 original size:18 final size:18
Alignment explanation
Indices: 258534--258570 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
258524 GTCACGGCCG
258534 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
258552 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
258570 A
1 A
258571 CAAGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATCGTCACTATCATCA
Left flanking sequence: Indices 258034 -- 258533
TACTAATCGATAGGGCCTCATCGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATG
GACCCGAATCCATTAGTATAGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTGGAACATCTTTCACAATCCCTGGAGAGATAGTTCACTAATAAACCGAGGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATAGGTCTATTTCCGGCATCATATCCATAGTTAGCGCA
TTCATCATAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGGCCG
Right flanking sequence: Indices 258571 -- 259070
CAAGAAAACCCTTGGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAAAGGAACATAG
GAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAAT
ACCCCTAGAGAGGGATAGGGCTAAACGGAGCGAAAAGGGTTTTCCATGAGATGGGAAATGAAAAC
TATTAGCCCCACAGGAGGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAATATCCGCCTT
TCTGCTAAACAGGATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGTCAACTAAGTA
TCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTTTGATAAATGAT
CACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGTGGAGAACTGA
ACCAAGAATTCTCTTTCTTTATCACCAATCGAATCACTGTTCGAG
Found at i:270603 original size:18 final size:18
Alignment explanation
Indices: 270563--270605 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
270553 ACCGCCCTGC
270563 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
270582 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
270599 CATAGTC
1 CATAGTC
270606 AACAAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 270063 -- 270562
GAAAGCTTTTTTTTCAAGTGTCAGTAGCGGAACGTTCTGTCAATCGGGGAAGGTTTTTGGTGACA
ACACCTGGAGATATCAGAAGTGAGAATGCTGACATGAGTAACGAAAAATCCTGTGAAAAACACGA
TCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAATCTACGCAGAGTGAATCGGTCCCTAAGGA
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGAATGATCGGGCCGAGGGCAGCCCCCTCTTCCCCTCACTCTC
CTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTAC
GCGACTGGCGCTTCAAAAGACGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCCTTTACTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 270606 -- 271105
AACAAGGTTTAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:277367 original size:26 final size:23
Alignment explanation
Indices: 277319--277371 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
277309 AGGAATGGGT
277319 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
277342 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
*
277365 GGACGGG
1 GAACGGG
277372 GCCTGTTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.40, T:0.19
Consensus pattern (23 bp):
GAACGGGAAACCTGTTGTTAGGA
Left flanking sequence: Indices 276819 -- 277318
GTTATTTAAAACCAATAACAACGTAAAAAACACGTGGTTTTGCATGTAGGTGAAGGGTCAAATTG
ATCAAAAAAGGAACGCTCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGCTAGGGCTAGATG
GATTTCGTGTCAAAAGAAAAACGAGTGAAAAGACCATTTCAAGCAAAAAAGACGGGGTTTTAGAC
TTTTTTCCAAAAAGCATGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCT
TTGGTATTGCGTCTCATCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCCTGCTTCTGAAA
GAAAAGAATCATATGACTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAA
TCGAAACTTATACGATATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATC
CTTACTTACCTCCTTATACTACTGTAAGCATATGAAGGAATGGGT
Right flanking sequence: Indices 277372 -- 277672
GCCTGTTGCCAAGGAGAACGGATAACATGGAAAGACAAGGAATACAAGGAAAGACAAGGAAAGCG
TGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGAGG
AATGGAATTCCTATTCAAATTCCCGGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGATCA
CCCCACAAGAGAAGCCACTCGAACGAATAGCTCCTTTCTTGCCGTGGAATTCCTCAAAGCTATAA
TATAAATGGAATTCTCCCTTGACTCGATCTTTAAAAAAATG
Found at i:277428 original size:10 final size:10
Alignment explanation
Indices: 277400--277434 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
277390 CGGATAACAT
277400 GGAAAGACAA
1 GGAAAGACAA
*
277410 GG-AATACAA
1 GGAAAGACAA
277419 GGAAAGACAA
1 GGAAAGACAA
277429 GGAAAG
1 GGAAAG
277435 CGTGGGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.57, C:0.09, G:0.31, T:0.03
Consensus pattern (10 bp):
GGAAAGACAA
Left flanking sequence: Indices 276900 -- 277399
TCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGCTAGGGCTAGATGGATTTCGTGTCAAAAG
AAAAACGAGTGAAAAGACCATTTCAAGCAAAAAAGACGGGGTTTTAGACTTTTTTCCAAAAAGCA
TGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCTTTGGTATTGCGTCTCA
TCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCCTGCTTCTGAAAGAAAAGAATCATATGA
CTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAATCGAAACTTATACGAT
ATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATCCTTACTTACCTCCTTA
TACTACTGTAAGCATATGAAGGAATGGGTGAACGGGAAACCTGTTGTTAGGAGAACGGGAAACCT
GTTGTTAGGAGGACGGGGCCTGTTGCCAAGGAGAACGGATAACAT
Right flanking sequence: Indices 277435 -- 277672
CGTGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGA
GGAATGGAATTCCTATTCAAATTCCCGGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGAT
CACCCCACAAGAGAAGCCACTCGAACGAATAGCTCCTTTCTTGCCGTGGAATTCCTCAAAGCTAT
AATATAAATGGAATTCTCCCTTGACTCGATCTTTAAAAAAATG
Done.