Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MT075725
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: 287405
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:2436 original size:34 final size:35
Alignment explanation
Indices: 2393--2468 Score: 136
Period size: 34 Copynumber: 2.2 Consensus size: 35
2383 AAAATCCTTA
2393 AAGTCTTAATGAGGACTCTTAACCTACGTT-AATC
1 AAGTCTTAATGAGGACTCTTAACCTACGTTAAATC
2427 AAGTCTTAATGAGGACTCTTAACCTACGTTAAATC
1 AAGTCTTAATGAGGACTCTTAACCTACGTTAAATC
*
2462 CAGTCTT
1 AAGTCTT
2469 TATAGTCTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 30 0.75
35 10 0.25
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (35 bp):
AAGTCTTAATGAGGACTCTTAACCTACGTTAAATC
Left flanking sequence: Indices 1893 -- 2392
CTGTTGACCAGGGAAAGCTAAGAAGCCTACTCAGCTAGATACCAGCGGAGGAGTACTAAGATCTA
TCCCCCCGGAAAAGAAAAAAGGGCTCTCAGCACGCTCCACGGGACCTTGGAGAAAAAATCCTCGT
GTGCTACCATTCACAAAAAGGAAAGAAAGCTGTTTCTCCTGTCATGATAGATACTTATATCTTAT
ATACAGGAGTTGTACTACGGCGGATCCTGGAATTATGACTTAAAGGATTCGTTCTGATATCTAAG
ATAGGGTTTTAGTGATCTAATCACACACAACTCAGTGATCTCTGGTCCTCGCAGCATGCACTCGG
CTAATAGTAACTATTTTTACTAGCAGTGAACATATACATCATTTATCTATTAAAGAATAATGATA
GAGTTCATATTCCCCTGGGAGGAGTGCCCCTCAAGGCGGGGTAATGACAGAGATATAGTCTTAGT
GCGAATAGAGACTTTATAAGACTCGTCAAGTACGTAAAATCCTTA
Right flanking sequence: Indices 2469 -- 2968
TATAGTCTTCACAAAAGTACAGGGTACAGAAGAATAAATCCCATTCTATAAACCTCTATCAAATG
TTGAAAACACAAAAATGTTAAATCGTTCAATTTTATCTCGCACTCTTTCTTCTGGAGATCCTTGA
TCTAGGACCGAGCTGTGACATTCTACCCGATATGCCGGGGAGGGAGGGGAGACCCTCTTTCTTTA
CTGCTGGTTGAGGACTTTTTCCTTTGTGCGAGCAGGAACTTCCTTCGATTGAGAACGTGCGTCTA
CTCCCCTTATTCACGGGGCTAATCTTTAGCTATAGCCTGTATGTAGCTCGGGGACTTTTCCTATA
GTCTCTCCAGAGGGAGAAGTTCGATATTATCTTTTTGACTTCCTATGGCCTAAGAAAGGGCTTCT
ATCTTTGCAAAGGGGCTAAAATGCAAGTGCAATGGTTCAGTTGATAAGCTGGTCTGCTCCGACAA
CTCATTCTAAAAGGTAGTGGAGGACGTCTCTTTTGCTGTATCTAC
Found at i:150124 original size:13 final size:13
Alignment explanation
Indices: 150106--150132 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
150096 CCAGTGCGCC
150106 ACCTTACTAATTA
1 ACCTTACTAATTA
150119 ACCTTACTAATTA
1 ACCTTACTAATTA
150132 A
1 A
150133 TAGGCAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (13 bp):
ACCTTACTAATTA
Left flanking sequence: Indices 149606 -- 150105
AACATGGTCACTCCCTTAGCGCTTCATGGTTGGGGTTGATGTTGACTGGCCTCTCTCGCGTACCA
ATAGCGAAAAGGTGACTTCCATTAACTAATCTAAAAGGAAGGTAGGACTAGCTCGACTGAAAGCC
AATCTACATGAAAAATGAACACTACCAAAAAGATAATAGTTAAGAAGCCAGCCTCACATAACGAA
GTGAGCCCACAGAAAAACCTGACAAAGAGAGGGACAAGTCCTCACTCTAAGAATCTTTATCACGT
GGATCTGATGCACCACCTGATAATGCTGAGTCACTCAGAGAATGAATCCGGAGCCACCCCTACAC
ACGAAATTCCACGATCCTATGTCGAAGAACTAAGTCTAAGATCTGAGGCAAATACAAAGTCAACT
GACGGCGGTCCGTCCATGACCAAAGCTGCGCCTTCTACGCCCTCAAGACCTGGCTCAGCCTTACC
AGACCGCTGTGCATCACCATGGCTTCGCTAAACATCCAGTGCGCC
Right flanking sequence: Indices 150133 -- 150632
TAGGCAACTTGTACAATCCAATTCATCAACACGTAGGTATGGGCTATAGTCCAACTCTAGGTTGA
TTCGTTCCAGGCTTTGCCTTTTTCGATCTTAAGAGCTTTCTTCTCGCTATGCTACTCGGGGTAGT
AGTCCAATCCTGGCGACCTATGGTTTTTGGTTGTTTCCAAAGCACTAAGCTTTAGTTACCCTTAA
AGTGAAAGAAACTAGAGGTAGAAGATCTATTCCTTATGGCGAAAGATAATCCTTTCAGTCCAGGC
ACTCAGTGCAGTCCAGACGCTCAGGGGAAGACTCCGGTTAGGAATGCTGATTGGAACCAATACGA
TTGCCCAGAGGAGTTTTCTAATGAAGTTAACCAAGTTGAGATGAGAAGTAGTGAACCAACTTATG
CCGAGTGTTTGGCTTTGATCACGTTTACGGACGATTACTTGCAACCAGGACTCATTAAGCATAAT
AGGCCTTTGTTCATTTCATAATTCCTTAATGGGTTGGAGATAACA
Found at i:177240 original size:16 final size:16
Alignment explanation
Indices: 177219--177250 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
177209 GGATAAGTTG
177219 GTTTTTCCTTTTTATC
1 GTTTTTCCTTTTTATC
*
177235 GTTTTTCTTTTTTATC
1 GTTTTTCCTTTTTATC
177251 TGATTATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (16 bp):
GTTTTTCCTTTTTATC
Left flanking sequence: Indices 176719 -- 177218
AAGAAGATCGTCAATCGAATTATGCATAGGTCCAATATCAAAGGAATTCGCTTCTCCAACTTAAT
GCGAAATGCAGCGAAAAGTCGATCCCATAAGGCAGCAGCAAACAAAAAAAATGAAAAGAAAATGG
TTAGAAACTTCATAATGGGTTTATTCTCCGTTATAGAATTCCTAGTCAATTTGTTTTCACTGTTT
ATGAAAACACTTTCTCATTCGATTTATATTCGTTTGAGGTTTTTCATCTTAAACAATTGCGGGTC
CGGGGCTTTCCTTTTTTTTTTACAGATCGGATTCATCGTCATGAGTTTTTGTCTCTTTATATTTT
GCGATAAATTGATGTTTCCCCATCTAGAAAAGGTTTCGAATCCCATTCAGGTTGTGGCACAACTT
TCCTGCTTTTTCTTTATCTTTAAATATAAAGATATAAGGCTAAGGCACCTCTGTCTTTTATCTTT
TGTTCTGACCCTTTTAAGCAGCTTGTACCTGAAGGGGATAAGTTG
Right flanking sequence: Indices 177251 -- 177750
TGATTATCATATGTTTCTTTCCTTTAGACTCTGATTTGGCCCTTTTTCTTTTATTTTATTTTTAC
AGCTTTGATCCGGGTATGTCAAAATGGGGGTTCTACCTAGTTTTCCAGCAGTTCTGCTTTTTTCT
TCTTACATTCTTTTTTAAAAAAGAACAGCCCTGCCCTAAGAAACGTCTTTTATACTTTGGTTGCA
TAGAGGCCTTTCTTTTGTGCAATGGATTCTTCAATTATAATGAATTCTATTTAGCAGAACCCTTG
AAGTTTGCCGTCCTGTTGTCGGGTGCCTGTATTATATACATAAGTTTCGAGAGGCGCACGATATG
GGAACTTTTCATTTTATTTTTTATTTATTTTACACTGAGTATCATCATTGCTATCTATATTTCAC
CTACAGAAAGAACTACCATATTGGGGATATCTTCAGGAATGTTCATTTTCGTTTCTGTGCACTTT
TGGGCTTTTCTTTGCTTGCTTTTTTTATGGGGCAATTTACCCAAC
Found at i:194254 original size:16 final size:17
Alignment explanation
Indices: 194224--194257 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
194214 TTGAATATAT
*
194224 ATATAATACATTAATTG
1 ATATAATACACTAATTG
194241 ATAT-ATACACTAATTG
1 ATATAATACACTAATTG
194257 A
1 A
194258 ATTGGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATAATACACTAATTG
Left flanking sequence: Indices 193724 -- 194223
TTGGCATCAATCCATCCAAAACAAAATGAGAGCCAGCTACCCGCATGCAGAGGATTTTCCATTTG
GTTCCCCGTTCTCTCACCAATGAGTACCTACTTAATACCACCCCCGCCTTTTGAACACTTGTTGG
GAATATCAACTAGTGAATACTTGGGAATACCACTCCCTACTTGGTGCTTACCCATGTACGGACTG
TACACACCGATTGGAATATTCCGATGGATTAGATATTCACACTGATAGATTCTATTCATACTAAC
TGGGGGTATATTCATATAACTACTGACTACCTACCCACCATTGAACACTTGTTTGGAATACCCGC
CAGTGCTGCACTTCAATTCCTACTCTTTCTCACTCCCCTGTGAATGGGGTGAATACTCACTACCA
CCCACTCAATACCCTACCCCTAGGAATACCGTTTGCTAACCACAGTTTGTTTGGTTTGCTTACCA
CCGTTCTCTTCGCACTGATTGATTGTATACACTGTTTGAATATAT
Right flanking sequence: Indices 194258 -- 194757
ATTGGGAAATTCATTCACATTGATACTAGTTTCTGCTCTAGTTCGGCTTTCTGCTCGTTGATTTG
GTCTATTCGATCCAGCTTCTTCTTTTTCCGTGGAGAAGTCAGAAGCTCATTTTGGTTGAAGCTGG
TGCAACGACTCGGGGAGAGCGGAGGAGTGGGCGGCCGTCATCAGTCCTTAAGACAAGTCTTGACC
AGGGAAGAGAGGTGTTTCATCCGAGTTCAATTCTTCATTGTCATAAGACAAGGTACACCATGTTC
GAAGACAGGATATGGAGAACGGAGATTTGAGATAGGCTTACACTTCTTTTTCTATTGGTATAACC
AACTACTAAGTTTTGCCCGCTTGAGTCTTCCAATTGGTATAACCTAAATGAGCATTCTTGCTGAG
ATCAAACGGACACTTATAACCAGAGTCAAGAAGCCCTATTCGTTTCACTAAAAATCTATTTTTGG
GGCTTGGGATACCATAAAATCTTTTAGTGATATTCTTTATCCGCG
Found at i:194260 original size:21 final size:21
Alignment explanation
Indices: 194204--194261 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
194194 TGATTGATTG
**
194204 TATACACTGTTTGAATAT-ATA
1 TATACACTAATTGAAT-TGATA
194225 TATA-A-TACATT-AATTGATA
1 TATACACTA-ATTGAATTGATA
194244 TATACACTAATTGAATTG
1 TATACACTAATTGAATTG
194262 GGAAATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 7 0.23
21 11 0.37
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (21 bp):
TATACACTAATTGAATTGATA
Left flanking sequence: Indices 193704 -- 194203
GAGGTCACGGCACCGCGAACTTGGCATCAATCCATCCAAAACAAAATGAGAGCCAGCTACCCGCA
TGCAGAGGATTTTCCATTTGGTTCCCCGTTCTCTCACCAATGAGTACCTACTTAATACCACCCCC
GCCTTTTGAACACTTGTTGGGAATATCAACTAGTGAATACTTGGGAATACCACTCCCTACTTGGT
GCTTACCCATGTACGGACTGTACACACCGATTGGAATATTCCGATGGATTAGATATTCACACTGA
TAGATTCTATTCATACTAACTGGGGGTATATTCATATAACTACTGACTACCTACCCACCATTGAA
CACTTGTTTGGAATACCCGCCAGTGCTGCACTTCAATTCCTACTCTTTCTCACTCCCCTGTGAAT
GGGGTGAATACTCACTACCACCCACTCAATACCCTACCCCTAGGAATACCGTTTGCTAACCACAG
TTTGTTTGGTTTGCTTACCACCGTTCTCTTCGCACTGATTGATTG
Right flanking sequence: Indices 194262 -- 194761
GGAAATTCATTCACATTGATACTAGTTTCTGCTCTAGTTCGGCTTTCTGCTCGTTGATTTGGTCT
ATTCGATCCAGCTTCTTCTTTTTCCGTGGAGAAGTCAGAAGCTCATTTTGGTTGAAGCTGGTGCA
ACGACTCGGGGAGAGCGGAGGAGTGGGCGGCCGTCATCAGTCCTTAAGACAAGTCTTGACCAGGG
AAGAGAGGTGTTTCATCCGAGTTCAATTCTTCATTGTCATAAGACAAGGTACACCATGTTCGAAG
ACAGGATATGGAGAACGGAGATTTGAGATAGGCTTACACTTCTTTTTCTATTGGTATAACCAACT
ACTAAGTTTTGCCCGCTTGAGTCTTCCAATTGGTATAACCTAAATGAGCATTCTTGCTGAGATCA
AACGGACACTTATAACCAGAGTCAAGAAGCCCTATTCGTTTCACTAAAAATCTATTTTTGGGGCT
TGGGATACCATAAAATCTTTTAGTGATATTCTTTATCCGCGTTCT
Found at i:279681 original size:17 final size:17
Alignment explanation
Indices: 279648--279681 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
279638 CGCTCCTGAC
* *
279648 TATTCATATTCACGGCT
1 TATTCATAATCAAGGCT
279665 TATTCATAATCAAGGCT
1 TATTCATAATCAAGGCT
279682 GTAACCTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (17 bp):
TATTCATAATCAAGGCT
Left flanking sequence: Indices 279148 -- 279647
GCGTTTAAAAAAGAAAGCCCATTCTCGAATCCTGTATTCGACTCTATGAAGCCAGTAATCTCATC
AGAAATGACGAATCTTCTCAAAGACATCTCTGCAAATAGCGGAAGTAATGTGATGTCTGATCTTT
TCTTTATCTTGCAGACGGGTGAAGAAAGTGCTCAATCAGACCTTCTTTTAGGTGGCCTGCTCCCT
ATAGTTGATAGTGGGACCTCCTTGCTCTTCTTCTTGACCCTGAAGAAAGGGCGGGTTCACTCCGT
CACCTATTGGGCAAGCGGCTTTGCTCTTCTATCCCATCCTGACTCGTACCTTCAACCGACATTGT
CCTCTAAGGCAAGGCTGATAGCGCCTGGAAACAAATCAAAGCTTTCCCCGCTCGTTGTCCAGTGA
TAGTACAGAGTAGGCTTCTTTCTTTCCTTTCTCGTGGAATGAGCACACCTTCAACTAGTCAGCAG
TGCCGAAATAGTCTGTCTCTTCCAGCTCGTAATCTCGCTCCTGAC
Right flanking sequence: Indices 279682 -- 280181
GTAACCTCCTAATCAAGGAGTGGAATTCTCTGCCCGAGTGAAACAAGTGAATCCGGAAGGAAAGG
GACTGATTTCCTCCCGACGTGCATGCTCAGTGAGCATTTTCTTGTCTATCCCCGAGTCAGTCAAA
GATGTCTGGTGATAGAGCCCTTCTTTCTTAGTCTGATTCTTTCCTTACTTGAAACCAAAGCAACT
CTTTAACCTCTCCACGGACACTGTCACTAAACCATAGCTACTTTCATCATCGATAACGTGGCATT
CTGTCTTTCATTCCCTCCACCTTACGGTAGACCATCTTCAGCTCCTCTTCGACGATTCACTCTTA
CTGGAACAATCTTTCTAGCCTCGTGCGAGAAAAGAGGGAAAGTGCTAAGACCGGTAATGCAGCTA
GAGAGTTGGAGTGTGGTTATTCCGCCAAAAGCTAGGCCAAGAAGCACAAGGTGAGACAGATAGAA
TTCCTTCTTTTAAGTAAGGTGTTGTTGGAGCAAGTTCGGAAGACC
Done.