Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: OM066870
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: 48380
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:5261 original size:24 final size:26
Alignment explanation
Indices: 5227--5274 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5217 AAAGGTGGTA
*
5227 CGCTCTCTCGAA-AACAGGAAGAGGG
1 CGCTCTCTCGAAGAACAGCAAGAGGG
5252 CGCTC-CTCGAAGAACAGCAAGAG
1 CGCTCTCTCGAAGAACAGCAAGAG
5275 CTCATTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.33, C:0.27, G:0.29, T:0.10
Consensus pattern (26 bp):
CGCTCTCTCGAAGAACAGCAAGAGGG
Left flanking sequence: Indices 4727 -- 5226
TTGAAATAGTGTTTTTGCCTTGGCAAAGACTCCTTACCTGCTGAATGGATCTTGCCACATAAAGT
AAATCAATATTCAGCCCTGAACATGGATTCCCGATAACTAGCTTGCCCTGGACAAGAAACTCCAA
TTCCATATAAGAAAAAGTAATAAAGCAGACCTGTAATCTTTATTGGAAAAAGTCCGGGACTATGG
AACTACCAAGGCTATCCAGTGTCTTGCAATAAGTAGCGAACCAGTCTTTTCTCTTTATAGCCTAT
CCCCTCTCCTTCCCTATCGATAGAGTGAATTAGGCATCGAACCTGACCTTTTCACGCAAAGAAGT
TCCCCTTTTTATATACCGAGCGAGACCAAGCCAGACGGAGAGTCAGCCCTTCCCATTCTACGCGT
GTCAAGTTGAAGAAATGAATGCAGCTTCATTCTTCTTTTGCTGGTTTACATTCTTAAGGTGGAAA
GACCTTTTAGGACCGACTACAACACGACTAAAATCAAAGGTGGTA
Right flanking sequence: Indices 5275 -- 5774
CTCATTGTTCGGGCTGTCACCCGCGGTCACCGGGGGGACTAGAAGAGTCCGTCGACTCTTTCTAG
AAGATTTAAATAAGTAGTCCGTCGACGCAAAGTAGTGTGTTTTAATGCATGGCTTTCTTTGTCTT
TGTTTGGTGGAGATCTACTCCTATGCTTACTGGAGATAGACTCCTATGCTAAGTGTCTTAGTTTG
GTTTTATTTGTTGTGTTTGCATGTATGGGCCAAAACCTAGTCTAAAGTGTTCAATGCTTATGTTA
ATATAATAATAATAACTTTTTCGTAAAAATGTGCTGAAAATTCATGTGAAAGTTGAAATAAGGCC
GAAGGGCTAAGTGTACTATTGGAGATGTGCTTATTAAGCCTTTCCAGCTCTGAAGCTTCCTTCTT
CCTTGAGTCTGCGCCGTCTGAAATACCAAACCCTAAATCTTGCTAGTTCAGTTCGTGTGTTTTAC
GTGAGCGCGCTTCACTAGTGTGCGTAGAAAAAACACACTAACTTG
Found at i:13718 original size:14 final size:14
Alignment explanation
Indices: 13695--13727 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13685 GTACCAACAT
*
13695 AATACGAATTCAGG
1 AATACCAATTCAGG
13709 AATACCAATTCAGG
1 AATACCAATTCAGG
13723 AATAC
1 AATAC
13728 GAATACGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.21
Consensus pattern (14 bp):
AATACCAATTCAGG
Left flanking sequence: Indices 13195 -- 13694
TTTAAGGGATTAGTGGACTCAGCCTGTCCGTTTTCTCTTTTTGGTAATAAAGTTGGGTTCTTCTG
AGTAATCATGAATGATGATGTTAGATGTTGAATAGTCTGAGGAAATGCGTACCTCGATCGCTTGG
TTGCTCCTGGGGACATCCAAACCGCACAAGAATCTCCTCATAGAGCCGGCAGAATTTTCTCGCAA
AGCCCTTTCTCATTATCACCTACACCCCTTTCTTCCGTTGCTGTAATAATGTACCTGTTCCTTAT
TATAAATAATAAGCATATAGATTCCTTCTATCTATAGCCGAAATCTTAAAAAAAGAAAAAGACGC
CTTCTTCTAGTTCTAGCTAGCTGGTTGCTGCGACATAAGTTCGTTCAGAATGGGCAGTTTTTTAG
GATTTCTACTTTGTTTGATGGGGATTTAGGGATAACACATGCACATGAATAAGAAAAAGCAATCG
CGGAATAAGCAGAATACTCAATAGCATTGGAAAAAGTACCAACAT
Right flanking sequence: Indices 13728 -- 14227
GAATACGGAATAGTAACAACATACTAATTAGAGGGTGAAGTAGTAGCTAATCACTAATCAAATAA
TAGGGAGGAGGTTATGAAATAACGGGAAAAAAAAATAATGGTAAACCAGAGTCACCGGTTGGCGG
GAGTTCCTACTTCCAAAAGAGGAAGGCCGCTAAGGTCCATAAAATGGATTCATGAGAGGGAGGCG
TTTACGTCTTTCCTGTAGTAGTTGGAGTTGGAGGTGTGGCACACCAGCTTGGTCTTTCTGTAAAA
ATGTATTTGCCGGTTGGCTGGTCAACGGTTGAGCTGTCTGGTCAATCCAGTTCTTCTTTTTACAA
ATATATGCCGGCATATATATTTGCTCAAAATGATTCAGGAGACCTCTCTTCCTCTTTTTGCCTGT
TTAATAGCTTGAGACGAGTACAATGAGGATCAGAACCGGACAACCCCCTTTAGTCAAGCCCAGTT
TAAATGCCAGTCAGGAAGGCTCTCGGAAAGTTAGGAAGGACAGCT
Found at i:26542 original size:32 final size:32
Alignment explanation
Indices: 26501--26564 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
26491 CCCCTACTTA
26501 GTCTTACCTAGGAAGTGGAAAATACATTCCCT
1 GTCTTACCTAGGAAGTGGAAAATACATTCCCT
26533 GTCTTACCTAGGAAGTGGAAAATACATTCCCT
1 GTCTTACCTAGGAAGTGGAAAATACATTCCCT
26565 TGTTTGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (32 bp):
GTCTTACCTAGGAAGTGGAAAATACATTCCCT
Left flanking sequence: Indices 26001 -- 26500
GGGTCCGTGTAACCATACCGAATTCGCACCTCCAGGCGCCCCCCTAAAGCTCACTTCCTTCTTGG
GGACCACGACAATGAGTGTATAACGCATTTGACGCCCCCGAGAATGGTTAACGGGCAACCGTAGA
GAGAGAAGCCCTTATTCAATGCTTCATTCATAGGAGACCACGCAGAGCAGGTGTAGCCTTCGTAG
CAACCGAACCATACTACTTGACTATGTCATTAGTTGAGGAAAGTCAGTCACCCACCAAGTCAATC
GAAAATTTCTATGCTTGGTTCAAAGGCGCAAGCGCCTTATGTCGCCCAAGCCTCCTTAACTCCTT
TTAGCTAGCCTTTCCGTCCCTGCACCTAAGACTTTGTTGCCTTACTTCACTTCCCTTTGATGAAA
GCCCTAAGCTCGAAGTCAAGGCAAGGTGTATTAATGCTGCTCGACCTTTCGAACGAACTGATCAT
GATGTATGGGAGCATTGACATGAGAAGCTCGTTCGCCCCTACTTA
Right flanking sequence: Indices 26565 -- 27064
TGTTTGAAACCATCTTATTGGATGCCTATTCTGATACGGAGGGACCGGTACCCGCTCCTTCTGCT
TAGGATTCCTTACCTTACTTAACGCTCCCTTTCACAAACGCAAGCGCCTCCGTTGTGAAGAAAAC
AGCAGGCTCCCCTCTATCCGTGAAGGCCGGAGCATGAACGGGGATATCGACCTTCGGAAAAGCAT
TGGTTTCAGCGAGCATACGAGCATAAGACTTATGCATGGTGGAGGCAGCAGGCGCAGAAGACGTT
TGGGGGGGCTGCCCGCCCCCCTCCAGCCCGGCCATGAGGCCGGCGGCCTCAGGCAGCAGAAACCC
TAGGAAACCCTAGCTAAACCCTAAGACTCTGGCTGAGTCTCTTGAGGAGAGACTCGATGTGAGGA
CCCCTCAAAGCCTCACTAGACCGGAAGCGTCCTTCCGATATAGCTTATAGTTGACGCACGTCTGC
GCCAACTGGCTTATCTGTAGGACAACCGCACTTGCGGCCTTACCT
Found at i:43405 original size:21 final size:22
Alignment explanation
Indices: 43374--43418 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
43364 ATGACTTTCC
*
43374 TTCGTCACCTTGCTTGCCGATA
1 TTCGTCACCTTGATTGCCGATA
43396 TTCGT-ACCTTGATTGCCGATA
1 TTCGTCACCTTGATTGCCGATA
43417 TT
1 TT
43419 GGGGATATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.40
Consensus pattern (22 bp):
TTCGTCACCTTGATTGCCGATA
Left flanking sequence: Indices 42874 -- 43373
TAGTCGCTTATGACTTAGTCCTGACCAAGCAAGGCCTCTTTTAGATTGACTGTTGGCAGATCGAG
ATTGAAAGCCAGTAGCAAGGAAGTGCTTTCTTGTAGTAGATCCGTCTAGTCGAAGAGCATTCTGT
CTAGTCTCCCTTGTTTCGCTTGTGAGAAGAAGCTGTGGCACTTTCGGAAATAGGCTTTGATGGAT
TGCACAGATTACCTTCGCTCCTTTCCTGCTTTCCGGCTTAGACTGATTTAGTGAAGTATGCCAGT
TTGCTAACTCCTTGCTCTGACTCTGCCTTATTAACGGAATTATCCGAAGCTACCTTCTCAGATGC
GGCATTACCTTACCGCTGTTCTGTATTTTTACTTTTTGACTTGCCTTGCTTTCTTGCTTTACTTA
TTTACTTTGCCTCTCGATACGCACCTTCTCTTGCTATTGAATCCAGTACTATTGAATTTAGCGCT
GCACATGAATAGGCTCTTAGCCTGAGCCTGGCCTGATGACTTTCC
Right flanking sequence: Indices 43419 -- 43918
GGGGATATTGATTAACTGCCCGAGAAGAGAAGATCATCTGCAATCACATTTGAGGAATCCAGGGG
AAACTACTGGCTCTAAGCGCCTATGCACATGAATCAGAAGCTGTGGCACTTCTGCCTTTAATCCT
TATAAGGATTTCAGGAGGCATGCTAAGTACAGACGATGGCATCGAATGCAAAATAGGGTGTGGCA
CTTTCGGGATAGACTAGGCTGTTCGGGATTCACCTGATTGACCATAAATCCGCTATTGCCCACCT
ATATATATCCGATTTTTCTTTCTCAGATAAGACCTTACGCCCCTAACTCTCTGGGCCTGGCTTAG
AAGAACTAGGCTTATGCTAAAGGAAGCAGTACAACCATCCAATTGCAATTGCATGTCTTAACCAT
AGTGACAGTGACACAGATCCCTTGGATCAAATAGTGGATTCTAAACCTTGCGTCTTGCAACTGCT
ACTGCCTCTGTAGCACTCAGACTAGCAGGGAATTCAATAGCAATA
Found at i:47633 original size:15 final size:15
Alignment explanation
Indices: 47613--47646 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
47603 TAGCTGCTGA
*
47613 TTCTGTAACAGCTTG
1 TTCTGTAACAGCTTC
*
47628 TTCTGTCACAGCTTC
1 TTCTGTAACAGCTTC
47643 TTCT
1 TTCT
47647 TATCAACCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (15 bp):
TTCTGTAACAGCTTC
Left flanking sequence: Indices 47113 -- 47612
TTCTTCCTCCAACAACGGCCAACAAGACCAAGAGCAGCGGATTCTATAACACCGGATTTGCGGCA
TCAGCGTATTCTCTTCCTGAGACACCTTCCTCCAGGATAAGTCAATTAGGTCAATCCCTTTTTGA
AGAACCTCTTCTGATTAACTTCCTCCAGGTTTAGAAAGACCCAGGGGGAGTTCTCGCCTTTTGCC
TGCTTTGATTAGGACTTTGCCCCGGGAAGAGCTCATCGGGGAAGAACTAAAAAAAGAAAATTTAA
GTCGAAGTAAGTCGGATTCGCTAGCCTTTGGGCTTAAAGAATCGCTCTTTGCTAATAGACTGGAC
TGGCTTAGAATCAATGCTTTGACCGCTAATGCCGATTCCCAGACCAGGTTCACGCTTGTGAGCCA
GAGCTAGTCTTCTTCCCACTGACCGCTACTAATAAGATAAGAGCTGCCGAACCACTACCTACTAG
TAGGTAGTGCCTTCCTCCAACAGATGGGGGTTCAATAGCTGCTGA
Right flanking sequence: Indices 47647 -- 48146
TATCAACCTCCCCCAGGGAAGTAAGTAAGTAAGGTAGCAGGAATAGATCTACTATAAAAAGCCTT
GAGTCGGGTTTGAACTCCTCTCCTCTCACTACTCTCTTTGGTTCTGCCTTTAAGAGGCCTGTAGA
GGGGGAATTTCCACTGCCGCAAGCGCCTCGGTCTCTACGATTGCTTGACTTAAACAAGTGACTTC
ACTCTCTTTTCTTTCATCTTAGAGATAATGTCTCTAATTCACTCTCGGATCTCACTCTCTTTCTT
TCGGGCCTAGCCCGTGGGAAGAGAGTTTAGTCATTGATATCCATATTAAAAGGCGGGTATTCCCA
CAAAACAAAAGCGCTAGAACCGATTACATCGCCTTTACTTTAATCAACAAGGCTGCTTTCCCTGC
TAACCCTTCTCGGGAGATTGCCAGGTGTGAGACGATCCCTTCTCGCCAAGGAAAGAAGTCCAATA
GCAGCTGATCTTAGCTTTGAGCGCTTATTCCTTTTGTTCCCAGAT
Done.