Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: OM066873
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: 35805
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Found at i:535 original size:15 final size:15
Alignment explanation
Indices: 515--557 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
505 GCCTCTCTCT
*
515 CTCCTAGGGTTAAAA
1 CTCCTAGGGCTAAAA
530 CTCCTAGGGGGCTAAAA
1 CTCCTA--GGGCTAAAA
547 CTCCTAGGGCT
1 CTCCTAGGGCT
558 GCGCCGACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (15 bp):
CTCCTAGGGCTAAAA
Left flanking sequence: Indices 15 -- 514
CCCCAGTCGTACTCCATTCTACCCATTGAGTAGGTTACTACGGTTCCCATGCCTCCTGCTTTAAC
TTGAGTTCCATCAGGCAAGACATCATCCTTGCGGATGCCTTTTGGGTCCTACACAGACACAGAAA
AGATCACATCTTAACAGCCTTCTATGAAAGTAAGCTGCATTGGTGGTCTTAGCTGGGTTGATGGA
AGGTCATAGAGAGCACACCCAAATTTGAGCCACAAGGACTGCTCTTAATTCCAAGGTTTACAATA
ACGAATGTACTAAGAATAGGGTCTCATTTTCGGAGCTTGGAGGGCTAGGCGTGGGTCACCTGAGG
AACGGCAGGGTGCAGCCGGAGAGTCTCCGTAATGGATGCATGTAGGATAACTTTGCCAAGGAAAA
GTAGGTCAAGAGCCCTGCAAGCCGAAGATAACCTTGTTTCAAGGGCTTTATATATCTCAGCCTAT
AACTATAAGTGGGATTGCAATTTGGAAGATTTTGAGCCTCTCTCT
Right flanking sequence: Indices 558 -- 1057
GCGCCGACCCTAACTCCCTGTTAGGGTTTCGGCCATGGTTCGGGGGGCCACCACCCGCCCCCTCC
TTCTTCTTCCTCTCCTGCTAGCGCCCTCCTCCGTTCTTTCCCGGGCTGAAAGGGCAAAGTAGCTC
CCTTTTTTTCAACTCTAATCTGCCTTTTTTGGATCCAATACCGATACTGATCACCGGACTCACCC
GCTACTCGTAGTTAATGAAGTATGGCTTTCTTCTTTTCTCTTAAATAAAACGTCGGCAATCAAAC
CAATCCACTCTTGGAAAGTGCCATAGCACCTGCCTTCAATTTGAAAGAAATGCCTGCTGATGATG
CATCCTCTCTTGAACTGCCTAGTACCTTACCAATTGAATTTCTTTGCCTTAGAGAAAGCATAGCC
TCTACCTGTGACAGCCTTTCTAGTTATAGGCGAGTGTGGCATATTCCTTTGAGGAGCTGCCTGCC
CTTTACTGTCAATTCCCGTTCCTTCCCTACTGGTTGAACTGTTAG
Found at i:10658 original size:24 final size:24
Alignment explanation
Indices: 10626--10671 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
10616 GCCCCCTTTT
*
10626 AGCGATATCCCTTTCAAACATGTC
1 AGCGATATCCCCTTCAAACATGTC
10650 AGCGATATCCCCTTCAAACATG
1 AGCGATATCCCCTTCAAACATG
10672 AGTAGGAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.26
Consensus pattern (24 bp):
AGCGATATCCCCTTCAAACATGTC
Left flanking sequence: Indices 10126 -- 10625
CAGCCCTTCCCGGTCAACTGCGGAAAACCTTATCAATGAAATTGCCGATTTTTGAGCCTATCTCG
CTAGTTCAAGCCCTCTTATGGGTCTTTTTACTAGTTCTGCTTTAACATGCTAGAGAACTTGCCCT
GATCTGCCGTCCAATCCACATACATTCATTCCACTCGGTAAATATGGCTTAGCTGGCTCTCTGCC
CGCCTCTCTATTATTGTATTGATAGGCTCGGTAGGCTAAGTAAGTACTTCCATTGGCCAGTACTT
CTCTTGTTAGGCTAGCTAGTAAGTAACGTAGACGTAGTTGGCAAGTTTGCTAGTAGCTTATGAGT
CAGATGCCTCTTCTCTCTCCTTCTTTCGAGCTTATCAATACGCTTCTGTTGGATGTCGCTTAGTT
TATATGTCAATCATCTTTTTCCTTAAACCAGAGGCCCCTCGAAAAAGTGGAAATACATTTGAAAT
ACATACACCACCGCCTGTAACAGGATTGCTAGTTGGCCCCCTTTT
Right flanking sequence: Indices 10672 -- 11171
AGTAGGAGACTTATTTTTGAGAAAGTCGTGGAGTTCTAATAAGCTGTAGTCTATTGAGTTGAAGC
TGCAGTCGTTGACTTGTAAGCCGTAGTCTTCGACGAACTTTGCGGAGTCGAAGCAAGCTTCCCTT
GCTGAATAGAAGAGGAAGCTTCTGCCCCTCTCCCTTCTTTTGAGTCTACGCGCTTCTGCTTAGTT
TGTCGTTTATATGCTCCTTAAGCCAGAGGCCAGTTCAATTGATCTTCTCATAGGTGGAACACACT
GCCTGTAATTAGCGATCTTCCTCTTTTTAAGAAGCATGAGTAGGCAAGCTTGTCTTGTTGGGAAA
GTCATCCTTGGCATAAGCTCTAGTGGATCTCTGTTATGGCATTCCCATATGCTTCCTAATTCCTA
TATGTTTCCATATTCCCTATAGTGCTATACCATTCCCTCTCTTTTCTTCCCACTCCCTCACCGGG
TCCCCTCTGTAAAGATCTTTTCCTGCTTAGGCTAGCTCTACTTCC
Found at i:10736 original size:21 final size:22
Alignment explanation
Indices: 10711--10765 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
10701 GGAGTTCTAA
*
10711 TAAGCTGTAGTCTATTGAGTTG
1 TAAGCTGTAGTCTATTGACTTG
* *
10733 -AAGCTGCAGTC-GTTGACTTG
1 TAAGCTGTAGTCTATTGACTTG
*
10753 TAAGCCGTAGTCT
1 TAAGCTGTAGTCT
10766 TCGACGAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (22 bp):
TAAGCTGTAGTCTATTGACTTG
Left flanking sequence: Indices 10211 -- 10710
GGTCTTTTTACTAGTTCTGCTTTAACATGCTAGAGAACTTGCCCTGATCTGCCGTCCAATCCACA
TACATTCATTCCACTCGGTAAATATGGCTTAGCTGGCTCTCTGCCCGCCTCTCTATTATTGTATT
GATAGGCTCGGTAGGCTAAGTAAGTACTTCCATTGGCCAGTACTTCTCTTGTTAGGCTAGCTAGT
AAGTAACGTAGACGTAGTTGGCAAGTTTGCTAGTAGCTTATGAGTCAGATGCCTCTTCTCTCTCC
TTCTTTCGAGCTTATCAATACGCTTCTGTTGGATGTCGCTTAGTTTATATGTCAATCATCTTTTT
CCTTAAACCAGAGGCCCCTCGAAAAAGTGGAAATACATTTGAAATACATACACCACCGCCTGTAA
CAGGATTGCTAGTTGGCCCCCTTTTAGCGATATCCCTTTCAAACATGTCAGCGATATCCCCTTCA
AACATGAGTAGGAGACTTATTTTTGAGAAAGTCGTGGAGTTCTAA
Right flanking sequence: Indices 10766 -- 11265
TCGACGAACTTTGCGGAGTCGAAGCAAGCTTCCCTTGCTGAATAGAAGAGGAAGCTTCTGCCCCT
CTCCCTTCTTTTGAGTCTACGCGCTTCTGCTTAGTTTGTCGTTTATATGCTCCTTAAGCCAGAGG
CCAGTTCAATTGATCTTCTCATAGGTGGAACACACTGCCTGTAATTAGCGATCTTCCTCTTTTTA
AGAAGCATGAGTAGGCAAGCTTGTCTTGTTGGGAAAGTCATCCTTGGCATAAGCTCTAGTGGATC
TCTGTTATGGCATTCCCATATGCTTCCTAATTCCTATATGTTTCCATATTCCCTATAGTGCTATA
CCATTCCCTCTCTTTTCTTCCCACTCCCTCACCGGGTCCCCTCTGTAAAGATCTTTTCCTGCTTA
GGCTAGCTCTACTTCCTAGCCTGCCTGGTCTACGCCCATCCAAATTTAGCATTGTGTCTCGATGG
CAATATCTCTTTAGGTTGAGTAAGAAGCTATATCTCCATAGGTTG
Found at i:30326 original size:22 final size:22
Alignment explanation
Indices: 30294--30339 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
30284 TGTCGTCCAG
*
30294 CGGAGCTTAGAAGAAGGTGACT
1 CGGAGCCTAGAAGAAGGTGACT
30316 CGGAGCCTAGAAGAAGGTGACT
1 CGGAGCCTAGAAGAAGGTGACT
30338 CG
1 CG
30340 CGCAGACAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.37, T:0.15
Consensus pattern (22 bp):
CGGAGCCTAGAAGAAGGTGACT
Left flanking sequence: Indices 29794 -- 30293
CGGAAGCCAATGTCCCGGGGTCCCGGGGACTCATTCTGACTGAAACAAGGGGTGGGTCTTTACCA
AAAGTAAAATCCAAGATTTCAGGGAAGAAAAAAGAGGGGCAAGGCACTCTTCATTCTTCATTCGA
AACTCATGAATGTCGGGTCGGGGGTTTCTGCCTTGTTATAAAAAAGGGGAGTTGGGTAAAGCAAA
CTCCCTCCTTGGACGAGCATGGGGCTTAGTCAAGTAGAACCGGGTTGCGCTGCTTGATGCTCCGA
TCGAAAACAAATCAGTGGGGCCTGATTAAAACCGGTACGACAGAATATGCGTTAGAAAGGTCAAT
CCCTCCCCCCCTTTATTATTAAGTAAATAAAACCGGGCCGAACTTCTAAAAAGCAGCCCGCCCGC
TTCCATAGAACAATATCGTGGCAACGTAGACCTAAGTGAGTTTATTGGATCCTGGGAACCATCAC
AAGTACGGCCGGCCTATATTTGAACGAGAATGCCGTGTCGTCCAG
Right flanking sequence: Indices 30340 -- 30839
CGCAGACAGCTGACTCCTTTTCAATAGAAAGGAATAGCCAAACCAACCCAGCTGGCTGGTCAATC
TCAATGATCTTATCGGCCGGCAAACCGGAGACGGACGACCACGGTCCCGACCTTACCAGCACCGT
AGGTTTACTAATCAATGAACCCCCGAAACCTACTGTCTTTTCTGAGAAAGTCAACAAAGCCGGAA
CAAACCGGACTAAAAAAGTCACGACATGTTGTTGATATTGATGGAGTTGGAGGGAGTCAGAGACT
ACCACTGAATCCATCCATAAACCGTCACCTTCCTTCGTAACCAGCACTTTTCCAAAGGTTACCCG
TCATCGAATCTCCAGTAGGGGGGCAAGGAGGAGCACGTAGGAATGCCGACCACTACATAAGCCGC
TGGCGGCTGAGGCGAGCAGCAAGCGGGGGAGAGTCAAGTAAAGTACAACAACGTTGGGGTGGGAC
GCTAGTACTTAAACTAGGGTTGCTTCTTAGCGCTAATCTTGCCTT
Found at i:33010 original size:31 final size:31
Alignment explanation
Indices: 32972--33037 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
32962 AGAATTGTAA
*
32972 AGCCTTTCTCTAGCCC-CGAACTACTGAACTT
1 AGCCTTTCTC-AGCCCGAGAACTACTGAACTT
* *
33003 AGCCTTTCTCGGCCCGAGAAGTACTGAACTT
1 AGCCTTTCTCAGCCCGAGAACTACTGAACTT
33034 AGCC
1 AGCC
33038 CCCTTTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (31 bp):
AGCCTTTCTCAGCCCGAGAACTACTGAACTT
Left flanking sequence: Indices 32472 -- 32971
AGCGCACAAAAGCAAGGGTGGTGAGTGGGTCCAGAAAGACTCATCCTATAGGTAGGAATTGGAAC
GAAGATGCGTGCGAGATAAAGTTTCAAATAAAGAGGAAGAGGATCACAAAGAAAAGAGTACCAAA
GGCTCTGTTATTTCGAATTAAAGTAGTGCGCAGGCCTTCATAAAGGCAGTTTATTTAACACGGGA
CACTTTACTTTCCTATTAACACATAGGCTTCGCCTTTTTAGAATGCTTTTAGTAGGTCACTACAA
AAGAAGAAGAACGGGCCAGCCACAAAAAGATCCACTGATCCAGGGCTAGGGTGGGGTAGGGGCAG
GGCGCAGCGTCGGTATTGCCTCTTCTCCCGTTGGCAGGGGTTCCTCCAGTCTCCAGTCCCTGCCT
GCTGGTTGAGGGAGGAGAGAGACGGAATCCATACGGGCTACGTGAGTGAACTCACTGCATTTGGT
CAGCAGGTGAGGAGCAAAAGAGAATTGAAAGAAGAAGAATTGTAA
Right flanking sequence: Indices 33038 -- 33537
CCCTTTCTCTAGTGGTTCTTGCCCTTAAAACTAGAACTAATCAGTACAGTAGAGACCAAGGAAAA
GGAACCAATGCACTGATGGAAGTAAACCTTGCTTCATTCACCTTGTTACTCCTGCTCTGTCATCA
TCCACCGATCTCTGCTAACTGACACCCTTCCCCTTCCTTGGCTCCGAACCCCCAATAGCTAAGGG
TTTGTGAGAATAAAGGGCCATTTTCAAAGAATAATCTTTTATCCCCATTGTAGTTGTTGGAACTG
TTGCTTCAAAGATCCGCTGCATTCTACGCTGTTGATTGTATTGATCCGCTTTTTTTTCTTACCCG
AATAATAATAATAATAATAGTTAGTTGCCCCGGCTCGGTGAGTCCTTCCTTCCGTGATGAACTGT
TGGTACCAGTCCTATATTTTTTCTCTGTGGACCGAGGAGAAAGGGGGCTCCGCGGGAAGAGGGTT
GTACCATGAAGAGAAGCAAGGAGGTCAACCTGTTTCAAATATACA
Found at i:33693 original size:11 final size:11
Alignment explanation
Indices: 33671--33716 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
33661 GTATTTCTAT
33671 TACTAT-TTAA
1 TACTATGTTAA
33681 TACTATGTTAA
1 TACTATGTTAA
*
33692 TA-AATGAATTAA
1 TACTATG--TTAA
33704 TACTATGTTAA
1 TACTATGTTAA
33715 TA
1 TA
33717 AATGAAGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.30
11 12 0.40
12 6 0.20
13 3 0.10
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (11 bp):
TACTATGTTAA
Left flanking sequence: Indices 33171 -- 33670
ACCGATCTCTGCTAACTGACACCCTTCCCCTTCCTTGGCTCCGAACCCCCAATAGCTAAGGGTTT
GTGAGAATAAAGGGCCATTTTCAAAGAATAATCTTTTATCCCCATTGTAGTTGTTGGAACTGTTG
CTTCAAAGATCCGCTGCATTCTACGCTGTTGATTGTATTGATCCGCTTTTTTTTCTTACCCGAAT
AATAATAATAATAATAGTTAGTTGCCCCGGCTCGGTGAGTCCTTCCTTCCGTGATGAACTGTTGG
TACCAGTCCTATATTTTTTCTCTGTGGACCGAGGAGAAAGGGGGCTCCGCGGGAAGAGGGTTGTA
CCATGAAGAGAAGCAAGGAGGTCAACCTGTTTCAAATATACAACATGGATTCTAGCAATGCAATG
TAGTTGGACCCTCATGTCGATCCGAATGAATCAGTCTTTCCACGGAAGTCTATTCTTGCCTGCTA
GGCAAGAGGATAACAAGTTACAAATTCTGTCACATGTATTTCTAT
Right flanking sequence: Indices 33717 -- 34216
AATGAAGTAGTTAATGGTGGGCATTATCCTTTTTGTAGTGACGAATCTTGTATGTGTTCCCAAGA
AAAGGAATTTGTCCATTTCATTTTTCGAGGTTTCAAAAAAAGGGCGTGGAAACACATAGAACTCT
TGAATGGAAATTGAAAAGAGATGTAGCTACAGTTCCTTCGGAACTGGTAAGATCTTTGGCGCAAG
AAGAACGGGGTGATCCGTATCATCTTGACTTGGTTCTGCTTCCTATCCTTTTATTTAACAATACC
GAGTCGGGTTCTTCTCCTACCAGTATCGAATAGAACATGCTGAACAAAATCTTCTTCATGTAAAA
CCTGCTCGATTTAGATCGGAAAAATCGTACGGATTTTATGAAACCATGTGCTATGGCTCGAATCT
GTAGTCAATCCTATTTCCGATAGGAGCAGTTGACAATTGAATCCAATTTTTCCCATCCGTAATAG
TGCGAAAAGAAGGCCCGGCTACAAGTTAAGTTGTTTAGGAATAGT
Found at i:33703 original size:23 final size:23
Alignment explanation
Indices: 33677--33722 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
33667 CTATTACTAT
33677 TTAATACTATGTTAATAAATGAA
1 TTAATACTATGTTAATAAATGAA
33700 TTAATACTATGTTAATAAATGAA
1 TTAATACTATGTTAATAAATGAA
33723 GTAGTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
TTAATACTATGTTAATAAATGAA
Left flanking sequence: Indices 33177 -- 33676
CTCTGCTAACTGACACCCTTCCCCTTCCTTGGCTCCGAACCCCCAATAGCTAAGGGTTTGTGAGA
ATAAAGGGCCATTTTCAAAGAATAATCTTTTATCCCCATTGTAGTTGTTGGAACTGTTGCTTCAA
AGATCCGCTGCATTCTACGCTGTTGATTGTATTGATCCGCTTTTTTTTCTTACCCGAATAATAAT
AATAATAATAGTTAGTTGCCCCGGCTCGGTGAGTCCTTCCTTCCGTGATGAACTGTTGGTACCAG
TCCTATATTTTTTCTCTGTGGACCGAGGAGAAAGGGGGCTCCGCGGGAAGAGGGTTGTACCATGA
AGAGAAGCAAGGAGGTCAACCTGTTTCAAATATACAACATGGATTCTAGCAATGCAATGTAGTTG
GACCCTCATGTCGATCCGAATGAATCAGTCTTTCCACGGAAGTCTATTCTTGCCTGCTAGGCAAG
AGGATAACAAGTTACAAATTCTGTCACATGTATTTCTATTACTAT
Right flanking sequence: Indices 33723 -- 34222
GTAGTTAATGGTGGGCATTATCCTTTTTGTAGTGACGAATCTTGTATGTGTTCCCAAGAAAAGGA
ATTTGTCCATTTCATTTTTCGAGGTTTCAAAAAAAGGGCGTGGAAACACATAGAACTCTTGAATG
GAAATTGAAAAGAGATGTAGCTACAGTTCCTTCGGAACTGGTAAGATCTTTGGCGCAAGAAGAAC
GGGGTGATCCGTATCATCTTGACTTGGTTCTGCTTCCTATCCTTTTATTTAACAATACCGAGTCG
GGTTCTTCTCCTACCAGTATCGAATAGAACATGCTGAACAAAATCTTCTTCATGTAAAACCTGCT
CGATTTAGATCGGAAAAATCGTACGGATTTTATGAAACCATGTGCTATGGCTCGAATCTGTAGTC
AATCCTATTTCCGATAGGAGCAGTTGACAATTGAATCCAATTTTTCCCATCCGTAATAGTGCGAA
AAGAAGGCCCGGCTACAAGTTAAGTTGTTTAGGAATAGTGGCGTT
Done.