Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: OM066869
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: 56458
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Found at i:11273 original size:21 final size:21
Alignment explanation
Indices: 11224--11275 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
11214 CGAAAGCTAC
* * *
11224 GCCAACTGCCACTGGATATAA
1 GCCAACTGCAACTCGATAGAA
*
11245 GCCGACTGCAACTCGATAGAA
1 GCCAACTGCAACTCGATAGAA
*
11266 TCCAACTGCA
1 GCCAACTGCA
11276 TCTAAGCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (21 bp):
GCCAACTGCAACTCGATAGAA
Left flanking sequence: Indices 10724 -- 11223
CTTTAAAGTCTTTCAACAAGGAAAAAGGAACTTCAAGAAGATACTGCTGCTTTATTTGATACTGT
TGGTTTACTGGCTGGAATAGATCTCCCAGCGAAAAGGGAGAAAACTAGATATGGCACCCCAACTG
GATAGGCAGAAGCAATAGAACTCCCAGTTTAATTTGATGGAGGGGCTTGCCTTAACACTTCAATT
GGATAGACTGGAAATATGGCAGTAGCAGGGGAAAAGACTAAAACTAGATCGATGCGAATTGGCTT
GGGTAGTAGTAGAGTAGGTTTACCCCAGTACTTCAGCTCGAAGGAATAAGGAAAGGTAGGGGATA
TAACAGAAGTCGTAGGGATAGAAGTAGAACTGGCTTACACGATCCAAAAGGGCAGGGCTTCTTAC
AAACCAAAAGAGGCAGGAACTGCTGTATTGGGATTATAAGCGCTTAGCAATAACAGTATAAAAAC
TGCCACGAAAACCGTATTAGTAGCGGAAGGGCGAACGAAAGCTAC
Right flanking sequence: Indices 11276 -- 11775
TCTAAGCTTTCTCCAACTAGAATATGATGTTACCGACTGTAAAATATACTGCTTACTGACTTTCA
AAGGAGCTTAAAAAAGCAATTACAAAAGAGGCTTACTGCAGATCTTATAAATGGGATGAAAAAAG
AGATTACCCCAGCTTATATAGGACTATAAAGGCATCTGTAACAGGCACTTAAACTAGATCAATGT
CTGAAAATGGTTGGGAAGGACAAAGAAAGAACTCAAACTGCAGGAACTTAAACTAAAACCCCATA
TAAAAGAGAAGGATAGGCAACAAAGAGATCAATTTGAACTTCACCACTACATGGGAAATGAGCTC
CTAGCTGCAACTACCTTTTCTATCTTTCCCAAATCTGGTATATAAAGCATATATGTGAGATTAAG
TACATCGTTCAGAACTTCTCCTTACGACACAAAATCGCTCTTCGGCTCGATACCCTGCTTCTTCT
CCGGCCGGAGCTGGGTTTTGCCACAAACCAAGGGTCCCAGGAAAC
Found at i:31904 original size:40 final size:40
Alignment explanation
Indices: 31849--31924 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
31839 TTCTTTTTGT
*
31849 AGAAGTACTTTCTTCTAATTTATCCTTACGTAAGATTTCA
1 AGAAGTACTATCTTCTAATTTATCCTTACGTAAGATTTCA
*
31889 AGAAGTACTATCTTCTAATTTATCCTTCCGTAAGAT
1 AGAAGTACTATCTTCTAATTTATCCTTACGTAAGAT
31925 GTTTAGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (40 bp):
AGAAGTACTATCTTCTAATTTATCCTTACGTAAGATTTCA
Left flanking sequence: Indices 31349 -- 31848
ACGAGTAACACAAGTGTTCGGGGGATGCGCCTCACTCTCGCTCTCGGGAAATCGACTAACAGATG
CAGTCTTGGCTCAGTCAATCAATCACTACTATAAAAAAAATCCATGATACCATAAAGAGAAGTTA
CACAGCAGAAGGTGCTGCGGGATAAGGAGAAGAAGTGCGGGATACAAGTACCAGTGCCATAAAGA
AATGTCACGAAAGCCGAGAGCCATCACGCCCGAACCAGCAACCCCTTCTTATGCTGCTTGCAACT
CCGAGGTTTCTGATTTACTTAACTTTCATTTAACCAGGAATAGCCAGCAAGAAATCCATTGCTTG
TTCGTTAGTCACGCGCAGTAGTTTTATTGCTCCAATAGTCTTCGCCTTTCCGCCGCAAGCGCCTA
TACTATCTGGTAGACTTTAGAGAAAAAATAGAAACTAACTTACGGAACGCTTGTTCAAAGTGTTC
AGCTTGTTCAGTTTTACGGAACGCTTGTTCAGTGGTTCTTTTTGT
Right flanking sequence: Indices 31925 -- 32424
GTTTAGTCAATAAAAGCGGAATTCCGAAATGTAAAGTCTTGTCCATATTCTATTTTTGCAAGGAA
TCTATATGCTTATTATTTATAATAAGGGTAGGGATAATAAAATTCATATATTTACATATATAATG
ATATTTCACCGTGTGGAGACCGCAGTCAGCTCTATACCAATGAATGTTGGTGACTTCTGTCCAAA
TGGATCGAACTGGTAACAGTATGGTCTTAGTGCACCCATTGGACGCAGGATCTAATGTTCTACAC
ACAGAAGGACTGCCCCTATTCACTCGTTGTTTATAAGAAATAAAAATAAAATTAAAAAATACCTC
TTTTTAAAGAATTAACTTCTTAAAAACCTGAGTTCAGAGAACTACCTAATTATGACTTAACTAAT
ACAGTTCAGCAAGCAGGAAGGAGTATCTCAAGCGAGCTGTCAAGGGAAAGAAAGTTATAATATCC
TCGCATATTATCTGTATTACTATAGGATATTTCCTGTTTCCAATT
Found at i:37792 original size:34 final size:34
Alignment explanation
Indices: 37754--37821 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
37744 AGCACCAAAG
37754 CGAAACACCTACTTCAAGGAGAGCAGACCAAGTC
1 CGAAACACCTACTTCAAGGAGAGCAGACCAAGTC
37788 CGAAACACCTACTTCAAGGAGAGCAGACCAAGTC
1 CGAAACACCTACTTCAAGGAGAGCAGACCAAGTC
37822 GAAGAAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (34 bp):
CGAAACACCTACTTCAAGGAGAGCAGACCAAGTC
Left flanking sequence: Indices 37254 -- 37753
GAGCCTAGGGGATTGGCTTTCCTAGTCCTAACATAATACCTAAAAGTAGAGCTGTGTCAGTTCAC
AAAGACCTGTTCCTGTGGTTGAGGTTGCCAGTGCCAATGCGCCTCTGCTTGCAAACAAATGGATG
GCTCGCTCTTTTAGTGATTATTCTAATAATACCTTCCTTTCGATTGATTGGATAAGGGACAAAAG
AAGCTTAGTTAACAGAGACCGGAGGACCAGAAGAGGTTATTAAAGGTACAGTGGAAGGCGACGAG
TTGGCTTTCGGTTCCTTCCTTGGCCTTAGCTTGTGCCTACCCCGTGTCCATGGGAAATAAGATTT
CAGCTAAGGATGATTGCCTTCTATCCGTCAGGAAAGAGTTGCTTGCCTTTACCCACCTTCCTAAC
CCGTGGAACTGCTTGCCCGGTGGATGAGAAAGCTTACTTCGCCCTCCAAACCTGATCTGTGTGGA
GCAGGAAAGAGGAGATCGGAGTCAAAGGGGAGGATAGCACCAAAG
Right flanking sequence: Indices 37822 -- 38321
GAAGAAATAGGTTTTAAGAAACCAAGTCAGCAAGTCGAAGCTCAAGGACGAATGAGTTCTTGAGT
CAGCAAGCTTTCTCCTCTTTGGCCCTCTTTCAAGCACCAAGGCACCAACCAAAGCGAAGCGTAGC
GACCAAATCGAAGAAGAGAAGGCGCTTGCAGTTCAGAGAGGTAAATGCTCAATACCCTTCGATCA
TGATCAAGTGCTTTTTGGACCGTCTCATGCTGGTGTTGGTACCCACAATATCTCTAGTCTTCTTA
CAAAAAAAGGATTTACTTTTTACTATAACAGTCGTCACTCTGACATCCCTTGTTTCACTCCTATA
GTCTCATAGATCGGGGTCGATGCAGAGGAAATGAATGCATTTCCGTACTTAAATAAAGTAAGTGG
AATAGCTATAACATAATATGGATCATGCCACATCACTTATTTTAGTGGATCTTATGGAGCCTGCT
CATGGACGACATGATTCGGGTCTGATCATAGAAAAGGTTCGCTTG
Found at i:43641 original size:24 final size:24
Alignment explanation
Indices: 43546--43633 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
43536 CAGAATGATT
*
43546 AGAATTAGAGGGACAATCAGAAGA
1 AGAATTAGAGGGACGATCAGAAGA
43570 AGAATTAGAGGGACGATCAGAAGA
1 AGAATTAGAGGGACGATCAGAAGA
*
43594 AGAATTAGAGGGACGATCCGAAGA
1 AGAATTAGAGGGACGATCAGAAGA
*
43618 AGAATTAGATGGACGA
1 AGAATTAGAGGGACGA
43634 GAAGAAGATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.45, C:0.09, G:0.32, T:0.14
Consensus pattern (24 bp):
AGAATTAGAGGGACGATCAGAAGA
Left flanking sequence: Indices 43046 -- 43545
CATCTTTTAAACTACTGACTATATGGTCGATAAAATCGGAAGGGGTAATATCCAAAAAGGCTGGA
TTCCGCGAGAGAAAGAGAAGACAGCCTAAAGACAATGAAGGCAAGACTACCTGAAGAAGATCAGC
CGATGCGGTATAACAGAATAAATAACTAAAGGCATCATAATACTTTTCTTCTCGAGAAACCACTG
ACCAACCTATAACATTACCGAAGCCACGGTCGGGAGAACGATAAAGTTGAGAACGGCGGGAAATG
CAATAAGCTGGCGAAGAGCCCAACTTTGGAACACCAACAATAGGATTAATTGGAAACTTCCCAGC
CGAAAGACCAGAAAATGAATGTCGCATTTCTGGCAGCTGCCTGTGGAACAGACTCGACTGACGAC
CATGAATAAAAGATTTTTCTTTTAAAGAATGAAAACCTTCAAGCTTCAAATCTTTTGGGCGATAC
CCAAGCATTTCCTAGAATCTTAGAAGAACTCTTCTCAGAATGATT
Right flanking sequence: Indices 43634 -- 44133
GAAGAAGATAGTCTTGTCTTTGCCAAACCTAATATGTTTTTCAAAGCAATCATACTTTTAAAATT
TAATTAATATTCTGTGTCACTTGAAACAAGTAACAACTTATATACTATATGGGAGGGGGGTTTAC
CCCCTAAAAGAGTGGACTTTAGCAATACTAATCCTATTTGATTTAGCTTCACCAATCTTCCATAA
TTATGGTGGCCATTTAGGCAAATTACGAAAAATACACCCAGGTACTCTTTAATCCGACATCTTCG
GAGCTGCGAAAGTTAGCATCATGTCTAGTGACATACAGGCATGCCAACATAATGGCAGAGACTTC
CCTTGACTTATTAGGAGTCACCCGTATTCACAACAAAAACAGAACCCTCTTTATTAAGAAATAGA
AGACCTCCAGGGCATTCCACCGCATCACCACCTGCCCCATGCATAAGGGCTTATCCTAATCGGGG
GCCTGGAACGACAATGACAGAACACTGATTGGGAAAGGCCTAGAA
Found at i:54551 original size:19 final size:20
Alignment explanation
Indices: 54527--54570 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
54517 ACGTAATGAT
54527 GTGAGAT-GCTCGATATGCC
1 GTGAGATAGCTCGATATGCC
54546 GTGAGATACGCTCGATATGCC
1 GTGAGATA-GCTCGATATGCC
54567 GTGA
1 GTGA
54571 TAAGAGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
21 16 0.70
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (20 bp):
GTGAGATAGCTCGATATGCC
Left flanking sequence: Indices 54027 -- 54526
CAGTTAAAGATACACTGCTGATGGCTTTAGCCATACCCCGATTAAACTCATCTGTTGGGTAGCTG
AGAACAACTACCTCTGTATGGGAACTACTACCACTGGCGGAAAGTGTACTATTAGTTAGTTCGAA
TGATCGTTGTAAGCACAATGGGTCGAATGATAATGGTAATGTAGCGGAAAATGAATCAATCACCT
TACTGATTAAACAGTTTAAACAATCTGGGCTGCAGCTAATGTAAAACATATGAATAATCAACAGA
GGGGGTAACCACGAGCTTATAAGACTCGTTGTGGAATCCCTGATCAAACATCGGCTAGCCTATGA
TTAATAATATCTCTCATTGGTGAGATCCCGGGCGATCGTGGGAATACTTCTAAGGTCGGCAACCC
GTTTTGCTAGGAGACGGGATCTGCCCCACAACCCGTAAGGAACTCTACCTGCCGAGACTTGTGAA
GGTGCACTCGCAATCGACTGTGTGTCCTGACACAAACGTAATGAT
Right flanking sequence: Indices 54571 -- 55070
TAAGAGGAATGCATCAGAAGTCGGTGTGGAACGAAAATAATAACTTCCAGCCGGAAAGATGGATG
TTTTAGGAAACAATGATGCCTGTGTACCTACTTTGATCAGGCTTGGCATTCTAGTGTGGGTAGAA
CCGGAAGACGACGAAAGGGATGAACTATCAGGCTTACTCGATAGACGTTCCTTCACAGCTTGTGT
TAAGTTTTTGATCGTGGGTTAATTTTTTCTCGTTTCTCCGCGGCCATCATGTGTGACCGACTTTG
ATTTTAGGGTTCTGGGAAGGGTTACTCCACAAAAGCTTGGGAATTCGTATGTAAGTTAAGCATAT
GTGCTAGAAACTCATCAAGTGAAAAGTACACTACCAGATTATGTAGTGTACTTTTCTTTCTTGTT
CAGAGGAAGAGCCATAAAGACTTCGTGTATGTATCTCGCATAAGAAAAATCGTGGTGGAAATGCG
GTTGAAAGCTGAAATGAGACGACAGAACGAGTGAAAGAAGTTACT
Found at i:56108 original size:40 final size:40
Alignment explanation
Indices: 56053--56128 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
56043 TTCTTTTTGT
*
56053 AGAAGTACTTTCTTCTAATTTATCCTTACGTAAGATTTCA
1 AGAAGTACTATCTTCTAATTTATCCTTACGTAAGATTTCA
*
56093 AGAAGTACTATCTTCTAATTTATCCTTCCGTAAGAT
1 AGAAGTACTATCTTCTAATTTATCCTTACGTAAGAT
56129 GTTTAGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (40 bp):
AGAAGTACTATCTTCTAATTTATCCTTACGTAAGATTTCA
Left flanking sequence: Indices 55553 -- 56052
TCTACTATCTGGTAGACTTTAGGGAAAAAATAGAAACTAAACCTTATGGAATCTTTAGTCTTATG
GGATATATGTACACCCACATAGATAGCAGGGAAGGCCATCCAACCTAAATAGGCATCCCACAACA
TGCCATTTAATGGTAAAGGCGCCACTCCACTCCACTCCCCTGAAATAGGTCCCCAAAGCCTGTCT
TCTCTACGTGTGTGTCCACAGTCTGATGAGACACACTATTAGAGGAGGAAAAAAGAGGGAAGCAA
CAAAACGATGCTTTCCTGGGTAAGGCAACGGGAGTTGAGGGAAACCCATGCTGCTACGTGGAGAA
TGAATGCCCTATCGTACACACGCTAAATTATACCATGCTACGCTCGTACCGTAACCAAGATAACA
ACGATTGCACCATCGTACGGAATTCACAGTATCTCCACCTTACGGAACGCTTGTTCAAAGTGTTC
AGCTTGTTCAGTTTTACGGAACGCTTGTTCAGTGGTTCTTTTTGT
Right flanking sequence: Indices 56129 -- 56458
GTTTAGTCAATAAAAGCGGAATTCCGAAATGTAAAGTCTTGTCCATATTCTATTTTTGCAAGGAA
TCTATATGCTTATTATTTATAATAAGGGTAGGGATAATAAAATTCATATATTTACATATATAATG
ATATTTCACCGTGTGGAGACCGCAGTCAGCTCTATACCAATGAATGTTGGTGACTTCTGATCGCA
GGTTTCATTTGAAGACCCCAACGCCATTATTTGATTTTGTGAGTTTAAGAGCGCCATTCAGATTG
CGTCAAATCCGGTCTTTCATGCAAGAGTTTTTTAGGCCAAACATATCGAAGTTGATTGCCACGCT
AGTAT
Done.