Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_056836
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: 256961
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:30900 original size:28 final size:28
Alignment explanation
Indices: 30852--30905 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
30842 GGTAGTGTGG
*
30852 TTAGCCTACTGGATAGAGAGTTTAGTCA
1 TTAGCCTACTGAATAGAGAGTTTAGTCA
* *
30880 TTAGCCTACTGAATCGGGAGTTTAGT
1 TTAGCCTACTGAATAGAGAGTTTAGT
30906 ACCAGTACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (28 bp):
TTAGCCTACTGAATAGAGAGTTTAGTCA
Left flanking sequence: Indices 30352 -- 30851
AGGTTACCTAGAAACTAGTCTTTGCTTTTAGAGTCTCTATCCCTATTGGGACTGCCCCGGAGAAT
CTCCTAATGAGACTGATTGGGATGTAGAAGGATAAAATAGTTCATAATTTGCTTTCTTCAACCGT
ACTGGATACTCTTTTCTCGGCTAGACTAAACTGGCTCTGCCTCACCAGGTCTACTAGAGGCAAGT
CTATAAACTGCGCAACCCTATATGCATTCCTACACCGAGGGAGGCCTCCTTCATACACATAAGTG
GAAAGAGCTGCAGTTTTCTTCTCCTTCGCCCGAGGAGCCTATCCCTGCTTTGTTTGATAAGCCGC
GGATTCCCCCGGTTCCAGAGAAGGGGCTATATTATATTGTCACAATCGTTGCACGAATTGGGTAT
ACTCTAAGCTTTGTATCCACCTTTAGAGTAGAGATAGGGGCTTACGACTTTATCGAAGGTAACGT
CAATTGTAGTCAGTGCCTAAAAGCGCTATCATTATGGTAGTGTGG
Right flanking sequence: Indices 30906 -- 31405
ACCAGTACCTAAATTGGTACCTTTCCTTTGAGTCGAGCCAGTTGCAAGCGGAGGCTGACGACTGA
ATATATAGTTCATGTTTCTCCCTCTATTCGTTAGGTGGTTTATTCAATTAAGGAGGTTAGTAGTG
AATAGGGACGTGAGGCTGCTGCTTCAGAAACGGAATCCACGGCTTCAAAGTAAACTCGATAGACT
GATTCACCTAGATCCACTTCTGAAACGAGATCAACTGCTTCGGATGAACCAGGTAACTTCAGAAT
CAAGAGAATCAACTGAAGTTCCTTTCTTTGAAGAAGTCATTGGGTGATCTCCTGCCTCTGGATTG
CCTACGAAATGCAACTGGGGACATAGGAACGACCAGGCCTTTCCTGATAGTAGTGTGCCTCTATA
TCAGTAAGTAGTTTCCCGCTTTCCAGAAGAAGTCGCTATTGCTCCTAAAGGCAAGAGTAGGGTCC
TGCTCTGTTCCCTACTAATTGCGTAGTAAGAGAAGCAGTTGCCCT
Found at i:68728 original size:16 final size:17
Alignment explanation
Indices: 68709--68745 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
68699 CAGGAAGAGG
68709 ACCAAAAAG-AAAGACC
1 ACCAAAAAGTAAAGACC
*
68725 ACC-AAAAGTAACGACC
1 ACCAAAAAGTAAAGACC
68741 ACCAA
1 ACCAA
68746 GATACGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 12 0.67
17 1 0.06
ACGTcount: A:0.57, C:0.30, G:0.11, T:0.03
Consensus pattern (17 bp):
ACCAAAAAGTAAAGACC
Left flanking sequence: Indices 68209 -- 68708
TAACTTACTGTATAATGCCCCTTCCCCGATACTCCAACATTGTCCTATCCATCGCTGTGGATGTT
CACCCGTCTATCCAATAAGTCAAAGGTGCATAAGCCTGCTCCTCGAGAAAGCCTTGTTCGAAAAT
CCCTTGCCGGCCGACGGGACTCTACGTCTGGGTCTTATTCCATCTCAAACTCGGATTAGGAAGAG
TGCCCTTGAACTACAGATCAATCATAATAAACAATACAAGAAAAGAAATGGATTCTCCTGCCGGA
GAGAAAGGCAAAAAGGGGGGGAAATAGGGAAGAGGAGATTAAGGATAGTCACTCCACTCCATAGA
TAGTGAACTTGTTTCATTTTCAATTCCTTTCGGGTCGAAAACGGCGGGGCACAATCCGGGGTCTT
TTTGAAATTAATCAATCAATTTTATAACTGAGTGGAGTTTTACAATTAGAATCGAATTCTAAACC
GGCGTGGCGATGCTGGATGCTTCTGATCAATAGAACAGGAAGAGG
Right flanking sequence: Indices 68746 -- 69245
GATACGCATAGTGATTCGATCTTTTGATCACCCATTTTTTGAAAACCTTTTTTGGGGGCTTCCGC
CTTACACACGGAAGATTGGATTGCCTGAATCACGAGTCTTATATACTGTGTTACGATCGCCTCAT
ATTGATAAAAAGTCCAGAGAACAATTTGAAATGGAAATAAAGAAAGAATTTCTGGTCATAAAAAC
AGAAAGGCATGAATTGCGCAAGAAGTTCTTTTGGTTAAAACGCCGTGCGACTCGGAGGACATAAG
ACTTCTTGGTCAAGCCAAAAAGATTGCCGACTGGATGCTCCTACCCCACCATGCCTGGCCCTTTA
CCTTACCTTAAGAAGAAAGAGGGGGGGTATGAAGCGTGGGAAACAATGCAAGAAGTGTATGATAC
AACAGGTAACCTTAAGTGTTGGAGTGGCGGCAAAACTCTTGATTGATCAACGCGAGTGAACTGTG
CTTAGACGCTTCGTAAAACCGCACCGATCTACGAGAGGAGTTGTT
Found at i:88405 original size:28 final size:28
Alignment explanation
Indices: 88365--88421 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
88355 GCAATTCTCT
*
88365 TACTTTCTTATATTAAATCATATATTCA
1 TACTTTATTATATTAAATCATATATTCA
88393 TACTTTATTATATTAAATCATATATTCA
1 TACTTTATTATATTAAATCATATATTCA
88421 T
1 T
88422 TTAAATATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (28 bp):
TACTTTATTATATTAAATCATATATTCA
Left flanking sequence: Indices 87865 -- 88364
TCCCTTACTTACCATCTATGCCGTCCAAGTGAAGCGGTTCAGGTCACAGAAGGTAAGATTGGCTC
TTTCTTTTTGAATTGCATCCGGGAGCACGCGTCAATAAGAATTTGTCATTTTCCATTTAGAGTGA
GAAGCCGCAGTCAAAAAGTTGGTTGTGCATTGCCAAGGGACCCAGTCCATGATAAAAGAAAAGAG
AGGCTTTGCTCTGGAAACGAAAGTAAACTGCATCTTCTTAGATCAAACGAAGTGTACGTACAGTT
CATCAGGTCCCCATGCTACGGGCGAAGCAGGTGGGGTATCTCTTGAGAGCCAAGGACGGGGTCGA
ACCGTCATTCCAGGATTTGCAGTCCGATACATTTCCATTATGTTACCTAGCCAAACCCGCCACCT
CATGTGCCAAAGTCAAACGGCTGTTCTTCCTTCCCCGGTCCGCTTTTCTAAAGTAAGATGAGACA
ATACCCTTATGATATGCCCCTAGGCTAAAGAAGGTGCAATTCTCT
Right flanking sequence: Indices 88422 -- 88921
TTAAATATTGTACTTTCTTTCTTTCTTTTCTCATATTATCACATAGTCTTACTTGATTTAATAGA
AAATAGAATACCAGAATGTCCGAAAAGCATTGATTCGCATCTCATACAACCGACACTGTTTGCCT
TATCTTCTTATCTTTCCTAGGGTTCATAATCAAGAAAAGAAAATAGTGACATGACTTCTCTGTCA
AAATGTAGCTTGTTCGGAAAAGAGGCTGTAGACCGTGGGGAAAAGGAAGAGGTTTTTAGCGCTTA
TGATAAATGAATTATTAGAGATGTTATAGAGATAGAGATGAATCCTCTAGCTAGCAATAGTAGTT
ATTCATCAATAGGGTACTCAACCGGCAACCGATCAAGGAAAGGGTTCCGGCCTCCACCTAAGAAA
GCAGGAGCCAGGGAGACATGACATGAGCTTAGAGGAGTCGAATTGCCTCGCCCTCTACCCATATA
GGATGCAGCTTTTTTTGATGAAGCAGGAATTCAGGGAAAAGTTAA
Found at i:152982 original size:12 final size:12
Alignment explanation
Indices: 152965--152989 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
152955 TATCCGGAGG
152965 ATGCCTTATCTT
1 ATGCCTTATCTT
152977 ATGCCTTATCTT
1 ATGCCTTATCTT
152989 A
1 A
152990 CTATCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (12 bp):
ATGCCTTATCTT
Left flanking sequence: Indices 152465 -- 152964
GTGCGAAATTGAATTAATAGTATATATGAGTAATTCAAAGAAAAAATATAAATATTTGTTTTCTC
AAAAAAAGAAATAAATAAAGTAGTCGATTAATCCTCATTTATTCCTTTGCTTACGAATGTGCGTC
TTTTTTCGCCTGCCTTCATAGGAGGTCGGGCTGTGCACTTCAGCCCACCACATCAAGGTGACAGG
ATTCGAACCTATGGCCCTCTGTACCCAAAACAGATGCGCTGACCAGACTGCGCTACACCTCGTCT
CACCCCCCCGGAGCATATAGATCCACCCGATCGATGAACACTCGAACCTCCACGCTCTTTAGCAC
GAGATTTTGAGTCTCGCGTGTCTACCATTTCACCACCAAGGCATCTTGAAAGTGAATCGTATATG
ATGTATGGAATATATGACAAAGGTGGAGTGTTGGAGTATTTCTATTGATCGGTCATGCCATATAG
GCCCGAGTCATATATCCAATTGCTTCGATTTGAATTATCCGGAGG
Right flanking sequence: Indices 152990 -- 153489
CTATCTTAATCTTATATCTTATATATATCATATATATTATATCAAAAAGATGGACAGGACAATCA
AACCTATTTCTCCATTCAATAGAAGTCCAAAGAGGTGATATAGGGGCCAAAATAACAATAACGAG
AAAGAGTAAAGTACCAAATTTATCCTGTGCCAGGAACCAGATTTGAACTGGTGACACGAGGATTT
TCAGTCCTCTGCTCTACCGTTTGATTCTAAGTTACTATACGCTGTTTAGAATACATACGTTCGGA
AAGAGCTGTTTCCCTCATATAAAAGGAAGAACAAAGCCTTGTTCCTTTAGCTGCTTTATTCCCGG
AATGCCTTCTTTTTCAAAGTTCTGTTAGGTTCTTAGTAGCGCGACCTTTTCTTCTTTTACTTCAC
ATAGCTTTTCGTCTCTTTGATAGCTGGAAGTTCTCCAAAAGTATGAAAAGCAGGAGGACTTTGTA
CCATCCATTCCGGTGTGGTTGGATTCTGTTCAACAGCCCAAGGAC
Found at i:225696 original size:18 final size:18
Alignment explanation
Indices: 225673--225715 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
225663 CGCCAAAGTG
225673 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
225691 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
225709 GACTATG
1 GACTATG
225716 GCAGGGCGGT
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:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 225173 -- 225672
CGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGAGAC
AGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTACCTT
AGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCTCCT
TCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGTCCT
GTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGAGAG
CACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAGCGC
CCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACTGGGAGGATCGC
CCTCCCAATTCGAAGTTTTTTCCTGGAAGCCTAAACGCCAAAGTG
Right flanking sequence: Indices 225716 -- 226215
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTTACT
ATAGATAGGCTGAAGATTCAAAAGGCGAGCACTGAAATGAGAAAGGCTTGTAGACTCGTGACGCT
GAACGACACATTGACAAAAAACAGCGCACAGACGAAAGCGCTTCGAAAGGTGTCAGCAGGTGCGC
GGAGCCGGAGCCCTAAATGTTCGCCCGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTT
TAGATAACAAAAAGTGTCCGCCCCTTAGGTCGCCAAACTACGACGACTCGAAGAATTCCCCTTAG
CACAAGCACTAAGTAAGCAAGCTACCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGCC
GAGTCAGAAAGGCTTTGATGACTCAAGGTGAATATTAGGGAAAGGAGAGTGAGGGGAAGAGGAGA
GGAAGTGAAACGAACTCGGCCCGATCATCCAATTCGCTCCAACAG
Found at i:250060 original size:15 final size:16
Alignment explanation
Indices: 250032--250068 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
250022 AAGAATTCCT
250032 CTAGTAGCTTCCTATC
1 CTAGTAGCTTCCTATC
250048 CTAGTAG-TTCCTATC
1 CTAGTAGCTTCCTATC
*
250063 CCAGTA
1 CTAGTA
250069 AGTGGCTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.35
Consensus pattern (16 bp):
CTAGTAGCTTCCTATC
Left flanking sequence: Indices 249532 -- 250031
TTCCCTCTCCGTTGAATGAACTAACTACGGGCTGCATTCGTCTCCCGAGCCAGAAAGCAAGACAA
AATGAGGGGTCGGGTCGATGGAATATCCCTGCTGTTTCAGGAAGCGACCTGTGCGTAACAAAGGG
CTTTCTTCATGACAGGGTTGGATTCAGTCTAGGGTTCATCATGAAATCGGGGTCCTTACCTCAGC
TCTTTCGAAGGTGTTGGGTACGTCGGGTCCTTCTACTTTTGCTGCAGCTGTTGTAATTTCATCAT
CATAAGCTGGACATTAAGAAAAATAGGTTGCTCTTGTTCTTGTCTGTTGAGGTTAGGAAGCTAGG
TCTATCTAATTGGTAGTCGTAGAGCGGGCAAGGGGAGTTTCGGGATATCTATACCTGAGGCAGGC
TGCTACTTGACTGTAGGGTTATAACAAGCAAAGCCAGATAAGAATGTTTTAGATTTAGCACTGGT
AGTAGCTAGGCGTAGGATGTAGCTTTAGGATGTTTAAGAATTCCT
Right flanking sequence: Indices 250069 -- 250568
AGTGGCTAGGTTGTTAGAGAGCAGCAGACAATCTTATGAATTATAAGACAATCTCAACATTGTCT
GCTGTTAGATAACATTGTCTTGTATCTCCTATAGGTTTATATCAAGATAGGACGTATAAGACTGT
ATTCTATCACTACGCCTTCCTTCTGTTATACCTCTAAGGGTAATCCCCGCTCTAACTCTATTTAA
GTAATTGGAGTATAATCTTGTGTTGGCAGTTAGCTATCGATGAGCGATGAAACCACATCCTGGTA
AAATAATTGCTTCACACAAATTCAATGAACCTTATCCTATTATTAACGAAACAGACCTACTCAGC
ATTGCAGTAATGGATCTCTTAATCCAGTTTGCTTACCCCTCTATATCTGGATACAGTAAATTCAC
AATTCAATTGAGTATGAAGCAATACTTTGATTCAATTCATTTTACGGTTGGTCCAGCAATACCCT
TGACTTTTGAGAATGGTGATTTCATTCCAAAGAGCCTTGTTTATG
Found at i:252967 original size:15 final size:15
Alignment explanation
Indices: 252947--252980 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
252937 CTACAATACC
*
252947 AAGGCTGAGGCTAAG
1 AAGGCTAAGGCTAAG
252962 AAGGCTAAGGCTAAG
1 AAGGCTAAGGCTAAG
252977 AAGG
1 AAGG
252981 ACCACGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (15 bp):
AAGGCTAAGGCTAAG
Left flanking sequence: Indices 252447 -- 252946
ATTGCTACACCACATCAGAAGATGGCAATCATCATGTCATGAAGTTCAAGGGAGCTGCTAAAAGC
ATTATAAATCCTGAATGGTTTGAGCAACAGTACGCTGACCCCTATCGGGCGATTCAGGCTTCGGT
GACATCGAATTTTAGGATAAATTGGTCGGAACTTGAGGTCATAAAGAAAGAGAGTACTTTCACTC
TTAGGATAGCGCTGAACAGAAAGAGGATAGCCATAATTCAAGATCAAAAATGGGTTGATACCAAT
CCTATTGAAATCTCAGACTTGTCCGCTCTAGATAACATTGGAAAACAAATAATCAAATTTCTAAG
AAAACAACTTGATTATTTGAATTCTGAAAAAAACAATATCATCTCTCATGAGATATTATCTCAAA
GGGAAAGGGAGATAGACCAGAGGAAAGACGAGAGATACAAATCAGAAATATTAAACTCCACTACT
TCAGGTCAAAAGACCACTACTGTTCAACCAACTCTCTACAATACC
Right flanking sequence: Indices 252981 -- 253480
ACCACGACAATAGCACTCCCGATAGACCCAAACCAGATGAATAAAAGCAAGAAGGGCCCTTCCTT
GTCTCCCAACTCTCCGGTTCAACCGTTAGACCGGTCCCCTAATCTCTTCGTTGACACGAGAAACA
AACCAATCAAAAAGCACTAATCATAGACCCGATTCCCACATACACTACTACTTTCGGGAACTTCC
TTTCTTTCTGTAAAGGCAAGGAACTTCTTTCACTAGTATCGGGGACATGCCCAGAAGAGGATTTA
ATAGTTCCAGAGACATGCAAACAAAGCCATGCTTACTTCATCTTCACTTCATGCTTATACACCTG
CTGGGCTGGGGCCCAACTTATTTCTAAAGGGGGCTTGCCTACAGAATCTTGTTCAGCTTAACTGA
GCCAGAATCAAGCCCAATGTAGTTCTGTTCTTCCTTTGAGGCCTACATGTTTTCTGGATTGGGTT
GTTCCTGTACCTTGGATCTCTCTGTGTATGTCAAATAAAACCAGG
Done.