Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_059792
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: 379922
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:31404 original size:18 final size:19
Alignment explanation
Indices: 31370--31405 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31360 GAAAGAAGAA
*
31370 TGCACCAAAATGCAGGTGC
1 TGCACCAAAACGCAGGTGC
31389 TGCACC-AAACGCAGGTG
1 TGCACCAAAACGCAGGTG
31406 GTTGTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (19 bp):
TGCACCAAAACGCAGGTGC
Left flanking sequence: Indices 30870 -- 31369
AGGATGAGTCCTTCTTTTTCCTTCTCGCGAACCACGGGAGCGCCTAGCACCCAGAGGAGCAAAGC
TAATTATCCTTTCAGGGTAAAGCGGCGCATAAAAAAGGGCTGGCCCGTCAAACGTCCGGTTCCTT
CGCGAACGAAGTTCAGAATCAACAAGGGTTCGTAGAACGAAGGGAGTGTACAACTGGGGCGCAGC
CCCAGTTTTTTGTTCGTAACGAGGGAGAGATAGAATGGAGTTCTTCACGAAGTTCGAGACAAAGT
AATACAAAACTTCTCTATGGCCTCCTCGTTTTGAGACATTATGGCTTTGGGGTCGACCCCGGTAA
CAAAGAAGGAATCCATAAAAACGTGGGATCCGACACCATGATAAAATACTACCCTCATGATTAGA
CCATGTCCCTGAGATTTGATAAAAGAAAGGTGCATTAGCGGTTAATACGTTGTAATTGGATAAGT
TATTAGGAATATGACGGAACGAAAGACCGAGGAAAGAAAGAAGAA
Right flanking sequence: Indices 31406 -- 31905
GTTGTTTCTTGTTGTAAGTGAATGCAACGAAAAGACCCGGAAATAACGATAAATGAAAGAATTCA
TATATTATGTACATTTCGTGCTCTGCTCATTTATAAATTTCTGCTTTGTTATTCCCATCATCCGG
TAACCACAGGATGATCCACAAGAAAGGTGGCAGGATTCGAACCTATGGCCGGCCCGCCCCTGACC
TGCTGGGTTGGGTGGCCGGGTTAGCACCCCTCTAAGCCCCTGTACCCGAAACAGATGCGCTGCGC
TACCCAGCGCTACACCTTGTCTCCCCTACTCCTCTTCTGGTTATGCCATTACCAATCGCGGGTAA
CCCCCGGGCCGGCCGCCCCTGACCTAATAAGATAAGAACTATTATCCTTATGACCAAACAGCGAT
AGTTTCACGATCCCGACCAGCAACTTGTTGGGAGTAGGGGCATCCAAGCTTGCCCAACCTAGACA
TTGTAACTGAAAGTCCTGCCTACTTGTAGGCTTAGGGTAGTCCTC
Found at i:75240 original size:30 final size:30
Alignment explanation
Indices: 75190--75261 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
75180 CTAAAACCGG
* *
75190 AACCTCTGGGGGAGCAGGGGGCACCTCAAA
1 AACCTCCGGGGCAGCAGGGGGCACCTCAAA
*
75220 AACCTCCGGGGCAGCGGGGGGCACCTCAAA
1 AACCTCCGGGGCAGCAGGGGGCACCTCAAA
75250 AACCTCCGGGGC
1 AACCTCCGGGGC
75262 TACCCGAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.32, G:0.36, T:0.08
Consensus pattern (30 bp):
AACCTCCGGGGCAGCAGGGGGCACCTCAAA
Left flanking sequence: Indices 74690 -- 75189
GGATCCGAACGAATTTAGTTTTCATTTTCCCGTATGGAGCACTGAGTCACAAACGTTACGATATT
AGGTTGGTTGCCCCCCGTCCTTTCTTGCTCTCGGTCCCACCCAGTGCCGCTACCCACCTCTACTC
GGATCTCTTCCTAGAGCCATAGATCATAGTTTCTTACCGCCGTCATAAGACGTTGGAAGGCCCGT
GTGTCTCGGGTACCCAACCGGTAGATACTTCGTAGATGGGAGCGGTACTGCCGCAAGGATAGTGC
CCTACCTCGAGGATAAAAAACTATCCCTCTTATCCGATGGCGGTTCTCAAAGATCCGAGTCGGAT
TGAATCCGCTATGAACTAAAGCGGATTCAATTAGCCTTTCTATCCTGGTTTGTACCGAGATAGTC
TCGGTAATTCTACGTAGGGTTGGATTTTCCCCTAACGTATTGACCAAGAATCTACTTCGTAGCTC
CCCCTCCCTTTGGAGGTCCGGTATTATTTGCTGCGCTAAAACCGG
Right flanking sequence: Indices 75262 -- 75761
TACCCGAATCCCCACAACTGGCGGTGAAGGAGGTCCCTCCACACCTCCCACCCCATCGCATGTTG
CGACGTCCCCGGCAGAAAAACTAACTATATATATCAAAATATTTATTAAAATAATATATAAACTT
GAGCTGGTCAATTCGAGATAAAAACCAGAAAAAAAAGAAAAAAGCCGAATTCTACCTGCGCCTGT
CTGGTCCGACCGTTTTGCGGCTCTTTCTAAGAGACGGGAATGTAAATAGAAAACATCGCCTGGGA
AAGCCTCACGGCCTGGTGGTCGGCGTAACAATAATGACATTTGTCGATATGCCACGGCCTGTTTA
CTAAGATCATCATAGATTATTAATGCGTGCATTCCATTATCGCGGAAATATTCCCCCATGGCACA
CCCAGAATATGGGGCCAGAAATTGCAGAGGTGCTGGATCCGAAGCGGTGGCTGCTACAAGAATGG
AATATTCTAAAGCATTCGCTTCTGAAAGAATTTGAACTAATTGTG
Found at i:197773 original size:5 final size:5
Alignment explanation
Indices: 197763--197792 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
197753 AAATCCCCTC
197763 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT
197793 AAGGCAGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTCTT
Left flanking sequence: Indices 197263 -- 197762
GTTGGCTCTAGCATAAGGAGTCAACTCACAAAACATAAAGAAAGCTGCGGGACTCACAGAGTAGA
GATGCCTGAGAGGTATCCGTAATCGCTGCAGCGACTAGGACATTGGCTTAACAGGCCAAACGCCT
TAGGGCAACAAAATAAAAAACCTTCCAGACAAGGCCGAACCGGACCAAAGTCGGTCGATTCAACC
TGCCATTTCCGGTTCACGAATGGTGCGTCTAAGAGATCCTGGATGGTTACGCCTGGAGATACTGC
AACCATGTAGTACCACTTGACGCAGTTAAGCCATTGTCGGACCCACGACCTTACCTTAAGGTTGT
GTACTCCGCGAACTCGCGACTACCATCGGTGACGATAACCTACCTCGTCAGGATAGAGGCACAGG
TCCTTTGGAGCCATTTCCCTGCGGAAAAAATTTACAAAGATTCCTGACTCTAACAAGTAAGCAAG
TAAACTACCTTTAGGAATTTTCATTCCATTCTTCGAAATCCCCTC
Right flanking sequence: Indices 197793 -- 198292
AAGGCAGTCGAGGGAAGCGGTTTATGGGGTGGGCTGCTAAGGCCCGGGGAGCAAAATCGGGTCAA
ACATCGATAGGGAGAAAGAGGTAAATGACTCTTCCTTTCCTTTCCTTTCCTTTCCTCCCGATTGG
CAATGATATATCTTTCTTCTGCCATTGCGAGACAAGACAGCTTCGTTCGGGCGATCTAACCAACT
TAGGGAAGGTATGCCCTCTCTGCTTCTCCACTCGAACCATAACCTGAACTAGAAATGGAACTGGT
CAGCTGCCAAAGGAATGAAACAAATGCTCAACACATGCCTCCTATTGGAGAAGCTTCTTTCATTC
ATTTCCCTTACCAGCCGGGACATCTGCTCCTAAAATGGTAACTTCACTCTGCCCGCTCCGTTTGG
TTCATCATGTGGACAATTCCTCCACAAAAAATATTCTTGTCTGGAAATGCATGCTTTTATGGAGG
GGTTATTTCCCTCGTCGCTTACCCGCATTTCTCTTGGTATACCTA
Found at i:197899 original size:5 final size:5
Alignment explanation
Indices: 197889--197913 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
197879 TAAATGACTC
197889 TTCCT TTCCT TTCCT TTCCT TTCCT
1 TTCCT TTCCT TTCCT TTCCT TTCCT
197914 CCCGATTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCCT
Left flanking sequence: Indices 197389 -- 197888
GCCTTAGGGCAACAAAATAAAAAACCTTCCAGACAAGGCCGAACCGGACCAAAGTCGGTCGATTC
AACCTGCCATTTCCGGTTCACGAATGGTGCGTCTAAGAGATCCTGGATGGTTACGCCTGGAGATA
CTGCAACCATGTAGTACCACTTGACGCAGTTAAGCCATTGTCGGACCCACGACCTTACCTTAAGG
TTGTGTACTCCGCGAACTCGCGACTACCATCGGTGACGATAACCTACCTCGTCAGGATAGAGGCA
CAGGTCCTTTGGAGCCATTTCCCTGCGGAAAAAATTTACAAAGATTCCTGACTCTAACAAGTAAG
CAAGTAAACTACCTTTAGGAATTTTCATTCCATTCTTCGAAATCCCCTCCTCTTCTCTTCTCTTC
TCTTCTCTTCTCTTAAGGCAGTCGAGGGAAGCGGTTTATGGGGTGGGCTGCTAAGGCCCGGGGAG
CAAAATCGGGTCAAACATCGATAGGGAGAAAGAGGTAAATGACTC
Right flanking sequence: Indices 197914 -- 198413
CCCGATTGGCAATGATATATCTTTCTTCTGCCATTGCGAGACAAGACAGCTTCGTTCGGGCGATC
TAACCAACTTAGGGAAGGTATGCCCTCTCTGCTTCTCCACTCGAACCATAACCTGAACTAGAAAT
GGAACTGGTCAGCTGCCAAAGGAATGAAACAAATGCTCAACACATGCCTCCTATTGGAGAAGCTT
CTTTCATTCATTTCCCTTACCAGCCGGGACATCTGCTCCTAAAATGGTAACTTCACTCTGCCCGC
TCCGTTTGGTTCATCATGTGGACAATTCCTCCACAAAAAATATTCTTGTCTGGAAATGCATGCTT
TTATGGAGGGGTTATTTCCCTCGTCGCTTACCCGCATTTCTCTTGGTATACCTACCAGTGTGCCT
CCTAATTCCGTGAAGTCCTTGGAGCATGTGCTATTTTTTCAGGATCCTTGTCAAGAAGTCAGTCC
CTTCTTATTTCTTTTATGTTAAATTACTCGAAGAGGGAGTCGATT
Found at i:350744 original size:13 final size:13
Alignment explanation
Indices: 350722--350753 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
350712 TTCTTTTGAT
*
350722 CGATGGGAGTTAG
1 CGATGAGAGTTAG
350735 CGATGAGAGTTAG
1 CGATGAGAGTTAG
350748 CGATGA
1 CGATGA
350754 ATCAAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.09, G:0.41, T:0.22
Consensus pattern (13 bp):
CGATGAGAGTTAG
Left flanking sequence: Indices 350222 -- 350721
CGTTTCAACCAAATGGACTGGACAACAGAACTCAAATCGATAAAAGGAATGGCGGGAGGATAAAC
TTCAACGATCGGCGGGGAAAGAGAAACTACAAGAAGTCTACGAAAGTAAGGTTGTTAGCAACTTC
AGTAGTTCGAATATCTATCTACTAGTGAGAAGGTTAAGCTCAAAGAAAGTATTAGTTAGAAGCTC
AAGGAAAGCACTTAAAGGCAGCTTCAGGATAAAAAGATTTTAGAGTGAATAGCCCGTAGCTCACT
TCTGGAAGTGTTCCCGTATATTCGTAGGCGGGAAGCGAAGCAACTACTCAACGATGTGAGCCGGG
TTTGTCGTTAGCTGTCGAAGTAGGGGGAGGGAAGTCCGGAGACTATAGCTCAGTCGAACTTATAA
TCCAGCCACGAAACTTAAAATAGAACTCAAATAGATAGTACATTCAAGTGGGCAAGGTAAGCTCA
GTCTCAGGCGAAGGAAGCTTTTAGGCCGTTAATCTTTCTTTTGAT
Right flanking sequence: Indices 350754 -- 351253
ATCAAAGAAGTTGTCAGTGAAGAAGTTCTCTAAAACAGGAATGTAAATCCAATAAGTCCAGTTCT
GTAGGCCGAATCTAATAAGGTAGGCGAACCTGGCAAGTAGTTAACAGGCTCATTTTCCGTTCTAT
GCCCGTTCCTGATTCTAAGCCCGTTCCCGATTCTAACCCCGATCTTTCAGCGAGCTACAAGAGAG
GGTCTATTTGGTCACTATGCCTGTGGGTGGAAAAATCCTCCTGATTCAATCCCGGTAGATACATC
TTTTGTTTCAAGTCATACCAGACTAGACGACCTACCTTGTGTCTCTGTATTTCCCTAAGCCAACT
TATACAAAAAAGAATGAAGCAAGGATAGTCGTAGACTACTTGCCCTATCTCTTAAAGCTTCACTA
GCGAAAACTGTTAACTCTTTCATTTCTACGACCAACCGAGAGTCCCTGTGCTATGGCTCACACCC
GGAATAAGGTTTTTTTTCGTGATCTGCTTTAGCCGTTGTTTAAAG
Found at i:350905 original size:18 final size:18
Alignment explanation
Indices: 350878--350924 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
350868 TCATTTTCCG
* *
350878 TTCTATGCCCGTTCCTGA
1 TTCTAAGCCCGTTCCCGA
350896 TTCTAAGCCCGTTCCCGA
1 TTCTAAGCCCGTTCCCGA
*
350914 TTCTAACCCCG
1 TTCTAAGCCCG
350925 ATCTTTCAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.32
Consensus pattern (18 bp):
TTCTAAGCCCGTTCCCGA
Left flanking sequence: Indices 350378 -- 350877
GAGAAGGTTAAGCTCAAAGAAAGTATTAGTTAGAAGCTCAAGGAAAGCACTTAAAGGCAGCTTCA
GGATAAAAAGATTTTAGAGTGAATAGCCCGTAGCTCACTTCTGGAAGTGTTCCCGTATATTCGTA
GGCGGGAAGCGAAGCAACTACTCAACGATGTGAGCCGGGTTTGTCGTTAGCTGTCGAAGTAGGGG
GAGGGAAGTCCGGAGACTATAGCTCAGTCGAACTTATAATCCAGCCACGAAACTTAAAATAGAAC
TCAAATAGATAGTACATTCAAGTGGGCAAGGTAAGCTCAGTCTCAGGCGAAGGAAGCTTTTAGGC
CGTTAATCTTTCTTTTGATCGATGGGAGTTAGCGATGAGAGTTAGCGATGAATCAAAGAAGTTGT
CAGTGAAGAAGTTCTCTAAAACAGGAATGTAAATCCAATAAGTCCAGTTCTGTAGGCCGAATCTA
ATAAGGTAGGCGAACCTGGCAAGTAGTTAACAGGCTCATTTTCCG
Right flanking sequence: Indices 350925 -- 351424
ATCTTTCAGCGAGCTACAAGAGAGGGTCTATTTGGTCACTATGCCTGTGGGTGGAAAAATCCTCC
TGATTCAATCCCGGTAGATACATCTTTTGTTTCAAGTCATACCAGACTAGACGACCTACCTTGTG
TCTCTGTATTTCCCTAAGCCAACTTATACAAAAAAGAATGAAGCAAGGATAGTCGTAGACTACTT
GCCCTATCTCTTAAAGCTTCACTAGCGAAAACTGTTAACTCTTTCATTTCTACGACCAACCGAGA
GTCCCTGTGCTATGGCTCACACCCGGAATAAGGTTTTTTTTCGTGATCTGCTTTAGCCGTTGTTT
AAAGCCTTGTTGAGCTTTAAAGTACTTTTTGCAACTGTAACCGCGGTTACAGAAATAAGAAACTT
CTCTTTGACTGAAGCACTTGAACTTCACTTTCCAACTTGTTGGGAGTAGGGGCTTTCACTGGAAC
TGAAACTCTATCTTCTGTTCAACTCGGCTTCCTTAACTTAATTTG
Done.