Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold331
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1033222
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.30
Warning! 83795 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:996436 original size:30 final size:30
Alignment explanation
Indices: 996400--996461 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
996390 AGTGCAGTGC
996400 TCACAAAAACTTAACTTTCCAACTCCAATG
1 TCACAAAAACTTAACTTTCCAACTCCAATG
996430 TCACAAAAACTTAACTTTCCAACTCCAATG
1 TCACAAAAACTTAACTTTCCAACTCCAATG
996460 TC
1 TC
996462 TTTAAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.31, G:0.03, T:0.27
Consensus pattern (30 bp):
TCACAAAAACTTAACTTTCCAACTCCAATG
Found at i:1005740 original size:7 final size:7
Alignment explanation
Indices: 1005730--1005762 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1005720 TTTAAATTTC
1005730 ATATTGA
1 ATATTGA
1005737 ATATTGA
1 ATATTGA
1005744 ATATTGA
1 ATATTGA
1005751 ATATTGA
1 ATATTGA
1005758 ATATT
1 ATATT
1005763 TCAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (7 bp):
ATATTGA
Found at i:1006249 original size:18 final size:17
Alignment explanation
Indices: 1006226--1006259 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1006216 ATTTGTATGG
1006226 CTTTATCTTTCTTTATTT
1 CTTTAT-TTTCTTTATTT
*
1006244 CTTTATTTTTTTTATT
1 CTTTATTTTCTTTATT
1006260 ATACTAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTATTTTCTTTATTT
Found at i:1007888 original size:28 final size:27
Alignment explanation
Indices: 1007855--1007953 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
1007845 TAATGAGATT
1007855 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* *
1007882 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
* * *
1007911 AGCACTAAATGGGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
1007939 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
1007954 TACTTATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 54 0.92
29 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:1010129 original size:91 final size:92
Alignment explanation
Indices: 1009971--1010156 Score: 347
Period size: 91 Copynumber: 2.0 Consensus size: 92
1009961 ATACGAGTTT
1009971 GCTTAGTGCTTGAATTTAAATAAATGTCTGTTTTGATCTGTGCTATGTTTGATAATGCCTCATAA
1 GCTTAGTGCTT--ATTTAAATAAATGTCTGTTTTGATCTGTGCTATGTTTGATAATGCCTCATAA
1010036 CCCTAATTCGGCAACGGATACGGGTTAGG
64 CCCTAATTCGGCAACGGATACGGGTTAGG
1010065 GCTTAGTGCTT-TTTAAATAAATGTCTGTTTTGATCTGTGCTATGTTTGATAATGCCTCATAACC
1 GCTTAGTGCTTATTTAAATAAATGTCTGTTTTGATCTGTGCTATGTTTGATAATGCCTCATAACC
1010129 CTAATTCGGCAACGGATACGGGTTAGG
66 CTAATTCGGCAACGGATACGGGTTAGG
1010156 G
1 G
1010157 GTGTTACAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 81 0.88
94 11 0.12
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (92 bp):
GCTTAGTGCTTATTTAAATAAATGTCTGTTTTGATCTGTGCTATGTTTGATAATGCCTCATAACC
CTAATTCGGCAACGGATACGGGTTAGG
Found at i:1013164 original size:249 final size:245
Alignment explanation
Indices: 1012692--1013183 Score: 539
Period size: 249 Copynumber: 2.0 Consensus size: 245
1012682 TTAATATATA
* * * *
1012692 TATATATAACTATTATTATACTATAGATTATAATAAAAGGTATAATATTATATGATATTATAATG
1 TATATATAACTATTATTATA-TATAGATTATAATAAAAGATATAATATTACATAAGATTATAATG
* * * *
1012757 TTTAATCATCGATGTATGTATATAAATTATTAATATATGATATGATATGATATAGCATTATATAA
65 TTTAATCATCGATGCA-GTATATAAACTATTAATATATGATATGATATGATATAACATTATACAA
* * *** *
1012822 AATAGTAGAAAGACTAACTTTTAAATGTATGAAAAATATAGGGGCTTAGAGCATATTTCAACTAT
129 AATAGTAGAAAGACTAACTTTCAAATGTAGGAAAAATATAGAAACTTAGAGCATATTTCAACTAG
1012887 TATAATAATGAACAATAATATTTAATAATAAGTAATATATAATGTACTACTAT
194 TATAATAA-GAACAATAATATTTAATAATAAGTAATATATAATGTACTACTAT
*
1012940 TATATATAACTATTA-TAT-TATAGATTATGATAAAAGATATAATATTACATAAGATTATAAT-T
1 TATATATAACTATTATTATATATAGATTATAATAAAAGATATAATATTACATAAGATTATAATGT
* * *
1013002 TTAATCATTGATGCA-TATATAAACTATTAATATATTATAAACTATATGATGTGATATAACATTA
66 TTAATCATCGATGCAGTATATAAACTATT-A-ATA-TAT----GATATGATATGATATAACATTA
* *** ** * *
1013066 TACAATATAGTAGGCTGGTTAACTTTCGAATGTAGGAAAAGTATAGAAACTTAGAGCATATTTCA
124 TACAAAATAGTAGAAAGACTAACTTTCAAATGTAGGAAAAATATAGAAACTTAGAGCATATTTCA
* * * * * **
1013131 A-TCAGTATGAT-A-AACAATAATATATGATAATAATTCATATATTGTGTACTACT
189 ACT-AGTATAATAAGAACAATAATATTTAATAATAAGTAATATATAATGTACTACT
1013184 CTACTATTAT
Statistics
Matches: 203, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
242 12 0.06
243 1 0.00
244 17 0.08
245 41 0.20
246 35 0.17
247 3 0.01
248 17 0.08
249 77 0.38
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (245 bp):
TATATATAACTATTATTATATATAGATTATAATAAAAGATATAATATTACATAAGATTATAATGT
TTAATCATCGATGCAGTATATAAACTATTAATATATGATATGATATGATATAACATTATACAAAA
TAGTAGAAAGACTAACTTTCAAATGTAGGAAAAATATAGAAACTTAGAGCATATTTCAACTAGTA
TAATAAGAACAATAATATTTAATAATAAGTAATATATAATGTACTACTAT
Found at i:1021450 original size:24 final size:23
Alignment explanation
Indices: 1021419--1021463 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1021409 TCAAAATCAA
1021419 GGAACAAAAACCTGCAAAGAAAAG
1 GGAACAAAAA-CTGCAAAGAAAAG
* *
1021443 GGAACAAACACTGGAAAGAAA
1 GGAACAAAAACTGCAAAGAAA
1021464 GATCTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.58, C:0.16, G:0.22, T:0.04
Consensus pattern (23 bp):
GGAACAAAAACTGCAAAGAAAAG
Found at i:1026491 original size:41 final size:40
Alignment explanation
Indices: 1026385--1026494 Score: 109
Period size: 41 Copynumber: 2.8 Consensus size: 40
1026375 GAATAATTCG
* *
1026385 AAGTAATAATTTGACACCTAGTGTCTCATCG-GCTAAACTA
1 AAGTAATAA-TTGACACCTAGTGTCTCATCGAACTAAACCA
* * * * *
1026425 AAGT-A-AATTGGCACCCAGTGCCTCATCGAATTAATCCA
1 AAGTAATAATTGACACCTAGTGTCTCATCGAACTAAACCA
*
1026463 CAGTAATAGATTGACACCTAGTGTCTCATCGA
1 AAGTAATA-ATTGACACCTAGTGTCTCATCGA
1026495 CTCGAAGTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
37 18 0.33
38 10 0.18
39 2 0.04
40 5 0.09
41 20 0.36
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (40 bp):
AAGTAATAATTGACACCTAGTGTCTCATCGAACTAAACCA
Found at i:1026697 original size:24 final size:26
Alignment explanation
Indices: 1026666--1026724 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
1026656 ATATTCCAAT
1026666 TCAA-TTCAATCA-ATAT-AAATTCAA
1 TCAATTTCAATCATATATCAAA-TCAA
1026690 T-AATTTC-ATCATATATCAAATCAA
1 TCAATTTCAATCATATATCAAATCAA
*
1026714 TCTATTTCAAT
1 TCAATTTCAAT
1026725 TGTAAAACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 6 0.21
24 13 0.45
25 8 0.28
26 2 0.07
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (26 bp):
TCAATTTCAATCATATATCAAATCAA
Found at i:1027487 original size:22 final size:21
Alignment explanation
Indices: 1027458--1027526 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 21
1027448 TTTTCGTTTC
1027458 TTTATTTATT-TCATTTACTTA
1 TTTATTTATTAT-ATTTACTTA
1027479 TTTATTTTATTATATTTACTTTA
1 TTTA-TTTATTATATTTAC-TTA
1027502 TTATTATATTATATATATTTACTTA
1 -T-TTAT-TTAT-TATATTTACTTA
1027527 AATATTAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
21 4 0.10
22 12 0.29
23 4 0.10
24 2 0.05
25 10 0.24
26 9 0.22
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTATTTATTATATTTACTTA
Found at i:1027496 original size:14 final size:14
Alignment explanation
Indices: 1027477--1027522 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1027467 TTCATTTACT
1027477 TATTTATTTTATTA
1 TATTTATTTTATTA
*
1027491 TATTTACTTTATTA
1 TATTTATTTTATTA
* *
1027505 T-TATATTATA-TA
1 TATTTATTTTATTA
1027517 TATTTA
1 TATTTA
1027523 CTTAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:1027522 original size:26 final size:27
Alignment explanation
Indices: 1027471--1027525 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1027461 ATTTATTTCA
*
1027471 TTTACTTATTTATTTTATTATATTTAC
1 TTTACTTATTTATTATATTATATTTAC
1027498 TTTA-TTATTATATTATA-TATATTTAC
1 TTTACTTATT-TATTATATTATATTTAC
1027524 TT
1 TT
1027526 AAATATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTACTTATTTATTATATTATATTTAC
Found at i:1027532 original size:26 final size:25
Alignment explanation
Indices: 1027480--1027533 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1027470 ATTTACTTAT
* * *
1027480 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
1027505 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
1027531 TTA
1 TTA
1027534 AGTAATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:1027545 original size:26 final size:26
Alignment explanation
Indices: 1027490--1027547 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1027480 TTATTTTATT
* * * *
1027490 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
1027516 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
1027542 ATATTT
1 ATATTT
1027548 TATTAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:1028011 original size:25 final size:25
Alignment explanation
Indices: 1027979--1028031 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1027969 CATCTGTGAG
*
1027979 AAAAAATGGGGTTATAGACAATTAA
1 AAAAAATGAGGTTATAGACAATTAA
*
1028004 AAAAAATGAGGTTATGGACAATTAA
1 AAAAAATGAGGTTATAGACAATTAA
1028029 AAA
1 AAA
1028032 TTTTTTAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.23
Consensus pattern (25 bp):
AAAAAATGAGGTTATAGACAATTAA
Found at i:1033171 original size:29 final size:30
Alignment explanation
Indices: 1033130--1033193 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
1033120 AAGCTAAATA
*
1033130 TTAATTCTATTTAATAATATAAA-AATTAAT
1 TTAATTCTATTTAATAATA-AAATAACTAAT
1033160 TTAATT-TATTTAATAATAAAATAACTAAT
1 TTAATTCTATTTAATAATAAAATAACTAAT
1033189 TTAAT
1 TTAAT
1033194 CTAATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 3 0.09
29 23 0.72
30 6 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAATTCTATTTAATAATAAAATAACTAAT
Done.