Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3174
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: 36960
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:7204 original size:43 final size:44
Alignment explanation
Indices: 7142--7231 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 44
7132 TTCACCAAGC
* * *
7142 CTTAAACCCCTAAGCAGTAGGGTAACAGG-TTAAATTTACAGAT
1 CTTAAACCCCTAAGAAGTAGGGTAACAGGCTAAAAATTACAGAT
* *
7185 CTTAACCCCCTAAGAAGTAGGGTAATAGGCTAAAAATTACAGAT
1 CTTAAACCCCTAAGAAGTAGGGTAACAGGCTAAAAATTACAGAT
7229 CTT
1 CTT
7232 GTCTCCCTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 26 0.63
44 15 0.37
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (44 bp):
CTTAAACCCCTAAGAAGTAGGGTAACAGGCTAAAAATTACAGAT
Found at i:7772 original size:87 final size:86
Alignment explanation
Indices: 7611--7777 Score: 217
Period size: 86 Copynumber: 1.9 Consensus size: 86
7601 GACTGAATAT
* * * *
7611 CTACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCGAATGCAATAGGTCTTAAACCCCTAA
1 CTACAGATCTTATCACCCTAAGCAGCAGGGAAACAGATCGAAGGCAAAAGGCCTTAAACCCCTAA
*
7676 GCAGTAGGGTAACAGACCGAA
66 GCAATAGGGTAACAGACCGAA
* * * * * * *
7697 CTACAGATCTTATCTCCCTCAGTAGCAGGGAAATAGATTGAAGGTAAAAGAGCCTTAAACCTCTA
1 CTACAGATCTTATCACCCTAAGCAGCAGGGAAACAGATCGAAGGCAAAAG-GCCTTAAACCCCTA
7762 AGCAATAGGGTAACAG
65 AGCAATAGGGTAACAG
7778 GATGAATTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 41 0.60
87 27 0.40
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (86 bp):
CTACAGATCTTATCACCCTAAGCAGCAGGGAAACAGATCGAAGGCAAAAGGCCTTAAACCCCTAA
GCAATAGGGTAACAGACCGAA
Found at i:9933 original size:20 final size:20
Alignment explanation
Indices: 9908--9946 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9898 CATTTCATAT
*
9908 ATATATCCCGTATATTTTTA
1 ATATATCACGTATATTTTTA
*
9928 ATATATCATGTATATTTTT
1 ATATATCACGTATATTTTT
9947 TTTTGTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (20 bp):
ATATATCACGTATATTTTTA
Found at i:10026 original size:25 final size:26
Alignment explanation
Indices: 9959--10026 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
9949 TTGTTTCTAT
9959 TATTATATATATATTTTAATACCATATG
1 TATTAT-TAT-TATTTTAATACCATATG
** *
9987 TATTATTATCGTTTT-ATACTAT-TG
1 TATTATTATTATTTTAATACCATATG
10011 CTATTATTATTATTTT
1 -TATTATTATTATTTT
10027 CGTTATCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 2 0.06
25 19 0.56
26 4 0.12
27 3 0.09
28 6 0.18
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (26 bp):
TATTATTATTATTTTAATACCATATG
Found at i:11173 original size:33 final size:33
Alignment explanation
Indices: 11136--11233 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
11126 TATATCAATG
*
11136 TGCGAGTCGTAATGATGTGTGAGCTGTGTAATT
1 TGCGAGTCATAATGATGTGTGAGCTGTGTAATT
* *
11169 TGCGAGTCATAGTGATGTGTGAGCTGTGTAATG
1 TGCGAGTCATAATGATGTGTGAGCTGTGTAATT
* * * *
11202 TGTGAG-CTACAATGATGTGCGAGTTGTGTAAT
1 TGCGAGTC-ATAATGATGTGTGAGCTGTGTAAT
11234 GAGCAAGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.22, C:0.09, G:0.34, T:0.35
Consensus pattern (33 bp):
TGCGAGTCATAATGATGTGTGAGCTGTGTAATT
Found at i:11234 original size:33 final size:31
Alignment explanation
Indices: 11132--11269 Score: 116
Period size: 33 Copynumber: 4.2 Consensus size: 31
11122 TGTATATATC
11132 AATGTGCGAGTCGTAATGATGTGTGAGCTGTGT
1 AATGTGCGAGTC--AATGATGTGTGAGCTGTGT
*
11165 AATTTGCGAGTCATAGTGATGTGTGAGCTGTGT
1 AATGTGCGAGTCA-A-TGATGTGTGAGCTGTGT
* * *
11198 AATGTGTGAGCTACAATGATGTGCGAGTTGTGT
1 AATGTGCGAG-T-CAATGATGTGTGAGCTGTGT
* * * *
11231 AATGAGCAAG-CTATGTAATGTATGAGCTGTAGT
1 AATGTGCGAGTCAATG--ATGTGTGAGCTGT-GT
11264 AATGTG
1 AATGTG
11270 TGAGCTGTGA
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.05
31 1 0.01
32 11 0.13
33 65 0.76
34 2 0.02
35 2 0.02
ACGTcount: A:0.25, C:0.09, G:0.33, T:0.33
Consensus pattern (31 bp):
AATGTGCGAGTCAATGATGTGTGAGCTGTGT
Found at i:11267 original size:17 final size:17
Alignment explanation
Indices: 11245--11277 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11235 AGCAAGCTAT
11245 GTAATGTATGAGCTGTA
1 GTAATGTATGAGCTGTA
*
11262 GTAATGTGTGAGCTGT
1 GTAATGTATGAGCTGT
11278 GAAAATATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.33, T:0.36
Consensus pattern (17 bp):
GTAATGTATGAGCTGTA
Found at i:15165 original size:16 final size:18
Alignment explanation
Indices: 15141--15193 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
15131 ATGTAAAAAA
* *
15141 ATTAAAATATAAAAATTT
1 ATTAATATATATAAATTT
15159 ATTAATATGTATATAAATTT
1 ATTAATA--TATATAAATTT
*
15179 ATTAATATATGTAAA
1 ATTAATATATATAAA
15194 AATAACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.43
20 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTAATATATATAAATTT
Found at i:15188 original size:22 final size:20
Alignment explanation
Indices: 15148--15196 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
15138 AAAATTAAAA
15148 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
15168 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
15188 TGTAAAAAT
1 TATAAAAAT
15197 AACTTTAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:15243 original size:32 final size:32
Alignment explanation
Indices: 15207--15284 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
15197 AACTTTAAAG
*
15207 GAAAATATTTTCAGGAA-ATC-TGCCAAACAACA
1 GAAAATATTTTCA-CAACATCAT-CCAAACAACA
* *
15239 GAAAATATTTTACACAACTTCATCCAAACACCA
1 GAAAATATTTT-CACAACATCATCCAAACAACA
15272 GAAAATATTTTCA
1 GAAAATATTTTCA
15285 ATAAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 15 0.38
33 24 0.60
34 1 0.03
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCACAACATCATCCAAACAACA
Found at i:15315 original size:20 final size:20
Alignment explanation
Indices: 15286--15324 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15276 ATATTTTCAA
*
15286 TAAATTATTTTCCAGAAAAG
1 TAAATCATTTTCCAGAAAAG
*
15306 TAAATCATTTTCCGGAAAA
1 TAAATCATTTTCCAGAAAA
15325 CATTTTACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAG
Found at i:17974 original size:19 final size:20
Alignment explanation
Indices: 17947--17985 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
17937 GACCAGGTTT
17947 AAGGATTTTTAGGGT-TTTA
1 AAGGATTTTTAGGGTATTTA
*
17966 AAGGGTTTTTAGGGTATTTA
1 AAGGATTTTTAGGGTATTTA
17986 TCTTTTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
AAGGATTTTTAGGGTATTTA
Found at i:18795 original size:19 final size:19
Alignment explanation
Indices: 18771--18817 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
18761 CAAGATTTTC
18771 AATCAAAGGATTTAGAACG
1 AATCAAAGGATTTAGAACG
18790 AATCAAAGGATTTAGAACG
1 AATCAAAGGATTTAGAACG
18809 AATCAAAGG
1 AATCAAAGG
18818 TAATTATCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (19 bp):
AATCAAAGGATTTAGAACG
Found at i:20213 original size:127 final size:127
Alignment explanation
Indices: 20003--20233 Score: 324
Period size: 127 Copynumber: 1.8 Consensus size: 127
19993 CATGCATTGA
* *
20003 AATTTTAAAAGGATATTCGGTTATTTGGTCAAACGACAAATCGACACCCAGCACGTTAGGGCACG
1 AATTTTAAAAGGATATTCGGTCATTTGGTCAAACGACAAATCGAAACCCAGCACGTTAGGGCACG
*
20068 ATTTCTCGAACTCCCAAAC-TCGAAATATTGCCTTGTTTTCTAATTGAAGAAATCACAGACGG
66 ATTTCTCGAACTCCCAAACAT-GAAATATTGCCTTATTTTCTAATTGAAGAAATCACAGACGG
* * *
20130 AATTTTAAAAAGGGTATTTGGTCATTTGGTCAAACAGA-AAATTGAAACCCAGCACG-TAGGGCA
1 AATTTT-AAAAGGATATTCGGTCATTTGGTCAAAC-GACAAATCGAAACCCAGCACGTTAGGGCA
* ** *
20193 CGATTTCTCGAATTTTCAAACATGAAATATTTCCTTATTTT
64 CGATTTCTCGAACTCCCAAACATGAAATATTGCCTTATTTT
20234 GAGAATTTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
127 47 0.52
128 42 0.46
129 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (127 bp):
AATTTTAAAAGGATATTCGGTCATTTGGTCAAACGACAAATCGAAACCCAGCACGTTAGGGCACG
ATTTCTCGAACTCCCAAACATGAAATATTGCCTTATTTTCTAATTGAAGAAATCACAGACGG
Found at i:21044 original size:3 final size:3
Alignment explanation
Indices: 21036--21069 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
21026 ACTTAATATA
21036 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21070 GAAGGTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27675 original size:16 final size:15
Alignment explanation
Indices: 27651--27684 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
27641 ACAATATGAT
*
27651 AAAATATATTTTATAA
1 AAAAAATATTTTA-AA
27667 AAAAAATATTTTAAA
1 AAAAAATATTTTAAA
27682 AAA
1 AAA
27685 TAACAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAAATATTTTAAA
Found at i:28162 original size:18 final size:19
Alignment explanation
Indices: 28139--28180 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
28129 ACTAATAACG
28139 AAATAAATATTT-ATATGA
1 AAATAAATATTTAATATGA
*
28157 AAATAAATATTTAATTTGA
1 AAATAAATATTTAATATGA
28176 AAATA
1 AAATA
28181 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATAAATATTTAATATGA
Found at i:28541 original size:25 final size:24
Alignment explanation
Indices: 28505--28572 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
28495 AAAAATATTT
*
28505 TTAA-ATTTAATAATA-AATTTAATA
1 TTAATATTAAATAATATAA-TT-ATA
28529 TTAATATTAAATAAATATAATTATA
1 TTAATATTAAAT-AATATAATTATA
*
28554 TTAATATTAAATAACATAA
1 TTAATATTAAATAATATAA
28573 AAATCCCCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 10 0.26
25 21 0.54
26 6 0.15
27 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATATTAAATAATATAATTATA
Found at i:31602 original size:20 final size:20
Alignment explanation
Indices: 31565--31603 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31555 GTCTGATATA
31565 TTTTGAAAAGTATTTATTAAT
1 TTTTGAAAAG-ATTTATTAAT
31586 TTTTGAAAA-ATTGTATTA
1 TTTTGAAAAGATT-TATTA
31604 GCTTTGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 5 0.29
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTGAAAAGATTTATTAAT
Found at i:33939 original size:38 final size:38
Alignment explanation
Indices: 33805--33953 Score: 190
Period size: 39 Copynumber: 3.9 Consensus size: 38
33795 AAAAGTATGG
* * *
33805 TTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAA
1 TTTTAATTAACAATAAAACAAAATAGCATGGGGAA-TAA
* *
33844 TTTTAATTAACAATAAAACAAAATAGTATGGGGAAATAG
1 TTTTAATTAACAATAAAACAAAATAGCATGGGG-AATAA
* *
33883 TTTTAATTAACAATAAAACAAAATAGCATGGGGATTAT
1 TTTTAATTAACAATAAAACAAAATAGCATGGGGAATAA
* * *
33921 TTTTTATTAATAATAAAACAAAGTAGCATGGGG
1 TTTTAATTAACAATAAAACAAAATAGCATGGGG
33954 GGAGTGGAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 33 0.33
39 65 0.65
40 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (38 bp):
TTTTAATTAACAATAAAACAAAATAGCATGGGGAATAA
Found at i:34702 original size:18 final size:18
Alignment explanation
Indices: 34665--34702 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
34655 TTAATAGTTG
*
34665 TTTCTAATATTATGATTA
1 TTTCTAATATTATGAATA
34683 TTTCTAATATGTAT-AATA
1 TTTCTAATAT-TATGAATA
34701 TT
1 TT
34703 ATGTATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTCTAATATTATGAATA
Done.