Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold577
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: 25090
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Found at i:40 original size:13 final size:13
Alignment explanation
Indices: 22--57 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12 CGGCCCTAAT
22 TATTTATATTTTA
1 TATTTATATTTTA
*
35 TATTTATATTTTT
1 TATTTATATTTTA
48 TATATTATAT
1 TAT-TTATAT
58 AAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:66 original size:22 final size:22
Alignment explanation
Indices: 24--67 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
14 GCCCTAATTA
* *
24 TTTATATTTTATATTTATATTT
1 TTTATATTATATAATTATATTT
46 TTTATATTATATAAATT-TATTT
1 TTTATATTATAT-AATTATATTT
68 ATAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATATTATATAATTATATTT
Found at i:2191 original size:16 final size:16
Alignment explanation
Indices: 2170--2219 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2160 AGATTTTAAA
2170 AAAATTTATAAATATT
1 AAAATTTATAAATATT
* *
2186 AAAATTTAAATAATTTT
1 AAAATTTATA-AATATT
2203 AAAA-TTATTAAATATT
1 AAAATTTA-TAAATATT
2219 A
1 A
2220 TTTTATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTTATAAATATT
Found at i:2204 original size:17 final size:16
Alignment explanation
Indices: 2170--2208 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2160 AGATTTTAAA
*
2170 AAAATTTATAAATATT
1 AAAATTTAAAAATATT
*
2186 AAAATTTAAATAATTTT
1 AAAATTTAAA-AATATT
2203 AAAATT
1 AAAATT
2209 ATTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTTAAAAATATT
Found at i:2207 original size:25 final size:27
Alignment explanation
Indices: 2164--2214 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2154 TTTCAAAGAT
2164 TTTAAAAAAATTTATAAA-TATTAAAA
1 TTTAAAAAAATTTATAAATTATTAAAA
* *
2190 TTTAAATAATTTTA-AAATTATTAAA
1 TTTAAAAAAATTTATAAATTATTAAA
2215 TATTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAAAAAAATTTATAAATTATTAAAA
Found at i:2260 original size:37 final size:35
Alignment explanation
Indices: 2193--2261 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
2183 ATTAAAATTT
* *
2193 AAATAATTTTAAAATTATTAAATATTATTTTATAA
1 AAATAATTTTAAAATAATTAAATATAATTTTATAA
2228 AAATAATTATATAAAATAATTAAAT-TAAATTTTA
1 AAATAATT-T-TAAAATAATTAAATAT-AATTTTA
2262 AGTGCCTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 8 0.28
36 2 0.07
37 19 0.66
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
AAATAATTTTAAAATAATTAAATATAATTTTATAA
Found at i:10859 original size:22 final size:23
Alignment explanation
Indices: 10831--10884 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
10821 TTTTAATTTA
*
10831 TAAATAAAAAACTAAA-TTAAAT
1 TAAATAAAAAACTAAACTAAAAT
10853 TAAAT-AAAAACTAAACTAAAAT
1 TAAATAAAAAACTAAACTAAAAT
10875 T-AATAAAAAA
1 TAAATAAAAAA
10885 TCAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (23 bp):
TAAATAAAAAACTAAACTAAAAT
Found at i:10861 original size:21 final size:22
Alignment explanation
Indices: 10831--10883 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
10821 TTTTAATTTA
*
10831 TAAATAAAAAACTAAA-TTAAAT
1 TAAAT-AAAAACTAAACTAAAAT
10853 TAAATAAAAACTAAACTAAAAT
1 TAAATAAAAACTAAACTAAAAT
10875 T-AATAAAAA
1 TAAATAAAAA
10884 ATCAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAAACTAAACTAAAAT
Found at i:11179 original size:24 final size:24
Alignment explanation
Indices: 11152--11200 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11142 TTTTTAGTTT
11152 AGATTTAAGTTGAATTAATTCACC
1 AGATTTAAGTTGAATTAATTCACC
11176 AGATTTAAGTTGAATTAATTCACC
1 AGATTTAAGTTGAATTAATTCACC
11200 A
1 A
11201 ACTTATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (24 bp):
AGATTTAAGTTGAATTAATTCACC
Found at i:11258 original size:24 final size:25
Alignment explanation
Indices: 11203--11287 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 25
11193 ATTCACCAAC
11203 TTAT-ATTATATTTTAAAATAATAT
1 TTATAATTATATTTTAAAATAATAT
* * * *
11227 TAAAAATTAT-TTTTATATTAATAT
1 TTATAATTATATTTTAAAATAATAT
* * *
11251 TTATAATTAAAATTATATAATAATAT
1 TTATAATT-ATATTTTAAAATAATAT
* *
11277 TTTTTATTATA
1 TTATAATTATA
11288 AAAATAATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
24 20 0.43
25 8 0.17
26 18 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATAATTATATTTTAAAATAATAT
Found at i:11630 original size:11 final size:12
Alignment explanation
Indices: 11601--11636 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
11591 ATATCGTATA
11601 ATATTTTATATT
1 ATATTTTATATT
11613 ATATTTTA-ATT
1 ATATTTTATATT
*
11624 ATTTTTTATATT
1 ATATTTTATATT
11636 A
1 A
11637 CATTCATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:11750 original size:21 final size:21
Alignment explanation
Indices: 11724--11765 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11714 AATCTTTTTT
11724 AAATTATTTTATATATTTAAA
1 AAATTATTTTATATATTTAAA
11745 AAATTATTTTATATATTTAAA
1 AAATTATTTTATATATTTAAA
11766 TATATATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTATTTTATATATTTAAA
Found at i:14850 original size:23 final size:24
Alignment explanation
Indices: 14807--14855 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
14797 TCAACTTAGA
*
14807 ATTTTTTTATTCACTATTATATTT
1 ATTTTTTTATTCACTATTATAATT
14831 ATTTATTTTATT-A-TATTATAATT
1 ATTT-TTTTATTCACTATTATAATT
14854 AT
1 AT
14856 ATAATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 5 0.22
25 7 0.30
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTTTTATTCACTATTATAATT
Found at i:14867 original size:28 final size:26
Alignment explanation
Indices: 14806--14874 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 26
14796 TTCAACTTAG
14806 AATT-TTTTTATTCACTATTATATTTAT
1 AATTATTTTTATT-A-TATTATATTTAT
14833 --TTA-TTTTATTATATTATAATTATAT
1 AATTATTTTTATTATATTAT-ATT-TAT
*
14858 AATTATTTTTAATATAT
1 AATTATTTTTATTATAT
14875 ATTTCATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
23 6 0.17
24 4 0.11
25 12 0.34
27 3 0.09
28 10 0.29
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (26 bp):
AATTATTTTTATTATATTATATTTAT
Found at i:15087 original size:23 final size:24
Alignment explanation
Indices: 15039--15087 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
15029 CAAAATTAAT
**
15039 ATTTAATAATAAAAAATTATTTAA
1 ATTTAATAATAAAAAATTATGAAA
*
15063 ATTTAATTATAAAAAA-TATGAAA
1 ATTTAATAATAAAAAATTATGAAA
15086 AT
1 AT
15088 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
ATTTAATAATAAAAAATTATGAAA
Found at i:15682 original size:2 final size:2
Alignment explanation
Indices: 15677--15720 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
15667 CCCTTTTTTA
* * *
15677 AT AT AT AC AT AT AT AC AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15719 AT
1 AT
15721 TGATTGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:16154 original size:31 final size:31
Alignment explanation
Indices: 16115--16188 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
16105 CATATTTAAA
** *
16115 ATAT-TTTATATTTGTATAAATTTTG-ATAC
1 ATATATTTATATTAATATAAATTTTGAAAAC
16144 ATATAATTTAT-TTAATATAAATTTTGAAAAC
1 ATAT-ATTTATATTAATATAAATTTTGAAAAC
*
16175 TTATATTTATATTA
1 ATATATTTATATTA
16189 TATCAAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 4 0.11
30 19 0.51
31 14 0.38
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (31 bp):
ATATATTTATATTAATATAAATTTTGAAAAC
Found at i:18337 original size:17 final size:17
Alignment explanation
Indices: 18315--18349 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18305 TGAACATATC
18315 CATATCAGACACACACA
1 CATATCAGACACACACA
* *
18332 CATATCTGACACTCACA
1 CATATCAGACACACACA
18349 C
1 C
18350 CCAAATCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.37, G:0.06, T:0.17
Consensus pattern (17 bp):
CATATCAGACACACACA
Found at i:19277 original size:16 final size:16
Alignment explanation
Indices: 19226--19277 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
19216 TCTCGAACTT
*
19226 AAAAAAATCTAAATTC
1 AAAAAAACCTAAATTC
*
19242 AAAAAAACTTAAATTC
1 AAAAAAACCTAAATTC
* *
19258 -AAAAGACCTAAATCC
1 AAAAAAACCTAAATTC
19273 AAAAA
1 AAAAA
19278 TCTTGAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAAAAACCTAAATTC
Found at i:19376 original size:20 final size:21
Alignment explanation
Indices: 19351--19391 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19341 TAGTTCAATT
19351 AAAAA-TAATTTAAATATAAA
1 AAAAATTAATTTAAATATAAA
* *
19371 AAAAATTATTTTAAATTTAAA
1 AAAAATTAATTTAAATATAAA
19392 TAAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATTAATTTAAATATAAA
Found at i:20076 original size:13 final size:13
Alignment explanation
Indices: 20060--20085 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20050 ACATTTGGTT
20060 ATGGATTTTGATA
1 ATGGATTTTGATA
20073 ATGGATTTTGATA
1 ATGGATTTTGATA
20086 TCCGAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
ATGGATTTTGATA
Found at i:21349 original size:32 final size:33
Alignment explanation
Indices: 21267--21349 Score: 87
Period size: 39 Copynumber: 2.4 Consensus size: 33
21257 ATTAAAATCC
* *
21267 TATAATAATGTCTTAGTTTACCAATTAATTCATA
1 TATAATTATGTCTTAATTTACCAATTAATTCA-A
21301 TAAATAGTATTAATGTCTTAATTTACCAATTAATTC-A
1 T--ATA--ATT-ATGTCTTAATTTACCAATTAATTCAA
21338 TATAATTATGTC
1 TATAATTATGTC
21350 ATCATTAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
32 5 0.12
33 3 0.07
34 1 0.02
35 3 0.07
36 3 0.07
37 2 0.05
38 2 0.05
39 23 0.55
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.45
Consensus pattern (33 bp):
TATAATTATGTCTTAATTTACCAATTAATTCAA
Found at i:22201 original size:2 final size:2
Alignment explanation
Indices: 22196--22226 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22186 TTTTCTTTAC
*
22196 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22227 GTTTAGATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24095 original size:21 final size:22
Alignment explanation
Indices: 24071--24125 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
24061 ATATATTAAT
24071 ATTTATT-TTAAATAAAAAATA
1 ATTTATTATTAAATAAAAAATA
* *
24092 ATTT-TTATTATATAAATAATA
1 ATTTATTATTAAATAAAAAATA
*
24113 ATTTA-AATTAAAT
1 ATTTATTATTAAAT
24126 TAATTCGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTATTATTAAATAAAAAATA
Found at i:24312 original size:20 final size:20
Alignment explanation
Indices: 24272--24343 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
24262 TTTTTAAAAA
* *
24272 AATTAAA-TAAAATTAATTT
1 AATTAAATTATAATTTATTT
*
24291 AATTAAATTATTATTTATTT
1 AATTAAATTATAATTTATTT
* *
24311 AATAAAATAATAATTT-TTT
1 AATTAAATTATAATTTATTT
*
24330 AAATTTAATTATAA
1 -AATTAAATTATAA
24344 AATTAAATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
19 10 0.24
20 32 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAATTATAATTTATTT
Found at i:24835 original size:19 final size:21
Alignment explanation
Indices: 24813--24854 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
24803 ATTATGATGT
24813 AAAAAATAATT-TA-TTTATA
1 AAAAAATAATTATATTTTATA
*
24832 AAAAAATTATTATATTTTATA
1 AAAAAATAATTATATTTTATA
24853 AA
1 AA
24855 TAAAGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAAATAATTATATTTTATA
Done.