Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold257
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: 47767
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:133 original size:30 final size:30
Alignment explanation
Indices: 83--144 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
73 CACATGTTAC
83 ATTGACCTTTGAAAGTTTTACTTTATGTCA
1 ATTGACCTTTGAAAGTTTTACTTTATGTCA
113 ATTGA-CTTTGAAA-TCCTTTACTTTATGTCA
1 ATTGACCTTTGAAAGT--TTTACTTTATGTCA
143 AT
1 AT
145 CTATATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 1 0.03
29 8 0.27
30 21 0.70
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (30 bp):
ATTGACCTTTGAAAGTTTTACTTTATGTCA
Found at i:1037 original size:2 final size:2
Alignment explanation
Indices: 1030--1054 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1020 TGTCTGTCTG
1030 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1055 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1301 original size:15 final size:15
Alignment explanation
Indices: 1281--1317 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1271 TGAATTAGGG
1281 TTTTTTTTT-CCT-T
1 TTTTTTTTTCCCTCT
1294 TTTTTTTTCTCCCTCT
1 TTTTTTTT-TCCCTCT
1310 TTTTTTTT
1 TTTTTTTT
1318 GGTTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 3 0.14
16 9 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTTCCCTCT
Found at i:4581 original size:11 final size:11
Alignment explanation
Indices: 4562--4599 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4552 TTGTCTTGTA
4562 TTTTCTTTCTTT
1 TTTTCTTT-TTT
*
4574 TTTT-TTTCTT
1 TTTTCTTTTTT
4584 TTTTCTTTTTT
1 TTTTCTTTTTT
4595 TTTTC
1 TTTTC
4600 CATTTATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 6 0.26
11 13 0.57
12 4 0.17
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:5559 original size:29 final size:30
Alignment explanation
Indices: 5504--5562 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
5494 TATAAATTAC
*
5504 AAAAAATATTTAAAAACAATAGGAAATATA
1 AAAAAATATTTAAAAACAATAGCAAATATA
*
5534 AAAAAATTATTT-AAAA-AATTGCAAATATA
1 AAAAAA-TATTTAAAAACAATAGCAAATATA
5563 TTATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 10 0.38
31 5 0.19
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAAAATATTTAAAAACAATAGCAAATATA
Found at i:5968 original size:22 final size:22
Alignment explanation
Indices: 5922--5969 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5912 TTTATTATTA
*
5922 TTTT-TAAATAATGTTTAAATT
1 TTTTGTAAATAATGTTTAAATG
*
5943 TTTTGTAAATTAT-TTTATAATG
1 TTTTGTAAATAATGTTTA-AATG
5965 TTTTG
1 TTTTG
5970 CACTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.60
Consensus pattern (22 bp):
TTTTGTAAATAATGTTTAAATG
Found at i:11010 original size:22 final size:25
Alignment explanation
Indices: 10972--11019 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
10962 ATTGTCCACA
10972 TATATATATTTTAAATATTT-ATAT
1 TATATATATTTTAAATATTTAATAT
10996 TATAT-TATTTT-AATATTTAATAT
1 TATATATATTTTAAATATTTAATAT
11019 T
1 T
11020 TAATAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TATATATATTTTAAATATTTAATAT
Found at i:11028 original size:23 final size:22
Alignment explanation
Indices: 10974--11030 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
10964 TGTCCACATA
* *
10974 TATATATTTTAAATATTTATAT
1 TATATAATTTTAATATTTATAT
*
10996 TATATTATTTTAATATTTAATAT
1 TATATAATTTTAATATTT-ATAT
11019 T-TAATAATTTTA
1 TAT-ATAATTTTA
11031 TACAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATAATTTTAATATTTATAT
Found at i:11101 original size:58 final size:58
Alignment explanation
Indices: 10999--11111 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 58
10989 TTTATATTAT
** * *
10999 ATTATTTTAATATTTAATATTTAATAATTTTATACAATTTTTATATAATTATTTTAAC
1 ATTATTTTAATATTTAATATAGAATAATATTATACAATTTTTATAGAATTATTTTAAC
* * *
11057 ATTATTTTAATATTTACGT-TAGAATAATATTATA-TATTTCTTATAGATTTATTTT
1 ATTATTTTAATATTTA-ATATAGAATAATATTATACAATTT-TTATAGAATTATTTT
11112 TTTAATGTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 4 0.09
58 41 0.89
59 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (58 bp):
ATTATTTTAATATTTAATATAGAATAATATTATACAATTTTTATAGAATTATTTTAAC
Found at i:12282 original size:15 final size:15
Alignment explanation
Indices: 12262--12290 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12252 CGAAGCTTTG
12262 TGTAGTTGATTTTAT
1 TGTAGTTGATTTTAT
12277 TGTAGTTGATTTTA
1 TGTAGTTGATTTTA
12291 ATGGAGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (15 bp):
TGTAGTTGATTTTAT
Found at i:12298 original size:15 final size:15
Alignment explanation
Indices: 12265--12298 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12255 AGCTTTGTGT
* *
12265 AGTTGATTTTATTGT
1 AGTTGATTTTAATGG
12280 AGTTGATTTTAATGG
1 AGTTGATTTTAATGG
12295 AGTT
1 AGTT
12299 TGTTTAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (15 bp):
AGTTGATTTTAATGG
Found at i:15401 original size:5 final size:5
Alignment explanation
Indices: 15391--15415 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15381 TATATTTTGG
15391 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
15416 CATTTCAACT
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:21251 original size:31 final size:31
Alignment explanation
Indices: 21193--21252 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
21183 ACCAGCTTAA
* *
21193 GAAAAAGTGTCAAGTTTAGGTATCAAATTAG
1 GAAAAAGTGTCAAGTTGAGGTACCAAATTAG
*
21224 GAAAATGTGTCAAGTTCGA-GTACCAAATT
1 GAAAAAGTGTCAAGTT-GAGGTACCAAATT
21253 GGACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (31 bp):
GAAAAAGTGTCAAGTTGAGGTACCAAATTAG
Found at i:21418 original size:17 final size:20
Alignment explanation
Indices: 21386--21424 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
21376 TTGAAGAATA
21386 TTTATAATATATTTATA-AT
1 TTTATAATATATTTATATAT
21405 TTTA-AATA-ATTTATATAT
1 TTTATAATATATTTATATAT
21423 TT
1 TT
21425 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 8 0.42
19 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAATATATTTATATAT
Found at i:21425 original size:17 final size:19
Alignment explanation
Indices: 21383--21427 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
21373 ATTTTGAAGA
21383 ATATTTATAATATATTTAT
1 ATATTTATAATATATTTAT
21402 A-ATTT-TAA-ATAATTTAT
1 ATATTTATAATAT-ATTTAT
21419 ATATTTATA
1 ATATTTATA
21428 TTTTTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.09
17 10 0.43
18 8 0.35
19 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTATAATATATTTAT
Found at i:25397 original size:441 final size:441
Alignment explanation
Indices: 24575--25445 Score: 1733
Period size: 441 Copynumber: 2.0 Consensus size: 441
24565 CCAAATGCAT
24575 AACGTAGTTATCACAAGTGCCTCTCAACCAAAATGATCAGTGGTTAAGGTGATACTTTAGGAGCA
1 AACGTAGTTATCACAAGTGCCTCTCAACCAAAATGATCAGTGGTTAAGGTGATACTTTAGGAGCA
24640 AAAGGGGTTAGGCAGGAGGACCCTTTGTCCCCATACTTGTTCATCATAGGGATGAATGTGCTTTC
66 AAAGGGGTTAGGCAGGAGGACCCTTTGTCCCCATACTTGTTCATCATAGGGATGAATGTGCTTTC
24705 AGGCTTATAAAGACTGTTGATGCAAGTGGAGTGTCCGTGTATCACCCAAAATGTAAAAAATTGGA
131 AGGCTTATAAAGACTGTTGATGCAAGTGGAGTGTCCGTGTATCACCCAAAATGTAAAAAATTGGA
24770 GCTCACCATACTCTGTTTCGCAGATAACTTGCTAGTGTTCACAAAGGGATTGTTCGAATCGGTTC
196 GCTCACCATACTCTGTTTCGCAGATAACTTGCTAGTGTTCACAAAGGGATTGTTCGAATCGGTTC
24835 TTGCTATTAGTAATATTTTGAATATTTTTATAAAATATCAGAACTGCAAATGAACAACTCTAAGA
261 TTGCTATTAGTAATATTTTGAATATTTTTATAAAATATCAGAACTGCAAATGAACAACTCTAAGA
24900 GTGAGTTATTTAGTGTTAGAATATGTCAGAATGAGTTATAGAAGATTGTGAAGCAAACTGATCTG
326 GTGAGTTATTTAGTGTTAGAATATGTCAGAATGAGTTATAGAAGATTGTGAAGCAAACTGATCTG
24965 GAAATGGGAACCCTTCCTATTGGGTACCTTAGTGTACCATCTGGAAATGGG
391 GAAATGGGAACCCTTCCTATTGGGTACCTTAGTGTACCATCTGGAAATGGG
*
25016 AACGTAGTTATCACAAGTGCCTCTCAACCAAAATGATCAGTTGTTAAGGTGATACTTTAGGAGCA
1 AACGTAGTTATCACAAGTGCCTCTCAACCAAAATGATCAGTGGTTAAGGTGATACTTTAGGAGCA
25081 AAAGGGGTTAGGCAGGAGGACCCTTTGTCCCCATACTTGTTCATCATAGGGATGAATGTGCTTTC
66 AAAGGGGTTAGGCAGGAGGACCCTTTGTCCCCATACTTGTTCATCATAGGGATGAATGTGCTTTC
25146 AGGCTTATAAAGACTGTTGATGCAAGTGGAGTGTCCGTGTATCACCCAAAATGTAAAAAATTGGA
131 AGGCTTATAAAGACTGTTGATGCAAGTGGAGTGTCCGTGTATCACCCAAAATGTAAAAAATTGGA
25211 GCTCACCATACTCTGTTTCGCAGATAACTTGCTAGTGTTCACAAAGGGATTGTTCGAATCGGTTC
196 GCTCACCATACTCTGTTTCGCAGATAACTTGCTAGTGTTCACAAAGGGATTGTTCGAATCGGTTC
25276 TTGCTATTAGTAATATTTTGAATATTTTTATAAAATATCAGAACTGCAAATGAACAACTCTAAGA
261 TTGCTATTAGTAATATTTTGAATATTTTTATAAAATATCAGAACTGCAAATGAACAACTCTAAGA
25341 GTGAGTTATTTAGTGTTAGAATATGTCAGAATGAGTTATAGAAGATTGTGAAGCAAACTGATCTG
326 GTGAGTTATTTAGTGTTAGAATATGTCAGAATGAGTTATAGAAGATTGTGAAGCAAACTGATCTG
25406 GAAATGGGAACCCTTCCTATTGGGTACCTTAGTGTACCAT
391 GAAATGGGAACCCTTCCTATTGGGTACCTTAGTGTACCAT
25446 TGGTAACAAG
Statistics
Matches: 429, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
441 429 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (441 bp):
AACGTAGTTATCACAAGTGCCTCTCAACCAAAATGATCAGTGGTTAAGGTGATACTTTAGGAGCA
AAAGGGGTTAGGCAGGAGGACCCTTTGTCCCCATACTTGTTCATCATAGGGATGAATGTGCTTTC
AGGCTTATAAAGACTGTTGATGCAAGTGGAGTGTCCGTGTATCACCCAAAATGTAAAAAATTGGA
GCTCACCATACTCTGTTTCGCAGATAACTTGCTAGTGTTCACAAAGGGATTGTTCGAATCGGTTC
TTGCTATTAGTAATATTTTGAATATTTTTATAAAATATCAGAACTGCAAATGAACAACTCTAAGA
GTGAGTTATTTAGTGTTAGAATATGTCAGAATGAGTTATAGAAGATTGTGAAGCAAACTGATCTG
GAAATGGGAACCCTTCCTATTGGGTACCTTAGTGTACCATCTGGAAATGGG
Found at i:29062 original size:25 final size:25
Alignment explanation
Indices: 29034--29084 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29024 TATGACATCA
29034 ATTGAAAGAGACGAAATAAAAAATT
1 ATTGAAAGAGACGAAATAAAAAATT
29059 ATTGAAAGAGACGAAATAAAAAATT
1 ATTGAAAGAGACGAAATAAAAAATT
29084 A
1 A
29085 AGCAAGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.04, G:0.16, T:0.20
Consensus pattern (25 bp):
ATTGAAAGAGACGAAATAAAAAATT
Found at i:43845 original size:3 final size:3
Alignment explanation
Indices: 43837--43864 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43827 TCCATTAACA
43837 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
43865 GAGAATTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:45615 original size:99 final size:99
Alignment explanation
Indices: 45444--45643 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 99
45434 CATAGATTTT
45444 GATGATCTGTAAATATATCATGTTTGAGTTTGTGCGTGCACAGGGATTTTTAAGTGCGAGCAGAG
1 GATGATCTGTAAATATATCATGTTTGAGTTTGTGCGTGCACAGGGATTTTTAAGTGCGAGCAGAG
45509 AACAGCGGGAAAAGAGCTAACCTGGGGAAGCACA
66 AACAGCGGGAAAAGAGCTAACCTGGGGAAGCACA
* *
45543 GATGATCTGTAAATATATCATGTTTGAGTTTGTGTGTGCAGAGGGATTTTTAAGTGCGAGCAGAG
1 GATGATCTGTAAATATATCATGTTTGAGTTTGTGCGTGCACAGGGATTTTTAAGTGCGAGCAGAG
45608 AACAGCGGGAAAAGAGCTAACCTGGGGAAGCACA
66 AACAGCGGGAAAAGAGCTAACCTGGGGAAGCACA
45642 GA
1 GA
45644 AAGTCCACCA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (99 bp):
GATGATCTGTAAATATATCATGTTTGAGTTTGTGCGTGCACAGGGATTTTTAAGTGCGAGCAGAG
AACAGCGGGAAAAGAGCTAACCTGGGGAAGCACA
Done.