Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2007
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: 53116
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:6023 original size:40 final size:40
Alignment explanation
Indices: 5924--6154 Score: 304
Period size: 40 Copynumber: 5.8 Consensus size: 40
5914 TGGATGATAA
* * * * **
5924 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
5964 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * *
6003 CCGGGCTAAGTACCGAAGGCATTTCTGCGAATTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
6043 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * *
6083 CCGGGCTAAGTCCCGAAGGCAATTGTGCAAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
6123 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
6155 AGCTATATCC
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
39 33 0.20
40 133 0.79
41 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:12484 original size:13 final size:13
Alignment explanation
Indices: 12466--12490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12456 GGTTTCTTTA
12466 TTAAACTAATTAT
1 TTAAACTAATTAT
12479 TTAAACTAATTA
1 TTAAACTAATTA
12491 AATAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:15427 original size:6 final size:6
Alignment explanation
Indices: 15418--15497 Score: 63
Period size: 6 Copynumber: 13.0 Consensus size: 6
15408 AATAAAATTT
* * * * *
15418 AAATAA AAATAA AAATCA AAAGAA AAAGAA AAA-GA AAATAA ATAAAATA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-AATA-A
* *
15467 AAATAA AAATAA GAATAA ATAAAAA AAATAA
1 AAATAA AAATAA AAATAA A-AATAA AAATAA
15498 GAAGATTCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
5 4 0.07
6 42 0.71
7 11 0.19
8 2 0.03
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:15462 original size:4 final size:5
Alignment explanation
Indices: 15397--15497 Score: 59
Period size: 6 Copynumber: 19.6 Consensus size: 5
15387 ATATGTCTTT
* *
15397 TAAAA TAAAA T--AA TAAAA TTTAAA TAAAAA TAAAAA TCAAAA GAAAAA
1 TAAAA TAAAA TAAAA TAAAA -TAAAA T-AAAA T-AAAA T-AAAA -TAAAA
* *
15445 GAAAAA GAAAA T-AAA TAAAA TAAAA TAAAAA TAAGAA T-AAA TAAAA
1 -TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAA-AA TAAAA TAAAA
15491 -AAAA TAA
1 TAAAA TAA
15498 GAAGATTCAA
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.04
4 11 0.14
5 30 0.38
6 36 0.45
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:15475 original size:26 final size:25
Alignment explanation
Indices: 15418--15497 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
15408 AATAAAATTT
* *
15418 AAATAAAAATAAAAATCAA-AAGAA
1 AAATAAAAATAAAAATAAATAAAAA
* *
15442 AAAGAAAAA-GAAAATAAATAAAATA
1 AAATAAAAATAAAAATAAATAAAA-A
*
15467 AAATAAAAATAAGAATAAATAAAAA
1 AAATAAAAATAAAAATAAATAAAAA
15492 AAATAA
1 AAATAA
15498 GAAGATTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.15
24 11 0.24
25 16 0.35
26 12 0.26
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (25 bp):
AAATAAAAATAAAAATAAATAAAAA
Found at i:15493 original size:49 final size:49
Alignment explanation
Indices: 15398--15494 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
15388 TATGTCTTTT
* * *
15398 AAAATAAAATAATAAAATTTAAATAAAAATAAAAATCAAAAGAAAAAGA
1 AAAAGAAAATAATAAAATTAAAATAAAAATAAAAATCAAAAAAAAAAGA
* *
15447 AAAAGAAAATAAATAAAA-TAAAATAAAAATAAGAATAAATAAAAAAAA
1 AAAAGAAAAT-AATAAAATTAAAATAAAAATAAAAATCAA-AAAAAAAA
15495 TAAGAAGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 27 0.66
50 14 0.34
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (49 bp):
AAAAGAAAATAATAAAATTAAAATAAAAATAAAAATCAAAAAAAAAAGA
Found at i:17316 original size:46 final size:46
Alignment explanation
Indices: 17266--17441 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
17256 TGGTTGAGCA
17266 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
17312 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
17357 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
17405 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17442 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:17422 original size:93 final size:93
Alignment explanation
Indices: 17263--17434 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
17253 GGATGGTTGA
* *
17263 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
17328 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
17356 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
17421 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
17435 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19435 original size:24 final size:23
Alignment explanation
Indices: 19399--19444 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
19389 TATATTAGTG
*
19399 AAAGATTTATTGATCAGAAGCAT
1 AAAGATTTATTGAGCAGAAGCAT
* *
19422 AAAGAATTTCTTGAGCTGAAGCA
1 AAAG-ATTTATTGAGCAGAAGCA
19445 AGGTAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (23 bp):
AAAGATTTATTGAGCAGAAGCAT
Found at i:24854 original size:46 final size:46
Alignment explanation
Indices: 24804--24979 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
24794 TGGTTGAGCA
24804 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
24850 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
24895 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * ** *
24943 CCCGAGCTCATTTCGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
24980 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.55
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:24961 original size:93 final size:93
Alignment explanation
Indices: 24801--24972 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
24791 GGATGGTTGA
* * *
24801 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
24866 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * **
24894 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTTCGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
24959 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
24973 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27828 original size:21 final size:21
Alignment explanation
Indices: 27802--27854 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
27792 AGCGGTGGCG
*
27802 GTGAGATTAGTTACTGTAGCC
1 GTGAGATTAGATACTGTAGCC
* * *
27823 GTGAGATTGGATATTGTAGCG
1 GTGAGATTAGATACTGTAGCC
27844 GTGAGATTAGA
1 GTGAGATTAGA
27855 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCC
Found at i:28285 original size:17 final size:17
Alignment explanation
Indices: 28265--28309 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
28255 TATTAGTAGA
28265 AATTTTTAATTATAAAT
1 AATTTTTAATTATAAAT
** *
28282 AATTTAAAATAATAAAT
1 AATTTTTAATTATAAAT
28299 AATTTTTAATT
1 AATTTTTAATT
28310 TTTAATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTTAATTATAAAT
Found at i:52198 original size:6 final size:5
Alignment explanation
Indices: 52175--52274 Score: 66
Period size: 5 Copynumber: 19.2 Consensus size: 5
52165 TGAAATCTCC
52175 TATTT TATCTT TA-TT TATTCT TATTTT TATTT TA-TT TATTT TATTT
1 TATTT TAT-TT TATTT TATT-T TA-TTT TATTT TATTT TATTT TATTT
* *
52221 TATATT T-TTC T-TTT GATTTT TATTT TCATTT TCAATTT TATTAT TA-TT
1 TAT-TT TATTT TATTT TA-TTT TATTT T-ATTT T--ATTT TATT-T TATTT
52269 TATTT T
1 TATTT T
52275 GAAGACATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
4 15 0.19
5 31 0.40
6 25 0.32
7 7 0.09
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:52201 original size:21 final size:19
Alignment explanation
Indices: 52175--52274 Score: 80
Period size: 18 Copynumber: 5.1 Consensus size: 19
52165 TGAAATCTCC
52175 TATTTTATCTTTATTTATTCT
1 TATTTTAT-TTTATTTATT-T
52196 TATTTTTATTTTATTTATTT
1 TA-TTTTATTTTATTTATTT
* *
52216 TATTTTATATT-TTTCTTT
1 TATTTTATTTTATTTATTT
*
52234 TGATTTTTATTTTCA-TT-TTC
1 T-A-TTTTATTTT-ATTTATTT
*
52254 AATTTTATTATTATTTATTT
1 TATTTTATT-TTATTTATTT
52274 T
1 T
52275 GAAGACATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
18 15 0.23
19 14 0.22
20 15 0.23
21 14 0.22
22 6 0.09
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (19 bp):
TATTTTATTTTATTTATTT
Found at i:52203 original size:12 final size:11
Alignment explanation
Indices: 52175--52274 Score: 66
Period size: 12 Copynumber: 9.0 Consensus size: 11
52165 TGAAATCTCC
*
52175 TATTTTATCTT
1 TATTTTATTTT
*
52186 TA-TTTATTCT
1 TATTTTATTTT
52196 TATTTT-TATTT
1 TATTTTAT-TTT
52207 TA-TTTA-TTT
1 TATTTTATTTT
52216 TATTTTATATTTT
1 TA-TTT-TATTTT
*
52229 TCTTTTGATTTT
1 TATTTT-ATTTT
52241 TATTTTCATTTT
1 TATTTT-ATTTT
* *
52253 CAATTTTATTAT
1 -TATTTTATTTT
52265 TA-TTTATTTT
1 TATTTTATTTT
52275 GAAGACATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
9 5 0.07
10 19 0.27
11 13 0.19
12 24 0.34
13 9 0.13
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:52203 original size:16 final size:15
Alignment explanation
Indices: 52175--52220 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
52165 TGAAATCTCC
52175 TATTTTATCTTTATT
1 TATTTTATCTTTATT
*
52190 TATTCTTATTTTTATT
1 TATT-TTATCTTTATT
52206 T-TATTTAT-TTTATT
1 TAT-TTTATCTTTATT
52220 T
1 T
52221 TATATTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 12 0.43
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTATCTTTATT
Found at i:52241 original size:7 final size:6
Alignment explanation
Indices: 52188--52269 Score: 65
Period size: 6 Copynumber: 13.2 Consensus size: 6
52178 TTTATCTTTA
* * * *
52188 TTTATT CTTATT TTTATT TTATTTAT TTTATT TTATATT TTTCTT TTGATT
1 TTTATT TTTATT TTTATT TT-TAT-T TTTATT TT-TATT TTTATT TTTATT
* * * *
52239 TTTATT TTCATT TTCAAT TTTATT ATTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT T
52270 ATTTTGAAGA
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
6 46 0.78
7 10 0.17
8 3 0.05
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (6 bp):
TTTATT
Done.