Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1675
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: 36615
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:6731 original size:38 final size:38
Alignment explanation
Indices: 6658--6823 Score: 262
Period size: 38 Copynumber: 4.3 Consensus size: 38
6648 TCCAATTACT
* *
6658 AGCATAAAGCCTG-GGGAACTATAAACCCGAATATAATACC
1 AGCATTAAGCCTGCGGG-ACT-T-AACCCGGATATAATACC
6698 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
6736 AGCATTAAGCCTGCGGGATTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
6774 AGCATTAAGCCTGCAGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
6812 AGCATTAAGCCT
1 AGCATTAAGCCT
6824 ATTTAATCAT
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
38 101 0.84
39 1 0.01
40 15 0.12
41 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (38 bp):
AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
Found at i:10200 original size:27 final size:26
Alignment explanation
Indices: 10137--10248 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
10127 AGCATGGCTG
* *
10137 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
10163 CCAAAAGCAGATAATCGTGGCAGAGCCA
1 CCAGAA-CAGATAAT-GTGGCAGAGCCA
* *
10191 CTAGAACAGATATATGTGGCAAAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
10218 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
10245 CCAG
1 CCAG
10249 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.08
27 51 0.70
28 16 0.22
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:11518 original size:39 final size:36
Alignment explanation
Indices: 11465--11548 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 36
11455 TATAGAGCAA
*
11465 AAAAGAAAAAGAAGAGGAAAA-AGTAGATGGAGAGAAGAAG
1 AAAAG-AAAAGAAGAAGAAAAGAG--GATGGA-AGAAG-AG
11505 AAAAGAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
1 AAAAGAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
*
11541 AGAAGAAA
1 AAAAGAAA
11549 CGATGAAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 9 0.22
37 5 0.12
38 6 0.15
39 14 0.34
40 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (36 bp):
AAAAGAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
Found at i:12434 original size:38 final size:37
Alignment explanation
Indices: 12392--12473 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
12382 TATAGAGCAA
*
12392 AAAAGAAAAAGAAGAGGAAAA-AGTAGATGGAGAGAA-AG
1 AAAAGAAAAAGAAGAAGAAAAGAG--GATGGA-AGAAGAG
12430 AAAAG-AAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
1 AAAAGAAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
*
12466 AGAAGAAA
1 AAAAGAAA
12474 CGATGAAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 4 0.10
36 12 0.31
37 16 0.41
38 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.04
Consensus pattern (37 bp):
AAAAGAAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
Found at i:12457 original size:36 final size:36
Alignment explanation
Indices: 12392--12473 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
12382 TATAGAGCAA
*
12392 AAAAGAAAAAGAAGAGGAAAAAGTAGATGGAGAGAA-AG
1 AAAAG-AAAAGAAGAAGAAAAAG-AGATGGA-AGAAGAG
12430 AAAAGAAAAGAAGAAG-AAAAGAGGATGGAAGAAGAG
1 AAAAGAAAAGAAGAAGAAAAAGA-GATGGAAGAAGAG
*
12466 AGAAGAAA
1 AAAAGAAA
12474 CGATGAAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
35 5 0.12
36 20 0.50
37 10 0.25
38 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.04
Consensus pattern (36 bp):
AAAAGAAAAGAAGAAGAAAAAGAGATGGAAGAAGAG
Found at i:17981 original size:18 final size:19
Alignment explanation
Indices: 17957--17999 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17947 ATATAAAGAT
17957 ATATAAGTAAA-AT-AAATA
1 ATATAAG-AAATATCAAATA
*
17975 TTATAAGAAATATCAAATA
1 ATATAAGAAATATCAAATA
17994 ATATAA
1 ATATAA
18000 CATAGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 10 0.48
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
ATATAAGAAATATCAAATA
Found at i:21634 original size:18 final size:16
Alignment explanation
Indices: 21610--21652 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
21600 AATGTTAAGA
21610 ATTTTTTATTAAATTT
1 ATTTTTTATTAAATTT
21626 AAGTTTTTTA-TAAATTT
1 -A-TTTTTTATTAAATTT
21643 ATTTTTTATT
1 ATTTTTTATT
21653 GTATGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.29
16 2 0.08
17 8 0.33
18 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTTTTATTAAATTT
Found at i:21639 original size:17 final size:15
Alignment explanation
Indices: 21610--21651 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 15
21600 AATGTTAAGA
21610 ATTTTTTATTAAATTT
1 ATTTTTTA-TAAATTT
21626 AAGTTTTTTATAAATTT
1 -A-TTTTTTATAAATTT
21643 ATTTTTTAT
1 ATTTTTTAT
21652 TGTATGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.33
16 1 0.04
17 8 0.33
18 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTTTTTATAAATTT
Found at i:22177 original size:11 final size:11
Alignment explanation
Indices: 22161--22186 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22151 GTCGCCTCTT
22161 CCTTCGTTCTA
1 CCTTCGTTCTA
22172 CCTTCGTTCTA
1 CCTTCGTTCTA
22183 CCTT
1 CCTT
22187 TGCCTCCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:25217 original size:16 final size:16
Alignment explanation
Indices: 25196--25237 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
25186 TTATTAAATT
*
25196 ATATATTTTAATTATA
1 ATATATTTTAATAATA
25212 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
25227 AT-TATGTTTAA
1 ATATAT-TTTAA
25238 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:25222 original size:15 final size:15
Alignment explanation
Indices: 25187--25228 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25177 TTAAGAATTT
*
25187 TATTAAATTAT-ATA
1 TATTTAATTATAATA
25201 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
25215 TATTTAATAATAAT
1 TATTTAATTATAAT
25229 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:25368 original size:18 final size:17
Alignment explanation
Indices: 25340--25374 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25330 ATTATTAAGA
*
25340 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
25357 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
25375 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:25457 original size:157 final size:157
Alignment explanation
Indices: 25171--25480 Score: 557
Period size: 157 Copynumber: 2.0 Consensus size: 157
25161 ATAAGAATAT
* *
25171 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
*
25236 AAATATGATTAAAATATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
25301 TAATAATTTACCAAAACAAATTTCTAC
131 TAATAATTTACCAAAACAAATTTCTAC
*
25328 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATTTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
* *
25393 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAATAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
25458 TAATCATTTACCAAAACAAATTT
131 TAATAATTTACCAAAACAAATTT
25481 ATGCTAAGGG
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 146 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTCTAC
Found at i:25631 original size:16 final size:16
Alignment explanation
Indices: 25610--25677 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
25600 GATTTGCTAT
25610 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
25626 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
25642 TACAGCTCTAATCCAA
1 TACACCTCTAATCCAA
25658 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
25674 TACA
1 TACA
25678 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:26996 original size:16 final size:16
Alignment explanation
Indices: 26963--26996 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26953 GACAACTGTT
* *
26963 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
26979 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
26995 AA
1 AA
26997 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:29821 original size:21 final size:21
Alignment explanation
Indices: 29795--29835 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29785 AGACGAGCAA
* *
29795 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
29816 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
29836 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:34593 original size:16 final size:16
Alignment explanation
Indices: 34574--34606 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34564 TTTTTAAAAC
*
34574 TAATATTCCTTAATAA
1 TAATAGTCCTTAATAA
34590 TAATAGTCCTTAATAA
1 TAATAGTCCTTAATAA
34606 T
1 T
34607 TTAGTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATAGTCCTTAATAA
Done.