Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3251
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: 33089
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Found at i:11128 original size:43 final size:43
Alignment explanation
Indices: 10989--11160 Score: 190
Period size: 43 Copynumber: 4.0 Consensus size: 43
10979 ACATAGGATC
* * *
10989 CGATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
*
11032 CGACT-TATGATTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGA-TATTTGATTT-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
11076 CG-TACTTGATTTTGTGTAAGACC-CTGTCTGGGACAG-TGGTAT
1 CGATATTTGATTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* * *
11118 TGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
11161 TATATGAGCT
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 27 0.25
43 47 0.44
44 33 0.31
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:11157 original size:85 final size:87
Alignment explanation
Indices: 10998--11160 Score: 235
Period size: 85 Copynumber: 1.9 Consensus size: 87
10988 CCGATATGTG
*
10998 TTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGACTTATGATTTACGTGTAAGACCACGTCT
1 TTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCT
11063 GGGACGTTGGCATCGTACTTGA
66 GGGACGTTGGCATCGTACTTGA
* * * *
11085 TTTT-GTGTAAGACCCTGTCTGGGACAG-TGGTATTGA-TATTTGA-TTACATGTAAGACCACGT
1 TTTTCGTGTAAGACCATGTCTGGGAC-GTTGGCATCGACT-TATGATTTACATGTAAGACCACGT
11146 CTGGGACGTTGGCAT
64 CTGGGACGTTGGCAT
11161 TATATGAGCT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
85 33 0.48
86 31 0.45
87 5 0.07
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (87 bp):
TTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCT
GGGACGTTGGCATCGTACTTGA
Found at i:13252 original size:46 final size:46
Alignment explanation
Indices: 13202--13377 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
13192 TGTTTGGGCA
13202 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13248 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
13293 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * **
13341 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13378 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13357 original size:93 final size:93
Alignment explanation
Indices: 13198--13368 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
13188 AGGATGTTTG
* *
13198 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
13263 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
13291 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
13356 TTGAGTCCGAGTT
66 TTGAGTCCGAGTT
13369 TGCTTATGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:19447 original size:6 final size:6
Alignment explanation
Indices: 19410--19521 Score: 70
Period size: 6 Copynumber: 18.3 Consensus size: 6
19400 AAGAAACATT
* *
19410 ATCAGA A-CTAGA ATCAAA ATAAGA CA-CAGA ATCAGA ATCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA -ATCAGA ATCAGA ATCAGA ATCAGA
* * * * *
19458 ATCAGA ATCAAA ATTAG- GTGACAGA ATTAGA ATCAGT ATCAGGTA AT-AGA
1 ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
19508 ATCAAA ATCAGA AT
1 ATCAGA ATCAGA AT
19522 GTGAATGCAA
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
5 6 0.08
6 65 0.81
7 6 0.08
8 3 0.04
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:19501 original size:25 final size:25
Alignment explanation
Indices: 19454--19517 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
19444 GAATCAGAAT
*
19454 CAGAATCAGAATCAAAATTAGGTGA
1 CAGAATCAGAATCAAAATCAGGTGA
* ** *
19479 CAGAATTAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAAAATCAGGTGA
* *
19504 TAGAATCAAAATCA
1 CAGAATCAGAATCA
19518 GAATGTGAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.22
Consensus pattern (25 bp):
CAGAATCAGAATCAAAATCAGGTGA
Found at i:19696 original size:27 final size:28
Alignment explanation
Indices: 19640--19702 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
19630 GTGAGGCTGC
*
19640 CAGATAT-TGTGACGAAGTCACCAGATA
1 CAGATATATGTGACGAAGCCACCAGATA
* *
19667 CAGATATATGTGGCGAGGCCACCAGA-A
1 CAGATATATGTGACGAAGCCACCAGATA
19694 CAGATATAT
1 CAGATATAT
19703 ATATGTGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (28 bp):
CAGATATATGTGACGAAGCCACCAGATA
Found at i:20505 original size:27 final size:27
Alignment explanation
Indices: 20441--20578 Score: 134
Period size: 27 Copynumber: 5.1 Consensus size: 27
20431 TAAGGGTAAA
* * *
20441 TCGGTAGTCCTACCCTGCAGGGGTATT
1 TCGGTATTTCTACCCTACAGGGGTATT
** *
20468 TTAGTAATTCTACCCTACAGGGGTATT
1 TCGGTATTTCTACCCTACAGGGGTATT
* * *
20495 TCGGTATTTCTACTCAACAAGGGTATT
1 TCGGTATTTCTACCCTACAGGGGTATT
* *
20522 TCGATATTTCTACCCTAC-GAAGGTATT
1 TCGGTATTTCTACCCTACAG-GGGTATT
* **
20549 TTGGTATTTCTACCCTACAAAGGTATT
1 TCGGTATTTCTACCCTACAGGGGTATT
20576 TCG
1 TCG
20579 AAAATTTTGT
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
TCGGTATTTCTACCCTACAGGGGTATT
Found at i:20577 original size:54 final size:54
Alignment explanation
Indices: 20475--20579 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
20465 ATTTTAGTAA
* * *
20475 TTCTACCCTACAGGGGTATTTCGGTATTTCTACTCAACAAGGGTATTTCGATAT
1 TTCTACCCTACAGAGGTATTTCGGTATTTCTACCCAACAAAGGTATTTCGATAT
* *
20529 TTCTACCCTAC-GAAGGTATTTTGGTATTTCTACCCTACAAAGGTATTTCGA
1 TTCTACCCTACAG-AGGTATTTCGGTATTTCTACCCAACAAAGGTATTTCGA
20580 AAATTTTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
53 1 0.02
54 44 0.98
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (54 bp):
TTCTACCCTACAGAGGTATTTCGGTATTTCTACCCAACAAAGGTATTTCGATAT
Found at i:20653 original size:27 final size:26
Alignment explanation
Indices: 20623--20832 Score: 206
Period size: 27 Copynumber: 7.8 Consensus size: 26
20613 TATAAACTGG
* *
20623 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAATC-A
** **
20650 GGGTATTTCAGTAATTTTACAGGTCGA
1 GGGTATTTTGGTAATTTTACAAATC-A
** *
20677 GGGTATTTCAGTAATTTCACAAATCA
1 GGGTATTTTGGTAATTTTACAAATCA
*
20703 GGGGTATTTTGGTAATTTTACAAACTAA
1 -GGGTATTTTGGTAATTTTACAAA-TCA
*
20731 GGGTATTTTGGTAATTTTACAAACCA
1 GGGTATTTTGGTAATTTTACAAATCA
* * *
20757 GGGGTATTTTCGTAATTTTATAAACCAA
1 -GGGTATTTTGGTAATTTTACAAATC-A
*
20785 GGGTATTTTAGTAA-TTTACAAATCA
1 GGGTATTTTGGTAATTTTACAAATCA
*
20810 GGGGTATTTTGGTAATTCTACAA
1 -GGGTATTTTGGTAATTTTACAA
20833 CTTATCCACT
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.01
26 23 0.15
27 130 0.83
28 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAATCA
Found at i:20762 original size:81 final size:81
Alignment explanation
Indices: 20622--20832 Score: 232
Period size: 81 Copynumber: 2.6 Consensus size: 81
20612 CTATAAACTG
* * * ** ***
20622 GGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTACAGGTCGAGGGTA-TTTC
1 GGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTC
*
20686 AGTAATTTCACAAATCA
66 -GTAATTTCACAAACCA
20703 GGGGTATTTTGGTAATTTTACAAA-CTAAGGGTATTTTGGTAATTTTACAAACC-AGGGGTATTT
1 GGGGTATTTTGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTACAAACCGA-GGGTATTT
* *
20766 TCGTAATTTTATAAACCA
64 TCGTAATTTCACAAACCA
* * * *
20784 AGGGTATTTTAGTAA-TTTACAAATCAGGGGTATTTTGGTAATTCTACAA
1 GGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAA
20833 CTTATCCACT
Statistics
Matches: 111, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
80 32 0.29
81 75 0.68
82 4 0.04
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (81 bp):
GGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTC
GTAATTTCACAAACCA
Found at i:24653 original size:40 final size:40
Alignment explanation
Indices: 24569--24752 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
24559 TTGAATGCTG
* * * *
24569 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
24608 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
24649 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
24689 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
24729 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
24753 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:24706 original size:80 final size:81
Alignment explanation
Indices: 24569--24749 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
24559 TTGAATGCTG
* * *
24569 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
24633 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
24649 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
24710 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
24729 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
24750 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:24773 original size:39 final size:38
Alignment explanation
Indices: 24650--24799 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
24640 GTTATTAATT
* ** * *
24650 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
24690 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
24729 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
24769 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
24800 GAGCTATATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:24807 original size:40 final size:39
Alignment explanation
Indices: 24690--24812 Score: 97
Period size: 40 Copynumber: 3.1 Consensus size: 39
24680 GATACTAATT
* ** ** *
24690 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
24729 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
24769 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
24809 CCGG
1 CCGG
24813 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.36
40 44 0.64
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Found at i:32201 original size:40 final size:39
Alignment explanation
Indices: 32105--32204 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 39
32095 CTCATTCAAT
* * *
32105 GCCTTCGGGACTTAACCCGGATTTTTAAAACTCCACGAAT
1 GCCTTCGGGACTTAACCCGGA-TATTAAAACTCCACAAAG
* *
32145 GCGCTTCGGGAC-TAACCCGGA-ATTAGTATCTCGCACAAAG
1 GC-CTTCGGGACTTAACCCGGATATTA-AAACTC-CACAAAG
32185 GCCTTCGGGACTTAACCCGG
1 GCCTTCGGGACTTAACCCGG
32205 GGAATTAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
38 3 0.06
39 13 0.25
40 26 0.51
41 9 0.18
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (39 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCCACAAAG
Done.