Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1513
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: 32728
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:587 original size:52 final size:51
Alignment explanation
Indices: 307--588 Score: 234
Period size: 51 Copynumber: 5.4 Consensus size: 51
297 AATTCTCCAC
* * *
307 ATCGGGGATTATTCCAACTCCGATTTTATTT-C-AAAACACTTAATTTTCTATA
1 ATCGGGGA-TACTCCAACTCCGATTTTATTTCCAAAAACAC-CAATTTTC-ACA
*
359 AT-GGGGATACTCTAACGTATCCGATTTTATTTCCAAACAAACACCAATTTCTTCACA
1 ATCGGGGATACTCCAAC---TCCGATTTTATTTCC-AA-AAACACCAA-TT-TTCACA
* * ** * *
416 ATCGGGGATACTCCAACCCCG-GTTTATCACTAAAAACACTAATTTTCCACA
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTT-CACA
* * * * **
467 ATCGGGGATACTCCAA-TCCCGGTTTTATTTTC-AAAACGCCAATTTCCTTTA
1 ATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAATTTTC-ACA
*
518 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTCACA
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTCACA
*
569 ATCGAGGATTACTCCAACTC
1 ATCGGGGA-TACTCCAACTC
589 GTTATTTTCA
Statistics
Matches: 183, Mismatches: 30, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
50 10 0.05
51 78 0.43
52 39 0.21
53 15 0.08
54 7 0.04
55 3 0.02
56 3 0.02
57 12 0.07
58 16 0.09
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.32
Consensus pattern (51 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTCACA
Found at i:5456 original size:13 final size:13
Alignment explanation
Indices: 5438--5462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5428 CAAAGATCAG
5438 TGTATCGATACAA
1 TGTATCGATACAA
5451 TGTATCGATACA
1 TGTATCGATACA
5463 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5544 original size:13 final size:13
Alignment explanation
Indices: 5526--5550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5516 AAAAAAAATA
5526 TGTATCGATACAT
1 TGTATCGATACAT
5539 TGTATCGATACA
1 TGTATCGATACA
5551 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6085 original size:13 final size:13
Alignment explanation
Indices: 6067--6091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6057 GGAAATTCAA
6067 TGTATCGATACAC
1 TGTATCGATACAC
6080 TGTATCGATACA
1 TGTATCGATACA
6092 GGGGGATTAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:8679 original size:20 final size:20
Alignment explanation
Indices: 8650--8705 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
8640 GGCAGTAGCC
*
8650 AAATTGTATCGATACAC-CA
1 AAATTGTATCGATACACAAA
*
8669 AAGTATGTATCGATACACAAA
1 AAAT-TGTATCGATACACAAA
8690 AAATTGTATCGATACA
1 AAATTGTATCGATACA
8706 TTGGCTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.09
20 25 0.78
21 4 0.12
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (20 bp):
AAATTGTATCGATACACAAA
Found at i:15478 original size:10 final size:8
Alignment explanation
Indices: 15449--15479 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
15439 TATAGTATGA
15449 TATATATT
1 TATATATT
15457 TATATATT
1 TATATATT
*
15465 TATATATG
1 TATATATT
15473 TATATAT
1 TATATAT
15480 GTTTTTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
TATATATT
Found at i:15480 original size:8 final size:8
Alignment explanation
Indices: 15438--15481 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
15428 ATCTTTAATG
15438 GTATAGTAT
1 GTATA-TAT
15447 GATATATAT
1 G-TATATAT
*
15456 TTATATAT
1 GTATATAT
*
15464 TTATATAT
1 GTATATAT
15472 GTATATAT
1 GTATATAT
15480 GT
1 GT
15482 TTTTAGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 24 0.75
9 4 0.12
10 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
GTATATAT
Found at i:17240 original size:13 final size:13
Alignment explanation
Indices: 17222--17247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17212 CAATTTTTTG
17222 TGTATCGATACAT
1 TGTATCGATACAT
17235 TGTATCGATACAT
1 TGTATCGATACAT
17248 ACTTACTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17975 original size:21 final size:21
Alignment explanation
Indices: 17934--17977 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17924 CTTCCCTTTA
* *
17934 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
17955 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
17976 TC
1 TC
17978 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:19802 original size:13 final size:13
Alignment explanation
Indices: 19784--19822 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
19774 ATAATCACCC
19784 TGTATCGATACAA
1 TGTATCGATACAA
19797 TGTATCGATACAA
1 TGTATCGATACAA
19810 TGTATCGATACAA
1 TGTATCGATACAA
19823 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:21913 original size:15 final size:15
Alignment explanation
Indices: 21893--21923 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21883 ATTTCGTTTG
*
21893 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
21908 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
21923 G
1 G
21924 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:23756 original size:21 final size:21
Alignment explanation
Indices: 23727--23771 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23717 AAGTTTTCAT
*
23727 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
23747 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
23769 TTT
1 TTT
23772 CATCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:26099 original size:34 final size:35
Alignment explanation
Indices: 26061--26127 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
26051 CCTTACAACA
26061 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
26095 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
26128 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:26603 original size:13 final size:13
Alignment explanation
Indices: 26585--26610 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26575 CAATTTTTTG
26585 TGTATCGATACAT
1 TGTATCGATACAT
26598 TGTATCGATACAT
1 TGTATCGATACAT
26611 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26675 original size:21 final size:21
Alignment explanation
Indices: 26649--26724 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
26639 CTGCCAAGAA
26649 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
26670 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
26690 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
*
26711 ATATATCGATACAT
1 ATGTATCGATACAT
26725 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:26694 original size:20 final size:20
Alignment explanation
Indices: 26669--26742 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
26659 ACATCTTTTT
26669 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
26689 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
*
26710 CATATATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
26730 CATGTATCGATAC
1 CATGTATCGATAC
26743 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:26706 original size:41 final size:41
Alignment explanation
Indices: 26649--26742 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
26639 CTGCCAAGAA
*
26649 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATATATCGATACATTGCAAC
26690 ATGTATCGATACATCTTTTTCATATATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATATATCGATACATTGCAAC
26731 ATGTATCGATAC
1 ATGTATCGATAC
26743 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATATATCGATACATTGCAAC
Found at i:28538 original size:13 final size:13
Alignment explanation
Indices: 28520--28544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28510 ACTGAAGCAA
28520 TGTATCGATACAT
1 TGTATCGATACAT
28533 TGTATCGATACA
1 TGTATCGATACA
28545 ATCTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:30143 original size:84 final size:84
Alignment explanation
Indices: 29988--30152 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
29978 CATTTTCCAC
* * * *
29988 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAGGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAGGAATTATTCTCTAAAC
30053 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
30072 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTTCAA-GAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAGGAAT-T-ATTCTCTA
* * *
30134 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
30153 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 4 0.06
83 11 0.16
84 54 0.78
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAGGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:31719 original size:34 final size:35
Alignment explanation
Indices: 31681--31747 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
31671 CCTTACAACA
31681 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
31715 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
31748 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:32221 original size:13 final size:13
Alignment explanation
Indices: 32203--32228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32193 ACAATTTTTG
32203 TGTATCGATACAT
1 TGTATCGATACAT
32216 TGTATCGATACAT
1 TGTATCGATACAT
32229 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:32225 original size:32 final size:32
Alignment explanation
Indices: 32184--32246 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
32174 TACAAGCCAA
**
32184 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
32216 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
32247 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:32291 original size:20 final size:20
Alignment explanation
Indices: 32266--32341 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
32256 ACTGCCAAGA
32266 ATGTATCGATACATCTTTTC
1 ATGTATCGATACATCTTTTC
***
32286 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCT-TTTC
32306 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATC-TTTTC
*
32327 ATATATCGAGTACAT
1 ATGTATCGA-TACAT
32342 TGCAACATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.02
20 29 0.64
21 9 0.20
22 6 0.13
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATCTTTTC
Found at i:32321 original size:40 final size:42
Alignment explanation
Indices: 32266--32359 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
32256 ACTGCCAAGA
*
32266 ATGTATCGATACATC-TTTTCATGTATCGA-TACATTGCAAC
1 ATGTATCGATACATCTTTTTCATATATCGAGTACATTGCAAC
32306 ATGTATCGATACATCTTTTTCATATATCGAGTACATTGCAAC
1 ATGTATCGATACATCTTTTTCATATATCGAGTACATTGCAAC
32348 ATGTATCGATAC
1 ATGTATCGATAC
32360 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 15 0.29
41 13 0.25
42 23 0.45
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTCATATATCGAGTACATTGCAAC
Found at i:32354 original size:21 final size:20
Alignment explanation
Indices: 32285--32359 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 20
32275 TACATCTTTT
32285 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
32305 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
*
32326 CATATATCGAGTACATTGCAA
1 CATGTATCGA-TACATTGCAA
32347 CATGTATCGATAC
1 CATGTATCGATAC
32360 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 18 0.42
21 20 0.47
22 5 0.12
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Done.