Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold635
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: 97374
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4748 original size:11 final size:11
Alignment explanation
Indices: 4732--4772 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
4722 ATTTCATATT
4732 TTTTTTCTTTC
1 TTTTTTCTTTC
4743 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
4756 TTCTTTCTTTC
1 TTTTTTCTTTC
4767 TTTTTT
1 TTTTTT
4773 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:4786 original size:24 final size:22
Alignment explanation
Indices: 4732--4786 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
4722 ATTTCATATT
**
4732 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
4754 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
4780 TTTTTTC
1 TTTTTTC
4787 AACCCATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 18 0.67
25 2 0.07
26 4 0.15
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTTTCTAAA
Found at i:5154 original size:24 final size:23
Alignment explanation
Indices: 5127--5173 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5117 CCACTCAATC
5127 GGAAAACCCACTTTGGTTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTTT
* **
5151 GGAAAGCCCCTTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTTT
5174 TTTTTTTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (23 bp):
GGAAAACCCCTTTGGTTTTTTTT
Found at i:6256 original size:21 final size:21
Alignment explanation
Indices: 6215--6258 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6205 CTCCCCTTTA
* *
6215 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
6236 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
6257 TC
1 TC
6259 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:10166 original size:15 final size:15
Alignment explanation
Indices: 10146--10176 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10136 ATTTCGTTTG
*
10146 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
10161 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
10176 G
1 G
10177 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:12026 original size:21 final size:21
Alignment explanation
Indices: 11980--12024 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
11970 AAGTTTTCAT
11980 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
12000 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
12022 TTT
1 TTT
12025 CAACTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:14259 original size:13 final size:13
Alignment explanation
Indices: 14241--14266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14231 CAATTTTTTG
14241 TGTATCGATACAT
1 TGTATCGATACAT
14254 TGTATCGATACAT
1 TGTATCGATACAT
14267 AATTGCTGTA
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:17095 original size:20 final size:20
Alignment explanation
Indices: 17048--17122 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
17038 AAAAAGACAT
* ** *
17048 AATGTATCGATACACTGTAG
1 AATGTATCGATACATTCAAA
* *
17068 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
17088 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
17108 AATGTATCGATACAT
1 AATGTATCGATACAT
17123 CAGGGTATGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:17116 original size:40 final size:39
Alignment explanation
Indices: 17045--17122 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
17035 GGTAAAAAGA
* *
17045 CATAATGTATCGATACACTGTAGAATATATCGATACATT
1 CATAATGTATCGATACACTGAAAAATATATCGATACATT
* * *
17084 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACACTGAAAAATATATCGATACAT
17123 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACACTGAAAAATATATCGATACATT
Found at i:17446 original size:19 final size:19
Alignment explanation
Indices: 17403--17473 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
17393 CACACCTAGA
* *
17403 TGTATCGATACATTATACTT
1 TGTATCGATACATGAT-CAT
*
17423 TGTATCGATACATGCTCAT
1 TGTATCGATACATGATCAT
17442 TGTATCGATACATGGA-CAAT
1 TGTATCGATACAT-GATC-AT
17462 TGTATCGATACA
1 TGTATCGATACA
17474 CGAAACTGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.36
20 29 0.64
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:17530 original size:20 final size:20
Alignment explanation
Indices: 17505--17557 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
17495 TACCACTGTT
* *
17505 TGTATCGATGCATGGT-ACAA
1 TGTATCGATACATGATGA-AA
17525 TGTATCGATACATGATGAAA
1 TGTATCGATACATGATGAAA
17545 TGTATCGATACAT
1 TGTATCGATACAT
17558 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:23743 original size:13 final size:13
Alignment explanation
Indices: 23725--23749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23715 CAACATTCCT
23725 TGTATCGATACAA
1 TGTATCGATACAA
23738 TGTATCGATACA
1 TGTATCGATACA
23750 TGGGTTACTA
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:25645 original size:20 final size:18
Alignment explanation
Indices: 25601--25661 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
25591 TTTTTTATTC
25601 TAAG-GGGAGAAAATTTT
1 TAAGAGGGAGAAAATTTT
25618 TAAGAGGGAGAAAATCTTTT
1 TAAGAGGGAGAAAA--TTTT
* *
25638 ATCAAGGGGGAGAAATTTTT
1 -T-AAGAGGGAGAAAATTTT
25658 TAAG
1 TAAG
25662 CATTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 4 0.11
18 12 0.32
19 1 0.03
20 8 0.22
21 1 0.03
22 11 0.30
ACGTcount: A:0.39, C:0.03, G:0.28, T:0.30
Consensus pattern (18 bp):
TAAGAGGGAGAAAATTTT
Found at i:26252 original size:13 final size:13
Alignment explanation
Indices: 26234--26258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26224 CATTATGCTT
26234 TGTATCGATACAA
1 TGTATCGATACAA
26247 TGTATCGATACA
1 TGTATCGATACA
26259 TGCTCATTGT
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:26255 original size:33 final size:32
Alignment explanation
Indices: 26213--26277 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
26203 ACACACCCAG
* *
26213 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATGAT-CATTGTATCGATACA
*
26246 ATGTATCGATACATGCTCATTGTATCGATACA
1 ATGTATCGATACATGATCATTGTATCGATACA
26278 TGGATAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATGATCATTGTATCGATACA
Found at i:26289 original size:20 final size:19
Alignment explanation
Indices: 26247--26297 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
26237 ATCGATACAA
* *
26247 TGTATCGATACATGCTCAT
1 TGTATCGATACATGATAAT
26266 TGTATCGATACATGGATAAT
1 TGTATCGATACAT-GATAAT
*
26286 TGTATCAATACA
1 TGTATCGATACA
26298 CGAAACTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:27585 original size:41 final size:41
Alignment explanation
Indices: 27544--27624 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
27534 TTAAAATATA
* *
27544 AAATTAATTAAAA-AT-ATTTAAATTTTATTTTTTATTTTAT
1 AAATTAATTAAAATATAATTTAAATTTT-TATATTATTTTAT
**
27584 AAATTTTTTAAAATATAATTTAAATTTTTATATTATTTTAT
1 AAATTAATTAAAATATAATTTAAATTTTTATATTATTTTAT
27625 TAACTGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 11 0.31
41 13 0.37
42 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (41 bp):
AAATTAATTAAAATATAATTTAAATTTTTATATTATTTTAT
Found at i:28537 original size:2 final size:2
Alignment explanation
Indices: 28530--28564 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
28520 TTACATGTGA
*
28530 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28565 GTTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29495 original size:15 final size:15
Alignment explanation
Indices: 29475--29503 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29465 TAAAAATTTA
29475 ATATTTAATTTTTTG
1 ATATTTAATTTTTTG
29490 ATATTTAATTTTTT
1 ATATTTAATTTTTT
29504 AATTTACCAA
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATATTTAATTTTTTG
Found at i:38195 original size:17 final size:17
Alignment explanation
Indices: 38173--38206 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38163 CAGTCAACTG
38173 AGTAAAAAAGAAAAAGA
1 AGTAAAAAAGAAAAAGA
* *
38190 AGTAAATAAGTAAAAGA
1 AGTAAAAAAGAAAAAGA
38207 TGGAGACAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (17 bp):
AGTAAAAAAGAAAAAGA
Found at i:38652 original size:21 final size:21
Alignment explanation
Indices: 38606--38653 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
38596 TTTTTAAAAA
* *
38606 AATAATGTATTTATATATTTT
1 AATATTGTATTTATATATTGT
*
38627 GATATTGTATTT-TATTATTGT
1 AATATTGTATTTATA-TATTGT
38648 AATATT
1 AATATT
38654 TAAGATATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (21 bp):
AATATTGTATTTATATATTGT
Found at i:39104 original size:17 final size:17
Alignment explanation
Indices: 39082--39128 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
39072 AATCCGTTAA
*
39082 ATTTAATTTAAATAATT
1 ATTTAATTTAAATAAAT
*
39099 ATTTAATAATAAA-AAAT
1 ATTTAAT-TTAAATAAAT
*
39116 ATTTTATTTAAAT
1 ATTTAATTTAAAT
39129 TTAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAATTTAAATAAAT
Found at i:48746 original size:22 final size:23
Alignment explanation
Indices: 48698--48747 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
48688 ATATTTTTTT
* *
48698 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAATAAACATA
48721 ATTTTTTAAAA-AAA-AAACATA
1 ATTTTTTAAAACAAATAAACATA
*
48742 AATTTT
1 ATTTTT
48748 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTTTTTAAAACAAATAAACATA
Found at i:49298 original size:17 final size:17
Alignment explanation
Indices: 49276--49311 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49266 CATTTCATAT
* *
49276 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
49293 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
49310 TT
1 TT
49312 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:50611 original size:32 final size:32
Alignment explanation
Indices: 50556--51094 Score: 893
Period size: 32 Copynumber: 16.8 Consensus size: 32
50546 AAAATGGTGA
* * *
50556 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
50588 TTTTAAATGGGTTACCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
50620 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
** *
50652 TTTGAAAAAGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
50684 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
50716 TTT-AGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
50748 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
50780 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
50812 TTTGAAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
50845 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
50877 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
50909 TTTGAAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
50941 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
50973 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
51005 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
51037 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
51069 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
51095 GATTTAAAAG
Statistics
Matches: 481, Mismatches: 23, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
31 14 0.03
32 434 0.90
33 33 0.07
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:51112 original size:27 final size:27
Alignment explanation
Indices: 51077--51815 Score: 1146
Period size: 27 Copynumber: 27.1 Consensus size: 27
51067 GCTTTGAAAT
* *
51077 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
51104 GGACGCCACGGAGTTGTGGAGTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51131 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
51158 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51185 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
51213 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
51240 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
51268 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
51295 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
51322 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51349 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
51377 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
51404 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
51432 GGGTG-CACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51458 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51485 GGGTGCCACGGAGTTGTGG-C-T-AAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
51509 -GGTGCCACGGAGTTGTAGGTCTTTTAAAA
1 GGGTGCCACGGAGTTGT-GGAC--TTAAAA
*
51538 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51565 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
51593 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
51620 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
51648 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51675 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
51702 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
51730 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
51757 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
51784 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
51812 GGGT
1 GGGT
51816 CACAGTACTA
Statistics
Matches: 656, Mismatches: 40, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
23 16 0.02
24 5 0.01
25 2 0.00
26 26 0.04
27 402 0.61
28 183 0.28
29 6 0.01
30 16 0.02
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:51369 original size:164 final size:163
Alignment explanation
Indices: 51080--51815 Score: 1169
Period size: 164 Copynumber: 4.5 Consensus size: 163
51070 TTGAAATGGG
* * ** *
51080 TGCCACAGAGTTGTGGATTTAAAAGGACGCCACGGAGTTGTGGAGTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
51145 TGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTA
51210 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
131 AAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GA
*
51244 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
51309 TGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTA
51374 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
131 AAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GA
*
51408 TGCCACGGAGTTATGGACTTAAAAGGGTG-CACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
51472 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-CT--AAA-GGTGCCACGGAGTTGTAGGTCTTT
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGT-GGAC-TT
* * *
51533 TAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGG
129 TAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
51568 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGA
* *
51633 GTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-T
64 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTT
* * *
51697 TAAAAGGGTGCCACGGAGTTGTGGTCTTTAAAAGGG
129 TAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGA
*
51733 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
51798 TGTGGACTTTAAAAGGGT
66 TGTGGAC-TTAAAAGGGT
51816 CACAGTACTA
Statistics
Matches: 537, Mismatches: 24, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
159 16 0.03
160 24 0.04
161 44 0.08
162 23 0.04
163 127 0.24
164 255 0.47
165 26 0.05
166 6 0.01
167 16 0.03
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (163 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTA
AAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:52854 original size:15 final size:15
Alignment explanation
Indices: 52836--52865 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52826 TGGGTGAAAA
52836 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
52851 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
52866 AGGATTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GGTTTTTTTTTTTTT
Found at i:59614 original size:10 final size:10
Alignment explanation
Indices: 59601--59630 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
59591 CCATTTCATA
59601 TTTTTTCTTT
1 TTTTTTCTTT
59611 TTTTTTCTTT
1 TTTTTTCTTT
*
59621 TTCTTTCTTT
1 TTTTTTCTTT
59631 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:59623 original size:16 final size:17
Alignment explanation
Indices: 59602--59636 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
59592 CATTTCATAT
*
59602 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
59618 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
59635 TT
1 TT
59637 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:68588 original size:3 final size:3
Alignment explanation
Indices: 68580--68605 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
68570 AAAAATCATT
68580 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
68606 GAGAAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:69907 original size:14 final size:14
Alignment explanation
Indices: 69888--69946 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
69878 TTTTTAAGTA
69888 AAATTTAATATATT
1 AAATTTAATATATT
*
69902 AAATTTAAATATTTT
1 AAATTT-AATATATT
*
69917 AAATTAAGAATATATT
1 AAATT--TAATATATT
69933 AAATATT-ATATATT
1 AAAT-TTAATATATT
69947 TAATAATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 13 0.35
15 12 0.32
16 11 0.30
17 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATTTAATATATT
Found at i:69945 original size:16 final size:15
Alignment explanation
Indices: 69888--69949 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
69878 TTTTTAAGTA
69888 AAATTT-AATATATT
1 AAATTTAAATATATT
*
69902 AAATTTAAATATTTT
1 AAATTTAAATATATT
*
69917 AAATTAAGAATATATT
1 AAATTTA-AATATATT
*
69933 AAATATTATATAT-TT
1 AAAT-TTAAATATATT
69948 AA
1 AA
69950 TAATATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.15
15 17 0.43
16 15 0.38
17 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AAATTTAAATATATT
Found at i:69951 original size:14 final size:14
Alignment explanation
Indices: 69895--69959 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
69885 GTAAAATTTA
69895 ATATATTAAATTTAA-
1 ATATATTAAA--TAAT
* *
69910 ATATTTTAAATTAAGA
1 ATATATTAAA-TAA-T
*
69926 ATATATTAAATATT
1 ATATATTAAATAAT
*
69940 ATATATTTAATAAT
1 ATATATTAAATAAT
69954 ATATAT
1 ATATAT
69960 AATAATTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
14 22 0.52
15 11 0.26
16 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATATTAAATAAT
Found at i:72006 original size:23 final size:22
Alignment explanation
Indices: 71962--72006 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
71952 AAATTGTTCA
*
71962 TCATATATTTTTTTACTGATAC
1 TCATATATTTTTTTACTAATAC
* *
71984 TCATGTATTTTTTATGCTAATAC
1 TCATATATTTTTT-TACTAATAC
72007 GTGTCCCGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (22 bp):
TCATATATTTTTTTACTAATAC
Found at i:80561 original size:27 final size:27
Alignment explanation
Indices: 80527--80584 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
80517 CATTTCTTCA
80527 TGTA-TCGATACAATGTATCGATACAT
1 TGTACTCGATACAATGTATCGATACAT
*
80553 TGTACTCGATACAATGTATCGATGCAT
1 TGTACTCGATACAATGTATCGATACAT
80580 TGTAC
1 TGTAC
80585 CATGTATCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (27 bp):
TGTACTCGATACAATGTATCGATACAT
Found at i:80583 original size:13 final size:13
Alignment explanation
Indices: 80526--80575 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
80516 ACATTTCTTC
80526 ATGTATCGATACA
1 ATGTATCGATACA
80539 ATGTATCGATACA
1 ATGTATCGATACA
*
80552 TTGTACTCGATACA
1 ATGTA-TCGATACA
80566 ATGTATCGAT
1 ATGTATCGAT
80576 GCATTGTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 22 0.65
14 12 0.35
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:80653 original size:20 final size:19
Alignment explanation
Indices: 80628--80700 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
80618 CTGCCAGTTT
**
80628 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
80648 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
80667 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
80687 CATGTATCGATACA
1 CATGTATCGATACA
80701 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:81789 original size:18 final size:19
Alignment explanation
Indices: 81757--81792 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
81747 ATCAAAACAT
81757 AAATATGTCACAAATATAC
1 AAATATGTCACAAATATAC
*
81776 AAATGTGTCA-AAATATA
1 AAATATGTCACAAATATA
81793 TATAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (19 bp):
AAATATGTCACAAATATAC
Found at i:82423 original size:2 final size:2
Alignment explanation
Indices: 82321--82406 Score: 61
Period size: 2 Copynumber: 43.0 Consensus size: 2
82311 ATCTTCGGTG
* * * * *
82321 TA TA TA TA -A TA TG CA TA TA TA TA TA TA TA TA TA AA GTG CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
82363 TA TA TA GCA T- TA GTA TA TA CA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82405 TA
1 TA
82407 CACACACAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
1 3 0.05
2 58 0.91
3 3 0.05
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (2 bp):
TA
Found at i:91671 original size:300 final size:296
Alignment explanation
Indices: 91208--91803 Score: 1005
Period size: 300 Copynumber: 2.0 Consensus size: 296
91198 TTTAGGAGCA
* * *
91208 TGCATTTGAGGTAATAAACAATGAGTAACTTTAATAAGATCCTATTTTCCGTTCAGCAGTCTTGT
1 TGCATTTGAGATAATAAACAATGAGTAACCTCAATAAGATCCTATTTTCCGTTCAGCAGTCTTGT
91273 TTTGTTGTGGACTGTAATAATAAGATTGAATCATAACATATGCATGAAGGTATCTAGGAGTTAGA
66 TTTGTTGTGGACTGTAATAATAAGATTGAATCATAACATATGCATGAAGGTATCTAGGAGTTAGA
* *
91338 AAATATTCTTGAGCATTATAATTGTGAAGTACTCAAATAGAGAGATTAAATTGAGATTAATTTCA
131 AAATATTCTTGAGCATCATAATTGTAAAGTACTCAAATAGAGAGATTAAATTGAGATTAATTTCA
*
91403 GCACACAAGGCA-ATGAAATTGAAAACAACTGAGAACAATCTTTCATTAGATAAAACCATGTAAC
196 GCACAAAAGGCACATGAAATTGAAAACAACTGAGAACAATCTTTCATTAGATAAAACCATGTAAC
91467 ACAAGAATAATCATCCACAAAGGCAACAAAGTAGTG
261 ACAAGAATAATCATCCACAAAGGCAACAAAGTAGTG
* **
91503 TGCATTTGAGATAATAAACAATGAGTGACCTCAATAAGATCCTATTTTTCCGTTCAGTGGTCTTG
1 TGCATTTGAGATAATAAACAATGAGTAACCTCAATAAGATCCTA-TTTTCCGTTCAGCAGTCTTG
* * * *
91568 TTTTGTTGTGGAGTGTAATTATAAGATTGAATCATACCATACTCGTGCATGAAGGTATTTAGGAG
65 TTTTGTTGTGGACTGTAATAATAAGATTGAATCATAACATA----TGCATGAAGGTATCTAGGAG
*
91633 TTGGAAAATATTCTTGAGCATCATAATTGTAAAGTACTCAAATAGAGAGATTAAATTGAGATTAA
126 TTAGAAAATATTCTTGAGCATCATAATTGTAAAGTACTCAAATAGAGAGATTAAATTGAGATTAA
*
91698 TTTCAGCACAAAAGGCACATGAAATTGAAAACATCTGAGAACAATCTTTCATTAGATAAAACCAT
191 TTTCAGCACAAAAGGCACATGAAATTGAAAACAACTGAGAACAATCTTTCATTAGATAAAACCAT
91763 GTAACACAAGAATAATCATCCACAAAGGCAACAAAGTAGTG
256 GTAACACAAGAATAATCATCCACAAAGGCAACAAAGTAGTG
91804 AAATCCCAAT
Statistics
Matches: 280, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
295 40 0.14
296 56 0.20
300 97 0.35
301 87 0.31
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (296 bp):
TGCATTTGAGATAATAAACAATGAGTAACCTCAATAAGATCCTATTTTCCGTTCAGCAGTCTTGT
TTTGTTGTGGACTGTAATAATAAGATTGAATCATAACATATGCATGAAGGTATCTAGGAGTTAGA
AAATATTCTTGAGCATCATAATTGTAAAGTACTCAAATAGAGAGATTAAATTGAGATTAATTTCA
GCACAAAAGGCACATGAAATTGAAAACAACTGAGAACAATCTTTCATTAGATAAAACCATGTAAC
ACAAGAATAATCATCCACAAAGGCAACAAAGTAGTG
Done.