Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1612
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: 21633
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:5437 original size:23 final size:24
Alignment explanation
Indices: 5389--5438 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
5379 TATTTTTTTA
* *
5389 TTTTTTAAAACAAATAAAGATCAT
1 TTTTTTAAAACAAATAAACATAAT
*
5413 TTTTTTAAAA-AAA-AAACATAAA
1 TTTTTTAAAACAAATAAACATAAT
5435 TTTT
1 TTTT
5439 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 3 0.13
24 10 0.43
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTTTTAAAACAAATAAACATAAT
Found at i:7285 original size:32 final size:32
Alignment explanation
Indices: 7236--7544 Score: 461
Period size: 32 Copynumber: 9.8 Consensus size: 32
7226 AAAATGGTGA
* * *
7236 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
7268 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
7300 TTTTAAGTGGGTTGCCACCAACTTCTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
7332 TTTG-AATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
7363 TTTGAAATGGGTTGCCA-CGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
7394 TTTGAAATGGGTTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TTGCCACCGACTTGTGTGGGC
7427 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
7459 TTTGGAATGGGTTGCCACCGACTTGTGT-GG-
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
7489 TTT-AAATGGGTTGCCACCG-CTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
7519 TTTGGAATGGGTTGCCACCGA-TTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
7545 GATTTAAAAG
Statistics
Matches: 256, Mismatches: 14, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
28 7 0.03
29 17 0.07
30 6 0.02
31 75 0.29
32 126 0.49
33 25 0.10
ACGTcount: A:0.15, C:0.19, G:0.34, T:0.32
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:7620 original size:53 final size:54
Alignment explanation
Indices: 7531--8406 Score: 1382
Period size: 53 Copynumber: 16.5 Consensus size: 54
7521 TGGAATGGGT
* *
7531 TGCCACCGA-TTGTGGATTTAAAAGGGATGCCAC-GAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
7584 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC-GAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
7637 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC-GAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
7691 TGCCACGGAGTTGTGGACTTAAAAGGGAGCCAC-GAGTTGTGGACTTAAAA-GA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
7743 TGCCACAG-GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
7795 TGCCACGGAGTTGTGG-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
7848 ATGCCACGGAGTTGTGGACTTAAAA-GGTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
7902 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
7956 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
8011 TGCCACGGAGTTGTGGACTTAAAA-GGTGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGG-G
8065 TGCCAC--AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
8117 TGCCAC-GAGTTGTGGACTTAAAA-GG-ACCA-TGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
8167 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
8221 TGCCAC-GAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
8274 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
8329 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCAC--AGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
8382 TGCCAC-GAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
8407 AAAATGCCAC
Statistics
Matches: 779, Mismatches: 22, Indels: 45
0.92 0.03 0.05
Matches are distributed among these distances:
50 26 0.03
51 46 0.06
52 105 0.13
53 264 0.34
54 210 0.27
55 128 0.16
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:7627 original size:26 final size:27
Alignment explanation
Indices: 7531--8406 Score: 1382
Period size: 27 Copynumber: 32.9 Consensus size: 27
7521 TGGAATGGGT
* *
7531 TGCCACCGA-TTGTGGATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7557 ATGCCAC-GAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
7584 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7611 TGCCAC-GAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7637 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
7665 TGCCAC-GAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7691 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
7718 AGCCAC-GAGTTGTGGACTTAAAA-GA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
7743 TGCCACAG-GTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7769 TGCCACGGAGTTGTGGACTT-AAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7795 TGCCACGGAGTTGTGG-CTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7821 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7848 ATGCCACGGAGTTGTGGACTTAAAA-GG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
7875 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7902 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7929 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
7956 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
7984 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8011 TGCCACGGAGTTGTGGACTTAAAA-GG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
8037 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
8065 TGCCAC--AGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8090 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8117 TGCCAC-GAGTTGTGGACTTAAAA-GG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
8142 -ACCA-TGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8167 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8194 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8221 TGCCAC-GAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
8247 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
8274 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
8302 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
8329 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
8357 TGCCAC--AGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
8382 TGCCAC-GAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
8407 AAAATGCCAC
Statistics
Matches: 798, Mismatches: 23, Indels: 56
0.91 0.03 0.06
Matches are distributed among these distances:
24 20 0.03
25 49 0.06
26 254 0.32
27 361 0.45
28 114 0.14
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:8429 original size:30 final size:30
Alignment explanation
Indices: 8381--8437 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
8371 ACTTAAAAGG
*
8381 ATGCCACGAGTTGTGGACTTT-AAAAGAAA
1 ATGCCACGAGTCGTGGACTTTGAAAAGAAA
8410 ATGCCACTGAGTCGTGGACTTTGAAAAG
1 ATGCCAC-GAGTCGTGGACTTTGAAAAG
8438 GTCACAGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (30 bp):
ATGCCACGAGTCGTGGACTTTGAAAAGAAA
Found at i:16244 original size:10 final size:10
Alignment explanation
Indices: 16231--16260 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16221 CCATTTCATA
16231 TTTTTTCTTT
1 TTTTTTCTTT
16241 TTTTTTCTTT
1 TTTTTTCTTT
*
16251 TTCTTTCTTT
1 TTTTTTCTTT
16261 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:16253 original size:16 final size:17
Alignment explanation
Indices: 16232--16266 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16222 CATTTCATAT
*
16232 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
16248 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
16265 TT
1 TT
16267 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:17426 original size:48 final size:45
Alignment explanation
Indices: 17374--17488 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 45
17364 ATGTGCCATT
* * *
17374 TCAAGGTCAACGACATCGGACTAAGGAAAAGTGGACCAATGTGCTGAC
1 TCAAGGCCAGCGACATCGGACTAA-GAAAAGT-G-CCAATATGCTGAC
* * * * *
17422 TCAAGGCCAGCGACATTGGGCTTAGAAAGGTGCCAATATGCTGAT
1 TCAAGGCCAGCGACATCGGACTAAGAAAAGTGCCAATATGCTGAC
*
17467 TCAAGGCCAGCGATATCGGACT
1 TCAAGGCCAGCGACATCGGACT
17489 TTAAGATGAC
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
45 30 0.54
46 1 0.02
47 6 0.11
48 19 0.34
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (45 bp):
TCAAGGCCAGCGACATCGGACTAAGAAAAGTGCCAATATGCTGAC
Found at i:17558 original size:32 final size:32
Alignment explanation
Indices: 17510--17969 Score: 738
Period size: 32 Copynumber: 14.6 Consensus size: 32
17500 AAAATGGTGA
* *
17510 TTTGAAA-GGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
17541 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
17573 TTTTAAAT-GGTTGCCACCAACTTGTG-GGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
17603 -TTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
17634 TTTGAAATGGGTTGCCACCTACTTGTG-GGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
17665 TTT-AGAATGGGTTGCCACCGACTTGTGTTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTG-TGGGC
17698 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
17730 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
17762 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
17794 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
17826 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
17858 TTTG-AATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
17889 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
17921 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
17953 TTTGGAATGGG-TGCCAC
1 TTTGAAATGGGTTGCCAC
17970 GATTTGGAAT
Statistics
Matches: 409, Mismatches: 11, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
29 5 0.01
30 22 0.05
31 91 0.22
32 261 0.64
33 29 0.07
34 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:18027 original size:27 final size:27
Alignment explanation
Indices: 17961--18791 Score: 1210
Period size: 27 Copynumber: 31.0 Consensus size: 27
17951 GCTTTGGAAT
*
17961 GGGTGCCAC-GA-TT-TGGAATTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17985 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
18013 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
18040 GGGTGCCAC--A---G-ACAC-TAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18060 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
18088 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
18115 -GATGCCACAGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18141 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
18168 GGGTGCTACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18195 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
18222 GGGATGCCATGGAGTTATGGACTT-AAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
18249 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18276 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18303 GGGTGCCACGGAGTTGTGGA-TTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
18329 GGAATGCCACAG-GTTGTGGACTTAAAA
1 GG-GTGCCACGGAGTTGTGGACTTAAAA
18356 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18383 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18410 GGGTGCCACGGAGTTGTGGTA-TTAAAA
1 GGGTGCCACGGAGTTGTGG-ACTTAAAA
* *
18437 GGAATGCCACAGAGTTGTGGACTTAAAA
1 GG-GTGCCACGGAGTTGTGGACTTAAAA
18465 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18492 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
18519 GGAATGCCA--GAGTTGTGGACTTAAAA
1 GG-GTGCCACGGAGTTGTGGACTTAAAA
18545 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
18572 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
18599 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
18626 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
18653 GGGTACCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
18681 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
18708 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
18736 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
18763 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
18791 G
1 G
18792 AAAATGCCAC
Statistics
Matches: 735, Mismatches: 45, Indels: 50
0.89 0.05 0.06
Matches are distributed among these distances:
20 14 0.02
21 2 0.00
22 2 0.00
24 3 0.00
25 13 0.02
26 88 0.12
27 473 0.64
28 140 0.19
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:20151 original size:21 final size:20
Alignment explanation
Indices: 20109--20158 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
20099 CATGTCCTCG
*
20109 TTTTTTTTTTGTTGTTCCCT
1 TTTTTTTTTTGTTGTTCACT
20129 TTTTTTTTTTGCTT-TTGCACT
1 TTTTTTTTTTG-TTGTT-CACT
20150 TTTTCTTTT
1 TTTT-TTTT
20159 CATTTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 13 0.50
21 9 0.35
22 4 0.15
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTTTTTTTGTTGTTCACT
Found at i:20152 original size:15 final size:16
Alignment explanation
Indices: 20134--20175 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
20124 TCCCTTTTTT
20134 TTTTTGCTTTTGCA-C
1 TTTTTGCTTTTGCATC
*
20149 TTTTT-CTTTT-CATT
1 TTTTTGCTTTTGCATC
20163 TTTTTGCTTTTGC
1 TTTTTGCTTTTGC
20176 TTTTGACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 2 0.09
14 10 0.43
15 10 0.43
16 1 0.04
ACGTcount: A:0.05, C:0.17, G:0.10, T:0.69
Consensus pattern (16 bp):
TTTTTGCTTTTGCATC
Found at i:20153 original size:35 final size:33
Alignment explanation
Indices: 20128--20192 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
20118 TGTTGTTCCC
20128 TTTTTTT-TTTTGCTTTTGCACTTTTTCTTTTCA
1 TTTTTTTCTTTTGCTTTTG-ACTTTTTCTTTTCA
*
20161 TTTTTTTGCTTTTGCTTTTGACTTTTTTTTTT
1 TTTTTTT-CTTTTGCTTTTGACTTTTTCTTTT
20193 GTCATTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.24
34 11 0.38
35 11 0.38
ACGTcount: A:0.05, C:0.12, G:0.08, T:0.75
Consensus pattern (33 bp):
TTTTTTTCTTTTGCTTTTGACTTTTTCTTTTCA
Found at i:20172 original size:21 final size:22
Alignment explanation
Indices: 20148--20189 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20138 TGCTTTTGCA
*
20148 CTTTTTCTTTTCA-TTTTTTTG
1 CTTTTGCTTTTCACTTTTTTTG
*
20169 CTTTTGCTTTTGACTTTTTTT
1 CTTTTGCTTTTCACTTTTTTT
20190 TTTGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (22 bp):
CTTTTGCTTTTCACTTTTTTTG
Found at i:20187 original size:29 final size:28
Alignment explanation
Indices: 20132--20186 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
20122 GTTCCCTTTT
*
20132 TTTTTTTGCTTTTGCACTTTTTCTTTTCA
1 TTTTTTTGCTTTTG-ACTTTTACTTTTCA
20161 TTTTTTTGCTTTTG-CTTTTGACTTTT
1 TTTTTTTGCTTTTGACTTTT-ACTTTT
20187 TTTTTTGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 5 0.21
29 14 0.58
ACGTcount: A:0.05, C:0.15, G:0.09, T:0.71
Consensus pattern (28 bp):
TTTTTTTGCTTTTGACTTTTACTTTTCA
Done.