Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1302
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: 52338
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:127 original size:32 final size:32
Alignment explanation
Indices: 40--1370 Score: 1383
Period size: 31 Copynumber: 43.8 Consensus size: 32
30 CAAATGGTGA
* ** **
40 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
72 TTTTAAATGGGTTGCC-CCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
103 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
135 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
165 TTTGAAATGGGTTGCCACCGACTTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-TTGTGTGGGC
198 TTTGAAA-GGGTTTGCCACCGACTAT-TGT-GGC
1 TTTGAAATGGG-TTGCCACCGACT-TGTGTGGGC
229 TTTTGAAATGGG-TGCCACCGACTTGTG-GGGC
1 -TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
260 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
292 -TTGGAATGGGTTG-CACCG-CTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
321 GTTGAAATGGGTTGCCACCGACTTGTGT-GGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
352 TTTG-AAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
382 TTTGGAAT--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
410 TTTGAAATGGATTG-CACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
439 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
467 TTTGAAA--GGATGCCACCAAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACC-GACTTGTGTGGGC
* * *
498 TTTGAAA--AGCTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
528 TTTGAAA-GGGTTGCCACCGACTTGTGT--GC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
557 TTTTGGAATGGGTTGCCA-CGACTTATGTGGGC
1 -TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
589 TTTGAAATGGG-TGCCACCGACTTGTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTG-TGTGGGC
621 -TTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
652 TTTGGAAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
683 TTTTGAAA-GGGTTG-C-CCGACTTGTGTGGGC
1 -TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
713 TTTGGAAT--GATGCCACTAAC-T-TG-GGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
740 TTTGAAATGGATTGCCACCG-C-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
769 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
797 TTTGAAA-GGATTTGCCACCAAC-TGTGTGGAC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* * *
828 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
858 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
886 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
918 TTTGAAATGGGTTG-CACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
949 TTTGGAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
980 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1012 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1044 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTGC
1 TTTGAAATGGGTTGCCACCGACTTGTGT-GG---GC
1080 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
1110 -TTGGAAT--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1137 TTTGAAATGGATTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1167 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1195 -TTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1224 TTTGAAA--GGATGCCACCAACTTGTG-GGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1253 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1281 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1313 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1345 TTTGGAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1371 GATTTAAAAG
Statistics
Matches: 1136, Mismatches: 97, Indels: 133
0.83 0.07 0.10
Matches are distributed among these distances:
27 58 0.05
28 118 0.10
29 125 0.11
30 243 0.21
31 269 0.24
32 262 0.23
33 33 0.03
34 3 0.00
35 1 0.00
36 24 0.02
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:164 original size:30 final size:30
Alignment explanation
Indices: 40--1371 Score: 1193
Period size: 32 Copynumber: 43.9 Consensus size: 30
30 CAAATGGTGA
* **
40 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTG--TGGGC
*
72 TTTTAAATGGGTTGCC-CCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
* *
103 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
135 TTTGAAATGGGTTGCCACCGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
165 TTTGAAATGGGTTGCCACCGACTTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC--T-TGTGGGC
198 TTTGAAA-GGGTTTGCCACCGACTAT-TGTGGC
1 TTTGAAATGGG-TTGCCACCGACT-TGTG-GGC
229 TTTTGAAATGGG-TGCCACCGACTTGTGGGGC
1 -TTTGAAATGGGTTGCCACCGACTTGT-GGGC
260 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
*
292 -TTGGAATGGGTTG-CACCG-CTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
*
321 GTTGAAATGGGTTGCCACCGACTTGTGTGGC
1 TTTGAAATGGGTTGCCACCGACTTGTG-GGC
352 TTTG-AAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
* * **
382 TTTGGAAT--GATGCCACTAACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
*
410 TTTGAAATGGATTG-CACCGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* *
439 TTTGAAA--GGATGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* *
467 TTTGAAA--GGATGCCACCAAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACC-GACTTGTG-GG-C
* * *
498 TTTGAAA--AGCTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
*
528 TTTGAAA-GGGTTGCCACCGACTTGTGTGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
*
557 TTTTGGAATGGGTTGCCA-CGACTTATGTGGGC
1 -TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
589 TTTGAAATGGG-TGCCACCGACTTGTTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC---TTGTGGGC
621 -TTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
*
652 TTTGGAAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
683 TTTTGAAA-GGGTTG-C-CCGACTTGTGTGGGC
1 -TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
* * **
713 TTTGGAAT--GATGCCACTAACTTG-GGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
*
740 TTTGAAATGGATTGCCACCG-CTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* *
769 TTTGAAA--GGATGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* * *
797 TTTGAAA-GGATTTGCCACCAACTGTGTGGAC
1 TTTGAAATGG-GTTGCCACCGACT-TGTGGGC
* *
828 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTG-GG-C
* * *
858 TTTGAAA--AGATGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
886 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
918 TTTGAAATGGGTTG-CACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
*
949 TTTGGAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
980 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
*
1012 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1044 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGT-GG---GC
1080 TTTGAAATGGGTTGCCACCGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* * **
1110 -TTGGAAT--GATGCCACTAACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
*
1137 TTTGAAATGGATTGCCACCGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* *
1167 TTTGAAA--GGATGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
* *
1195 -TTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTG-GG-C
* *
1224 TTTGAAA--GGATGCCACCAACTTGTGGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGGG-C
* * *
1253 TTTGAAA--AGATGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGGGC
1281 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1313 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
* * *
1345 TTTGGAATGGG-TGCCACAGAGTTGTGG
1 TTTGAAATGGGTTGCCACCGACTTGTGG
1372 ATTTAAAAGG
Statistics
Matches: 1131, Mismatches: 94, Indels: 153
0.82 0.07 0.11
Matches are distributed among these distances:
27 61 0.05
28 115 0.10
29 138 0.12
30 238 0.21
31 253 0.22
32 260 0.23
33 38 0.03
34 3 0.00
35 1 0.00
36 24 0.02
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (30 bp):
TTTGAAATGGGTTGCCACCGACTTGTGGGC
Found at i:1387 original size:27 final size:27
Alignment explanation
Indices: 1353--2458 Score: 1946
Period size: 27 Copynumber: 41.0 Consensus size: 27
1343 GCTTTGGAAT
* *
1353 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1380 GGATGCCACGGAGTTGTGGACTT-AAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1406 -GGTGCCA-GAGAGTTGTGGACTTAAAA
1 GGGTGCCACG-GAGTTGTGGACTTAAAA
1432 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1459 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1487 GGGGTGCCACAGAGTTGTGGACTTAAAA
1 -GGGTGCCACGGAGTTGTGGACTTAAAA
*
1515 GAGTGCCACGGAGTTGT-GACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1541 GGGTGCCACGGAGTTGTGGACCTACTAAA
1 GGGTGCCACGGAGTTGTGGACTTA--AAA
*
1570 GGGTGCCACGGAGTTGTGAACTT-AAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1596 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1624 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1651 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1678 GGGATGCCACGGAGTTGTGGACTTTAAAA
1 GGG-TGCCACGGAGTTGTGGAC-TTAAAA
*
1707 GGGTGCCACAGAGTT-TGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1733 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1760 GGGTGCCACGGAGTTGTGGACCTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1787 GGGTGCCACGGAG-TGTGAACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1813 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1840 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1867 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1894 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1921 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1948 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1975 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2002 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2029 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2056 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2083 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2110 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2137 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2164 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2191 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2218 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2245 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2272 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2299 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2326 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2353 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2380 --GTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2405 GGGTGCCA--GAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2430 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
2458 G
1 G
2459 AAATGTGACT
Statistics
Matches: 1037, Mismatches: 22, Indels: 39
0.94 0.02 0.04
Matches are distributed among these distances:
24 1 0.00
25 68 0.07
26 80 0.08
27 780 0.75
28 55 0.05
29 53 0.05
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:2484 original size:44 final size:44
Alignment explanation
Indices: 2421--2505 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
2411 CAGAGTTGTG
*
2421 GACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAAATGT
1 GACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAATGT
2465 GACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAA
1 GACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAA
2506 ATGCCACTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (44 bp):
GACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAATGT
Found at i:2500 original size:28 final size:28
Alignment explanation
Indices: 2468--2534 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
2458 GAAATGTGAC
*
2468 TTAAAAGGATGCCACGGAGTTGTGGACT
1 TTAAAAGGATGCCACGGAGTCGTGGACT
* *
2496 TTAAAAGAAAATGCCACTGAGTCGTGGACT
1 TTAAAAG--GATGCCACGGAGTCGTGGACT
2526 TTGAAAAGG
1 TT-AAAAGG
2535 TCACAGTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 7 0.22
30 20 0.62
31 5 0.16
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.24
Consensus pattern (28 bp):
TTAAAAGGATGCCACGGAGTCGTGGACT
Found at i:2512 original size:30 final size:31
Alignment explanation
Indices: 2476--2533 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
2466 ACTTAAAAGG
*
2476 ATGCCACGGAGTTGTGGACTTT-AAAAGAAA
1 ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
*
2506 ATGCCACTGAGTCGTGGACTTTGAAAAG
1 ATGCCACGGAGTCGTGGACTTTGAAAAG
2534 GTCACAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (31 bp):
ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
Found at i:3875 original size:22 final size:22
Alignment explanation
Indices: 3850--3897 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3840 TTTATTTTGC
*
3850 TTTTGCACTTTTTCTTTTCATT
1 TTTTGCACTTTTGCTTTTCATT
** *
3872 TTTTGTGCTTTTGCTTTTGATT
1 TTTTGCACTTTTGCTTTTCATT
3894 TTTT
1 TTTT
3898 TTTGTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.06, C:0.12, G:0.10, T:0.71
Consensus pattern (22 bp):
TTTTGCACTTTTGCTTTTCATT
Found at i:9913 original size:2 final size:2
Alignment explanation
Indices: 9906--9942 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9896 GATTTTCAAA
*
9906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9943 ATAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10335 original size:11 final size:11
Alignment explanation
Indices: 10319--10359 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
10309 ATTTCATATT
10319 TTTTTTCTTTC
1 TTTTTTCTTTC
10330 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
10343 TTCTTTCTTTC
1 TTTTTTCTTTC
10354 TTTTTT
1 TTTTTT
10360 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:10373 original size:24 final size:22
Alignment explanation
Indices: 10319--10373 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
10309 ATTTCATATT
**
10319 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
10341 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
10367 TTTTTTC
1 TTTTTTC
10374 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:10753 original size:1 final size:1
Alignment explanation
Indices: 10749--10779 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10739 AAAGCCCCTC
10749 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10780 GATCCCTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11714 original size:32 final size:32
Alignment explanation
Indices: 11640--11933 Score: 442
Period size: 32 Copynumber: 9.2 Consensus size: 32
11630 TAACTTGCAT
*
11640 GGCTTTTAAATGGGTTTGCC-CCGAACCTTGTGTG
1 GGCTTTGAAATGGG-TTGCCACCG-A-CTTGTGTG
*
11674 GGCTTTGAAAAGGGTTCGCCACCGACTTGTGT-
1 GGCTTTGAAATGGGTT-GCCACCGACTTGTGTG
11706 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
11738 GGCTTTGAAATGGGTTG-CACCGACTTGTGTG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
*
11769 GGCTTTGAAATGGGTTGCCACCGACTTATGTG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
11801 GGCTTTGAAATGGGTTGCCACCGACTTGTGT-
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
*
11832 GGCTTTGTAATGGGTTGCCACCGACTTGTGTGG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGT-G
11865 GGCTTTG-AATGGGTTGCCACCGACTTGTGT-
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
11895 GGCTTTCGAAATGGGTTGCCACCGA--TGTGTG
1 GGCTTT-GAAATGGGTTGCCACCGACTTGTGTG
11926 GGCTTTGA
1 GGCTTTGA
11934 TGATGCACTA
Statistics
Matches: 245, Mismatches: 6, Indels: 22
0.90 0.02 0.08
Matches are distributed among these distances:
30 13 0.05
31 83 0.34
32 114 0.47
33 16 0.07
34 16 0.07
35 3 0.01
ACGTcount: A:0.16, C:0.19, G:0.33, T:0.32
Consensus pattern (32 bp):
GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
Found at i:11791 original size:63 final size:64
Alignment explanation
Indices: 11640--12213 Score: 599
Period size: 63 Copynumber: 9.3 Consensus size: 64
11630 TAACTTGCAT
* *
11640 GGCTTTTAAATGGGTTTGCC-CCGAACCTTGTGTGGGCTTTGAAAAGGGTTCGCCACCGACTTGT
1 GGCTTTGAAATGGG-TTGCCACCG-A-CTTGTGTGGGCTTTGAAATGGGTT-GCCACCGACTTGT
11704 GT-
62 GTG
11706 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG-CACCGACTTGTGTG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
*
11769 GGCTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT-
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
*
11832 GGCTTTGTAATGGGTTGCCACCGACTTGTGTGGGGCTTTG-AATGGGTTGCCACCGACTTGTGT-
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGT-GGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
* *
11895 GGCTTTCGAAATGGGTTGCCACCGA--TGTGTGGGCTTTG--AT--GATG-CA-CTAC---T-TG
1 GGCTTT-GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
** * * *
11948 GGC-TTG-AATGCATTGCCACCGACTTG-GTGGGCCTGTG-AA--GGATGCCACTGAAC-T-TGT
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGG-CTTTGAAATGGGTTGCCACCG-ACTTGTGT
12005 G
64 G
* * * * * *
12006 GGCTTTGAAAT-GGATGCCACCAAC-TGTGTGGACTTTGAAA-AGATTGCCACTGACTTG-GT-
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
* *
12065 GGCTTTGAAA-GTGATTGCCACCAACTTGTGTGGGCTTTGAAAAT-GGTTGCCACCGGACTTGTG
1 GGCTTTGAAATG-GGTTGCCACCGACTTGTGTGGGCTTTG-AAATGGGTTGCCACC-GACTTGTG
12128 TG
63 TG
*
12130 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTT-TGTGG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT-G
12194 TGGCTTTG-AATGGG-TGCCAC
1 -GGCTTTGAAATGGGTTGCCAC
12214 AAGAGGTGTG
Statistics
Matches: 444, Mismatches: 29, Indels: 73
0.81 0.05 0.13
Matches are distributed among these distances:
50 14 0.03
51 6 0.01
52 9 0.02
53 9 0.02
54 2 0.00
56 5 0.01
57 3 0.01
58 14 0.03
59 30 0.07
60 28 0.06
61 20 0.05
62 29 0.07
63 122 0.27
64 78 0.18
65 58 0.13
66 17 0.04
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.31
Consensus pattern (64 bp):
GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
Found at i:11805 original size:95 final size:95
Alignment explanation
Indices: 11640--12213 Score: 593
Period size: 95 Copynumber: 6.2 Consensus size: 95
11630 TAACTTGCAT
* *
11640 GGCTTTTAAATGGGTTTGCC-CCGAACCTTGTGTGGGCTTTGAAAAGGGTTCGCCACCGACTTGT
1 GGCTTTGAAATGGG-TTGCCACCG-A-CTTGTGTGGGCTTTGAAATGGGTT-GCCACCGACTTGT
11704 GTGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
62 GTGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
*
11738 GGCTTTGAAATGGGTTG-CACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTATGTGG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT-G
11802 GCTTTGAAATGGGTTGCCACCGACTTGTGT-
65 GCTTTGAAATGGGTTGCCACCGACTTGTGTG
*
11832 GGCTTTGTAATGGGTTGCCACCGACTTGTGTGGGGCTTTG-AATGGGTTGCCACCGACTTGTGTG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGT-GGGCTTTGAAATGGGTTGCCACCGACTTGTGTG
11896 GCTTTCGAAATGGGTTGCCACCGA--TGTGTG
65 GCTTT-GAAATGGGTTGCCACCGACTTGTGTG
* * **
11926 GGCTTTG--AT--GATG-CA-CTAC---T-TGGGC-TTG-AATGCATTGCCACCGACTTG-GTGG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT-G
* * *
11978 GCCTGTG-AA--GGATGCCACTGAAC-T-TGTG
65 G-CTTTGAAATGGGTTGCCACCG-ACTTGTGTG
* * * * * *
12006 GGCTTTGAAAT-GGATGCCACCAAC-TGTGTGGACTTTGAAA-AGATTGCCACTGACTTG-GTGG
1 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
* *
12067 CTTTGAAA-GTGATTGCCACCAACTTGTGTG
66 CTTTGAAATG-GGTTGCCACCGACTTGTGTG
12097 GGCTTTGAAAAT-GGTTGCCACCGGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT
1 GGCTTTG-AAATGGGTTGCCACC-GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT
*
12161 GGGCTTTGGAATGGGTTGCCACCGACTT-TGTGG
64 -GGCTTTGAAATGGGTTGCCACCGACTTGTGT-G
12194 TGGCTTTG-AATGGG-TGCCAC
1 -GGCTTTGAAATGGGTTGCCAC
12214 AAGAGGTGTG
Statistics
Matches: 410, Mismatches: 31, Indels: 72
0.80 0.06 0.14
Matches are distributed among these distances:
79 9 0.02
80 12 0.03
81 5 0.01
82 26 0.06
83 11 0.03
84 3 0.01
85 4 0.01
87 5 0.01
88 11 0.03
89 23 0.06
90 13 0.03
91 11 0.03
92 15 0.04
93 7 0.02
94 58 0.14
95 121 0.30
96 24 0.06
97 31 0.08
98 21 0.05
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.31
Consensus pattern (95 bp):
GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
CTTTGAAATGGGTTGCCACCGACTTGTGTG
Found at i:11993 original size:29 final size:30
Alignment explanation
Indices: 11961--12159 Score: 103
Period size: 30 Copynumber: 6.5 Consensus size: 30
11951 TTGAATGCAT
11961 TGCCACCG-ACTTGGTGGGCCTGTG-AA-GGA
1 TGCCACCGAACTT-GTGGG-CTGTGAAATGGA
* *
11990 TGCCACTGAACTTGTGGGCTTTGAAATGGA
1 TGCCACCGAACTTGTGGGCTGTGAAATGGA
* * *
12020 TGCCACC-AACTGTGTGGACTTTGAAA-AGA
1 TGCCACCGAACT-TGTGGGCTGTGAAATGGA
* *
12049 TTGCCACTG-ACTTG-GTGGCTTTGAAA-GTGA
1 -TGCCACCGAACTTGTG-GGCTGTGAAATG-GA
* *
12079 TTGCCACC-AACTTGTGTGGGCTTTGAAAATGGT
1 -TGCCACCGAAC-T-TGTGGGCTGTG-AAATGGA
* * *
12112 TGCCACCGGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGAAC-T-TGTGGGCTGTGAAAT-GGA
12145 TGCCACCG-ACTTGTG
1 TGCCACCGAACTTGTG
12160 TGGGCTTTGG
Statistics
Matches: 143, Mismatches: 11, Indels: 31
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.03
29 31 0.22
30 50 0.35
31 2 0.01
32 22 0.15
33 32 0.22
34 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (30 bp):
TGCCACCGAACTTGTGGGCTGTGAAATGGA
Found at i:12106 original size:32 final size:32
Alignment explanation
Indices: 11946--12203 Score: 242
Period size: 32 Copynumber: 8.3 Consensus size: 32
11936 ATGCACTACT
*
11946 TGGGC-TTG-AATGCATTGCCACCGACTTG-G
1 TGGGCTTTGAAATGGATTGCCACCGACTTGTG
* *
11975 TGGGCCTGTG-AA-GGA-TGCCACTGAAC-T-TG
1 TGGG-CTTTGAAATGGATTGCCACCG-ACTTGTG
*
12004 TGGGCTTTGAAATGGA-TGCCACCAAC-TGTG
1 TGGGCTTTGAAATGGATTGCCACCGACTTGTG
* * *
12034 TGGACTTTGAAA-AGATTGCCACTGACTTG-G
1 TGGGCTTTGAAATGGATTGCCACCGACTTGTG
*
12064 T-GGCTTTGAAA-GTGATTGCCACCAACTTGTG
1 TGGGCTTTGAAATG-GATTGCCACCGACTTGTG
12095 TGGGCTTTGAAAATGG-TTGCCACCGGACTTGTG
1 TGGGCTTTG-AAATGGATTGCCACC-GACTTGTG
*
12128 TGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAATGGATTGCCACCGACTTGTG
* *
12160 TGGGCTTTGGAATGGGTTGCCACCGACTT-TG
1 TGGGCTTTGAAATGGATTGCCACCGACTTGTG
12191 TGGTGGCTTTGAA
1 T-G-GGCTTTGAA
12204 TGGGTGCCAC
Statistics
Matches: 194, Mismatches: 17, Indels: 32
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.02
29 33 0.17
30 51 0.26
31 11 0.06
32 58 0.30
33 36 0.19
34 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (32 bp):
TGGGCTTTGAAATGGATTGCCACCGACTTGTG
Found at i:12149 original size:65 final size:64
Alignment explanation
Indices: 12002--12213 Score: 246
Period size: 65 Copynumber: 3.4 Consensus size: 64
11992 CCACTGAACT
* * * *
12002 TGTGGGCTTTGAAAT-GGATGCCACCAAC-TGTGTGGACTTTGAAAA-GATTGCCACTGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAAATGGTTGCCACCGACTTG
*
12063 -GT-GGCTTTGAAA-GTGATTGCCACCAACTTGTGTGGGCTTTGAAAATGGTTGCCACCGGACTT
1 TGTGGGCTTTGAAATG-GGTTGCCACCAACTTGTGTGGGCTTTGAAAATGGTTGCCACC-GACTT
12125 G
64 G
* *
12126 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTG-GAATGGGTTGCCACCGACTT-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAAAT-GGTTGCCACCGACTTG
12189 TGTGGTGGCTTTG-AATGGG-TGCCAC
1 TGT-G-GGCTTTGAAATGGGTTGCCAC
12214 AAGAGGTGTG
Statistics
Matches: 132, Mismatches: 8, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
59 10 0.08
60 13 0.10
61 16 0.12
62 8 0.06
63 15 0.11
64 17 0.13
65 52 0.39
66 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (64 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAAATGGTTGCCACCGACTTG
Found at i:12393 original size:27 final size:27
Alignment explanation
Indices: 12240--12487 Score: 274
Period size: 28 Copynumber: 9.1 Consensus size: 27
12230 AAATGAACGG
12240 CACGGAGTTGTGGACTTAAAA-GGTGC
1 CACGGAGTTGTGGACTTAAAAGGGTGC
*
12266 CAACGTAGTTAGTGGACTTAAAAGGGTGC
1 C-ACGGAGTT-GTGGACTTAAAAGGGTGC
** *
12295 CACGGAGTTGTTGGACTTCAACTGTGTGC
1 CACGGAGTTG-TGGACTT-AAAAGGGTGC
* * * *
12324 CACAGAGTTGTTGACATACCAAGGGTGC
1 CACGGAGTTGTGGACTTA-AAAGGGTGC
* * *
12352 CCCTGCGTTGTGGACTTTAAAAGGGTGC
1 CACGGAGTTGTGGAC-TTAAAAGGGTGC
*
12380 CAC-GAGTTGTGGAC-TAAAA-GATGC
1 CACGGAGTTGTGGACTTAAAAGGGTGC
*
12404 CAACGGAGTTATGGACTT-AAA-GGTGC
1 C-ACGGAGTTGTGGACTTAAAAGGGTGC
12430 CACGGAGTTGTGGACTTAAAAGGGTGC
1 CACGGAGTTGTGGACTTAAAAGGGTGC
12457 CACGGAGTTGTGGACTTAAAAGGGTGC
1 CACGGAGTTGTGGACTTAAAAGGGTGC
12484 CACG
1 CACG
12488 TTGTGACTTT
Statistics
Matches: 186, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
24 5 0.03
25 22 0.12
26 22 0.12
27 56 0.30
28 57 0.31
29 24 0.13
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (27 bp):
CACGGAGTTGTGGACTTAAAAGGGTGC
Found at i:12419 original size:26 final size:26
Alignment explanation
Indices: 12240--12487 Score: 250
Period size: 27 Copynumber: 9.2 Consensus size: 26
12230 AAATGAACGG
12240 CACGGAGTTGTGGACTTAAAAGGTGC
1 CACGGAGTTGTGGACTTAAAAGGTGC
*
12266 CAACGTAGTTAGTGGACTTAAAAGGGTGC
1 C-ACGGAGTT-GTGGACTTAAAA-GGTGC
**
12295 CACGGAGTTGTTGGACTTCAACTGTGTGC
1 CACGGAGTTG-TGGACTT-AAAAG-GTGC
* * * *
12324 CACAGAGTTGTTGACATACCAAGGGTGC
1 CACGGAGTTGTGGACTTA--AAAGGTGC
* * *
12352 CCCTGCGTTGTGGACTTTAAAAGGGTGC
1 CACGGAGTTGTGGAC-TTAAAA-GGTGC
*
12380 CAC-GAGTTGTGGAC-TAAAAGATGC
1 CACGGAGTTGTGGACTTAAAAGGTGC
*
12404 CAACGGAGTTATGGACTT-AAAGGTGC
1 C-ACGGAGTTGTGGACTTAAAAGGTGC
12430 CACGGAGTTGTGGACTTAAAAGGGTGC
1 CACGGAGTTGTGGACTTAAAA-GGTGC
12457 CACGGAGTTGTGGACTTAAAAGGGTGC
1 CACGGAGTTGTGGACTTAAAA-GGTGC
12484 CACG
1 CACG
12488 TTGTGACTTT
Statistics
Matches: 186, Mismatches: 21, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
24 5 0.03
25 22 0.12
26 22 0.12
27 58 0.31
28 54 0.29
29 25 0.13
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (26 bp):
CACGGAGTTGTGGACTTAAAAGGTGC
Found at i:12444 original size:78 final size:79
Alignment explanation
Indices: 12240--12487 Score: 268
Period size: 78 Copynumber: 3.1 Consensus size: 79
12230 AAATGAACGG
*
12240 CACGGAGTTGTGGACTTAAAAGGTGCCAACGTAGTTAGTGGACTTAAAAGGGTGCCACGGAGTTG
1 CACGGAGTTGTGGACTT-AAAGGTGCC-ACGGAGTT-GTGGACTTAAAAGGGTGCCACGGAGTTG
** *
12305 TTGGACTTCAACTGTGTGC
63 -TGGACTT-AAAAGTATGC
* * * * * *
12324 CACAGAGTTGTTGACATACCAAGGGTGCCCCTGCGTTGTGGACTTTAAAAGGGTGCCAC-GAGTT
1 CACGGAGTTGTGGACTTA--AA-GGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTT
12388 GTGGAC-TAAAAG-ATGC
62 GTGGACTTAAAAGTATGC
*
12404 CAACGGAGTTATGGACTTAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTG
1 C-ACGGAGTTGTGGACTTAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTG
**
12469 GACTTAAAAGGGTGC
65 GACTTAAAAGTATGC
12484 CACG
1 CACG
12488 TTGTGACTTT
Statistics
Matches: 138, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
77 15 0.11
78 28 0.20
79 11 0.08
80 8 0.06
81 16 0.12
82 1 0.01
83 6 0.04
84 26 0.19
85 21 0.15
86 6 0.04
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (79 bp):
CACGGAGTTGTGGACTTAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG
ACTTAAAAGTATGC
Found at i:12528 original size:41 final size:44
Alignment explanation
Indices: 12465--12553 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
12455 GCCACGGAGT
* *
12465 TGTGGACTTAAAAGGGTGCCAC-GTTGT-GACTTTAAAAGAAAA
1 TGTGAACTTAAAAGGATGCCACGGTTGTGGACTTTAAAAGAAAA
12507 TGTGAACTT-AAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAA
1 TGTGAACTTAAAAGGATGCCAC-G-GTTGTGGACTTTAAAAGAAAA
12552 TG
1 TG
12554 CCACTGAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
41 11 0.27
42 8 0.20
44 5 0.12
45 17 0.41
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (44 bp):
TGTGAACTTAAAAGGATGCCACGGTTGTGGACTTTAAAAGAAAA
Found at i:12555 original size:30 final size:31
Alignment explanation
Indices: 12521--12578 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
12511 AACTTAAAGG
*
12521 ATGCCACGGAGTTGTGGACTTT-AAAAGAAA
1 ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
*
12551 ATGCCACTGAGTCGTGGACTTTGAAAAG
1 ATGCCACGGAGTCGTGGACTTTGAAAAG
12579 GTCCAGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (31 bp):
ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
Found at i:13602 original size:1 final size:1
Alignment explanation
Indices: 13596--13620 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
13586 GGTGAAAAGG
13596 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
13621 AGCATTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20394 original size:11 final size:11
Alignment explanation
Indices: 20378--20418 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
20368 ATTTCATATT
20378 TTTTTTCTTTC
1 TTTTTTCTTTC
20389 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
20402 TTCTTTCTTTC
1 TTTTTTCTTTC
20413 TTTTTT
1 TTTTTT
20419 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:20432 original size:24 final size:22
Alignment explanation
Indices: 20378--20432 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
20368 ATTTCATATT
**
20378 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
20400 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
20426 TTTTTTC
1 TTTTTTC
20433 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:20799 original size:23 final size:22
Alignment explanation
Indices: 20773--20817 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20763 CCACTCAATC
20773 GGAAAACCCACTTTGGTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTT
* **
20796 GGAAAGCCCCTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTT
20818 TTTTTTTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (22 bp):
GGAAAACCCCTTTGGTTTTTTT
Found at i:32978 original size:73 final size:71
Alignment explanation
Indices: 32892--33064 Score: 172
Period size: 71 Copynumber: 2.4 Consensus size: 71
32882 GTATTTGAAC
* **
32892 TCATTTATCTTTTTTAGTCCTTAAAAAGTAGGATGCATTTTCTGTTTTCTTCAAAGCCCATGC-A
1 TCATTTATCTTTTTTAGTCCTTAAAAAGT-GGATGC-CTTT-T-TTTTCTTCAAAGCCCACACAA
** *
32956 -CTGTTGGCA
62 GCTGGCGCCA
* * * * *
32965 TCATTTATCTTTTTCAGTTC-TCAAGAGCTGGATGCCTTTTTTTTCTTCAAAGTCCACACAAGCT
1 TCATTTATCTTTTTTAGTCCTTAAAAAG-TGGATGCCTTTTTTTTCTTCAAAGCCCACACAAGCT
33029 GGCGCCA
65 GGCGCCA
*
33036 TCATTTATCTTTTCTAGTCCTTAAAAAGT
1 TCATTTATCTTTTTTAGTCCTTAAAAAGT
33065 CTTCAAATCC
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
69 16 0.20
70 2 0.03
71 27 0.34
72 16 0.20
73 19 0.24
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (71 bp):
TCATTTATCTTTTTTAGTCCTTAAAAAGTGGATGCCTTTTTTTTCTTCAAAGCCCACACAAGCTG
GCGCCA
Found at i:33094 original size:56 final size:56
Alignment explanation
Indices: 33008--33116 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 56
32998 GCCTTTTTTT
33008 TCTTCAAAGTCCACACAAGCTGGCGCCATCATTTATC-TTTTCTAGTCCTTAAAAAG
1 TCTTCAAAGTCCACACAAGCTGGCGCCATCATTTATCTTTTTCTA-TCCTTAAAAAG
* * *
33064 TCTTCAAA-TCCCACACAAGCTGGTGGCATCATTTTTCTTTTTCTATCCTTAAA
1 TCTTCAAAGT-CCACACAAGCTGGCGCCATCATTTATCTTTTTCTATCCTTAAA
33117 GAGCAAGACG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
55 1 0.02
56 40 0.83
57 7 0.15
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (56 bp):
TCTTCAAAGTCCACACAAGCTGGCGCCATCATTTATCTTTTTCTATCCTTAAAAAG
Found at i:33248 original size:77 final size:74
Alignment explanation
Indices: 33064--33312 Score: 253
Period size: 74 Copynumber: 3.4 Consensus size: 74
33054 CCTTAAAAAG
* *
33064 TCTTCAAATCCCACACAAGCTGGTGGCATCATTTTTCTTTTTCTA-TCCTTAAAGAGCAAGACGC
1 TCTTCAAAACCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGT-CTTAAAGAGCAAGACGC
33128 TTTTTCTTTT
65 TTTTTCTTTT
* *
33138 TCTTCAAAACCCACACAAGCTAGTGGCATCATTTATC-TTTTCTAGTCTTGAAAGAGCAAGATGC
1 TCTTCAAAACCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGTCTT-AAAGAGCAAGACG-
*
33202 CTTTTTTTTTTCT
64 C-TTTTTCTTT-T
* * *** * * *
33215 TCTTCAAAGCCCACACAAGTTGGTGGTGCCATTTA-CTTTTTCTAGTCCTCAAAGAGTAGGA--C
1 TCTTCAAAACCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGT-CTTAAAGAGCAAGACGC
*
33277 ATTTTC---T
65 TTTTTCTTTT
*
33284 TCTTCAAAACCCGCACAAGCTGGTGGCAT
1 TCTTCAAAACCCACACAAGCTGGTGGCAT
33313 TTACCTACTT
Statistics
Matches: 146, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
69 24 0.16
73 14 0.10
74 48 0.33
75 1 0.01
76 9 0.06
77 48 0.33
78 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (74 bp):
TCTTCAAAACCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGTCTTAAAGAGCAAGACGCT
TTTTCTTTT
Found at i:33342 original size:66 final size:69
Alignment explanation
Indices: 33209--33342 Score: 150
Period size: 69 Copynumber: 2.0 Consensus size: 69
33199 TGCCTTTTTT
* * ** * * **
33209 TTTTCTTCTTCAAAGCCCACACAAGTTGGTGGTGCCATTTACTTTTTCTAGTCCTCAAAGAGTAG
1 TTTTCTTCTTCAAAACCCACACAAGCTGGTGGTGCCATTTACTACTTCAAGTCCTCAAAAAACAG
33274 GACA
66 GACA
*
33278 TTTTCTTCTTCAAAACCCGCACAAGCTGGT-G-G-CATTTACCTACTT-AAGTCCTCAAAAAACA
1 TTTTCTTCTTCAAAACCCACACAAGCTGGTGGTGCCATTTA-CTACTTCAAGTCCTCAAAAAACA
33339 GGAC
65 GGAC
33343 GCTTACCCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
66 22 0.40
67 5 0.09
68 1 0.02
69 27 0.49
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (69 bp):
TTTTCTTCTTCAAAACCCACACAAGCTGGTGGTGCCATTTACTACTTCAAGTCCTCAAAAAACAG
GACA
Found at i:42651 original size:2 final size:2
Alignment explanation
Indices: 42644--42683 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
42634 GTTTACCTGC
42644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42684 GAGGCCTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46835 original size:16 final size:16
Alignment explanation
Indices: 46814--46845 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46804 AGCTACTGAT
46814 TCCATTTTTTTATTTA
1 TCCATTTTTTTATTTA
46830 TCCATTTTTTTATTTA
1 TCCATTTTTTTATTTA
46846 AAGAAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (16 bp):
TCCATTTTTTTATTTA
Done.