Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 46 of 199
Found at i:13325081 original size:44 final size:44
Alignment explanation
Indices: 13325006--13325252 Score: 318
Period size: 44 Copynumber: 5.6 Consensus size: 44
13324996 TTCGATTTGC
* **
13325006 TCCACTGCTGCTT-AGGGAGACAGGA-TCTACAATCTTTAACCTAT
1 TCCACTGCTG-TTCAGGGAGATAGGACT-TACAATCTTCCACCTAT
* * *
13325050 TCCATTGCTGTTCAGGGAGATAGGACATACAATCTTTCACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACCTAT
* *
13325094 TCCATTGCTGTTCAGGGAGCTAGGACTTACAATCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACCTAT
* * *
13325138 TCCACTACTGTTCAGGGAGCTAGGACTTACAATATTCCACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACCTAT
* * * *
13325182 TCCACTGCTGGTCAAGGAGATAGGACTTGCAATCTTCAACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACCTAT
*
13325226 TCCACTGCTGGTCAGGGAGATAGGACT
1 TCCACTGCTGTTCAGGGAGATAGGACT
13325253 AATGGCTTAA
Statistics
Matches: 183, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 2 0.01
44 181 0.99
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
TCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACCTAT
Found at i:13338262 original size:3 final size:3
Alignment explanation
Indices: 13338254--13338300 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
13338244 ATAATCAAAT
* *
13338254 ATA ATA ATA AAA ATA ATAA ATA GTA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
13338299 AT
1 AT
13338301 TAAGTGATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:13338283 original size:21 final size:21
Alignment explanation
Indices: 13338239--13338293 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
13338229 TATATATAGG
*
13338239 TAAATATAATCAAATATAATAA
1 TAAAAATAAT-AAATATAATAA
13338261 TAAAAATAATAAATAGTAA-AA
1 TAAAAATAATAAATA-TAATAA
*
13338282 TAATAATAATAA
1 TAAAAATAATAA
13338294 TAATAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAATAATAAATATAATAA
Found at i:13341836 original size:20 final size:20
Alignment explanation
Indices: 13341793--13341839 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13341783 TTACTCTTTT
*
13341793 ATATATACTTTATATTTTAC
1 ATATATACTTTATATTTTAA
*
13341813 ATATATACTTT-TCTTTGTAA
1 ATATATACTTTATATTT-TAA
13341833 ATATATA
1 ATATATA
13341840 GATATGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATATACTTTATATTTTAA
Found at i:13345414 original size:33 final size:35
Alignment explanation
Indices: 13345367--13345435 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 35
13345357 TATTTATATC
*
13345367 AAATAATTTCAAAAA-TAAAAAAGTTAAAATTAAAA
1 AAATAATTTCAAAAATTAAAAAAATT-AAATTAAAA
13345402 AAAT-ATTT-AAAAATTAAAAAAATTAAATTAAAA
1 AAATAATTTCAAAAATTAAAAAAATTAAATTAAAA
13345435 A
1 A
13345436 TTTATTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 15 0.47
34 13 0.41
35 4 0.12
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (35 bp):
AAATAATTTCAAAAATTAAAAAAATTAAATTAAAA
Found at i:13345735 original size:26 final size:28
Alignment explanation
Indices: 13345695--13345751 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
13345685 AAAAATATCT
13345695 AATATATTTTGTATA-A-TTATAAATTTAA
1 AATATATTTTGTATACACTTA-AAA-TTAA
13345723 AATATA-TTT-TATACACTTAAAATTAA
1 AATATATTTTGTATACACTTAAAATTAA
13345749 AAT
1 AAT
13345752 TGCATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 11 0.41
27 7 0.26
28 9 0.33
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (28 bp):
AATATATTTTGTATACACTTAAAATTAA
Found at i:13360340 original size:31 final size:31
Alignment explanation
Indices: 13360304--13360363 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
13360294 TGGATTTCTC
13360304 TTTTTGCATCTTCCAAATTTGAAAACCTCAA
1 TTTTTGCATCTTCCAAATTTGAAAACCTCAA
13360335 TTTTTGCATCTTCCAAATTTGAAAACCTC
1 TTTTTGCATCTTCCAAATTTGAAAACCTC
13360364 GTGAAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (31 bp):
TTTTTGCATCTTCCAAATTTGAAAACCTCAA
Found at i:13365664 original size:23 final size:20
Alignment explanation
Indices: 13365638--13365682 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
13365628 TTGCAAAACA
13365638 GTTTACTGAGTGAATTCCATTTT
1 GTTTACTGAG-GAATT--ATTTT
*
13365661 GTTTATTGAGGAATTATTTT
1 GTTTACTGAGGAATTATTTT
13365681 GT
1 GT
13365683 GAGAGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTTACTGAGGAATTATTTT
Found at i:13368718 original size:20 final size:20
Alignment explanation
Indices: 13368687--13368724 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13368677 GGTTTTTTTA
13368687 AAGGTCAGATTTTATTATTTC
1 AAGGTCAGATTTT-TTATTTC
13368708 AAGGT-AGATTTTTTATT
1 AAGGTCAGATTTTTTATT
13368725 ATTGTAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (20 bp):
AAGGTCAGATTTTTTATTTC
Found at i:13368720 original size:21 final size:22
Alignment explanation
Indices: 13368687--13368727 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13368677 GGTTTTTTTA
13368687 AAGGTCAGA-TTTTATTATTTC
1 AAGGTCAGATTTTTATTATTTC
13368708 AAGGT-AGATTTTTTATTATT
1 AAGGTCAGA-TTTTTATTATT
13368728 GTAAAGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 5 0.28
22 10 0.56
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (22 bp):
AAGGTCAGATTTTTATTATTTC
Found at i:13368900 original size:16 final size:16
Alignment explanation
Indices: 13368879--13368911 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13368869 TAATGATATT
*
13368879 TTTTATTTTTAAATAA
1 TTTTATTTTAAAATAA
13368895 TTTTATTTTAAAATAA
1 TTTTATTTTAAAATAA
13368911 T
1 T
13368912 AAGATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATTTTAAAATAA
Found at i:13369581 original size:23 final size:23
Alignment explanation
Indices: 13369554--13369599 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
13369544 AAGTTGATAA
13369554 AGGAGGAATAACACAATTTAAAG
1 AGGAGGAATAACACAATTTAAAG
*
13369577 AGGAGGAATAACACGATTTAAAG
1 AGGAGGAATAACACAATTTAAAG
13369600 CGCACATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (23 bp):
AGGAGGAATAACACAATTTAAAG
Found at i:13373416 original size:6 final size:6
Alignment explanation
Indices: 13373405--13373432 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13373395 AAGTGACTTT
13373405 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
13373433 TATGTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:13388745 original size:36 final size:36
Alignment explanation
Indices: 13388688--13388945 Score: 203
Period size: 36 Copynumber: 7.2 Consensus size: 36
13388678 GAAGCACAAA
*
13388688 AATTTTTTG-AAACACTG-AAATTTATGAAACACTGGC
1 AATTTTTTGAAAACAC-GAAAATTTATGAAACAC-GGG
* * * *
13388724 AA-TTTTTGAAAACGCAAAAATTTTTGAAAGACGGG
1 AATTTTTTGAAAACACGAAAATTTATGAAACACGGG
* *
13388759 AATTTTTTGCAAACACGGAAATTTATGAAACACGGG
1 AATTTTTTGAAAACACGAAAATTTATGAAACACGGG
*
13388795 AATTTTTTTTGAAAACACGAAAATTT-TCGAAACAC-GA
1 AA--TTTTTTGAAAACACGAAAATTTAT-GAAACACGGG
* * * *
13388832 AAATTTTTGAAAACACGATAATTTTTGAAAACAC-GA
1 AATTTTTTGAAAACACGAAAATTTATG-AAACACGGG
* * * *
13388868 AAATTGTTGAAAACACGAAAAAATTT-TGAAATACCGG
1 AATTTTTTGAAAACACG--AAAATTTATGAAACACGGG
* * *
13388905 -ATTTTTTGAAAACAAGAAGATTTTTGAAACAC--G
1 AATTTTTTGAAAACACGAAAATTTATGAAACACGGG
13388938 AATTTTTT
1 AATTTTTT
13388946 TATTTTATTT
Statistics
Matches: 184, Mismatches: 25, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
33 1 0.01
34 13 0.07
35 38 0.21
36 92 0.50
37 7 0.04
38 33 0.18
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (36 bp):
AATTTTTTGAAAACACGAAAATTTATGAAACACGGG
Found at i:13388780 original size:72 final size:69
Alignment explanation
Indices: 13388688--13388945 Score: 234
Period size: 72 Copynumber: 3.6 Consensus size: 69
13388678 GAAGCACAAA
* *
13388688 AATTTTTTG-AAACACTGAAATTTATGAAACACTGGCAATTTTTGAAAACGCAAAAATTTTTGAA
1 AATTTTTTGAAAACAC-GAAATTTATGAAACAC-GGAAATTTTTGAAAACACAAAAATTTTTGAA
*
13388752 AGACGGG
64 ACAC-GG
* * * *
13388759 AATTTTTTGCAAACACGGAAATTTATGAAACACGGGAATTTTTTTTGAAAACACGAAAATTTTCG
1 AATTTTTTGAAAACAC-GAAATTTATGAAACAC-GGAA--ATTTTTGAAAACACAAAAATTTTTG
*
13388824 AAACACGA
62 AAACACGG
* * * * *
13388832 AAATTTTTGAAAACACGATAATTTTTGAAAACACGAAAATTGTTGAAAACACGAAAAAATTTTGA
1 AATTTTTTGAAAACACGA-AATTTATG-AAACACGGAAATTTTTGAAAACAC-AAAAATTTTTGA
*
13388897 AATACCGG
63 AACA-CGG
* * *
13388905 -ATTTTTTGAAAACAAGAAGATTTTTGAAACAC-GAATTTTTT
1 AATTTTTTGAAAACACGAA-ATTTATGAAACACGGAAATTTTT
13388946 TATTTTATTT
Statistics
Matches: 154, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
70 6 0.04
71 28 0.18
72 61 0.40
73 27 0.18
74 32 0.21
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (69 bp):
AATTTTTTGAAAACACGAAATTTATGAAACACGGAAATTTTTGAAAACACAAAAATTTTTGAAAC
ACGG
Found at i:13388946 original size:17 final size:18
Alignment explanation
Indices: 13388686--13388939 Score: 175
Period size: 18 Copynumber: 14.1 Consensus size: 18
13388676 TAGAAGCACA
13388686 AAAATTTTTTG-AAACACTG
1 AAAA-TTTTTGAAAACAC-G
*
13388705 -AAATTTATG-AAACACTG
1 AAAATTTTTGAAAACAC-G
** * *
13388722 GCAATTTTTGAAAACGCA
1 AAAATTTTTGAAAACACG
*
13388740 AAAATTTTTGAAAGAC-GG
1 AAAATTTTTGAAA-ACACG
* * *
13388758 GAATTTTTTGCAAACACG
1 AAAATTTTTGAAAACACG
* *
13388776 GAAATTTATG-AAACACGGG
1 AAAATTTTTGAAAACAC--G
**
13388795 AATTTTTTTTGAAAACACG
1 AA-AATTTTTGAAAACACG
*
13388814 AAAATTTTCG-AAACACG
1 AAAATTTTTGAAAACACG
13388831 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
*
13388849 ATAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
*
13388867 AAAATTGTTGAAAACACG
1 AAAATTTTTGAAAACACG
*
13388885 AAAAAATTTTGAAATAC-CG
1 -AAAATTTTTGAAA-ACACG
* * *
13388904 -GATTTTTTGAAAACAAG
1 AAAATTTTTGAAAACACG
*
13388921 AAGATTTTTG-AAACACG
1 AAAATTTTTGAAAACACG
13388938 AA
1 AA
13388940 TTTTTTTATT
Statistics
Matches: 186, Mismatches: 36, Indels: 28
0.74 0.14 0.11
Matches are distributed among these distances:
16 2 0.01
17 55 0.30
18 91 0.49
19 25 0.13
20 7 0.04
21 6 0.03
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (18 bp):
AAAATTTTTGAAAACACG
Found at i:13389249 original size:5 final size:5
Alignment explanation
Indices: 13389239--13389263 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13389229 TAAAATTATT
13389239 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
13389264 ATTGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:13389463 original size:12 final size:12
Alignment explanation
Indices: 13389446--13389535 Score: 76
Period size: 12 Copynumber: 7.2 Consensus size: 12
13389436 AAATTGAACC
13389446 CTTTTTTTTCTT
1 CTTTTTTTTCTT
13389458 CTTTTTTTTC-T
1 CTTTTTTTTCTT
13389469 CTTTTTTTTCTT
1 CTTTTTTTTCTT
* *
13389481 TTTCTTTTTGTTTT
1 CTT-TTTTT-TCTT
*
13389495 CTTTTTTCTTTTTT
1 C-TTTTT-TTTCTT
*
13389509 CTTCTGTTTTC-T
1 CTT-TTTTTTCTT
13389521 CTTTTTTTTTCTT
1 C-TTTTTTTTCTT
13389534 CT
1 CT
13389536 CTGCTGGGCC
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
11 11 0.17
12 22 0.34
13 14 0.22
14 13 0.20
15 4 0.06
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (12 bp):
CTTTTTTTTCTT
Found at i:13389464 original size:11 final size:11
Alignment explanation
Indices: 13389448--13389535 Score: 69
Period size: 10 Copynumber: 8.1 Consensus size: 11
13389438 ATTGAACCCT
13389448 TTTTTTTCTTC
1 TTTTTTTCTTC
13389459 -TTTTTT-TTC
1 TTTTTTTCTTC
13389468 TCTTTTTT-TTC
1 T-TTTTTTCTTC
* *
13389479 TTTTTCTTTTTG
1 TTTTT-TTCTTC
*
13389491 TTTTCTTTTTTC
1 TTTT-TTTCTTC
13389503 -TTTTTTCTTC
1 TTTTTTTCTTC
*
13389513 TGTTTTCTCTT-
1 T-TTTTTTCTTC
13389524 TTTTTTTCTTC
1 TTTTTTTCTTC
13389535 T
1 T
13389536 CTGCTGGGCC
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
9 3 0.05
10 24 0.38
11 17 0.27
12 19 0.30
13 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:13389484 original size:17 final size:17
Alignment explanation
Indices: 13389462--13389529 Score: 95
Period size: 17 Copynumber: 3.9 Consensus size: 17
13389452 TTTCTTCTTT
13389462 TTTTTCTCTTTTTTTTC
1 TTTTTCTCTTTTTTTTC
13389479 TTTTTCT-TTTTGTTTTC
1 TTTTTCTCTTTT-TTTTC
13389496 TTTTT-TCTTTTTTCTTC
1 TTTTTCTCTTTTTT-TTC
13389513 TGTTTTCTCTTTTTTTT
1 T-TTTTCTCTTTTTTTT
13389530 TCTTCTCTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.15
17 25 0.54
18 6 0.13
19 8 0.17
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTCTCTTTTTTTTC
Found at i:13389488 original size:24 final size:24
Alignment explanation
Indices: 13389446--13389529 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 24
13389436 AAATTGAACC
*
13389446 CTTTTTTTTCTTCTT-TTTTTTCT
1 CTTTTTTTTCTTTTTCTTTTTTCT
*
13389469 CTTTTTTTTCTTTTTCTTTTTGTTTT
1 CTTTTTTTTCTTTTTC-TTTT-TTCT
* *
13389495 CTTTTTTCTTTTTTCTTCTGTTTTCT
1 CTTTTTT-TTCTTT-TTCTTTTTTCT
13389521 CTTTTTTTT
1 CTTTTTTTT
13389530 TCTTCTCTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
23 14 0.27
25 6 0.12
26 20 0.39
27 8 0.16
28 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.82
Consensus pattern (24 bp):
CTTTTTTTTCTTTTTCTTTTTTCT
Found at i:13389520 original size:7 final size:6
Alignment explanation
Indices: 13389450--13389533 Score: 63
Period size: 6 Copynumber: 14.3 Consensus size: 6
13389440 TGAACCCTTT
* *
13389450 TTTTTC TTCTTT- TTTTTC TCTTT- TTTTTC TTTTTC TTTTT- GTTTTC
1 TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
13389496 TTTTT- TCTTTT- TTCTTC TGTTTTC TCTTTT- TTTTTC TT
1 TTTTTC T-TTTTC TTTTTC T-TTTTC T-TTTTC TTTTTC TT
13389534 CTCTGCTGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
5 19 0.30
6 32 0.51
7 12 0.19
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:13389530 original size:24 final size:23
Alignment explanation
Indices: 13389446--13389533 Score: 56
Period size: 25 Copynumber: 3.7 Consensus size: 23
13389436 AAATTGAACC
* *
13389446 CTTTTTTTTCTTCTTTTTTTTCT
1 CTTTTTTTTTTTCTTTGTTTTCT
13389469 CTTTTTTTTCTTTTTCTTTTTGTTTTCT
1 C--TTTTTT-TTTTTC--TTTGTTTTCT
*
13389497 -TTTTTCTTTTTTC-TTCTGTTT-T
1 CTTTTT-TTTTTTCTTTGT-TTTCT
*
13389519 CTCTTTTTTTTTCTT
1 CTTTTTTTTTTTCTT
13389534 CTCTGCTGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
22 11 0.21
23 9 0.17
25 17 0.33
26 6 0.12
28 9 0.17
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (23 bp):
CTTTTTTTTTTTCTTTGTTTTCT
Found at i:13389646 original size:32 final size:30
Alignment explanation
Indices: 13389556--13389625 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
13389546 GACCTGTTAG
13389556 GCCTGCACACCTACTGGCTGCTGCTGGGCT
1 GCCTGCACACCTACTGGCTGCTGCTGGGCT
13389586 GCCTGCACACCTACTGGCTGCTGCTGGGCT
1 GCCTGCACACCTACTGGCTGCTGCTGGGCT
13389616 GCCTGCACAC
1 GCCTGCACAC
13389626 TAGGCCTGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.11, C:0.39, G:0.29, T:0.21
Consensus pattern (30 bp):
GCCTGCACACCTACTGGCTGCTGCTGGGCT
Found at i:13389683 original size:26 final size:25
Alignment explanation
Indices: 13389654--13389707 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
13389644 GGCCGCTGGG
* *
13389654 TTTTGGGCTGCTTCTTTCTTTTCTTT
1 TTTTCGGCTGCTTCTTTCTCTT-TTT
*
13389680 TTTTCTGCTGCTTCTTTCTCTTTTT
1 TTTTCGGCTGCTTCTTTCTCTTTTT
13389705 TTT
1 TTT
13389708 GCTTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.00, C:0.20, G:0.11, T:0.69
Consensus pattern (25 bp):
TTTTCGGCTGCTTCTTTCTCTTTTT
Found at i:13389687 original size:23 final size:23
Alignment explanation
Indices: 13389661--13389711 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
13389651 GGGTTTTGGG
13389661 CTGCTTCTTTCTTT-TCTTTTTTT
1 CTGCTTC-TTCTTTCTCTTTTTTT
*
13389684 CTGCTGCTTCTTTCTCTTTTTTT
1 CTGCTTCTTCTTTCTCTTTTTTT
13389707 -TGCTT
1 CTGCTT
13389712 TTTTTTGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.69
Consensus pattern (23 bp):
CTGCTTCTTCTTTCTCTTTTTTT
Found at i:13389822 original size:19 final size:19
Alignment explanation
Indices: 13389798--13389838 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13389788 TGTTAAAATT
13389798 TTTTTCTATTTT-TTCTTTC
1 TTTTTCT-TTTTCTTCTTTC
*
13389817 TTTTTCTTTTTCTTTTTTC
1 TTTTTCTTTTTCTTCTTTC
13389836 TTT
1 TTT
13389839 CCCCCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTTC
Found at i:13389833 original size:13 final size:13
Alignment explanation
Indices: 13389798--13389838 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13389788 TGTTAAAATT
13389798 TTTTTCTATTTTT-
1 TTTTTCT-TTTTTC
*
13389811 TCTTTC-TTTTTC
1 TTTTTCTTTTTTC
13389823 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
13389836 TTT
1 TTT
13389839 CCCCCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 5 0.21
12 5 0.21
13 14 0.58
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:13390006 original size:12 final size:12
Alignment explanation
Indices: 13389973--13390013 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
13389963 TGGTCTCCCC
13389973 TTTTTTCT-TTT
1 TTTTTTCTCTTT
*
13389984 TTCTTTGCTCTTT
1 TT-TTTTCTCTTT
13389997 TTTTTTCTCTTT
1 TTTTTTCTCTTT
13390009 TTTTT
1 TTTTT
13390014 CTTTTGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 2 0.08
12 19 0.73
13 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:13390181 original size:22 final size:21
Alignment explanation
Indices: 13390156--13390206 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
13390146 TGCTCAAAAA
13390156 TTTGTTTTTTTTCTTTTTTTGC
1 TTTGTTTTTTTTCTTTTTTT-C
*
13390178 TTTGTTTTTTTTGTTTTTTTC
1 TTTGTTTTTTTTCTTTTTTTC
13390199 TCTTGTTT
1 T-TTGTTT
13390207 CTCTTTGCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (21 bp):
TTTGTTTTTTTTCTTTTTTTC
Found at i:13390213 original size:23 final size:22
Alignment explanation
Indices: 13390156--13390213 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
13390146 TGCTCAAAAA
* *
13390156 TTTGTTTTTTTTCTTTTTTTGC
1 TTTGTTTTCTTTGTTTTTTTGC
*
13390178 TTTGTTTTTTTTGTTTTTTT-C
1 TTTGTTTTCTTTGTTTTTTTGC
13390199 TCTTGTTTCTCTTTG
1 T-TTGTTT-TCTTTG
13390214 CTGCTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 2 0.06
22 25 0.78
23 5 0.16
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (22 bp):
TTTGTTTTCTTTGTTTTTTTGC
Found at i:13390462 original size:30 final size:29
Alignment explanation
Indices: 13390414--13390512 Score: 119
Period size: 30 Copynumber: 3.4 Consensus size: 29
13390404 TTTTAGGGTC
*
13390414 AAATGTAA-TTCTAGAAAGTTCAAGGGTTA
1 AAATGTAATTTCAAGAAAGTT-AAGGGTTA
* *
13390443 AAATGTAATTTCAAGAAAGTTTAGAGGTTG
1 AAATGTAATTTCAAGAAAGTTAAG-GGTTA
* * *
13390473 AAATGTAATTTCAAAAAAGTTAGGGGTCA
1 AAATGTAATTTCAAGAAAGTTAAGGGTTA
13390502 AAATGTAATTT
1 AAATGTAATTT
13390513 TTTTTAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.40
30 36 0.60
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.32
Consensus pattern (29 bp):
AAATGTAATTTCAAGAAAGTTAAGGGTTA
Found at i:13390992 original size:77 final size:77
Alignment explanation
Indices: 13390795--13391415 Score: 821
Period size: 77 Copynumber: 8.1 Consensus size: 77
13390785 TTTTATTTAA
** * *
13390795 AAAAATACCTCAACATGTGACCCGAGGCTCAACTCACATCTCACAATATGAGTTGA-TTTTTGAA
1 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
* *
13390859 AAACTGAAATTTAA
66 AAACAGAAA-TT-G
* *
13390873 AAGAAATACCTC-GGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTG
1 AA-AAATACCTCAGG-ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
13390936 AAAAACAGAAATTG
64 AAAAACAGAAATTG
*
13390950 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG-
1 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGA
*
13391014 AAAACAGAAACTG
65 AAAACAGAAATTG
13391027 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA
1 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
*
13391091 AAACAGAAACTG
66 AAACAGAAATTG
*
13391103 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
1 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
* *
13391168 AAATAGAAACTG
66 AAACAGAAATTG
* * * * * *
13391180 AAAAATACCTCAAGATGTGATCCGAGGCTTAACTCACCTCTTGCAATATAAGTTGA-TTTTTAAA
1 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
*
13391244 AAACAGAAATTTA
66 AAACAGAAA-TTG
* *
13391257 AAAAATACCTC-GGCATGTGACCCGAGGCTCAACTCACCTCTCACAATCTGAGTTGATTTCTTTG
1 AAAAATACCTCAGG-ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TTTG
*
13391321 AAAAAAGAGAAATTG
64 -AAAAACAGAAATTG
* * * * *
13391336 GAAAATACCTC--GATGTGACTCGAAGCTCAACTCACCTCTCGCAATATGAGCT-AATTTTTGAA
1 AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
*
13391398 AAACATAAATTG
66 AAACAGAAATTG
13391410 AAAAAT
1 AAAAAT
13391416 GATTCTTGAA
Statistics
Matches: 486, Mismatches: 44, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
74 17 0.03
75 10 0.02
76 101 0.21
77 256 0.53
78 47 0.10
79 45 0.09
80 10 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (77 bp):
AAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
AAACAGAAATTG
Found at i:13391116 original size:153 final size:152
Alignment explanation
Indices: 13390703--13391415 Score: 851
Period size: 153 Copynumber: 4.6 Consensus size: 152
13390693 TTTTTTAACT
* * * * *
13390703 GAAATTGAAAAATACCTCGGCGTGTGACCTGAGGTTCAACTCACCTCTCACAATATGAGTTGATT
1 GAAACTGAAAAATACCTCGG-ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * ** *
13390768 TTTAAAAAATAGAAAATTTTTATTTAAAAAAATACCTCAACATGTGACCCGAGGCTCAACTCACA
65 TTTGAAAAACAG--AA-----A-TT-GAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACC
*
13390833 TCTCACAATATGAGTTGA-TTTTTGAAAAACT
121 TCTCACAATATGAGTTGATTTTTTGAAAAACA
* * * *
13390864 GAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 GAAA-CT-GAA-AAATACCTCGG-ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
13390928 ATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCG
62 A-TTTTTGAAAAACAGAAATTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCA
*
13390993 CATTATGAGTTGATTTTTTTG-AAAACA
126 CAATATGAGTTGA-TTTTTTGAAAAACA
13391020 GAAACTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 GAAACTGAAAAATACCTC-GGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
13391085 TTTGAAAAACAGAAACTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
65 TTTGAAAAACAGAAATTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCACAAT
* *
13391150 ATGAGTTGATTTTTGGAAAAATA
130 ATGAGTTGATTTTTTGAAAAACA
* * * * *
13391173 GAAACTGAAAAATACCTCAAGATGTGATCCGAGGCTTAACTCACCTCTTGCAATATAAGTTGATT
1 GAAACTGAAAAATACCTC-GGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
13391238 TTTAAAAAACAGAAATTTAAAAAATACCTC-GGCATGTGACCCGAGGCTCAACTCACCTCTCACA
65 TTTGAAAAACAGAAA-TTGAAAAATACCTCAGG-ATGTGACCCGAGGCTCAACTCACCTCTCACA
* *
13391302 ATCTGAGTTGATTTCTTTGAAAAAAGA
128 ATATGAGTTGATTT-TTTG-AAAAACA
* * * * * *
13391329 GAAATTGGAAAATACCTC-GATGTGACTCGAAGCTCAACTCACCTCTCGCAATATGAGCTAATTT
1 GAAACTGAAAAATACCTCGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
13391393 TTGAAAAACATAAATTGAAAAAT
66 TTGAAAAACAGAAATTGAAAAAT
13391416 GATTCTTGAA
Statistics
Matches: 490, Mismatches: 49, Indels: 34
0.86 0.09 0.06
Matches are distributed among these distances:
152 6 0.01
153 177 0.36
154 143 0.29
155 55 0.11
156 33 0.07
157 7 0.01
161 4 0.01
162 4 0.01
163 33 0.07
164 28 0.06
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (152 bp):
GAAACTGAAAAATACCTCGGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTGAAAAACAGAAATTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCACAATA
TGAGTTGATTTTTTGAAAAACA
Found at i:13391199 original size:230 final size:228
Alignment explanation
Indices: 13390703--13391415 Score: 869
Period size: 230 Copynumber: 3.1 Consensus size: 228
13390693 TTTTTTAACT
* * * * * *
13390703 GAAATTGAAAAATACCTC-GGCGTGTGACCTGAGGTTCAACTCACCTCTCACAATATGAGTTGAT
1 GAAATTGAAAAATACCTCAAG-ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGAT
* * **
13390767 TTTTAAAAAATAGAAAATTTTTATTTAAAAAAATACCTCAACATGTGACCCGAGGCTCAACTCAC
65 TTTTAAAAAACAG--AA-----ATCT-AAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCAC
* * * *
13390832 ATCTCACAATATGAGTTGATTTTTGAAAAACTGAAATTTAAAAGAAATACCTCGGCATGTG-TCC
122 CTCTCACAATATGAGTTGATTTTTGAAAAACAGAAA-TT-GAA-AAATACCTCGG-ATGTGACCC
*
13390896 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAACA
183 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACA
* * *
13390943 GAAATTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATT
1 GAAATTGAAAAATACCTCAAGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-T
** * *
13391008 TTTTTGAAAACAGAAA-CTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCGCA
65 TTTTAAAAAACAGAAATCTAAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCACA
*
13391072 ATATGAGTTGATTTTTGAAAAACAGAAACTGAAAAATACCTCAGGATGTGACCCGAGGCTCAACT
130 ATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC-GGATGTGACCCGAGGCTCAACT
*
13391137 CACCTCTCGCAATATGAGTTGATTTTTGGAAAAATA
194 CACCTCTCGCAATATGAGTTGATTTTT-GAAAAACA
* * * *
13391173 GAAACTGAAAAATACCTCAAGATGTGATCCGAGGCTTAACTCACCTCTTGCAATATAAGTTGATT
1 GAAATTGAAAAATACCTCAAGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
*
13391238 TTTAAAAAACAGAAATTTAAAAAATACCTC-GGCATGTGACCCGAGGCTCAACTCACCTCTCACA
66 TTTAAAAAACAGAAATCTAAAAAATACCTCAGG-ATGTGACCCGAGGCTCAACTCACCTCTCACA
* * * * *
13391302 ATCTGAGTTGATTTCTTTGAAAAAAGAGAAATTGGAAAATACCTC-GATGTGACTCGAAGCTCAA
130 ATATGAGTTGA-TT-TTTG-AAAAACAGAAATTGAAAAATACCTCGGATGTGACCCGAGGCTCAA
* *
13391366 CTCACCTCTCGCAATATGAGCTAATTTTTGAAAAACA
192 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
*
13391403 TAAATTGAAAAAT
1 GAAATTGAAAAAT
13391416 GATTCTTGAA
Statistics
Matches: 420, Mismatches: 43, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
229 36 0.09
230 171 0.41
231 47 0.11
232 72 0.17
233 23 0.05
234 1 0.00
239 2 0.00
240 55 0.13
241 13 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (228 bp):
GAAATTGAAAAATACCTCAAGATGTGACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
TTTAAAAAACAGAAATCTAAAAAATACCTCAGGATGTGACCCGAGGCTCAACTCACCTCTCACAA
TATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCGGATGTGACCCGAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTGAAAAACA
Found at i:13399718 original size:35 final size:35
Alignment explanation
Indices: 13399672--13399973 Score: 242
Period size: 35 Copynumber: 8.5 Consensus size: 35
13399662 AATACAAATT
* *
13399672 TTTTTTAAAACACGAGAATTTTAGAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTAGAAACACGAAAA
* **
13399707 TTTTTTG-AAACACGGAAA-TTTATGAAACACGGGCAA
1 -TTTTTGAAAACACGAAAATTTTA-GAAACAC-GAAAA
* * * * *
13399743 TTTTTGAAAACACAAAAATTTTTGAAAGACGGGAAT
1 TTTTTGAAAACACGAAAATTTTAGAAACAC-GAAAA
* * *
13399779 TTTTTGCAAACACGGAAA-TTTATGAAACACGAGAATTT
1 TTTTTGAAAACACGAAAATTTTA-GAAACACGA-AA--A
*
13399817 TTTTTGAAAACACGAAAATTTTCGAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTAGAAACACGAAAA
*
13399852 TTTTTGAAAACACGAAAATTTGT-GAAACACGAGAA
1 TTTTTGAAAACACGAAAATTT-TAGAAACACGAAAA
13399887 TTTTTGAAAACACGAAAATTGTT-GAAAACACGAAAAA
1 TTTTTGAAAACACGAAAATT-TTAG-AAACACG-AAAA
* * * * *
13399924 ATTTTG-AAACATCG-GAGTTTTTGAAAACACGAAGA
1 TTTTTGAAAACA-CGAAAATTTTAG-AAACACGAAAA
13399959 TTTTTG-AAACACGAA
1 TTTTTGAAAACACGAA
13399974 TTTTTTATTT
Statistics
Matches: 221, Mismatches: 29, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
34 6 0.03
35 95 0.43
36 76 0.34
37 15 0.07
38 26 0.12
39 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTAGAAACACGAAAA
Found at i:13399973 original size:17 final size:17
Alignment explanation
Indices: 13399673--13399973 Score: 262
Period size: 18 Copynumber: 16.9 Consensus size: 17
13399663 ATACAAATTT
* *
13399673 TTTTTAAAACACGAGAA
1 TTTTTGAAACACGAAAA
*
13399690 TTTTAGAAACACGAAAA
1 TTTTTGAAACACGAAAA
*
13399707 TTTTTTGAAACACGGAAA
1 -TTTTTGAAACACGAAAA
* **
13399725 TTTATGAAACACGGGCAA
1 TTTTTGAAACAC-GAAAA
*
13399743 TTTTTGAAAACACAAAAA
1 TTTTTG-AAACACGAAAA
* * *
13399761 TTTTTGAAAGACGGGAAT
1 TTTTTGAAACAC-GAAAA
*
13399779 TTTTTGCAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* *
13399797 TTTATGAAACACGAGAATTT
1 TTTTTGAAACACGA-AA--A
13399817 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
13399835 TTTTCGAAACACGAAAA
1 TTTTTGAAACACGAAAA
13399852 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
13399870 TTTGTGAAACACGAGAA
1 TTTTTGAAACACGAAAA
13399887 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
13399905 TTGTTGAAAACACGAAAAA
1 TTTTTG-AAACACG-AAAA
* * *
13399924 ATTTTGAAACATCG-GAG
1 TTTTTGAAACA-CGAAAA
*
13399941 TTTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
13399959 TTTTTGAAACACGAA
1 TTTTTGAAACACGAA
13399974 TTTTTTATTT
Statistics
Matches: 232, Mismatches: 37, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
17 85 0.37
18 111 0.48
19 21 0.09
20 7 0.03
21 8 0.03
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.28
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:13400290 original size:16 final size:16
Alignment explanation
Indices: 13400266--13400312 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
13400256 TTATTTAAAA
*
13400266 TAAAATAAAATTATAT
1 TAAATTAAAATTATAT
13400282 TAAATTAAAATTGA-AT
1 TAAATTAAAATT-ATAT
* *
13400298 TATATTAAAAATATA
1 TAAATTAAAATTATA
13400313 AATACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTAAAATTATAT
Found at i:13400290 original size:21 final size:21
Alignment explanation
Indices: 13400251--13400316 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
13400241 CTTTATTTAT
13400251 TAAAATTAT-TTAAAATAAAA
1 TAAAATTATATTAAAATAAAA
*
13400271 TAAAATTATATTAAATTAAAA
1 TAAAATTATATTAAAATAAAA
**
13400292 TTGAATTATATTAAAAATATAAA
1 TAAAATTATATT-AAAATA-AAA
13400315 TA
1 TA
13400317 CAAAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 9 0.24
21 20 0.53
22 5 0.13
23 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTATATTAAAATAAAA
Found at i:13400477 original size:10 final size:9
Alignment explanation
Indices: 13400463--13400529 Score: 64
Period size: 9 Copynumber: 7.0 Consensus size: 9
13400453 AAATTGAACC
13400463 CTTTTTTTT
1 CTTTTTTTT
*
13400472 CCTTTTTTT
1 CTTTTTTTT
13400481 CTTTTTTCTT
1 CTTTTTT-TT
*
13400491 -TTTGTTTT
1 CTTTTTTTT
13400499 CTTTTTTCTT
1 CTTTTTT-TT
13400509 CTTTTTTCCTCT
1 CTTTTTT--T-T
13400521 CTTTTTTTT
1 CTTTTTTTT
13400530 TTCTCTGCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
8 2 0.04
9 25 0.51
10 12 0.24
11 2 0.04
12 8 0.16
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:13400486 original size:18 final size:18
Alignment explanation
Indices: 13400463--13400515 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
13400453 AAATTGAACC
13400463 CTTTTTT-TTCCTTTTTTT
1 CTTTTTTCTT-CTTTTTTT
13400481 CTTTTTTCTT-TTTGTTTT
1 CTTTTTTCTTCTTT-TTTT
13400499 CTTTTTTCTTCTTTTTT
1 CTTTTTTCTTCTTTTTT
13400516 CCTCTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.09
18 24 0.75
19 5 0.16
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
CTTTTTTCTTCTTTTTTT
Found at i:13400803 original size:47 final size:46
Alignment explanation
Indices: 13400717--13400807 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
13400707 GGCTGTTAAA
13400717 TTTTTTTCTTTTTCTTTTTTCTTTCCCCCTTTCTTCTTCCTTCTTC
1 TTTTTTTCTTTTTCTTTTTTCTTTCCCCCTTTCTTCTTCCTTCTTC
*
13400763 TTTTTCTT-TTTTTCTTTATTTCTTCTTCCCCTTT-TTCTTCCTTCT
1 TTTTT-TTCTTTTTCTTT-TTTCTT-TCCCCCTTTCTTCTTCCTTCT
13400808 CCATTCAGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
46 14 0.34
47 19 0.46
48 8 0.20
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (46 bp):
TTTTTTTCTTTTTCTTTTTTCTTTCCCCCTTTCTTCTTCCTTCTTC
Found at i:13400945 original size:10 final size:12
Alignment explanation
Indices: 13400895--13400945 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
13400885 CCCTTTCCCC
*
13400895 CTTTTTCTTTTT
1 CTTTTTCTTTCT
*
13400907 C-TCTTCTTTCCT
1 CTTTTTCTTT-CT
13400919 CTTTTTCTTTCT
1 CTTTTTCTTTCT
13400931 CTTTTT-TTT-T
1 CTTTTTCTTTCT
13400941 CTTTT
1 CTTTT
13400946 GCTTGCAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.18
11 10 0.29
12 11 0.32
13 7 0.21
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
CTTTTTCTTTCT
Found at i:13401440 original size:29 final size:29
Alignment explanation
Indices: 13401339--13401447 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 29
13401329 TTGGGAAATT
13401339 TTAGGGTCAAAATATAA-TTC-TAGAAAAG
1 TTAGGGTCAAAATATAATTTCATA-AAAAG
** *
13401367 TTCAATAGTTAAAATATAATTTCA-AAAAAG
1 TT--AGGGTCAAAATATAATTTCATAAAAAG
*
13401397 TTTAGGGATTAAAATATAATTTCATAAAAA-
1 -TTAGGG-TCAAAATATAATTTCATAAAAAG
*
13401427 TTAGGAGTCAAAATACAATTT
1 TTAGG-GTCAAAATATAATTT
13401448 TTTTAAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
28 2 0.03
29 19 0.29
30 34 0.52
31 11 0.17
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (29 bp):
TTAGGGTCAAAATATAATTTCATAAAAAG
Found at i:13401702 original size:23 final size:23
Alignment explanation
Indices: 13401672--13401717 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
13401662 GACTTGGAAA
13401672 TTCTCAACTTTGCTTTTTTCCAT
1 TTCTCAACTTTGCTTTTTTCCAT
13401695 TTCTCAACTTTGCTTTTTTCCAT
1 TTCTCAACTTTGCTTTTTTCCAT
13401718 GCCTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.04, T:0.57
Consensus pattern (23 bp):
TTCTCAACTTTGCTTTTTTCCAT
Found at i:13412678 original size:29 final size:29
Alignment explanation
Indices: 13412623--13412679 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
13412613 TTCAAAAAAT
* *
13412623 TTAAAAATTCTAATTAAGCCTTTAATTTG
1 TTAAAAATTCTAATTAAACCTTAAATTTG
*
13412652 TTAAAAATTTTAATTAAAACC-TAAATTT
1 TTAAAAATTCTAATT-AAACCTTAAATTT
13412680 TTTTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (29 bp):
TTAAAAATTCTAATTAAACCTTAAATTTG
Found at i:13419271 original size:29 final size:27
Alignment explanation
Indices: 13419207--13419271 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 27
13419197 TTTTTATATG
*
13419207 TATAATTATACTAAATTAAAATTCATG
1 TATAATTATACTAAATTAAAATTCATA
*
13419234 TATTAAATTATACATTAAATTAAAGTTCATA
1 TA-T-AATTATAC--TAAATTAAAATTCATA
13419265 TATAATT
1 TATAATT
13419272 TTGAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 12 0.38
30 1 0.03
31 16 0.50
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (27 bp):
TATAATTATACTAAATTAAAATTCATA
Found at i:13421726 original size:15 final size:15
Alignment explanation
Indices: 13421706--13421734 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13421696 CAAATAAACT
13421706 GTAAAATATGAAATA
1 GTAAAATATGAAATA
13421721 GTAAAATATGAAAT
1 GTAAAATATGAAAT
13421735 TCGGTCATCT
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:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (15 bp):
GTAAAATATGAAATA
Found at i:13430109 original size:2 final size:2
Alignment explanation
Indices: 13430102--13430133 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13430092 AACATGCATA
13430102 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13430134 CAGTTTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13431387 original size:39 final size:39
Alignment explanation
Indices: 13431293--13431452 Score: 227
Period size: 39 Copynumber: 4.0 Consensus size: 39
13431283 GGCCCATTTT
*
13431293 TATTTTAAAAATTTTAAAAAATTAAAAAAAAGTATTTTAAAA
1 TATTTT-AAAATTTAAAAAAATT--AAAAAAGTATTTTAAAA
13431335 TA-TTTAAAA-TTAAAAAAATTAAAAAAGTATTTTAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAA
*
13431372 TATTTTAAAATTTAAAAAAATTTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTT-AAAA
13431412 TATTTTAAAATTTAAAAAAAATTTAAAAAA-TATTTTAAAA
1 TATTTTAAAATTT-AAAAAAA-TTAAAAAAGTATTTTAAAA
13431452 T
1 T
13431453 TAAAAAAATA
Statistics
Matches: 110, Mismatches: 3, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
37 19 0.17
38 7 0.06
39 33 0.30
40 26 0.24
41 16 0.15
42 9 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (39 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAA
Found at i:13431409 original size:12 final size:11
Alignment explanation
Indices: 13431356--13431451 Score: 75
Period size: 11 Copynumber: 9.4 Consensus size: 11
13431346 AAAAAAATTA
13431356 AAAAAGTATTTT
1 AAAAA-TATTTT
13431368 -AAAATATTTT
1 AAAAATATTTT
13431378 --AAA-A-TTT
1 AAAAATATTTT
*
13431385 AAAAA-AATTT
1 AAAAATATTTT
13431395 AAAAAGTATTTT
1 AAAAA-TATTTT
13431407 AAAAATATTTT
1 AAAAATATTTT
*
13431418 --AAA-ATTTA
1 AAAAATATTTT
* *
13431426 AAAAAAATTTA
1 AAAAATATTTT
13431437 AAAAATATTTT
1 AAAAATATTTT
13431448 AAAA
1 AAAA
13431452 TTAAAAAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
7 3 0.04
8 5 0.07
9 10 0.14
10 17 0.24
11 28 0.39
12 9 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:13431441 original size:30 final size:30
Alignment explanation
Indices: 13431388--13431460 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
13431378 AAAATTTAAA
** *
13431388 AAAATTTAAAAAGTATTTTAAAAATATTTT
1 AAAATTTAAAAAAAATTTAAAAAATATTTT
13431418 AAAATTTAAAAAAAATTTAAAAAATATTTT
1 AAAATTTAAAAAAAATTTAAAAAATATTTT
13431448 AAAA-TTAAAAAAA
1 AAAATTTAAAAAAA
13431461 TAAATATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 9 0.22
30 31 0.77
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTTAAAAAAAATTTAAAAAATATTTT
Found at i:13431451 original size:10 final size:10
Alignment explanation
Indices: 13431293--13431452 Score: 75
Period size: 10 Copynumber: 16.1 Consensus size: 10
13431283 GGCCCATTTT
13431293 TATTTTAAAA
1 TATTTTAAAA
13431303 -ATTTTAAAA
1 TATTTTAAAA
* **
13431312 AATTAAAAAAAA
1 TATT--TTAAAA
13431324 GTATTTTAAAA
1 -TATTTTAAAA
13431335 TA-TTT-AAA
1 TATTTTAAAA
*
13431343 -A-TTAAAAA
1 TATTTTAAAA
* **
13431351 AATTAAAAAA
1 TATTTTAAAA
13431361 GTATTTTAAAA
1 -TATTTTAAAA
13431372 TATTTT-AAA
1 TATTTTAAAA
*
13431381 -ATTTAAAAA
1 TATTTTAAAA
* *
13431390 AATTTAAAAA
1 TATTTTAAAA
13431400 GTATTTTAAAAA
1 -TATTTT-AAAA
13431412 TATTTTAAAA
1 TATTTTAAAA
**
13431422 T-TTAAAAAA
1 TATTTTAAAA
* *
13431431 AATTTAAAAAA
1 TATTT-TAAAA
13431442 TATTTTAAAA
1 TATTTTAAAA
13431452 T
1 T
13431453 TAAAAAAATA
Statistics
Matches: 117, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
7 3 0.03
8 10 0.09
9 25 0.21
10 38 0.32
11 30 0.26
12 8 0.07
13 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:13437958 original size:307 final size:306
Alignment explanation
Indices: 13437349--13438080 Score: 731
Period size: 307 Copynumber: 2.4 Consensus size: 306
13437339 TTATGCGCAT
* *
13437349 TTTAATCTTTTTTTTTTATTTTAACACCATACATATTTCATGTGTTATTATTAATTAGTTTCAAA
1 TTTAATCTTTTTTTTTTATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTC-AA
* * *
13437414 CCATACA-TTTCATTATTTATTGTATGTTACTTTTAAACACAAATTTACATTCTAAATACATGGT
65 CCATA-AGTTTCATTATTTATTGTATTTTA-TTTTTAACACATATTTACATTCTAAATACATGGT
* * ** * * * * *
13437478 TTTCATATGCGTACGCATGTTATAGAGTTTCTAGTATTAATAATATTGTTAATTGAATTGGTATC
128 TTCCACACACATACACATGTGATAGAGTTTCTA-TATAAATAATATTATTAATTGAATTGGTATC
* * * * * * *
13437543 ATGAATTAACTCGACACCAAATCATGGTTGATGACAACACATTGATCAATAATTGTATTCATTTA
192 ATAAATTAACTCGAAAACAAATCAAGGTTGATGACAACACATTGATAAACAATTATATTCATTTA
* * * * ** *
13437608 ATATTTTTAATTTGATTTATTTATGTGCTTAAAATTCGTTTTACTCACAA
257 ATATTCTAAATCTAACGTATTTATATGCTTAAAATTCGTTTTACTCACAA
* *
13437658 TTTAATCTTTTTTTTTTCATTTTAGCAACATACATATTTCATGTGCTATTATTAATTAGTTTTAG
1 TTTAATCTTTTTTTTTT-ATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTCA-
*** **
13437723 ACCATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATATTTGTGTTCTAAATATGTGGTT
64 ACCATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATATTTACATTCTAAATACATGGTT
* * * *
13437788 TCCACACATATACACAAT-TGATAGA-TATTCT-TATAAATAATATTATTGATTGAGTTGGTGTC
129 TCCACACACATACAC-ATGTGATAGAGT-TTCTATATAAATAATATTATTAATTGAATTGGTATC
* *
13437850 GTAAATTAACT-TAAAACAAA-CTAAGGATTGATGACAACACCA-TGATAAACAATTATATTCA-
192 ATAAATTAACTCGAAAACAAATC-AAGG-TTGATGACAACA-CATTGATAAACAATTATATTCAT
** * *
13437911 TTAAGTATTCTAAATCTAACGTATTTATATTTTTAAATTTTGTTTTACTCACAA
254 TTAA-TATTCTAAATCTAACGTATTTATATGCTTAAAATTCGTTTTACTCACAA
* * * *
13437965 TTTAA------TATTTTATTTTAGTAACGTACATATTTCATGTGTTATTGTTAATTA-TTTCAAC
1 TTTAATCTTTTTTTTTTATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTCAAC
* * * * *
13438023 TAATATGTTTTATTATTTATTATATTTTATTTTTAA-ACATATTTCTATATTCTAAATA
66 -CATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATA-TT-TACATTCTAAATA
13438081 TATAATTTCT
Statistics
Matches: 354, Mismatches: 57, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
298 7 0.02
299 37 0.10
300 47 0.13
301 5 0.01
305 1 0.00
306 13 0.04
307 106 0.30
308 3 0.01
309 65 0.18
310 70 0.20
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (306 bp):
TTTAATCTTTTTTTTTTATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTCAAC
CATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATATTTACATTCTAAATACATGGTTTC
CACACACATACACATGTGATAGAGTTTCTATATAAATAATATTATTAATTGAATTGGTATCATAA
ATTAACTCGAAAACAAATCAAGGTTGATGACAACACATTGATAAACAATTATATTCATTTAATAT
TCTAAATCTAACGTATTTATATGCTTAAAATTCGTTTTACTCACAA
Found at i:13440457 original size:17 final size:17
Alignment explanation
Indices: 13440435--13440487 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
13440425 ATATGGAATC
*
13440435 TAATCTTCTAAGATATG
1 TAATCTTATAAGATATG
*
13440452 TAATCTTAGATATGATATG
1 TAATCTT--ATAAGATATG
*
13440471 TAATCTTAGAAGATATG
1 TAATCTTATAAGATATG
13440488 ATTCCTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 15 0.50
19 15 0.50
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (17 bp):
TAATCTTATAAGATATG
Found at i:13447847 original size:3 final size:3
Alignment explanation
Indices: 13447841--13447960 Score: 68
Period size: 3 Copynumber: 40.0 Consensus size: 3
13447831 ACTAATAAAC
* * **
13447841 TAA TAA TAA GAA TAA TAA -AA TACA GTAA -AA TAA TAG TAA TCC TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA
* * * ** * *
13447886 -AA -AA TAC TAA GAA TAC TAA TGT TAA TAA TAA AAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
13447932 CAA TAA TAA TAAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA T-AA TAA TAA TAA
13447961 AAGCAAAAAC
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
2 8 0.09
3 68 0.79
4 8 0.09
5 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:13458896 original size:30 final size:30
Alignment explanation
Indices: 13458860--13458924 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
13458850 GAGATACTGT
*
13458860 TTGAGACAT-ATATAGAAGGTGAATCTAGAA
1 TTGAGAC-TCATATAGAAGGTGAATCCAGAA
* *
13458890 TTGAGACTCATATAGAAGGTGTATCCAGTA
1 TTGAGACTCATATAGAAGGTGAATCCAGAA
13458920 TTGAG
1 TTGAG
13458925 GATCTAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (30 bp):
TTGAGACTCATATAGAAGGTGAATCCAGAA
Found at i:13461738 original size:21 final size:21
Alignment explanation
Indices: 13461707--13461761 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
13461697 TTCCAAAGTG
13461707 TGTCATGACATCGAACCCCGA
1 TGTCATGACATCGAACCCCGA
* * *
13461728 TGT-AGTGACATAGAACCTCTA
1 TGTCA-TGACATCGAACCCCGA
13461749 TGTCATGACATCG
1 TGTCATGACATCG
13461762 CTGCAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TGTCATGACATCGAACCCCGA
Found at i:13474318 original size:23 final size:23
Alignment explanation
Indices: 13474288--13474334 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13474278 TTAGCACATG
*
13474288 TTAGACACATCTTTCATATTGTA
1 TTAGACACATCCTTCATATTGTA
13474311 TTAGACACATCCTTCATATTGTA
1 TTAGACACATCCTTCATATTGTA
13474334 T
1 T
13474335 GATTTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (23 bp):
TTAGACACATCCTTCATATTGTA
Found at i:13475375 original size:30 final size:29
Alignment explanation
Indices: 13475339--13475395 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
13475329 ACAATCTTTA
13475339 ATTTTTTAAAGGGCAACACCTATATACTCT
1 ATTTTTTAAAGGGCAACACCTAT-TACTCT
13475369 ATTTTTTAAAGGGCAACACCTATTACT
1 ATTTTTTAAAGGGCAACACCTATTACT
13475396 ATAACCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (29 bp):
ATTTTTTAAAGGGCAACACCTATTACTCT
Found at i:13481182 original size:23 final size:24
Alignment explanation
Indices: 13481132--13481182 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
13481122 AACACCGCTG
*
13481132 AAGCGGATAAACTGACCACCGTCA
1 AAGCGGATAAACTGACCACCGCCA
* * *
13481156 AAGCGGAT-AGCTGAGCACCGCCC
1 AAGCGGATAAACTGACCACCGCCA
13481179 AAGC
1 AAGC
13481183 AAATAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.33, C:0.31, G:0.25, T:0.10
Consensus pattern (24 bp):
AAGCGGATAAACTGACCACCGCCA
Found at i:13485143 original size:138 final size:138
Alignment explanation
Indices: 13484992--13485271 Score: 461
Period size: 138 Copynumber: 2.0 Consensus size: 138
13484982 AGTAGAAAGG
*
13484992 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTATTTTATATTTTGACCAAAATTAATTAA
* *
13485057 TATAACTGTTTATAATAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATAATAATAAATTCGGTAAAATATATACAATTAATATTTTATATAAATCAAATT
*
13485122 TATATATT
131 CATATATT
***
13485130 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTATTTTATATTTTGATTGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTATTTTATATTTTGACCAAAATTAATTAA
* * * *
13485195 TATAATTGTTTATATTCATAAATTCGGTAAAATATATATAATTAATATTTTATATAAATCAAATT
66 TATAACTGTTTATAATAATAAATTCGGTAAAATATATACAATTAATATTTTATATAAATCAAATT
13485260 CATATATT
131 CATATATT
13485268 AATT
1 AATT
13485272 TTATCTATAT
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
138 131 1.00
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (138 bp):
AATTATATTATTTCCAAAAGAATATTAATTTTCATGTATTTTATATTTTGACCAAAATTAATTAA
TATAACTGTTTATAATAATAAATTCGGTAAAATATATACAATTAATATTTTATATAAATCAAATT
CATATATT
Found at i:13487910 original size:13 final size:13
Alignment explanation
Indices: 13487892--13487920 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13487882 ATGGCCAAAA
13487892 TGATTGCATCCTT
1 TGATTGCATCCTT
13487905 TGATTGCATCCTT
1 TGATTGCATCCTT
13487918 TGA
1 TGA
13487921 GTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (13 bp):
TGATTGCATCCTT
Found at i:13491372 original size:32 final size:30
Alignment explanation
Indices: 13491315--13491382 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 30
13491305 TTCTAGAAAA
*
13491315 TTTTTAATTTTTTTAACTTTCTTTATATCT
1 TTTTTAATTTTTTTAAATTTCTTTATATCT
*
13491345 TTTTTGAATTTTTTTTGAAATTT-TTTATA-AT
1 TTTTT-AA-TTTTTTT-AAATTTCTTTATATCT
13491376 TTTTTAA
1 TTTTTAA
13491383 AAATATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 7 0.21
31 8 0.24
32 13 0.39
33 5 0.15
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (30 bp):
TTTTTAATTTTTTTAAATTTCTTTATATCT
Found at i:13491381 original size:10 final size:9
Alignment explanation
Indices: 13491315--13491380 Score: 51
Period size: 11 Copynumber: 6.4 Consensus size: 9
13491305 TTCTAGAAAA
13491315 TTTTTAATT
1 TTTTTAATT
13491324 TTTTTAACTT
1 TTTTTAA-TT
*
13491334 TCTTTATATCT
1 TTTTTA-AT-T
13491345 TTTTTGAATTT
1 TTTTT-AA-TT
13491356 TTTTTGAAATT
1 TTTTT--AATT
13491367 TTTTATAATT
1 TTTT-TAATT
13491377 TTTT
1 TTTT
13491381 AAAAATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
9 7 0.15
10 16 0.34
11 19 0.40
12 5 0.11
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTTAATT
Found at i:13491422 original size:19 final size:19
Alignment explanation
Indices: 13491377--13491439 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
13491367 TTTTATAATT
13491377 TTTTAAAAATATAAATTTTAGAA
1 TTTTAAAAA-AT--ATTTTA-AA
* *
13491400 TTTTTATAAATATTTTAAA
1 TTTTAAAAAATATTTTAAA
*
13491419 TTTTAAAAAATATTTTGAA
1 TTTTAAAAAATATTTTAAA
13491438 TT
1 TT
13491440 ATTTTGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 20 0.57
20 6 0.17
22 2 0.06
23 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTAAAAAATATTTTAAA
Found at i:13491864 original size:24 final size:25
Alignment explanation
Indices: 13491810--13491864 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
13491800 ATTTTCAATC
*
13491810 TTATTATTAAATTCACAGTTTAAAA
1 TTATTAATAAATTCACAGTTTAAAA
**
13491835 GAATTAATAATATTCA-A-TTTAAAA
1 TTATTAATAA-ATTCACAGTTTAAAA
13491859 TTATTA
1 TTATTA
13491865 GTTAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
24 11 0.46
25 8 0.33
26 5 0.21
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (25 bp):
TTATTAATAAATTCACAGTTTAAAA
Found at i:13493344 original size:29 final size:29
Alignment explanation
Indices: 13493304--13493374 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
13493294 CACAATAACG
* * *
13493304 TAAGTGACTAAAGCGCAATATTTCAAACA
1 TAAGTGACTAAAACGAAACATTTCAAACA
*
13493333 TCAGTGACTAAAACGAAACATTTCAAACA
1 TAAGTGACTAAAACGAAACATTTCAAACA
*
13493362 TAAGTGAGTAAAA
1 TAAGTGACTAAAA
13493375 TGTAACCTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (29 bp):
TAAGTGACTAAAACGAAACATTTCAAACA
Found at i:13497599 original size:8 final size:8
Alignment explanation
Indices: 13497586--13497614 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
13497576 ACCCGAGACT
13497586 CACTGTAA
1 CACTGTAA
13497594 CACTGTAA
1 CACTGTAA
13497602 CACTGTAA
1 CACTGTAA
13497610 CACTG
1 CACTG
13497615 ATCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:13502913 original size:65 final size:65
Alignment explanation
Indices: 13502809--13502938 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
13502799 CCAAAACTAT
*
13502809 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTCGTCTAG
1 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTAGTCTAG
*
13502874 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTTGATTAGTCTAG
1 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTAGTCTAG
13502939 GATGAACACG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (65 bp):
AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTAGTCTAG
Found at i:13503335 original size:69 final size:68
Alignment explanation
Indices: 13503236--13503370 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
13503226 TGATTAAACT
* *
13503236 TAATCACTTTAATATTAAATTAATATAATACTTATCAAAATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATAC-TATCAAAATAAATATTAAATTAAATTTAATATT
13503301 AAGA
65 AAGA
* * *
13503305 TAATCACTTTAATGTTAAATTAATAAAATACTATCAAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATCAAAATAAATATTAAATTAAATTTAATATTA
13503370 A
66 A
13503371 ATCTATTAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 32 0.52
69 29 0.48
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATCAAAATAAATATTAAATTAAATTTAATATTA
AGA
Found at i:13506531 original size:15 final size:17
Alignment explanation
Indices: 13506511--13506544 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13506501 CCCTACTTAG
13506511 AAAA-TTTCAT-CCTCT
1 AAAATTTTCATCCCTCT
13506526 AAAATTTTCATCCCTCT
1 AAAATTTTCATCCCTCT
13506543 AA
1 AA
13506545 TAGCCCAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTTTCATCCCTCT
Found at i:13517087 original size:30 final size:31
Alignment explanation
Indices: 13517053--13517116 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
13517043 ACTTAGTTTA
13517053 TTGTTAA-TTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
* * *
13517083 TTGTTAATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
13517114 TTG
1 TTG
13517117 CTTATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGACAT
Found at i:13517491 original size:29 final size:30
Alignment explanation
Indices: 13517459--13517545 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 30
13517449 TTTAATGTAT
13517459 AATTATATACAT-AAACTTTAATTTGGTAC
1 AATTATATACATGAAACTTTAATTTGGTAC
* * * *
13517488 AATTATACACGTGAAACTCTAATTGTGGTTC
1 AATTATATACATGAAACTTTAATT-TGGTAC
* * *
13517519 AAATGTATACTTGAAACTTTAATTTGG
1 AATTATATACATGAAACTTTAATTTGG
13517546 ATTTAATCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 10 0.21
30 13 0.28
31 24 0.51
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (30 bp):
AATTATATACATGAAACTTTAATTTGGTAC
Found at i:13517724 original size:31 final size:30
Alignment explanation
Indices: 13517686--13517745 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
13517676 GAATTGGATC
* *
13517686 AAATCAAAATTTCATGTATA-AATTTACACAA
1 AAATC-AAAGTTCATATATATAA-TTACACAA
13517717 AAATCAAAGTTCATATATATAATTACACA
1 AAATCAAAGTTCATATATATAATTACACA
13517746 TTAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATATATATAATTACACAA
Found at i:13517743 original size:30 final size:31
Alignment explanation
Indices: 13517686--13517772 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
13517676 GAATTGGATC
* *
13517686 AAATCAAAATTTCATGTATAAATTTACACAA
1 AAATCAAAAGTTCATATATAAATTTACACAA
*
13517717 AAATC-AAAGTTCATATATATAA-TTACACATT
1 AAATCAAAAGTTCATATATA-AATTTACACA-A
*
13517748 AAA-CTAAAA-TTCATATATAATTTTA
1 AAATC-AAAAGTTCATATATAAATTTA
13517773 ATATTTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
30 21 0.45
31 23 0.49
32 3 0.06
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (31 bp):
AAATCAAAAGTTCATATATAAATTTACACAA
Found at i:13522409 original size:186 final size:186
Alignment explanation
Indices: 13522095--13522469 Score: 732
Period size: 186 Copynumber: 2.0 Consensus size: 186
13522085 CTCCTTGGTC
*
13522095 TTGTGTTCAAATCTTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
1 TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
13522160 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
66 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
13522225 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
131 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
13522281 TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
1 TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
13522346 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
66 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
*
13522411 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTTGATATTTAGTTCTTCGTT
131 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
13522467 TTG
1 TTG
13522470 GTTTCTTCCT
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 187 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (186 bp):
TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
Found at i:13530525 original size:13 final size:13
Alignment explanation
Indices: 13530507--13530532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13530497 TAAGTAAAAC
13530507 TATTATATTATTA
1 TATTATATTATTA
13530520 TATTATATTATTA
1 TATTATATTATTA
13530533 GAAAAAGCAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:13530616 original size:16 final size:16
Alignment explanation
Indices: 13530595--13530630 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13530585 AACGAAACAG
* *
13530595 AGAAGAAAGGAAGGAA
1 AGAAGAAAAGAAAGAA
13530611 AGAAGAAAAGAAAGAA
1 AGAAGAAAAGAAAGAA
13530627 AGAA
1 AGAA
13530631 AAGGGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAGAAAGAA
Found at i:13531668 original size:20 final size:20
Alignment explanation
Indices: 13531613--13531672 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
13531603 TTTCCGATCT
*
13531613 GGCACTTTATGTGTCGTATCA
1 GGCAC-TTATGTGTCGTTTCA
*
13531634 GGCACCTTGTGTGTCGTTTCA
1 GGCA-CTTATGTGTCGTTTCA
13531655 GGCACTTATGTGTCGTTT
1 GGCACTTATGTGTCGTTT
13531673 ATTGATCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.37
21 21 0.60
22 1 0.03
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (20 bp):
GGCACTTATGTGTCGTTTCA
Found at i:13531750 original size:18 final size:18
Alignment explanation
Indices: 13531729--13531763 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13531719 GTGTGTTTGG
13531729 GTTGGAATCTGTGTATCT
1 GTTGGAATCTGTGTATCT
13531747 GTTGGAATCTGTGTATC
1 GTTGGAATCTGTGTATC
13531764 CGTCAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43
Consensus pattern (18 bp):
GTTGGAATCTGTGTATCT
Found at i:13537236 original size:18 final size:18
Alignment explanation
Indices: 13537213--13537249 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13537203 TTAAAAATGA
13537213 AACTGTATTAACAACACC
1 AACTGTATTAACAACACC
13537231 AACTGTATTAACAACACC
1 AACTGTATTAACAACACC
13537249 A
1 A
13537250 TTTATGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
AACTGTATTAACAACACC
Found at i:13539824 original size:22 final size:22
Alignment explanation
Indices: 13539799--13539859 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
13539789 AGGTGATTAA
13539799 TATGTGAACCCTTTATTTGTAC
1 TATGTGAACCCTTTATTTGTAC
*
13539821 TATGTGAACCATTTATTTGTAC
1 TATGTGAACCCTTTATTTGTAC
* *
13539843 TATGCGAACCCTATATT
1 TATGTGAACCCTTTATT
13539860 GCATAAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (22 bp):
TATGTGAACCCTTTATTTGTAC
Found at i:13539903 original size:23 final size:23
Alignment explanation
Indices: 13539877--13539940 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
13539867 AACCCTAAAC
*
13539877 ATTGTTACATACGAA-CTCTACAT
1 ATTGTTACATGCGAACCT-TACAT
* *
13539900 ATTGTTAGATGCGAACCTTTCAT
1 ATTGTTACATGCGAACCTTACAT
*
13539923 GTTGTTACATGCGAACCT
1 ATTGTTACATGCGAACCT
13539941 ATGTGTCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTGTTACATGCGAACCTTACAT
Found at i:13540068 original size:15 final size:15
Alignment explanation
Indices: 13540048--13540077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13540038 TATGTGCGAA
13540048 CTACTTGCATGAACC
1 CTACTTGCATGAACC
*
13540063 CTACTTGTATGAACC
1 CTACTTGCATGAACC
13540078 TCTAGGTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (15 bp):
CTACTTGCATGAACC
Found at i:13556473 original size:2 final size:2
Alignment explanation
Indices: 13556466--13556502 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13556456 TATGCAAGAA
13556466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13556503 AACGTTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13559974 original size:54 final size:54
Alignment explanation
Indices: 13559907--13560018 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
13559897 GGATTGGTGG
13559907 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
1 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
13559961 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
1 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
13560015 ACAC
1 ACAC
13560019 ACTTTTGTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (54 bp):
ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
Found at i:13564099 original size:14 final size:14
Alignment explanation
Indices: 13564062--13564119 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
13564052 ATGAAAGTCC
13564062 ATTAGGTTAATTTAG
1 ATTA-GTTAATTTAG
*
13564077 GTTAGTTAATTTA-
1 ATTAGTTAATTTAG
*
13564090 ATTAGTTTAA-TTAA
1 ATTAG-TTAATTTAG
*
13564104 AATA-TTAATTTAG
1 ATTAGTTAATTTAG
13564117 ATT
1 ATT
13564120 CGCACTACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.11
13 12 0.34
14 16 0.46
15 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
ATTAGTTAATTTAG
Found at i:13567785 original size:20 final size:21
Alignment explanation
Indices: 13567747--13567785 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13567737 TGCAACACGT
13567747 AGCCTTGTATTGAGCCACAAC
1 AGCCTTGTATTGAGCCACAAC
*
13567768 AGCCTTGTGTTG-GCCACA
1 AGCCTTGTATTGAGCCACA
13567786 TCAACCTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (21 bp):
AGCCTTGTATTGAGCCACAAC
Found at i:13569288 original size:73 final size:73
Alignment explanation
Indices: 13569196--13569354 Score: 300
Period size: 73 Copynumber: 2.2 Consensus size: 73
13569186 GACACAACCA
* *
13569196 TAGGATGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCATCAATGTCGCCAC
1 TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
13569261 ACAGGCAC
66 ACAGGCAC
13569269 TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
1 TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
13569334 ACAGGCAC
66 ACAGGCAC
13569342 TAGGGTGTCGCGA
1 TAGGGTGTCGCGA
13569355 CACCGACCCT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (73 bp):
TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
ACAGGCAC
Found at i:13571752 original size:24 final size:24
Alignment explanation
Indices: 13571716--13571761 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13571706 GTTTATTTCA
13571716 TTTCATTTTATTTATTA-ATATCT
1 TTTCATTTTATTTATTACATATCT
*
13571739 TTTCCTTTATATTTATTACATAT
1 TTTCATTT-TATTTATTACATAT
13571762 TTCATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCATTTTATTTATTACATATCT
Found at i:13576435 original size:6 final size:6
Alignment explanation
Indices: 13576424--13576457 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
13576414 ATCCAAAAGC
13576424 TTTTAA TTTTAA TTTTAA TTTTGCAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTT--AA TTTTAA TT
13576458 GTCTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:13578295 original size:12 final size:12
Alignment explanation
Indices: 13578279--13578312 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
13578269 AAACAGAGTC
13578279 ATAAATATTTTT
1 ATAAATATTTTT
*
13578291 GTAAATATTTTT
1 ATAAATATTTTT
13578303 ATAAATATTT
1 ATAAATATTT
13578313 ATGGAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:13579889 original size:20 final size:19
Alignment explanation
Indices: 13579864--13579934 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
13579854 AAGCTTATTA
*
13579864 TAAGTAAATGGAATTGAAGG
1 TAAGTAAATGGAATGGAA-G
*
13579884 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGG-AAG
13579904 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGGAATGG-AAG
13579924 TAAG-AAATGGA
1 TAAGTAAATGGA
13579935 GTGGTTCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 7 0.15
20 37 0.80
21 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (19 bp):
TAAGTAAATGGAATGGAAG
Found at i:13579914 original size:15 final size:16
Alignment explanation
Indices: 13579894--13579926 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13579884 TAAGTAAATG
13579894 AAATGGAA-AGTAAGT
1 AAATGGAATAGTAAGT
*
13579909 AAATGGAATGGTAAGT
1 AAATGGAATAGTAAGT
13579925 AA
1 AA
13579927 GAAATGGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.21
Consensus pattern (16 bp):
AAATGGAATAGTAAGT
Found at i:13580252 original size:92 final size:92
Alignment explanation
Indices: 13580095--13580282 Score: 376
Period size: 92 Copynumber: 2.0 Consensus size: 92
13580085 TAGGTTTATA
13580095 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
1 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
13580160 ATTCATTGCTTACGTAGTTATTTTCCT
66 ATTCATTGCTTACGTAGTTATTTTCCT
13580187 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
1 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
13580252 ATTCATTGCTTACGTAGTTATTTTCCT
66 ATTCATTGCTTACGTAGTTATTTTCCT
13580279 TTAC
1 TTAC
13580283 TTTTCAGATT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (92 bp):
TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
ATTCATTGCTTACGTAGTTATTTTCCT
Found at i:13585290 original size:20 final size:20
Alignment explanation
Indices: 13585239--13585290 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
13585229 CTTATGCTAG
* *
13585239 GTAAATGGAATGGAAAGAAA
1 GTAAATAGAATGAAAAGAAA
* * *
13585259 GTAAATAAAATGAAAAGTAT
1 GTAAATAGAATGAAAAGAAA
*
13585279 GTAAATTGAATG
1 GTAAATAGAATG
13585291 GTAAGTAAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (20 bp):
GTAAATAGAATGAAAAGAAA
Found at i:13601300 original size:16 final size:18
Alignment explanation
Indices: 13601262--13601302 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
13601252 ATATGAACAC
13601262 TGATTTACGAGCTCCTCA
1 TGATTTACGAGCTCCTCA
*
13601280 TGATTTGCGAGCT-CT-A
1 TGATTTACGAGCTCCTCA
13601296 TGATTTA
1 TGATTTA
13601303 GTAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 12 0.57
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (18 bp):
TGATTTACGAGCTCCTCA
Found at i:13605319 original size:130 final size:130
Alignment explanation
Indices: 13605070--13605682 Score: 474
Period size: 130 Copynumber: 4.7 Consensus size: 130
13605060 ACAGTTCACC
* * * * * * *
13605070 GATTTAATATCCCAATTGATATTATTAAGGCT-AGCTAATTTACTATCACAGCCTAAGTTCATT-
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCA-CTGATTTACGATCATAGTCTAAGTTCATTG
** * * * *
13605133 -TCAGACTATCATGAATAATCTTCTCTACGATAACTGATTTACTATCGCTACTCCAAATA-CTTC
65 AT-TTACTATCATGAACAATCTTCTCTAAGTTAGCTGATTTACTATCGCTACTCCAAATAGC-TC
*
13605196 ACT
128 GCT
* * * * *
13605199 GATTTAAGATCACAGCTGGTATTATTAAAGCTCATTGATTTACGATCATAGTCTAAGTTGATT-A
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTACGATCATAGTCTAAGTTCATTGA
* * *
13605263 TTTTACTATCATGAACAATCTTCTCTAAGTTAGCAT-ACTTGCTAACGCTACTCCAAATAGCTCG
66 -TTTACTATCATGAACAATCTTCTCTAAGTTAGC-TGATTTACTATCGCTACTCCAAATAGCTCG
*
13605327 TT
129 CT
* * * * * * *
13605329 GATTTAATATCATAATTGGTATTATTAAGGTTCGCTGATTT-CTAATCATAATCTAAGTTTATTG
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTAC-GATCATAGTCTAAGTTCATTG
* * * * * * *
13605393 ATTTACTGTCATTAAAAATCTTCTTTGAGTTAGTTGATTTACTATCGCTACTCCAAACAGCTCGC
65 ATTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATTTACTATCGCTACTCCAAATAGCTCGC
13605458 T
130 T
* * * * *
13605459 GATTTCATATCACAGTTGATATTATTATGGCTCACTGGTTTACGATCACAGGT-TAAGTTCATTG
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTACGATCATA-GTCTAAGTTCATTG
* * * * * * *** * *
13605523 ATTTACTATAATGAACAATCTTC-CATGAGTTAGCTGATTTTCCATAGCTATTTTGAACAACTCG
65 ATTTACTATCATGAACAATCTTCTC-TAAGTTAGCTGATTTACTATCGCTACTCCAAATAGCTCG
*
13605587 AT
129 CT
* *** * * * *
13605589 GATTTAATATCACA-ATGGATATTATTAAGGCTTGTTGATTTATGATGATAGCCTAAGTTTATTG
1 GATTTAATATCACAGTTGG-TATTATTAAGGCTCACTGATTTACGATCATAGTCTAAGTTCATTG
* * * *
13605653 ATTTACGAACCTGAATAATCTTCT-TAAGTT
65 ATTTACTATCATGAACAATCTTCTCTAAGTT
13605683 GATTTATGAT
Statistics
Matches: 379, Mismatches: 91, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
129 59 0.16
130 314 0.83
131 6 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (130 bp):
GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTACGATCATAGTCTAAGTTCATTGA
TTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATTTACTATCGCTACTCCAAATAGCTCGCT
Found at i:13605594 original size:260 final size:260
Alignment explanation
Indices: 13605167--13605658 Score: 577
Period size: 260 Copynumber: 1.9 Consensus size: 260
13605157 CTACGATAAC
* *
13605167 TGATTTACTATCGCTACTCCAAATACTTCACTGATTTAAGATCACAGCTGGTATTATTAAAGCTC
1 TGATTTACTATCGCTACTCCAAACACTTCACTGATTTAAGATCACAGCTGATATTATTAAAGCTC
* * * *
13605232 ATTGATTTACGATCATAGTCTAAGTTGATTATTTTACTATCATGAACAATCTTCTCTAAGTTAGC
66 ACTGATTTACGATCACAGTCTAAGTTCATTATTTTACTATAATGAACAATCTTCTCTAAGTTAGC
* * * * *
13605297 ATACTTGCTAACGCTACTCCAAATAGCTCGTTGATTTAATATCATAATTGG-TATTATTAAGG-T
131 ATACTTGCCAACGCTACTCCAAACAACTCGATGATTTAATATCACAA-TGGATATTATTAAGGCT
* *
13605360 TCGCTGATTTCTAATCATAATCTAAGTTTATTGATTTACTGTCATTAAAAATCTTCTTTGAGTTA
195 T-GCTGATTTATAATCATAACCTAAGTTTATTGATTTACTGTCATTAAAAATCTTCTTTGAGTTA
13605425 GT
259 GT
* * * * **
13605427 TGATTTACTATCGCTACTCCAAACAGC-TCGCTGATTTCATATCACAGTTGATATTATTATGGCT
1 TGATTTACTATCGCTACTCCAAACA-CTTCACTGATTTAAGATCACAGCTGATATTATTAAAGCT
* *
13605491 CACTGGTTTACGATCACAGGT-TAAGTTCATTGA-TTTACTATAATGAACAATCTTC-CATGAGT
65 CACTGATTTACGATCACA-GTCTAAGTTCATT-ATTTTACTATAATGAACAATCTTCTC-TAAGT
* * * ***
13605553 TAGC-TGATTTTCCATA-GCTATTTTGAACAACTCGATGATTTAATATCACAATGGATATTATTA
127 TAGCAT-ACTTGCCA-ACGCTACTCCAAACAACTCGATGATTTAATATCACAATGGATATTATTA
* * * *
13605616 AGGCTTGTTGATTTATGATGATAGCCTAAGTTTATTGATTTAC
190 AGGCTTGCTGATTTATAATCATAACCTAAGTTTATTGATTTAC
13605659 GAACCTGAAT
Statistics
Matches: 193, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
259 5 0.03
260 181 0.94
261 7 0.04
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (260 bp):
TGATTTACTATCGCTACTCCAAACACTTCACTGATTTAAGATCACAGCTGATATTATTAAAGCTC
ACTGATTTACGATCACAGTCTAAGTTCATTATTTTACTATAATGAACAATCTTCTCTAAGTTAGC
ATACTTGCCAACGCTACTCCAAACAACTCGATGATTTAATATCACAATGGATATTATTAAGGCTT
GCTGATTTATAATCATAACCTAAGTTTATTGATTTACTGTCATTAAAAATCTTCTTTGAGTTAGT
Found at i:13619861 original size:19 final size:18
Alignment explanation
Indices: 13619834--13619870 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
13619824 CTAGTTAGAA
*
13619834 TAATTTATTATTTGTAATT
1 TAATATATTATTT-TAATT
13619853 TAATATATTATTTTAATT
1 TAATATATTATTTTAATT
13619871 AGGGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATATATTATTTTAATT
Found at i:13625855 original size:3 final size:3
Alignment explanation
Indices: 13625847--13625877 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13625837 GCTATGGTAA
13625847 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
13625878 TTAGAGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:13630355 original size:90 final size:90
Alignment explanation
Indices: 13630233--13630516 Score: 464
Period size: 90 Copynumber: 3.2 Consensus size: 90
13630223 CTTAGGGAGG
*
13630233 TAAGATCT-GTAATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGTTTTCTTTCGA
1 TAAGATCTGGT-ATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGA
* *
13630297 TCTGCTTCACCACTAGTATGGGAAGA
65 TCTGCTTCGCCACCAGTATGGGAAGA
*
13630323 TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GAT
1 TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGAT
*
13630387 CTGCTTCGCCACCAGTATGGGAAGG
66 CTGCTTCGCCACCAGTATGGGAAGA
* * *
13630412 CAAGATCTGATATCTCTGATCTACTTCACGCCAGTTCATGAAGTCAAGATCTGCTTTCTTTCGAT
1 TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGAT
13630477 CTGCTTCGCCACCAGTATGGGAAGA
66 CTGCTTCGCCACCAGTATGGGAAGA
*
13630502 TAAGATCTGTTATCT
1 TAAGATCTGGTATCT
13630517 TTTCAACCTG
Statistics
Matches: 180, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
89 82 0.46
90 96 0.53
91 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (90 bp):
TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGAT
CTGCTTCGCCACCAGTATGGGAAGA
Found at i:13645615 original size:15 final size:17
Alignment explanation
Indices: 13645590--13645623 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
13645580 AATAATTTAA
13645590 ATTTCTTTTT-AAAATT
1 ATTTCTTTTTAAAAATT
13645606 ATTT-TTTTTAAAAATT
1 ATTTCTTTTTAAAAATT
13645622 AT
1 AT
13645624 GAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTCTTTTTAAAAATT
Found at i:13645640 original size:21 final size:21
Alignment explanation
Indices: 13645614--13645656 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13645604 TTATTTTTTT
* * *
13645614 TAAAAATTATGAAAAAATATA
1 TAAAAATCATAAAAAAAAATA
13645635 TAAAAATCATAAAAAAAAATA
1 TAAAAATCATAAAAAAAAATA
13645656 T
1 T
13645657 TTTGTTACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAATCATAAAAAAAAATA
Found at i:13651052 original size:15 final size:14
Alignment explanation
Indices: 13651032--13651078 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
13651022 GCCATTTTTA
*
13651032 TTTTTATTTTAATAT
1 TTTTTAATTTAAT-T
13651047 TTTTTAATTTAATT
1 TTTTTAATTTAATT
*
13651061 TTTTAAATTCTAATT
1 TTTTTAATT-TAATT
13651076 TTT
1 TTT
13651079 CTTTTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAATTTAATT
Found at i:13657869 original size:16 final size:16
Alignment explanation
Indices: 13657848--13657879 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13657838 CTTAGTTAAT
13657848 TCTTAGTTATTAGATC
1 TCTTAGTTATTAGATC
13657864 TCTTAGTTATTAGATC
1 TCTTAGTTATTAGATC
13657880 ACCTATTTCA
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:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
TCTTAGTTATTAGATC
Found at i:13660451 original size:25 final size:25
Alignment explanation
Indices: 13660423--13660480 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
13660413 CATGTAAACT
*
13660423 GGAAGCTCTTATGAGCCATATAACA
1 GGAAGCTCGTATGAGCCATATAACA
* * *
13660448 GGAAGCTCGTGTGAGCTATATAACG
1 GGAAGCTCGTATGAGCCATATAACA
13660473 GGAAGCTC
1 GGAAGCTC
13660481 AATCAAGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
GGAAGCTCGTATGAGCCATATAACA
Found at i:13660489 original size:25 final size:25
Alignment explanation
Indices: 13660461--13660527 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
13660451 AGCTCGTGTG
*
13660461 AGCTATATAACGGGAAGCTCAATCA
1 AGCTATATATCGGGAAGCTCAATCA
* * *
13660486 AGCTATATATCGAGAAACTTAATCA
1 AGCTATATATCGGGAAGCTCAATCA
13660511 AGCTATATATCGGGAAG
1 AGCTATATATCGGGAAG
13660528 TTCATGCGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (25 bp):
AGCTATATATCGGGAAGCTCAATCA
Found at i:13680350 original size:21 final size:22
Alignment explanation
Indices: 13680326--13680369 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13680316 ACTATATATT
13680326 AATTCAATC-ATAT-AACATTTC
1 AATTCAATCAAT-TCAACATTTC
*
13680347 AATTCACTCAATTCAACATTTC
1 AATTCAATCAATTCAACATTTC
13680369 A
1 A
13680370 TTCTCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTCAATCAATTCAACATTTC
Found at i:13680750 original size:18 final size:19
Alignment explanation
Indices: 13680710--13680756 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
13680700 GCTCCCAACT
13680710 CATTTCACAATTTCATATTC
1 CATTTCAC-ATTTCATATTC
*
13680730 CATTTCACATTTCA-CTTC
1 CATTTCACATTTCATATTC
13680748 CATTTCACA
1 CATTTCACA
13680757 CCATTTGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
19 6 0.23
20 8 0.31
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (19 bp):
CATTTCACATTTCATATTC
Found at i:13684477 original size:42 final size:43
Alignment explanation
Indices: 13684378--13684536 Score: 157
Period size: 43 Copynumber: 3.7 Consensus size: 43
13684368 GGCTCGTACA
* *
13684378 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAATAACG
* *
13684421 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATAT-ACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
* * *
13684463 ATGCCAATGCCCCAGACATGGTCTTACACGTTAATCTTAAAT--TG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG-TAATC--AAATAACG
* *
13684507 ATGCCAACGTCCTAGAC-GTGGTCTTACACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG
13684537 ATAACACATT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
42 30 0.31
43 38 0.39
44 27 0.28
45 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
Found at i:13689969 original size:16 final size:16
Alignment explanation
Indices: 13689942--13689976 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
13689932 AATTTGAATC
13689942 TAATAATAAATT-ATT
1 TAATAATAAATTAATT
13689957 TAATAAGTAAATTAATT
1 TAATAA-TAAATTAATT
13689974 TAA
1 TAA
13689977 ATATGGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAATAATAAATTAATT
Found at i:13691053 original size:19 final size:20
Alignment explanation
Indices: 13691008--13691062 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 20
13690998 ATCTTCAAGG
*
13691008 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATAT-AC
13691029 ATATGCAATCTTAGATAT-C
1 ATATGCAATCTTAGATATAC
13691048 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
13691063 AAAGATGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
ATATGCAATCTTAGATATAC
Found at i:13691822 original size:23 final size:22
Alignment explanation
Indices: 13691793--13691836 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
13691783 ATAATTCACA
*
13691793 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
13691816 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
13691837 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:13692013 original size:3 final size:3
Alignment explanation
Indices: 13692007--13692063 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
13691997 TTATCTTTTC
*
13692007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13692055 ATT ATT ATT
1 ATT ATT ATT
13692064 TTTGTTCTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13698631 original size:45 final size:45
Alignment explanation
Indices: 13698582--13699086 Score: 616
Period size: 45 Copynumber: 11.4 Consensus size: 45
13698572 GGAGTAGGTT
* * *
13698582 GAAGATAACAGATTTTGTCTTCCTGTATTGGCAGCGGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
13698627 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAATTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
13698672 GAAGATAGCAGATCTTGTCTTCCTATGTTGGCAACGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
13698717 GAAGGTAGTAGATCTTGTCTTCCTGTATTGGTAGCAAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
13698762 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
13698807 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
** *
13698852 GAAGATAGCAGGCCTTGTCTTCCTCTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
13698897 GAAGATAGCATATATTGTCTTCCTGTACT---AGC-----AG--C
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
13698932 GAAGATAGCAAATCTTGTTTTCCTGTATTAGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
13698977 AAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *
13699022 GAATATAGCAGATCCTGTCTTTCTGTATTGACAGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
***
13699067 GAAGATTTAAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCT
13699087 CCCTAAGCAG
Statistics
Matches: 393, Mismatches: 57, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
35 26 0.07
37 2 0.01
38 3 0.01
42 3 0.01
43 2 0.01
45 357 0.91
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:13698935 original size:35 final size:35
Alignment explanation
Indices: 13698896--13698970 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
13698886 CGAAGTAGAT
*
13698896 CGAAGATAGCATATATTGTCTTCCTGTACTAGCAG
1 CGAAGATAGCAAATATTGTCTTCCTGTACTAGCAG
* * *
13698931 CGAAGATAGCAAATCTTGTTTTCCTGTATTAGCAG
1 CGAAGATAGCAAATATTGTCTTCCTGTACTAGCAG
13698966 CGAAG
1 CGAAG
13698971 TAGATCAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (35 bp):
CGAAGATAGCAAATATTGTCTTCCTGTACTAGCAG
Found at i:13698949 original size:80 final size:80
Alignment explanation
Indices: 13698851--13699015 Score: 231
Period size: 80 Copynumber: 2.1 Consensus size: 80
13698841 CGAAGTAGAT
** * * *
13698851 CGAAGATAGCAGGCCTTGTCTTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCATATATTGTC
1 CGAAGATAGCAAACCTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTC
13698916 TTCCTGTACTAGCAG
66 TTCCTGTACTAGCAG
* * * *
13698931 CGAAGATAGCAAATCTTGTTTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTC
1 CGAAGATAGCAAACCTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTC
* *
13698996 TTCCTGTATTGGCAG
66 TTCCTGTACTAGCAG
13699011 CGAAG
1 CGAAG
13699016 TAGATTGAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (80 bp):
CGAAGATAGCAAACCTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTC
TTCCTGTACTAGCAG
Found at i:13699030 original size:125 final size:125
Alignment explanation
Indices: 13698806--13699031 Score: 362
Period size: 125 Copynumber: 1.8 Consensus size: 125
13698796 CGAAGTAGAT
* * * *
13698806 CGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAGGCCTTGTC
1 CGAAGATAGCAAATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTC
13698871 TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCATATATTGTCTTCCTGTACTAGCAG
66 TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCATATATTGTCTTCCTGTACTAGCAG
* * *
13698931 CGAAGATAGCAAATCTTGTTTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTC
1 CGAAGATAGCAAATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTC
* * *
13698996 TTCCTGTATTGGCAGCGAAGTAGATTGAATATAGCA
66 TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCA
13699032 GATCCTGTCT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
125 91 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (125 bp):
CGAAGATAGCAAATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTC
TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCATATATTGTCTTCCTGTACTAGCAG
Done.