Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 58 of 204
Found at i:18633165 original size:21 final size:21
Alignment explanation
Indices: 18633123--18633184 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
18633113 GCTAGGTGAA
* *
18633123 GTGGGACTGTAACTGGGGGAT
1 GTGGGACTGTAACTTGGAGAT
18633144 GTGGGACTGTAACTTGGAGAT
1 GTGGGACTGTAACTTGGAGAT
18633165 GTAGGG-CTGTAACTTGGAGA
1 GT-GGGACTGTAACTTGGAGA
18633185 GGTAGGGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.92
22 3 0.08
ACGTcount: A:0.23, C:0.10, G:0.42, T:0.26
Consensus pattern (21 bp):
GTGGGACTGTAACTTGGAGAT
Found at i:18633189 original size:21 final size:21
Alignment explanation
Indices: 18633150--18633208 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
18633140 GGATGTGGGA
*
18633150 CTGTAACTTGGAGATGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
18633171 CTGTAACTTGGAGAGGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
* * *
18633192 CTATAGCTTGGTGAGGT
1 CTGTAACTTGGAGAGGT
18633209 TGGAGAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.10, G:0.39, T:0.29
Consensus pattern (21 bp):
CTGTAACTTGGAGAGGTAGGG
Found at i:18633315 original size:21 final size:21
Alignment explanation
Indices: 18633252--18633394 Score: 126
Period size: 21 Copynumber: 6.8 Consensus size: 21
18633242 TGGACTTGTC
* * * *
18633252 GGACTGTATCCTGGTGAGCTA
1 GGACTGTAACCAGGAGAGGTA
** * * *
18633273 GGACTGTAAGTAGGTGATGTG
1 GGACTGTAACCAGGAGAGGTA
* *
18633294 GGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGAGAGGTA
* *
18633315 GGACTGTACCCAGGAGATGTA
1 GGACTGTAACCAGGAGAGGTA
18633336 GGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGAGAGGTA
* *
18633357 GGACTGTAACCAGGTGATG-A
1 GGACTGTAACCAGGAGAGGTA
*
18633377 CGGACTGTATCCAGGAGA
1 -GGACTGTAACCAGGAGA
18633395 TGATGGGCTG
Statistics
Matches: 99, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 1 0.01
21 98 0.99
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.20
Consensus pattern (21 bp):
GGACTGTAACCAGGAGAGGTA
Found at i:18633319 original size:42 final size:42
Alignment explanation
Indices: 18633273--18633409 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 42
18633263 TGGTGAGCTA
** * *
18633273 GGACTGTAAGTAGGTGATGTGGGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
* * *
18633315 GGACTGTACCCAGGAGATGTAGGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
* *
18633357 GGACTGTAACCAGGTGATG-ACGGACTGTATCCAGGAGATGATG
1 GGACTGTAACCAGGTGATGTA-GGACTGTAACCAGGAGA-GGTG
18633400 GG-CTGTAACC
1 GGACTGTAACC
18633410 GGGGGATGAC
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 76 0.94
43 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.20
Consensus pattern (42 bp):
GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
Found at i:18633396 original size:21 final size:20
Alignment explanation
Indices: 18633297--18633409 Score: 120
Period size: 21 Copynumber: 5.4 Consensus size: 20
18633287 TGATGTGGGG
18633297 CTGTAACCAGGAGAGGTG-GGA
1 CTGTAACCAGGAGA--TGAGGA
*
18633318 CTGTACCCAGGAGATGTAGGA
1 CTGTAACCAGGAGATG-AGGA
*
18633339 CTGTAACCAGGAGAGGTAGGA
1 CTGTAACCAGGAGATG-AGGA
*
18633360 CTGTAACCAGGTGATGACGGA
1 CTGTAACCAGGAGATGA-GGA
* *
18633381 CTGTATCCAGGAGATGATGGG
1 CTGTAACCAGGAGATGA-GGA
18633402 CTGTAACC
1 CTGTAACC
18633410 GGGGGATGAC
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 1 0.01
21 76 0.96
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (20 bp):
CTGTAACCAGGAGATGAGGA
Found at i:18640642 original size:19 final size:19
Alignment explanation
Indices: 18640618--18640657 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
18640608 AGGCGTCTCT
18640618 TTTGATATAATTACATGTA
1 TTTGATATAATTACATGTA
18640637 TTTGATATAATTACATGTA
1 TTTGATATAATTACATGTA
18640656 TT
1 TT
18640658 CTCATTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (19 bp):
TTTGATATAATTACATGTA
Found at i:18642471 original size:41 final size:40
Alignment explanation
Indices: 18642405--18642579 Score: 197
Period size: 41 Copynumber: 4.5 Consensus size: 40
18642395 AAATATATTT
* *
18642405 ATTTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
* *
18642445 ATTTTTTTAAATTTTAAAATA---CT----T--TTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
18642476 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTA
*
18642517 ATTTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATA-CTTTTTTA
**
18642558 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTTTTAA-TTTTAAAATA
18642580 AAAATGAGCC
Statistics
Matches: 116, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
31 27 0.23
33 1 0.01
34 1 0.01
37 1 0.01
38 1 0.01
40 20 0.17
41 55 0.47
42 10 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:18642473 original size:31 final size:30
Alignment explanation
Indices: 18642438--18642501 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 30
18642428 TTTTACATAC
18642438 TTTTTTAATTTTTTTAAATTTTAAAATACTT
1 TTTTTTAATTTTTTTAAATTTTAAAATA-TT
*
18642469 TTTTTTAATTTTTTTTAATTTTAAAATATT
1 TTTTTTAATTTTTTTAAATTTTAAAATATT
18642499 TTT
1 TTT
18642502 AAAATACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (30 bp):
TTTTTTAATTTTTTTAAATTTTAAAATATT
Found at i:18642482 original size:9 final size:10
Alignment explanation
Indices: 18642438--18642531 Score: 57
Period size: 10 Copynumber: 9.2 Consensus size: 10
18642428 TTTTACATAC
18642438 TTTTTTAATT
1 TTTTTTAATT
*
18642448 TTTTTAAATT
1 TTTTTTAATT
*** *
18642458 TTAAAATACTT
1 TT-TTTTAATT
18642469 TTTTTTAATT
1 TTTTTTAATT
18642479 TTTTTTAA--
1 TTTTTTAATT
**
18642487 TTTTAAAATAT
1 TTTTTTAAT-T
**
18642498 TTTTAAAATACT
1 TTTTTTAAT--T
18642510 TTTTTTAATT
1 TTTTTTAATT
18642520 TTTTTTAATT
1 TTTTTTAATT
18642530 TT
1 TT
18642532 AAAATATTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
8 6 0.09
10 36 0.56
11 14 0.22
12 8 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:18642513 original size:31 final size:30
Alignment explanation
Indices: 18642434--18642521 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
18642424 TATTTTTTAC
* *
18642434 ATACTTTTT-TAATTTTTTTAAATTTTAAA
1 ATACTTTTTAAAATTTTTTTTAATTTTAAA
**
18642463 ATACTTTTTTTTAATTTTTTTTAATTTTAAA
1 ATAC-TTTTTAAAATTTTTTTTAATTTTAAA
18642494 ATA-TTTTTAAAATACTTTTTTTAATTTT
1 ATACTTTTTAAAAT--TTTTTTTAATTTT
18642522 TTTTAATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
29 12 0.23
30 5 0.10
31 35 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (30 bp):
ATACTTTTTAAAATTTTTTTTAATTTTAAA
Found at i:18642530 original size:72 final size:71
Alignment explanation
Indices: 18642404--18642579 Score: 248
Period size: 72 Copynumber: 2.5 Consensus size: 71
18642394 TAAATATATT
* *
18642404 TATTTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAATTTTTTTAAATTTTAAAATACTT
1 TATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATA-TT
***
18642469 TTTTTTA
65 TTTAAAA
*
18642476 -ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTTAATTTTAAAATATT
1 TATTTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTTTTAAATTTTAAAATATT
18642540 TTTAAAA
65 TTTAAAA
*
18642547 TATTTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 TATTTTTTTTAA-TTTTAAAATATTTTTAAAATA
18642580 AAAATGAGCC
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
71 37 0.39
72 50 0.53
73 7 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (71 bp):
TATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATATTT
TTAAAA
Found at i:18642572 original size:31 final size:31
Alignment explanation
Indices: 18642517--18642579 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
18642507 ACTTTTTTTA
18642517 ATTTTTTTTAATTTTAAAATATTTTTAAAAT
1 ATTTTTTTTAATTTTAAAATATTTTTAAAAT
*
18642548 ATTTTTTTTAATTTTTTAAA-ATTTTTAAAAT
1 ATTTTTTTTAA-TTTTAAAATATTTTTAAAAT
18642579 A
1 A
18642580 AAAATGAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTTTTTTAATTTTAAAATATTTTTAAAAT
Found at i:18642574 original size:42 final size:41
Alignment explanation
Indices: 18642456--18642579 Score: 203
Period size: 41 Copynumber: 3.0 Consensus size: 41
18642446 TTTTTTTAAA
18642456 TTTTAAAATACTTTTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATA-TTTTTTTTAATTTTTTTTAATTTTAAAATAT
*
18642498 TTTTAAAATACTTTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTTTTAATTTTTTTTAATTTTAAAATAT
**
18642539 TTTTAAAATATTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTAAAATATTTTTTTTAATTTTTTTTAA-TTTTAAAATA
18642580 AAAATGAGCC
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 57 0.74
42 20 0.26
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (41 bp):
TTTTAAAATATTTTTTTTAATTTTTTTTAATTTTAAAATAT
Found at i:18643517 original size:18 final size:20
Alignment explanation
Indices: 18643468--18643534 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
18643458 AATTATGTCA
*
18643468 AATTAAAATACA-A-ATTTTA
1 AATTAAAA-ACATATATTTTT
*
18643487 AATATAAATACATAT-TTTTT
1 AAT-TAAAAACATATATTTTT
18643507 -ATTAAAAACATATACTTTTT
1 AATTAAAAACATATA-TTTTT
18643527 AATTAAAA
1 AATTAAAA
18643535 GAAAATCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 10 0.26
19 8 0.21
20 14 0.36
21 7 0.18
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTAAAAACATATATTTTT
Found at i:18645231 original size:14 final size:14
Alignment explanation
Indices: 18645212--18645238 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18645202 TTTGTACAAA
18645212 AATAATTAAGTCAT
1 AATAATTAAGTCAT
18645226 AATAATTAAGTCA
1 AATAATTAAGTCA
18645239 CCCTAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AATAATTAAGTCAT
Found at i:18646519 original size:25 final size:25
Alignment explanation
Indices: 18646484--18646543 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
18646474 TATATATTAA
*
18646484 ATATATATTATTTTTAATCAAATAT
1 ATATATTTTATTTTTAATCAAATAT
18646509 ATATATTTTATTTTTAATCAAATAT
1 ATATATTTTATTTTTAATCAAATAT
18646534 ATAT-TTTTAT
1 ATATATTTTAT
18646544 ATATTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 6 0.18
25 28 0.82
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATATTTTATTTTTAATCAAATAT
Found at i:18646550 original size:25 final size:25
Alignment explanation
Indices: 18646484--18646550 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
18646474 TATATATTAA
* *
18646484 ATATATATTATTTTTAATCAAATAT
1 ATATATTTTATTATTAATCAAATAT
*
18646509 ATATATTTTATTTTTAATCAAATAT
1 ATATATTTTATTATTAATCAAATAT
18646534 ATAT-TTTTATATATTAA
1 ATATATTTTAT-TATTAA
18646551 ATATATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 6 0.15
25 33 0.85
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATATTTTATTATTAATCAAATAT
Found at i:18646558 original size:25 final size:24
Alignment explanation
Indices: 18646473--18646558 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 24
18646463 CCGGCCCGAA
18646473 TTATATATTAAATATATAT-TATT
1 TTATATATTAAATATATATATATT
*
18646496 TT-TA-A-TCAA-ATATATATATT
1 TTATATATTAAATATATATATATT
* *
18646516 TTAT-T-TTTAATCAAATATATATTT
1 TTATATATTAAAT-ATATATATA-TT
18646540 TTATATATTAAATATATAT
1 TTATATATTAAATATATAT
18646559 TTAATATGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
19 6 0.12
20 9 0.18
21 5 0.10
22 2 0.04
23 10 0.20
24 6 0.12
25 6 0.12
26 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATATATTAAATATATATATATT
Found at i:18646560 original size:21 final size:21
Alignment explanation
Indices: 18646473--18646560 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 21
18646463 CCGGCCCGAA
*
18646473 TTATATATTAAATATATATTAT
1 TTATATATCAAATATATATT-T
*
18646495 TTTTA-ATCAAATATATATATT
1 TTATATATCAAATATATAT-TT
*
18646516 TTATTTTTAATCAAATATATATTT
1 TTA--TAT-ATCAAATATATATTT
*
18646540 TTATATATTAAATATATATTT
1 TTATATATCAAATATATATTT
18646561 AATATGGGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
21 29 0.53
22 7 0.13
23 1 0.02
24 5 0.09
25 13 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATATCAAATATATATTT
Found at i:18647114 original size:12 final size:10
Alignment explanation
Indices: 18647077--18647109 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
18647067 AATATATAAG
18647077 ATATAAAA-T
1 ATATAAAATT
18647086 -TATAAAATT
1 ATATAAAATT
18647095 ATATAAAATT
1 ATATAAAATT
18647105 ATATA
1 ATATA
18647110 TAAAAGCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.32
9 1 0.05
10 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATAAAATT
Found at i:18647840 original size:11 final size:11
Alignment explanation
Indices: 18647805--18647894 Score: 68
Period size: 11 Copynumber: 8.5 Consensus size: 11
18647795 ATTTTTTAAC
**
18647805 TTTAAAATACT
1 TTTAAAATTTT
18647816 TTTAAAATACTTT
1 TTTAAAAT--TTT
18647829 TTT-AAATTTT
1 TTTAAAATTTT
18647839 TTT--AA--T-
1 TTTAAAATTTT
18647845 TTTAAAATTTT
1 TTTAAAATTTT
18647856 TTTAAAATTTT
1 TTTAAAATTTT
18647867 TTTAAAATACTTT
1 TTTAAAAT--TTT
*
18647880 TTT-TAATTTT
1 TTTAAAATTTT
18647890 TTTAA
1 TTTAA
18647895 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
6 3 0.05
7 1 0.02
8 2 0.03
9 2 0.03
10 13 0.20
11 27 0.42
12 7 0.11
13 10 0.15
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:18647850 original size:40 final size:40
Alignment explanation
Indices: 18647796--18647948 Score: 117
Period size: 51 Copynumber: 3.5 Consensus size: 40
18647786 TTATTTTTTA
*
18647796 TTTTTTAACTTTAAAATACTTTTAAAATACTTTTTTAAAT
1 TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAAT
** * *
18647836 TTTTTTAATTTTAAAATTTTTTTAAAATTTTTTTAAAATACTTTTTTTAAT
1 TTTTTTAATTTTAAAATACTTTTAAAA------T--ACT--TTTT-TAAAT
*
18647887 TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAATTT
1 TTTTTTAATTTTAAAATACTTTTAAAATAC-TTTTTTAA-AT
18647929 TTATTTTAATTTTTAAAATA
1 TT-TTTTAA-TTTTAAAATA
18647949 AATTTTTGGT
Statistics
Matches: 88, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
40 24 0.27
41 2 0.02
42 7 0.08
43 7 0.08
44 11 0.12
45 1 0.01
46 1 0.01
48 2 0.02
50 4 0.05
51 29 0.33
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAAT
Found at i:18647852 original size:17 final size:17
Alignment explanation
Indices: 18647827--18647860 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18647817 TTAAAATACT
*
18647827 TTTTTAAATTTTTTTAA
1 TTTTAAAATTTTTTTAA
18647844 TTTTAAAATTTTTTTAA
1 TTTTAAAATTTTTTTAA
18647861 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAAATTTTTTTAA
Found at i:18647872 original size:51 final size:51
Alignment explanation
Indices: 18647805--18647920 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
18647795 ATTTTTTAAC
**
18647805 TTTAAAATACTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATTTT
1 TTTAAAATACTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATACT
** *
18647856 TTTAAAATTTTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATACT
1 TTTAAAATACTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATACT
18647907 TTTAAAATACTTTT
1 TTTAAAATACTTTT
18647921 TTTAATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (51 bp):
TTTAAAATACTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATACT
Found at i:18647887 original size:23 final size:22
Alignment explanation
Indices: 18647805--18647894 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 22
18647795 ATTTTTTAAC
**
18647805 TTTAAAATACTTTTAAAATACTTT
1 TTTAAAATTTTTTTAAAAT--TTT
18647829 TTT-AAATTTTTTT--AA---T
1 TTTAAAATTTTTTTAAAATTTT
18647845 TTTAAAATTTTTTTAAAATTTT
1 TTTAAAATTTTTTTAAAATTTT
*
18647867 TTTAAAATACTTTTTT-TAATTTT
1 TTTAAAAT--TTTTTTAAAATTTT
18647890 TTTAA
1 TTTAA
18647895 TTTTAAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 4 0.07
17 10 0.18
19 2 0.04
21 2 0.04
22 9 0.16
23 19 0.35
24 9 0.16
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTAAAATTTTTTTAAAATTTT
Found at i:18647909 original size:11 final size:11
Alignment explanation
Indices: 18647895--18647920 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18647885 ATTTTTTTAA
18647895 TTTTAAAATAC
1 TTTTAAAATAC
18647906 TTTTAAAATAC
1 TTTTAAAATAC
18647917 TTTT
1 TTTT
18647921 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:18651760 original size:37 final size:37
Alignment explanation
Indices: 18651717--18651789 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
18651707 AAAGACTTAT
18651717 ATACCATT-TACACGGTATTACCTCAAAGGACCAATAG
1 ATACCATTGT-CACGGTATTACCTCAAAGGACCAATAG
*
18651754 ATACCATTGTCACGGTGTTACCTCAAAGGACCAATA
1 ATACCATTGTCACGGTATTACCTCAAAGGACCAATA
18651790 AAAAATCGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 33 0.97
38 1 0.03
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (37 bp):
ATACCATTGTCACGGTATTACCTCAAAGGACCAATAG
Found at i:18651895 original size:28 final size:28
Alignment explanation
Indices: 18651855--18651916 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
18651845 GCTGCCAAAC
18651855 TCCCTTAAATCCCATAACAATCCGTCCA
1 TCCCTTAAATCCCATAACAATCCGTCCA
*
18651883 TCCCTTAAATCCCATAACAATTCGTCCA
1 TCCCTTAAATCCCATAACAATCCGTCCA
*
18651911 TTCCTT
1 TCCCTT
18651917 CATTACGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.31
Consensus pattern (28 bp):
TCCCTTAAATCCCATAACAATCCGTCCA
Found at i:18655495 original size:13 final size:13
Alignment explanation
Indices: 18655477--18655506 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18655467 AACCCAAACT
18655477 CAATTACCCAACC
1 CAATTACCCAACC
18655490 CAATTACCCAACC
1 CAATTACCCAACC
18655503 CAAT
1 CAAT
18655507 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:18655658 original size:9 final size:9
Alignment explanation
Indices: 18655646--18655704 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
18655636 AAAATAAAAA
18655646 AATTCGGGT
1 AATTCGGGT
18655655 AATTCGGGT
1 AATTCGGGT
*
18655664 ATTTTTC-GGT
1 A--ATTCGGGT
*
18655674 AATTCGGTT
1 AATTCGGGT
*
18655683 AATTCAGGT
1 AATTCGGGT
18655692 AATTCGGGT
1 AATTCGGGT
18655701 AATT
1 AATT
18655705 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 3 0.07
9 31 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:18666075 original size:22 final size:22
Alignment explanation
Indices: 18665987--18666074 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
18665977 GCTTGAACGA
* *
18665987 GATTTGCACTATGGTGCATACT
1 GATTTGCACTACGGTGCCTACT
* *
18666009 GATTTGCACTACAGTGCCTATT
1 GATTTGCACTACGGTGCCTACT
** *
18666031 GATTCACACTTCGGTGCCTACT
1 GATTTGCACTACGGTGCCTACT
18666053 -ACTTTGCACTACGGTGCCTACT
1 GA-TTTGCACTACGGTGCCTACT
18666075 ATTAAAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 1 0.02
22 52 0.98
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.34
Consensus pattern (22 bp):
GATTTGCACTACGGTGCCTACT
Found at i:18678405 original size:29 final size:28
Alignment explanation
Indices: 18678373--18678433 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
18678363 AAAAGCCCTT
*
18678373 TTTTTTTAAAATTTACCGAAATGGGCCGA
1 TTTTTTGAAAATTTACCGAAATGGGCC-A
** * *
18678402 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTGAAAATTTACCGAAATGGGCCA
18678430 TTTT
1 TTTT
18678434 CCGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (28 bp):
TTTTTTGAAAATTTACCGAAATGGGCCA
Found at i:18678793 original size:125 final size:126
Alignment explanation
Indices: 18678571--18678909 Score: 599
Period size: 126 Copynumber: 2.7 Consensus size: 126
18678561 CGTCTCTGGT
* * *
18678571 CAAATAGTATAAAATCGCTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATTGCGCCCTCG
1 CAAATAGTATAAAATTGATTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
*
18678636 TGGACGCGGTTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTCTAATGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTGAG
*
18678696 CAAATAGTATAAAATTGATTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCTCCCTCG
1 CAAATAGTATAAAATTGATTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
18678761 TGGACGCGATTTTGCTACAGTAGGTTATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTGAG
*
18678822 CAAATAGTATAAAATTGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATTGATTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
18678887 TGGACGCGATTTTGCTACAGTAG
66 TGGACGCGATTTTGCTACAGTAG
18678910 CAAGTTTGGG
Statistics
Matches: 204, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
125 98 0.48
126 106 0.52
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (126 bp):
CAAATAGTATAAAATTGATTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTGAG
Found at i:18682239 original size:29 final size:28
Alignment explanation
Indices: 18681788--18682213 Score: 603
Period size: 28 Copynumber: 15.1 Consensus size: 28
18681778 TACGGAACAA
*
18681788 TAGGGTTTTTAATTAATTTAGGTTAGAT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
* *
18681816 TAGGGTTTTTAGTTAATTTAGGTTAGAT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
18681844 TAGGGTTTTTAATTAATTTAGGTTAGGGT
1 TAGGGTTTTTAATTAATTTAGGTTA-GGT
* *
18681873 TAGGGTTTTAAATTAATTTAGGTTAGAT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
*
18681901 TAGGGTTTTTATTTAATTTAGGTTAGGTT
1 TAGGGTTTTTAATTAATTTAGGTTAGG-T
18681930 TAGGGTTTTTAATTAATTTTAGGTTAGGTT
1 TAGGGTTTTTAATTAA-TTTAGGTTAGG-T
18681960 TAGGGTTTTTAATTAATTTAGGTTAGGT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
* *
18681988 TAGGGTTTTTAGTTAATTTAGGTTAGAT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
18682016 TAGGGTTTTTAATTAA--T---TTAGGT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
* *
18682039 TAGGGTTTTAAATTAATTTAGGTTAGAT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
* *
18682067 TAGGGTTTTTAGTTAATTTATGTTAGGTT
1 TAGGGTTTTTAATTAATTTAGGTTAGG-T
18682096 TAGGGTTTTTAATTAATTTTAGGTTAGGTT
1 TAGGGTTTTTAATTAA-TTTAGGTTAGG-T
18682126 TAGGGTTTTTAATTAATTTAGGTTAGGT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
* * *
18682154 TAGGG-TTTTAGTTAATTTATGTTAGAT
1 TAGGGTTTTTAATTAATTTAGGTTAGGT
18682181 TAGGGTTTTTAATTAATTTAGGTTAGGGT
1 TAGGGTTTTTAATTAATTTAGGTTA-GGT
18682210 TAGG
1 TAGG
18682214 TTAGGGTTTT
Statistics
Matches: 359, Mismatches: 27, Indels: 23
0.88 0.07 0.06
Matches are distributed among these distances:
23 20 0.06
25 1 0.00
26 1 0.00
27 24 0.07
28 170 0.47
29 86 0.24
30 57 0.16
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (28 bp):
TAGGGTTTTTAATTAATTTAGGTTAGGT
Found at i:18682243 original size:166 final size:168
Alignment explanation
Indices: 18681788--18682216 Score: 749
Period size: 166 Copynumber: 2.5 Consensus size: 168
18681778 TACGGAACAA
*
18681788 TAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTT
1 TAGGGTTTTTAATTAATTTAGGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTT
*
18681853 TAATTAATTTAGGTTAGGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTATTTAAT
66 TAATTAATTTAGGTTAGGGTTA-GG--TTAAATT-ATTTAGGTTAGATTAGGGTTTTTAGTTAAT
18681918 TTAGGTTAGGTTTAGGGTTTTTAATTAATTTTAGGTTAGGTT
127 TTAGGTTAGGTTTAGGGTTTTTAATTAATTTTAGGTTAGGTT
18681960 TAGGGTTTTTAATTAATTTAGGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTT
1 TAGGGTTTTTAATTAATTTAGGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTT
18682025 TAATTAATTTAGGTTAGGGTT---TTAAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTA
66 TAATTAATTTAGGTTAGGGTTAGGTTAAATT-ATTTAGGTTAGATTAGGGTTTTTAGTTAATTTA
*
18682087 TGTTAGGTTTAGGGTTTTTAATTAATTTTAGGTTAGGTT
130 GGTTAGGTTTAGGGTTTTTAATTAATTTTAGGTTAGGTT
*
18682126 TAGGGTTTTTAATTAATTTAGGTTAGGTTAGGG-TTTTAGTTAATTTATGTTAGATTAGGGTTTT
1 TAGGGTTTTTAATTAATTTAGGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTT
18682190 TAATTAATTTAGGTTAGGGTTAGGTTA
66 TAATTAATTTAGGTTAGGGTTAGGTTA
18682217 GGGTTTTCAA
Statistics
Matches: 250, Mismatches: 4, Indels: 10
0.95 0.02 0.04
Matches are distributed among these distances:
165 51 0.20
166 111 0.44
168 3 0.01
172 85 0.34
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (168 bp):
TAGGGTTTTTAATTAATTTAGGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTT
TAATTAATTTAGGTTAGGGTTAGGTTAAATTATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAG
GTTAGGTTTAGGGTTTTTAATTAATTTTAGGTTAGGTT
Found at i:18682315 original size:26 final size:25
Alignment explanation
Indices: 18682284--18682332 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
18682274 CTTAAAAAAT
18682284 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
18682310 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
18682333 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:18682473 original size:24 final size:24
Alignment explanation
Indices: 18682446--18682498 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
18682436 AGCGGTTGTT
*
18682446 CTTCCTCTGGTGGTGATTGTGGTC
1 CTTCCTCCGGTGGTGATTGTGGTC
* *
18682470 CTTCCTCCGGTGGTGGTTGTGGTT
1 CTTCCTCCGGTGGTGATTGTGGTC
18682494 CTTCC
1 CTTCC
18682499 GGTTCCGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.02, C:0.25, G:0.32, T:0.42
Consensus pattern (24 bp):
CTTCCTCCGGTGGTGATTGTGGTC
Found at i:18684579 original size:30 final size:31
Alignment explanation
Indices: 18684526--18684589 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
18684516 GCCATTGATG
18684526 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
*
18684557 AAAATATAAAAAAA-TTATAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
18684587 AAA
1 AAA
18684590 TGGATTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:18684660 original size:22 final size:22
Alignment explanation
Indices: 18684635--18684685 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
18684625 AAATATGAGT
18684635 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
18684657 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
18684679 TTGAGAG
1 TTGAGAG
18684686 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:18684976 original size:29 final size:28
Alignment explanation
Indices: 18684918--18684983 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
18684908 GATTTCCCGG
* *
18684918 AAAATGGTCCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* **
18684946 AAAATCGGCCCATTTCGGTAAATTTTAAAA
1 AAAAT-GGCCCATTCCGGTAAATAAT-AAA
18684976 AAAATGGC
1 AAAATGGC
18684984 TTTTTCTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.16
29 19 0.61
30 7 0.23
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:18686308 original size:21 final size:21
Alignment explanation
Indices: 18686283--18686326 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18686273 AGAAAATAGC
18686283 AACAA-AACAATAATAATAAAA
1 AACAACAACAA-AATAATAAAA
*
18686304 AACAACAACAAAATAGTAAAA
1 AACAACAACAAAATAATAAAA
18686325 AA
1 AA
18686327 ACATTCGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.75, C:0.11, G:0.02, T:0.11
Consensus pattern (21 bp):
AACAACAACAAAATAATAAAA
Found at i:18686310 original size:24 final size:23
Alignment explanation
Indices: 18686282--18686327 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
18686272 AAGAAAATAG
18686282 CAACAA-AACAATAATAATAAAAAA
1 CAACAACAA-AATAATAA-AAAAAA
*
18686306 CAACAACAAAATAGTAAAAAAA
1 CAACAACAAAATAATAAAAAAA
18686328 CATTCGGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 13 0.65
25 2 0.10
ACGTcount: A:0.74, C:0.13, G:0.02, T:0.11
Consensus pattern (23 bp):
CAACAACAAAATAATAAAAAAAA
Found at i:18686329 original size:19 final size:19
Alignment explanation
Indices: 18686256--18686329 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
18686246 AAATGGTAGA
* * *
18686256 AAAATAGTGAAAGAACAAG
1 AAAATAGTAAAAAAACAAC
* * *
18686275 AAAATAGCAACAAAACAAT
1 AAAATAGTAAAAAAACAAC
18686294 AATAATA--AAAAACAACAAC
1 AA-AATAGTAAAAA-AACAAC
18686313 AAAATAGTAAAAAAACA
1 AAAATAGTAAAAAAACA
18686330 TTCGGTCCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 8 0.18
19 27 0.61
20 9 0.20
ACGTcount: A:0.70, C:0.11, G:0.08, T:0.11
Consensus pattern (19 bp):
AAAATAGTAAAAAAACAAC
Found at i:18687219 original size:15 final size:15
Alignment explanation
Indices: 18687196--18687225 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18687186 TAAATATATG
*
18687196 TTTTTATTTTTTTAA
1 TTTTAATTTTTTTAA
18687211 TTTTAATTTTTTTAA
1 TTTTAATTTTTTTAA
18687226 ATACTTTTTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAATTTTTTTAA
Found at i:18715718 original size:17 final size:17
Alignment explanation
Indices: 18715692--18715724 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18715682 ATATTTATGA
18715692 TTTTTTTATT-ATTTAT
1 TTTTTTTATTAATTTAT
18715708 TTTTGTTTATTAATTTA
1 TTTT-TTTATTAATTTA
18715725 AAAATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTTATTAATTTAT
Found at i:18717408 original size:16 final size:16
Alignment explanation
Indices: 18717387--18717420 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18717377 TTTAAATAAA
18717387 ATTAAAACTAATTGTT
1 ATTAAAACTAATTGTT
*
18717403 ATTAAAATTAATTGTT
1 ATTAAAACTAATTGTT
18717419 AT
1 AT
18717421 ACATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:18718521 original size:25 final size:23
Alignment explanation
Indices: 18718493--18718540 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 23
18718483 TAAATGAAAC
18718493 TAAAAATAAAAAAACTATTATATTT
1 TAAAAATAAAAAAA-TA-TATATTT
18718518 TAAAAATAAAAAAATATATATTT
1 TAAAAATAAAAAAATATATATTT
18718541 AATATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.30
24 2 0.09
25 14 0.61
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAAATAAAAAAATATATATTT
Found at i:18722225 original size:773 final size:775
Alignment explanation
Indices: 18719104--18722200 Score: 4918
Period size: 773 Copynumber: 4.0 Consensus size: 775
18719094 TACCAACTAC
* * * * *
18719104 AATTGGGAAGAAGAATTTTCCACCGAATGTCTTGGACATTAGATCTATGCATATGGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTCTTTCCC
* *
18719169 TACTGCAAGCCGCTTGTACAGGTTGATGACACCTAGTTATACGAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* *
18719234 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTGG
131 TATTGTGGTTGCACAAGACGGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTAG
*
18719299 AGAACATGAAATCGCCAGAATTCTTCTTGACGAACTTGAGGACGTATGTTGTTAGAGAAGACAAT
196 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGACAAT
* * ** * *
18719364 ATTTGTATCATATTTGATAGGTAG-A-AGACTAATTACCGCAATTAGGCGTTCCGGTGTTCCATG
261 ATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGCGATTAGGAGTTCCGGTGTTCCATG
* * * *
18719427 AAAATCTATTTACTGTATCCACCATATTGCTGCCAACTTCTACTGAGACTACATGAATGCAGACT
326 AAAATCTATTTACTGTATCCACCACATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGACT
*
18719492 AGCGCAAACAAGTAGTGAGCATGGGTAAATTTGGATTTCAACATATTTTTAAATATTCTTAATAC
391 AGCGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATAC
* * * *
18719557 TTCTATAAATTAATTCGAAAAGGTAGCATGTTTTTTCGAAATATATACGCAGTGTACGAGCTGGA
456 TTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGA
* * * *
18719622 ACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCTACAGTGAAGCAAATACTC
521 ACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACTC
18719687 TTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCT
586 TTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCT
* * * *
18719752 TGATATGGTCATATGACCACCAACCTAACAAGTGTTATTAACTTTATCATGAAGCAAACACGACA
651 CGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACA
* * * *
18719817 TTTTCCAATTTTATTTATTTTTTCAACTATATTTTATAGAGTGACAACATTTATGCCAAG
716 TTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTGACAACATTTATGCCAAG
* * *
18719877 AATTGGGAAGAAGAATTTTCCACAAAATGTCCTGGACATTCGATCTATGCATGTGGGTCTTTTCC
1 AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTCTTTCCC
* * *
18719942 TACTGCAAGCTGCTTGTGCAAGTTGATGACACCTGGTTATATGAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * *
18720007 TATTGTGGTTGCACAAGATGGGAACCAGAACTTGCTATCGATAGTGTTTGCCATTGTGGAGTTAA
131 TATTGTGGTTGCACAAGACGGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTAG
*
18720072 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGCGGACGTATGTTGTTAGAGAAGACAAT
196 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGACAAT
* *
18720137 ATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGTGATTAGGAGTTTCGGTGTTCCATG
261 ATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGCGATTAGGAGTTCCGGTGTTCCATG
* * * *
18720202 AAAATCTCTTTACTGTATCCGCCATATTACCGCCAACTTCCACTGAGACTACAAGAATGCAGACT
326 AAAATCTATTTACTGTATCCACCACATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGACT
18720267 AGCGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATA-TCTTAATAC
391 AGCGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATAC
* *
18720331 TTCCATAAATTAATTCGAAAATGTAGCTTGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGA
456 TTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGA
* *
18720396 ACAACACTGTTTCAAGCAAAGGCTGACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACAC
521 ACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACTC
* *
18720461 TTTTTTTAGAGTGGTTGGGTACCATGAAGCCATGGTAATGAACTCAAAGTTTTGATGACGGATCT
586 TTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCT
* * * **
18720526 CGATATGGTCATATGACCACCAACCTGACAAATGATATTAACTTTGTCTTAAAGCAAACACGATG
651 CGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACA
* * *
18720591 TTTTTTAATTTTATTTATTTTCTCAACTATATTTTACAGACCG-CAAACATTTATACCAAG
716 TTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTGAC-AACATTTATGCCAAG
* *
18720651 AATTGGAAAGAAGAATTTTTCACCAAATGTCCTGGATATTCGATCTATGCATGTGGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTCTTTCCC
* * *
18720716 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGATTATACGAAAAATATACTCAGATACTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * *
18720781 TATTATGGTTGCACAAGAC-GAATACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTG
131 TATTGTGGTTGCACAAGACGGGA-ACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTA
* *
18720845 GAGAACATGAAATCGCCAGAATTCTTCTTGACGAACTTGAGGACGTATGTTGTTAGAGAAG--AT
195 GAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGACAA
* * *
18720908 TATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGCGATTAGGAGATCCGATGTTTCAT
260 TATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGCGATTAGGAGTTCCGGTGTTCCAT
* * * *
18720973 GAAAATCTGTTTACTGTATCCGCCACATTGTCGCCAACTTCCACTGAGACTACAAGAATGCAGAA
325 GAAAATCTATTTACTGTATCCACCACATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGAC
*
18721038 TAGCGCAAAAAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
390 TAGCGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
*
18721103 CTTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTTGAAATACATACGCAGCGTACGAGCTGG
455 CTTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
* * *
18721168 AACAACACTGTTTCAAGCAAAGGCTGACCAGGCTTGAGGTTGATATCCACAGTGAAATGAATACT
520 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACT
* *
18721233 CTTTTTTTAGAGTGGTTGGGTACCAAGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACAGATC
585 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATC
*
18721298 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCGAACACGAC
650 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
*
18721363 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTAACAACATTTATGCCAAG
715 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTGACAACATTTATGCCAAG
*
18721424 AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGACATTCGATCTATGCATGTAGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTCTTTCCC
18721489 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * * *
18721554 TATTGTGGTTGCACAAGACGGGAACCATAACTTACTATCGATAGTGGTTGCCATTGTGGAGTTAG
131 TATTGTGGTTGCACAAGACGGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTAG
* *
18721619 AGAATATGAAATCACCAGAATTCTTCCTGACGAACTTGCA-GACGTATGTTGTTAGAGAAGACAA
196 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTG-AGGACGTATGTTGTTAGAGAAGACAA
* * * * *
18721683 TATTTGCATCATATTTGATAGGTAG-A-AGACTAATTGTCACGATTAGGCGTTCTGGTGTTCCAC
260 TATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGCGATTAGGAGTTCCGGTGTTCCAT
* *** * * *
18721746 GAAAATCTATTTACTGTATCCACCACACTGTTACCAACTTCTACCGAGACTACATGAATGCAGAC
325 GAAAATCTATTTACTGTATCCACCACATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGAC
* *
18721811 TAGGGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
390 TAGCGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
* * * *
18721876 CTTTCATAATTTAATTCGAAAAGGTAGCTTGTCTTTTCGAAATACATACACAGCGTACGAGCTGG
455 CTTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
*
18721941 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGTGGTTGATATCCACAGTAAAACGAATACT
520 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACT
* * *
18722006 TTTTTTTCTTGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTTAAAGTTTTGATGACGGAT
585 CTTTTTT-TAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGAT
* * * *
18722071 CCCGATATGGTCATATGACCACTAACCTGACAAATGTTATTAACTTTGTCTTGAAGCAAACACAA
649 CTCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGA
* * **
18722136 CATTTTCTAATTTTATTTATTTTTTCAACTATATTTTACAGATTGGTAACATTTATGCCAAG
714 CATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTGACAACATTTATGCCAAG
18722198 AAT
1 AAT
18722201 GAGGCTAAAA
Statistics
Matches: 2139, Mismatches: 174, Indels: 21
0.92 0.07 0.01
Matches are distributed among these distances:
772 176 0.08
773 1084 0.51
774 709 0.33
775 170 0.08
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (775 bp):
AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTCTTTCCC
TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
TATTGTGGTTGCACAAGACGGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTAG
AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGACAAT
ATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGTCGCGATTAGGAGTTCCGGTGTTCCATG
AAAATCTATTTACTGTATCCACCACATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGACT
AGCGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATAC
TTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGA
ACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACTC
TTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCT
CGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACA
TTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTGACAACATTTATGCCAAG
Found at i:18725497 original size:43 final size:43
Alignment explanation
Indices: 18725440--18725715 Score: 376
Period size: 43 Copynumber: 6.5 Consensus size: 43
18725430 TAAACGTTGT
* * * * *
18725440 TATAGACCATGACCTTTTGCAGCGCTTTTCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
* * * *
18725483 TATAAATCAGGACCTTTAGCGGTGATTTTTCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
* * *
18725526 TATAGATCAAGACCTTTAGCGACGC-TTTTGCACAAACACCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
*
18725568 TATAGATCAAGACCTTTAGCGGCGCTTTTTTCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
* *
18725611 TATAGCTCAAGACCTTTAGCGGCGCTTTTTCCATAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
**
18725654 TATAGATCAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
*
18725697 TATAGAACAA-ACCTTTAGC
1 TATAGATCAAGACCTTTAGC
18725716 AACGCTTCTC
Statistics
Matches: 206, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
42 48 0.23
43 158 0.77
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (43 bp):
TATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGC
Found at i:18725587 original size:85 final size:85
Alignment explanation
Indices: 18725440--18725736 Score: 373
Period size: 85 Copynumber: 3.5 Consensus size: 85
18725430 TAAACGTTGT
* * * * *
18725440 TATAGACCATGACCTTTTGC-AGCGCTTTTCCCACAAACGCCGCTATAAATCAGGACCTTTAGCG
1 TATAGATCAAGACCTTTAGCGA-CGCTTTT-CCACAAACGCCGCTATAGATCAAGACCTTTAGCG
* *
18725504 GTGATTTTTCCACAAACGCCGC
64 GCGCTTTTTCCACAAACGCCGC
* *
18725526 TATAGATCAAGACCTTTAGCGACGCTTTTGCACAAACACCGCTATAGATCAAGACCTTTAGCGGC
1 TATAGATCAAGACCTTTAGCGACGCTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGC
*
18725591 GCTTTTTTCACAAACGCCGC
66 GCTTTTTCCACAAACGCCGC
* * *
18725611 TATAGCTCAAGACCTTTAGCGGCGCTTTTTCCATAAACGCCGCTATAGATCAAGACCTTTAGCGG
1 TATAGATCAAGACCTTTAGCGACGC-TTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGG
**
18725676 CGCTTTCCCCACAAACGCCGC
65 CGCTTTTTCCACAAACGCCGC
* * * *
18725697 TATAGAACAA-ACCTTTAGCAACGCTTCTCGCAAAAACGCC
1 TATAGATCAAGACCTTTAGCGACGCTTTTC-CACAAACGCC
18725737 ACTAAAAACA
Statistics
Matches: 184, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
84 4 0.02
85 93 0.51
86 86 0.47
87 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (85 bp):
TATAGATCAAGACCTTTAGCGACGCTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGC
GCTTTTTCCACAAACGCCGC
Found at i:18725668 original size:128 final size:129
Alignment explanation
Indices: 18725440--18725736 Score: 391
Period size: 128 Copynumber: 2.3 Consensus size: 129
18725430 TAAACGTTGT
* * * *
18725440 TATAGACCATGACCTTTTGCAGCGCTTTTCCCACAAACGCCGCTATAAATCAGGACCTTTAGCGG
1 TATAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGG
* **
18725505 TGATTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTT-TGCACAAACACCGC
66 CGATTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTCCCCACAAACACCGC
* * ** **
18725568 TATAGATCAAGACCTTTAGCGGCGCTTTTTTCACAAACGCCGCTATAGCTCAAGACCTTTAGCGG
1 TATAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGG
* * * *
18725633 CGCTTTTTCCATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCGC
66 CGATTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTCCCCACAAACACCGC
* * * *
18725697 TATAGAACAA-ACCTTTAGCAACGCTTCTCGCAAAAACGCC
1 TATAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCC
18725737 ACTAAAAACA
Statistics
Matches: 145, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
128 125 0.86
129 20 0.14
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (129 bp):
TATAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGG
CGATTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTCCCCACAAACACCGC
Found at i:18727084 original size:40 final size:40
Alignment explanation
Indices: 18727021--18727145 Score: 121
Period size: 40 Copynumber: 3.1 Consensus size: 40
18727011 TAGCTTGAAT
* * *
18727021 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAGCAAAA
*
18727061 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAGCAAAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAGCAAAA
* * * * *
18727101 ATCAA-TCTTACAACAGTTT-ATGTGAAACAAATTAGCAAAA
1 ATCAACACTT-CAATA-TTTAATATGCAAGAAATTAGCAAAA
18727141 ATCAA
1 ATCAA
18727146 TTATTCATAG
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.04
40 65 0.90
41 4 0.06
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAGCAAAA
Found at i:18729567 original size:86 final size:86
Alignment explanation
Indices: 18729477--18729638 Score: 238
Period size: 86 Copynumber: 1.9 Consensus size: 86
18729467 TAATATTATA
18729477 TCTTTTACAATTATATAAGAAATTA-TTAAATATATAAATT-AAAAACACCAATTAACCTAAACC
1 TCTTTTACAATTATATAAGAAATTAGTT-AATATATAAATTAAAAAACACCAATTAACCTAAACC
18729540 CTAAACCCCTAACCCCTAACCCC
65 CTAAA-CCCTAACCCCTAACCCC
* * ** * *
18729563 TCTTTTACAATTATATAAGAACTTAGTTAATATATAAATTAAAAAATACTGATTAATCTAAACCT
1 TCTTTTACAATTATATAAGAAATTAGTTAATATATAAATTAAAAAACACCAATTAACCTAAACCC
18729628 TAAACCCTAAC
66 TAAACCCTAAC
18729639 ATGATCCCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
86 43 0.63
87 25 0.37
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.31
Consensus pattern (86 bp):
TCTTTTACAATTATATAAGAAATTAGTTAATATATAAATTAAAAAACACCAATTAACCTAAACCC
TAAACCCTAACCCCTAACCCC
Found at i:18729693 original size:7 final size:7
Alignment explanation
Indices: 18729683--18729747 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
18729673 TCTTAACATT
*
18729683 TAACCTC
1 TAACCCC
18729690 TAACCCC
1 TAACCCC
*
18729697 TAACCAC
1 TAACCCC
*
18729704 AAACCCC
1 TAACCCC
18729711 TAACCCC
1 TAACCCC
* *
18729718 AAACCCT
1 TAACCCC
18729725 TAACCCC
1 TAACCCC
**
18729732 TAACTAC
1 TAACCCC
18729739 TAACCCC
1 TAACCCC
18729746 TA
1 TA
18729748 TATCTTATTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.17
Consensus pattern (7 bp):
TAACCCC
Found at i:18729798 original size:7 final size:7
Alignment explanation
Indices: 18729786--18729826 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
18729776 ACTAATTAAT
18729786 CTAAACC
1 CTAAACC
18729793 CTAAACC
1 CTAAACC
18729800 CT-AACC
1 CTAAACC
18729806 C-AAATCC
1 CTAAA-CC
*
18729813 CTAACCC
1 CTAAACC
18729820 CTAAACC
1 CTAAACC
18729827 TTATTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 7 0.24
7 20 0.69
8 2 0.07
ACGTcount: A:0.39, C:0.46, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:18729814 original size:13 final size:13
Alignment explanation
Indices: 18729789--18729826 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
18729779 AATTAATCTA
18729789 AACCCTAAACCCT
1 AACCCTAAACCCT
18729802 AACCC-AAATCCCT
1 AACCCTAAA-CCCT
18729815 AACCCCTAAACC
1 AA-CCCTAAACC
18729827 TTATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 11 0.50
14 5 0.23
15 3 0.14
ACGTcount: A:0.39, C:0.47, G:0.00, T:0.13
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:18729870 original size:74 final size:75
Alignment explanation
Indices: 18729738--18729876 Score: 228
Period size: 74 Copynumber: 1.9 Consensus size: 75
18729728 CCCCTAACTA
* *
18729738 CTAACCCCTATATCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
1 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
18729803 ACCCAAATCC
66 ACCCAAATCC
*
18729813 CTAACCCCTAAACCTTATTT-A-ATATAAATTAAAACACACTAATTAATCTAAACCCTAAATCCT
1 CTAACCCCTAAACCTTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAACCCTAAACCCT
18729876 A
65 A
18729877 GCTTGACACC
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
73 13 0.22
74 29 0.48
75 18 0.30
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (75 bp):
CTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTA
ACCCAAATCC
Found at i:18729941 original size:14 final size:15
Alignment explanation
Indices: 18729922--18729954 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
18729912 CTTAAACCAG
18729922 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
18729936 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
18729951 AATC
1 AATC
18729955 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:18739945 original size:22 final size:21
Alignment explanation
Indices: 18739901--18739940 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
18739891 TTATTGAAAG
18739901 TTTTCATTTTATCATATCAAA
1 TTTTCATTTTATCATATCAAA
*
18739922 TTTTTATTTT-TCATATCAA
1 TTTTCATTTTATCATATCAA
18739941 TAATTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTCATTTTATCATATCAAA
Found at i:18743154 original size:24 final size:24
Alignment explanation
Indices: 18743089--18743154 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
18743079 ATGTATGCAT
*
18743089 ATAA-AAAATATTTATAAATATCAA
1 ATAATAAAATA-TAATAAATATCAA
* *
18743113 ATAATAAAAT-TAAGTAAATTTTAA
1 ATAATAAAATATAA-TAAATATCAA
18743137 AT-ATAAAATATACATAAA
1 ATAATAAAATATA-ATAAA
18743155 AATAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
23 9 0.26
24 20 0.57
25 6 0.17
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAATAAAATATAATAAATATCAA
Found at i:18743896 original size:25 final size:24
Alignment explanation
Indices: 18743868--18743925 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
18743858 AAAGAAAAAT
*
18743868 TAAACAAGCAAAACAAATTATTCCA
1 TAAACAAACAAAA-AAATTATTCCA
* *
18743893 TAAATTAAACAATAAAATTATTCCA
1 TAAA-CAAACAAAAAAATTATTCCA
18743918 TATAACAA
1 TA-AACAA
18743926 TTCATAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAACAAACAAAAAAATTATTCCA
Found at i:18744766 original size:13 final size:13
Alignment explanation
Indices: 18744748--18744772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18744738 GTATAGTAAA
18744748 ATATTTAAAAAAT
1 ATATTTAAAAAAT
18744761 ATATTTAAAAAA
1 ATATTTAAAAAA
18744773 AAGAGATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATTTAAAAAAT
Found at i:18744885 original size:16 final size:17
Alignment explanation
Indices: 18744866--18744897 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18744856 ATAATAATGC
18744866 ATATATAAAA-TTATTG
1 ATATATAAAACTTATTG
18744882 ATATATAAAACTTATT
1 ATATATAAAACTTATT
18744898 TTGGAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATAAAACTTATTG
Found at i:18746321 original size:22 final size:23
Alignment explanation
Indices: 18746277--18746324 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
18746267 AAACAAAGAG
18746277 ATTAAATTTCTTAAAATAAAAAA
1 ATTAAATTTCTTAAAATAAAAAA
*
18746300 ATTAAA-TTC-TAAATATATAAAA
1 ATTAAATTTCTTAAA-ATAAAAAA
18746322 ATT
1 ATT
18746325 GAAAAGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAAATTTCTTAAAATAAAAAA
Found at i:18747968 original size:24 final size:23
Alignment explanation
Indices: 18747940--18747985 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
18747930 TTTGGAGAAT
18747940 TTTGTATTT-ACGTTTTGAGGGTTC
1 TTTGT-TTTCACGTTTTG-GGGTTC
*
18747964 TTTGTTTTCAGGTTTTGGGGTT
1 TTTGTTTTCACGTTTTGGGGTT
18747986 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.07, G:0.28, T:0.57
Consensus pattern (23 bp):
TTTGTTTTCACGTTTTGGGGTTC
Found at i:18748435 original size:17 final size:17
Alignment explanation
Indices: 18748413--18748446 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18748403 ATCAAATACG
18748413 AACATTTCATATCATTT
1 AACATTTCATATCATTT
18748430 AACATTTCATATCATTT
1 AACATTTCATATCATTT
18748447 CCAGATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
AACATTTCATATCATTT
Found at i:18749309 original size:40 final size:42
Alignment explanation
Indices: 18749249--18749354 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 42
18749239 TTACGAAAGC
*
18749249 TGAACAAAAGCTCATGAGAGCT-A-AAAAAACCCATAAGGGT
1 TGAACAAAAGCTCATAAGAGCTGAGAAAAAACCCATAAGGGT
* * * *
18749289 TGAACGAAAGCTCGTAAGAGCTGAGCAGAAACCCATAAGGGT
1 TGAACAAAAGCTCATAAGAGCTGAGAAAAAACCCATAAGGGT
* * * *
18749331 TAAACAGAAGCTTAAAAGAGCTGA
1 TGAACAAAAGCTCATAAGAGCTGA
18749355 ACGGAAACTC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 19 0.36
41 1 0.02
42 33 0.62
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (42 bp):
TGAACAAAAGCTCATAAGAGCTGAGAAAAAACCCATAAGGGT
Found at i:18749342 original size:42 final size:42
Alignment explanation
Indices: 18749275--18749404 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 42
18749265 AGAGCTAAAA
* *
18749275 AAACCCATAAGGGTTGAAC-GAAAGCTCGTAAGAGCTGAGCAG
1 AAACCCATAAGGGTTAAACAG-AAGCTCGTAAGAGCTGAACAG
*** *
18749317 AAACCCATAAGGGTTAAACAGAAGCTTAAAAGAGCTGAACGG
1 AAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACAG
* * * * * * *
18749359 AAACTCATATGAGTTAAACAGAAACTCGTGAGAGCTAAACGG
1 AAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACAG
18749401 AAAC
1 AAAC
18749405 TAAACACGAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 71 0.99
43 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACAG
Found at i:18749397 original size:21 final size:20
Alignment explanation
Indices: 18749347--18749405 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
18749337 GAAGCTTAAA
*
18749347 AGAGCTGAACGGAAACTCAT
1 AGAGCTAAACGGAAACTCAT
* * *
18749367 ATGAGTTAAACAGAAACTCGT
1 A-GAGCTAAACGGAAACTCAT
18749388 GAGAGCTAAACGGAAACT
1 -AGAGCTAAACGGAAACT
18749406 AAACACGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (20 bp):
AGAGCTAAACGGAAACTCAT
Found at i:18752374 original size:3 final size:3
Alignment explanation
Indices: 18752366--18752457 Score: 107
Period size: 3 Copynumber: 30.7 Consensus size: 3
18752356 CTTGTCAATT
*
18752366 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
18752414 TTA CTA TTA TTA TTT TTA -TA TTCA TTA ATA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TT
18752458 GTTAGGTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
2 3 0.04
3 69 0.91
4 4 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18752648 original size:21 final size:21
Alignment explanation
Indices: 18752615--18752654 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18752605 GTCTATATAT
*
18752615 ATATATATTTTATATATTAAA
1 ATATATATATTATATATTAAA
*
18752636 ATATGTATATTATATATTA
1 ATATATATATTATATATTA
18752655 TTTTATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATATATATATTATATATTAAA
Found at i:18755293 original size:9 final size:9
Alignment explanation
Indices: 18755273--18755339 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
18755263 TTATAATAAA
18755273 TTTAATAGTT
1 TTTAATA-TT
18755283 TTT-ATATT
1 TTTAATATT
*
18755291 TTTAACATT
1 TTTAATATT
18755300 TTTGCAAT-TT
1 TTT--AATATT
* *
18755310 TATATTATT
1 TTTAATATT
*
18755319 TTTAATATA
1 TTTAATATT
18755328 TTTAATATT
1 TTTAATATT
18755337 TTT
1 TTT
18755340 TTATAACTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
8 7 0.16
9 29 0.64
10 7 0.16
11 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTAATATT
Found at i:18755324 original size:46 final size:47
Alignment explanation
Indices: 18755251--18755339 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
18755241 TTTATATAAT
*
18755251 TTTTTGCAATTTTTATAATAAATTTAATAGT-TTTTATATTTTTAACA
1 TTTTTGCAATTTTTATAATAAATTTAATA-TATTTAATATTTTTAACA
* **
18755298 TTTTTGCAA-TTTTATATTATTTTTAATATATTTAATATTTTT
1 TTTTTGCAATTTTTATAATAAATTTAATATATTTAATATTTTT
18755340 TTATAACTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.03
46 27 0.73
47 9 0.24
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (47 bp):
TTTTTGCAATTTTTATAATAAATTTAATATATTTAATATTTTTAACA
Found at i:18755419 original size:19 final size:21
Alignment explanation
Indices: 18755395--18755440 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
18755385 AAAGTTTAAG
*
18755395 TATTTTAAAT-ATTTTTTAT-
1 TATTTTAAATAAATTTTTATA
*
18755414 TATTTTTAATAAATTTTTATA
1 TATTTTAAATAAATTTTTATA
18755435 TATTTT
1 TATTTT
18755441 TCAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTAAATAAATTTTTATA
Found at i:18755420 original size:20 final size:21
Alignment explanation
Indices: 18755407--18755452 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
18755397 TTTTAAATAT
18755407 TTTTTAT-TATTTTTAATAAA
1 TTTTTATATATTTTTAATAAA
*
18755427 TTTTTATATATTTTTCAAAAAA
1 TTTTTATATATTTTT-AATAAA
18755449 TTTT
1 TTTT
18755453 ATAACTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 9 0.39
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTATATATTTTTAATAAA
Found at i:18755431 original size:21 final size:21
Alignment explanation
Indices: 18755397--18755452 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
18755387 AGTTTAAGTA
*
18755397 TTTTAAATATTTTTTAT-TAT
1 TTTTAAAAATTTTTTATATAT
18755417 TTTTAATAAA-TTTTTATATAT
1 TTTTAA-AAATTTTTTATATAT
*
18755438 TTTTCAAAAAATTTT
1 TTTT-AAAAATTTTT
18755453 ATAACTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 13 0.42
21 12 0.39
22 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAAAATTTTTTATATAT
Found at i:18755453 original size:21 final size:21
Alignment explanation
Indices: 18755408--18755455 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
18755398 TTTAAATATT
*
18755408 TTTTAT-TATTTTTAATAAAT
1 TTTTATATATTTTTAATAAAA
18755428 TTTTATATATTTTTCAA-AAAA
1 TTTTATATATTTTT-AATAAAA
18755449 TTTTATA
1 TTTTATA
18755456 ACTTTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATATATTTTTAATAAAA
Found at i:18756838 original size:14 final size:14
Alignment explanation
Indices: 18756819--18756845 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18756809 TTCTATATTC
18756819 TCAATCCTCAATTT
1 TCAATCCTCAATTT
18756833 TCAATCCTCAATT
1 TCAATCCTCAATT
18756846 ATATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
TCAATCCTCAATTT
Found at i:18758718 original size:63 final size:63
Alignment explanation
Indices: 18758641--18758777 Score: 157
Period size: 63 Copynumber: 2.2 Consensus size: 63
18758631 CATTCCCCGT
* * * * * * * * * * *
18758641 ATCAAAACCTTCAACTCTGGTTTATTTTACCCAAGCACCATAGCATGCACAATCATTTCTTAA
1 ATCAACACATTCAACACTAGTTTATTTTACACAACCACCACAACACGCACAATCATTCCCTAA
* *
18758704 ATCAACACATTCAACACTAGTTTATTTTACACAACCACCACAACACGCGCAATCATTCCCTAC
1 ATCAACACATTCAACACTAGTTTATTTTACACAACCACCACAACACGCACAATCATTCCCTAA
18758767 ATCAACACATT
1 ATCAACACATT
18758778 TAGGGATATA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.36, C:0.31, G:0.06, T:0.28
Consensus pattern (63 bp):
ATCAACACATTCAACACTAGTTTATTTTACACAACCACCACAACACGCACAATCATTCCCTAA
Found at i:18761672 original size:104 final size:104
Alignment explanation
Indices: 18761492--18761687 Score: 295
Period size: 104 Copynumber: 1.9 Consensus size: 104
18761482 GGCCAAAAAG
* * *
18761492 GTATCAATATTTTTTGAATTATCGATACCCCCTCTTAAAAGCGATACCAAAAATGCATTCTATTT
1 GTATCAATATTTTTTGAATTATCAATACCCCATCTTAAAAGCAATACCAAAAATGCATTCTATTT
*
18761557 TTCACAAACCCTACTAAGTATCGATACCTTTTTGGTCAA
66 TTCACAAACCCTACGAAGTATCGATACCTTTTTGGTCAA
* * * *
18761596 GTATCGATATTTTTTGAATTATCAATACCCTATCTTAAAAGCAATACC-AAAATAGCATTTTGTT
1 GTATCAATATTTTTTGAATTATCAATACCCCATCTTAAAAGCAATACCAAAAAT-GCATTCTATT
*
18761660 TTTCTCAAACCCTACGAAGTATCGATAC
65 TTTCACAAACCCTACGAAGTATCGATAC
18761688 GGTATCGATA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 5 0.06
104 77 0.94
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.36
Consensus pattern (104 bp):
GTATCAATATTTTTTGAATTATCAATACCCCATCTTAAAAGCAATACCAAAAATGCATTCTATTT
TTCACAAACCCTACGAAGTATCGATACCTTTTTGGTCAA
Found at i:18765262 original size:18 final size:19
Alignment explanation
Indices: 18765227--18765264 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
18765217 AAAAATCAGC
*
18765227 TAAAAATTCTAAATATTTT
1 TAAAAATTCTAAACATTTT
*
18765246 TAAAAA-TCTAACCATTTT
1 TAAAAATTCTAAACATTTT
18765264 T
1 T
18765265 TCCAAATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAATTCTAAACATTTT
Found at i:18765484 original size:2 final size:2
Alignment explanation
Indices: 18765477--18765512 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18765467 CAAAACTGTT
18765477 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18765513 TAGCAGAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18768947 original size:43 final size:43
Alignment explanation
Indices: 18768881--18768966 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
18768871 ATTTGCCTGT
*
18768881 GTCAGATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
1 GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
18768924 GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
1 GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
18768967 CTTTTTTGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (43 bp):
GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
Found at i:18772064 original size:28 final size:26
Alignment explanation
Indices: 18772008--18772066 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
18771998 ATATTTTGGT
*
18772008 AAAATATTATTTTTAAAATTATAAAA
1 AAAATATTATTTTTAAAATAATAAAA
*
18772034 AAAATATT-TTTTGTACAAATAAATAATA
1 AAAATATTATTTT-TA-AAAT-AATAAAA
18772062 AAAAT
1 AAAAT
18772067 TCAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.14
26 10 0.36
27 4 0.14
28 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATATTATTTTTAAAATAATAAAA
Found at i:18775550 original size:16 final size:16
Alignment explanation
Indices: 18775501--18775551 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
18775491 AAAAATAGTT
* *
18775501 TTTTTAATTTTAAAGA
1 TTTTTATTTTTAAAAA
* * *
18775517 GTTTTATTTTTCATAA
1 TTTTTATTTTTAAAAA
18775533 TTTTTATTTTTAAAAA
1 TTTTTATTTTTAAAAA
18775549 TTT
1 TTT
18775552 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (16 bp):
TTTTTATTTTTAAAAA
Found at i:18775576 original size:21 final size:20
Alignment explanation
Indices: 18775543--18775581 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
18775533 TTTTTATTTT
18775543 TAAAAATTTA-TTTAAAATA
1 TAAAAATTTATTTTAAAATA
18775562 TAAAAATAATTATTTTAAAA
1 TAAAAAT--TTATTTTAAAA
18775582 ATATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
21 3 0.18
22 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTTATTTTAAAATA
Found at i:18781514 original size:21 final size:21
Alignment explanation
Indices: 18781488--18781530 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18781478 CTTTTCCTAA
*
18781488 AATATGAATTGGATTGAATTG
1 AATATGAATTGGATTAAATTG
*
18781509 AATATGAATTGTATTAAATTG
1 AATATGAATTGGATTAAATTG
18781530 A
1 A
18781531 GTTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
AATATGAATTGGATTAAATTG
Found at i:18781951 original size:24 final size:23
Alignment explanation
Indices: 18781858--18781947 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 23
18781848 AAAGAGCATT
* *
18781858 CCGTTATTAGCCCTCTCGAGCTTC
1 CCGTTAATAGCTCT-TCGAGCTTC
* * *
18781882 CCGTTATATTGTTCTTACGAGTTTC
1 CCGTTA-ATAGCTCTT-CGAGCTTC
* *
18781907 CCGTTGATAGCTCTTGTGAGCTTC
1 CCGTTAATAGCTCTT-CGAGCTTC
18781931 CCGTTAATAGCTCTTCG
1 CCGTTAATAGCTCTTCG
18781948 GAGCATCCTG
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.02
24 34 0.67
25 16 0.31
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (23 bp):
CCGTTAATAGCTCTTCGAGCTTC
Found at i:18782154 original size:24 final size:24
Alignment explanation
Indices: 18782127--18782187 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
18782117 GGCTCTTCGA
*
18782127 AGCTACCCGTTATTGGCT-TTCATG
1 AGCTTCCCGTTATTGGCTCTT-ATG
18782151 AGCTTCCCGATTA-TGGCTCTTATG
1 AGCTTCCCG-TTATTGGCTCTTATG
*
18782175 AGCTTCTCGTTAT
1 AGCTTCCCGTTAT
18782188 ACAGCCCGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 3 0.09
24 24 0.75
25 5 0.16
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (24 bp):
AGCTTCCCGTTATTGGCTCTTATG
Found at i:18782244 original size:25 final size:25
Alignment explanation
Indices: 18782172--18782244 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
18782162 TATGGCTCTT
* * **
18782172 ATGAGCTTCTCGTTATACAGCCCGG
1 ATGAGCTTCTCGTTATATAGCTCAC
* * *
18782197 ATAAGCTTCTCGTTACATGGCTCAC
1 ATGAGCTTCTCGTTATATAGCTCAC
*
18782222 ATGAGCTTCTCATTATATAGCTC
1 ATGAGCTTCTCGTTATATAGCTC
18782245 GAGAGAGTGC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCTCGTTATATAGCTCAC
Found at i:18782855 original size:2 final size:2
Alignment explanation
Indices: 18782848--18782872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18782838 TCATGTTTTC
18782848 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 A
18782873 GTATTATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18788055 original size:26 final size:26
Alignment explanation
Indices: 18788007--18788058 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
18787997 TGGAAGGTGG
* *
18788007 AAAAAGAAAGATAAAGGAAAGAGAAA
1 AAAAAGAAAGAGAAAGAAAAGAGAAA
18788033 AAAAAGAAA-AGAAAGAAAGAGAGAAA
1 AAAAAGAAAGAGAAAGAAA-AGAGAAA
18788059 GACTAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAGAGAAAGAAAAGAGAAA
Found at i:18792310 original size:33 final size:33
Alignment explanation
Indices: 18792247--18792310 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
18792237 CTAGAGGGAA
*
18792247 TATTAGTTGTATATCACAGCCACGTTGCAAGCC
1 TATTAGTTGTATATCACAGCCACGTCGCAAGCC
*
18792280 TATTAGTTGTGTGAT-ACAGCCAAC-TCGCAAG
1 TATTAGTTGTAT-ATCACAGCC-ACGTCGCAAG
18792311 TCTGTTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (33 bp):
TATTAGTTGTATATCACAGCCACGTCGCAAGCC
Found at i:18812172 original size:31 final size:31
Alignment explanation
Indices: 18812137--18812204 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
18812127 GTCTAGTGAT
*
18812137 TTAAATAAAAACTTTCAAATAATTCAATGAC
1 TTAAATAAAAACTTTCAAATAATTCAATAAC
* ** *
18812168 TTAAATCAAAACTTTTGAATAGTTCAATAAC
1 TTAAATAAAAACTTTCAAATAATTCAATAAC
18812199 TTAAAT
1 TTAAAT
18812205 GAATATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAATTCAATAAC
Found at i:18818149 original size:38 final size:38
Alignment explanation
Indices: 18818028--18818176 Score: 136
Period size: 38 Copynumber: 3.9 Consensus size: 38
18818018 TAAAGACATG
* * * * ***
18818028 TATTAAAGATGTTTAAACTAGGACATATTTAAAATATA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
* * * *
18818066 TATTTAAGATGTCCTAAACTATGACATAATTAAAAACCCT
1 TATTAAAGATGTTC-AAATTATGACATAATT-AAAACCCA
* * *
18818106 TATTAAAGATGTTCAGATTATGATATAATTAAAACTCA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
* *
18818144 TATTAATGATGTTTAAATTATGACATAATTAAA
1 TATTAAAGATGTTCAAATTATGACATAATTAAA
18818177 TACTTAAACT
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
38 46 0.52
39 27 0.30
40 16 0.18
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (38 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
Found at i:18821991 original size:39 final size:38
Alignment explanation
Indices: 18821948--18822075 Score: 138
Period size: 39 Copynumber: 3.3 Consensus size: 38
18821938 TCTAAACTAG
* *
18821948 GACATATTTAAAATATATATTTAAGATGTCCTAAATTAT
1 GACATAATTAAAATATATATTTAAGATGTTC-AAATTAT
* *
18821987 GACATAATTAAAA-ACCCT-TATTAAAGATGTTCAGATTAT
1 GACATAATTAAAATA---TATATTTAAGATGTTCAAATTAT
18822026 GACATAATTAAAACT-TATA-TTAATGATGTTCAAATTAT
1 GACATAATTAAAA-TATATATTTAA-GATGTTCAAATTAT
18822064 GACATAATTAAA
1 GACATAATTAAA
18822076 GACTTAAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
37 4 0.05
38 28 0.37
39 31 0.41
40 12 0.16
41 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (38 bp):
GACATAATTAAAATATATATTTAAGATGTTCAAATTAT
Found at i:18822048 original size:38 final size:38
Alignment explanation
Indices: 18821929--18822087 Score: 162
Period size: 38 Copynumber: 4.1 Consensus size: 38
18821919 TAAAGACGTG
* * *
18821929 TTAAAGATG-TCTAAACTAGGACATATTTAAAA-TATATA
1 TTAAAGATGTTC-AAATTATGACATAATTAAAACT-TATA
* * *
18821967 TTTAAGATGTCCTAAATTATGACATAATTAAAAACCCT-TA
1 TTAAAGATGTTC-AAATTATGACATAATT-AAAA-CTTATA
*
18822007 TTAAAGATGTTCAGATTATGACATAATTAAAACTTATA
1 TTAAAGATGTTCAAATTATGACATAATTAAAACTTATA
* *
18822045 TTAATGATGTTCAAATTATGACATAATTAAAGACTTAAA
1 TTAAAGATGTTCAAATTATGACATAATTAAA-ACTTATA
18822084 TTAA
1 TTAA
18822088 TTTAACTAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
37 2 0.02
38 43 0.42
39 40 0.39
40 16 0.16
41 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (38 bp):
TTAAAGATGTTCAAATTATGACATAATTAAAACTTATA
Found at i:18824614 original size:9 final size:9
Alignment explanation
Indices: 18824600--18824655 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
18824590 ATAAAGTTCC
18824600 TATAATTTT
1 TATAATTTT
18824609 TATAATATTT
1 TATAAT-TTT
*
18824619 TATATATTGT
1 TATA-ATTTT
*
18824629 TATATTTATT
1 TATAATT-TT
*
18824639 TATAATTTC
1 TATAATTTT
18824648 TAT-ATTTT
1 TATAATTTT
18824656 ATGTATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
8 4 0.11
9 12 0.32
10 20 0.53
11 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TATAATTTT
Found at i:18824633 original size:10 final size:9
Alignment explanation
Indices: 18824606--18824664 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
18824596 TTCCTATAAT
18824606 TTTTATAATA
1 TTTTAT-ATA
18824616 TTTTATATA
1 TTTTATATA
18824625 TTGTTATAT-
1 TT-TTATATA
18824634 TTATT-TATA
1 TT-TTATATA
* *
18824643 ATTTCTATA
1 TTTTATATA
*
18824652 TTTTATGTA
1 TTTTATATA
18824661 TTTT
1 TTTT
18824665 TTTATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 5 0.12
9 24 0.59
10 12 0.29
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:18824635 original size:17 final size:16
Alignment explanation
Indices: 18824613--18824664 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
18824603 AATTTTTATA
18824613 ATATTTTATATATTGTT
1 ATATTTTATATATT-TT
*
18824630 ATATTTATTTATAATTTCT
1 ATATTT-TATAT-ATTT-T
*
18824649 ATATTTTATGTATTTT
1 ATATTTTATATATTTT
18824665 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
18 8 0.28
19 10 0.34
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (16 bp):
ATATTTTATATATTTT
Found at i:18825131 original size:9 final size:9
Alignment explanation
Indices: 18825102--18825146 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
18825092 AGTTTTTGGA
18825102 TTTTAGGG-
1 TTTTAGGGT
18825110 -TTTAGGG-
1 TTTTAGGGT
18825117 TTTTAGGGT
1 TTTTAGGGT
*
18825126 TTTTAGGAT
1 TTTTAGGGT
*
18825135 TTTTAAGGT
1 TTTTAGGGT
18825144 TTT
1 TTT
18825147 GGAGAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 7 0.22
8 7 0.22
9 18 0.56
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.56
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:18832880 original size:27 final size:27
Alignment explanation
Indices: 18832842--18832895 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
18832832 TCATGAGAAA
18832842 ATGAAAGGGTCAAGTCGAGGCACCGTG
1 ATGAAAGGGTCAAGTCGAGGCACCGTG
18832869 ATGAAAGGGTCAAGTCGAGGCACCGTG
1 ATGAAAGGGTCAAGTCGAGGCACCGTG
18832896 GATAGGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.37, T:0.15
Consensus pattern (27 bp):
ATGAAAGGGTCAAGTCGAGGCACCGTG
Found at i:18844616 original size:7 final size:7
Alignment explanation
Indices: 18844604--18844657 Score: 99
Period size: 7 Copynumber: 7.7 Consensus size: 7
18844594 GAAAAGTAAG
18844604 GGGGAAA
1 GGGGAAA
18844611 GGGGAAA
1 GGGGAAA
18844618 GGGGAAA
1 GGGGAAA
*
18844625 GGGAAAA
1 GGGGAAA
18844632 GGGGAAA
1 GGGGAAA
18844639 GGGGAAA
1 GGGGAAA
18844646 GGGGAAA
1 GGGGAAA
18844653 GGGGA
1 GGGGA
18844658 GAGGATCACG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GGGGAAA
Found at i:18845286 original size:13 final size:13
Alignment explanation
Indices: 18845268--18845297 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18845258 AGCCCAAACT
18845268 CAATTACCCAACC
1 CAATTACCCAACC
*
18845281 CAATTACCCAATC
1 CAATTACCCAACC
18845294 CAAT
1 CAAT
18845298 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:18845448 original size:9 final size:9
Alignment explanation
Indices: 18845436--18845499 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
18845426 AAATAAACAA
18845436 AATTCGGGT
1 AATTCGGGT
18845445 AATTCGGGT
1 AATTCGGGT
*
18845454 ATTTTTC-GGT
1 A--ATTCGGGT
18845464 AATTC-GG-
1 AATTCGGGT
*
18845471 --TTCGGTT
1 AATTCGGGT
18845478 AATTCGGGT
1 AATTCGGGT
18845487 AATTCGGGT
1 AATTCGGGT
18845496 AATT
1 AATT
18845500 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
5 3 0.07
6 1 0.02
8 5 0.11
9 29 0.64
10 4 0.09
11 3 0.07
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:18845677 original size:12 final size:12
Alignment explanation
Indices: 18845660--18845684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18845650 AGTAATTTTG
18845660 GGTCGGTTAACC
1 GGTCGGTTAACC
18845672 GGTCGGTTAACC
1 GGTCGGTTAACC
18845684 G
1 G
18845685 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:18853576 original size:13 final size:13
Alignment explanation
Indices: 18853558--18853583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18853548 AGAACATTGC
18853558 TCGTTGAATCTTT
1 TCGTTGAATCTTT
18853571 TCGTTGAATCTTT
1 TCGTTGAATCTTT
18853584 CATAATATCG
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TCGTTGAATCTTT
Found at i:18853723 original size:25 final size:24
Alignment explanation
Indices: 18853671--18853890 Score: 97
Period size: 25 Copynumber: 8.8 Consensus size: 24
18853661 AATTCATATT
* *
18853671 CGGGAATGCTCATAAGAGCACATAAA
1 CGGGAA-GCTCATGAGAGC-CATTAA
* *
18853697 CGGAAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATGAGAGCCAT-TAA
**
18853722 CGGGAAGCTTTTGAGAGCCATTAA
1 CGGGAAGCTCATGAGAGCCATTAA
* * *
18853746 CGGGAAGTTCAT-ACGAGCCAATAT
1 CGGGAAGCTCATGA-GAGCCATTAA
* * * * *
18853770 CGGGAAGGTTCAAGCGAGCCAATAT
1 CGGGAA-GCTCATGAGAGCCATTAA
*
18853795 CGGGAAGTTC-TGGAGAGCCAATTAA
1 CGGGAAGCTCAT-GAGAGCC-ATTAA
** *
18853820 TTAGGAAGCTCATGAAAGAGCCTTTAA
1 -CGGGAAGCTCATG--AGAGCCATTAA
*
18853847 TCGGGAAGCT--TCGAAGAGCCATATAT
1 -CGGGAAGCTCAT-G-AGAGCCAT-TAA
* *
18853873 CGGGACGCTCATAAGAGC
1 CGGGAAGCTCATGAGAGC
18853891 TACGGTGTGT
Statistics
Matches: 151, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
23 1 0.01
24 39 0.26
25 75 0.50
26 16 0.11
27 14 0.09
28 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (24 bp):
CGGGAAGCTCATGAGAGCCATTAA
Found at i:18853812 original size:24 final size:23
Alignment explanation
Indices: 18853722--18853816 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 23
18853712 AGCCATGTAA
* * *
18853722 CGGGAAGCTTTTGAGAGCCATTAA
1 CGGGAAG-TTCTGAGAGCCAATAT
18853746 CGGGAAGTTCAT-ACGAGCCAATAT
1 CGGGAAGTTC-TGA-GAGCCAATAT
* *
18853770 CGGGAAGGTTCAAGCGAGCCAATAT
1 CGGGAA-GTTC-TGAGAGCCAATAT
18853795 CGGGAAGTTCTGGAGAGCCAAT
1 CGGGAAGTTCT-GAGAGCCAAT
18853817 TAATTAGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
23 3 0.05
24 35 0.59
25 21 0.36
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.20
Consensus pattern (23 bp):
CGGGAAGTTCTGAGAGCCAATAT
Found at i:18864434 original size:20 final size:20
Alignment explanation
Indices: 18864409--18864453 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
18864399 ACAAATAAGA
*
18864409 GCACCGGAGTGCAATTAGAG
1 GCACCGGAGTGCAATCAGAG
*
18864429 GCACCGGAGTGCAATCAGTG
1 GCACCGGAGTGCAATCAGAG
18864449 GCACC
1 GCACC
18864454 TTTCTTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (20 bp):
GCACCGGAGTGCAATCAGAG
Found at i:18884671 original size:9 final size:9
Alignment explanation
Indices: 18884586--18884670 Score: 125
Period size: 9 Copynumber: 9.4 Consensus size: 9
18884576 GTAGTGATTC
*
18884586 AATTTGGTT
1 AATTCGGTT
18884595 AATTCGGTT
1 AATTCGGTT
*
18884604 AATTCGGGT
1 AATTCGGTT
*
18884613 AATTCGGGT
1 AATTCGGTT
18884622 AATTCGGTT
1 AATTCGGTT
*
18884631 AATTCGGGT
1 AATTCGGTT
18884640 AATTCGGTT
1 AATTCGGTT
18884649 AATTCGGTT
1 AATTCGGTT
*
18884658 AATTTGGTT
1 AATTCGGTT
18884667 AATT
1 AATT
18884671 TTTAACCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 70 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:18885193 original size:21 final size:20
Alignment explanation
Indices: 18885164--18885202 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
18885154 AATAAATAAC
* *
18885164 ATTTTTGGTGTAGGAAAAAT
1 ATTTTTGGTCTAAGAAAAAT
18885184 ATTTATTGGTCTAAGAAAA
1 ATTT-TTGGTCTAAGAAAA
18885203 TTATATGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTTGGTCTAAGAAAAAT
Found at i:18890323 original size:21 final size:21
Alignment explanation
Indices: 18890299--18890355 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
18890289 ATGAACAATT
*
18890299 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
18890320 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
18890340 AAGAAATAGAATCAAA
1 AAGAAAAAG-ATCAAA
18890356 GATTTGCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 13 0.42
21 12 0.39
22 6 0.19
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:18890340 original size:20 final size:23
Alignment explanation
Indices: 18890310--18890355 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
18890300 AGAAAAAGAG
18890310 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
18890331 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
18890353 AAA
1 AAA
18890356 GATTTGCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 9 0.39
22 6 0.26
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:18893199 original size:32 final size:32
Alignment explanation
Indices: 18893161--18893321 Score: 205
Period size: 35 Copynumber: 4.8 Consensus size: 32
18893151 AAATAATACA
*
18893161 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATAATG
*
18893193 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATAA--TG
*
18893228 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATAATG
* *
18893260 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAAGA-AATAAT--G
* *
18893295 TGAACAGGAAATATTCCCTGCAAGAAA
1 TGAACAGGAGAGATTCCCTGCAAGAAA
18893322 AGACAAGTGA
Statistics
Matches: 114, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
32 48 0.42
33 10 0.09
34 7 0.06
35 49 0.43
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (32 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATAATG
Found at i:18893259 original size:67 final size:67
Alignment explanation
Indices: 18893151--18893321 Score: 279
Period size: 67 Copynumber: 2.6 Consensus size: 67
18893141 GTCCAAAAAG
* * *
18893151 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
18893216 CA
66 CA
*
18893218 AAATAATGTGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
18893283 CA
66 CA
* * *
18893285 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
18893322 AGACAAGTGA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 96 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
CA
Found at i:18893610 original size:14 final size:13
Alignment explanation
Indices: 18893580--18893616 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
18893570 ATTTCCAAAA
*
18893580 TTTCAAATTAAGT
1 TTTCAAATTAAGC
18893593 TTTCAAACTTAAGC
1 TTTCAAA-TTAAGC
18893607 TTTCAAATTA
1 TTTCAAATTA
18893617 CAAATATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (13 bp):
TTTCAAATTAAGC
Found at i:18893823 original size:23 final size:23
Alignment explanation
Indices: 18893791--18893868 Score: 95
Period size: 23 Copynumber: 3.2 Consensus size: 23
18893781 CCCGACCCGT
18893791 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAATTATA
18893815 TTTTTATTAAAATTAAAATTA-A
1 TTTTTATTAAAATTAAAATTATA
*
18893837 TTGTTATTAAAATTGTATCAAATTATA
1 TTTTTATTAAAA-T-TA--AAATTATA
18893864 TTTTT
1 TTTTT
18893869 TTGTACTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.26
23 17 0.36
24 7 0.15
26 6 0.13
27 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTTTATTAAAATTAAAATTATA
Found at i:18894005 original size:93 final size:93
Alignment explanation
Indices: 18893895--18894078 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
18893885 TTTGTAAAAT
*
18893895 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATCATCAAATT
18893960 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
*
18893988 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATCATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATCATCAAATT
*
18894053 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
18894079 ATTAATTGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (93 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATCATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:18895068 original size:26 final size:25
Alignment explanation
Indices: 18895039--18895087 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
18895029 TTTATTGTAA
* *
18895039 AAATATTGTATTTTTTAAAATTATTT
1 AAATATGGTAGTTTTT-AAATTATTT
*
18895065 AAATATGGTGGTTTTTAAATTAT
1 AAATATGGTAGTTTTTAAATTAT
18895088 CTATGTCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (25 bp):
AAATATGGTAGTTTTTAAATTATTT
Done.