Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 188 of 198
Found at i:58494665 original size:29 final size:31
Alignment explanation
Indices: 58494601--58494665 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
58494591 AAAATTATAT
*
58494601 ATGAACTTTAATTTAATGTGTAATTATATAC
1 ATGAACTTTAATTTAATGTGTAATTATACAC
58494632 ATGAACTTTAATTT-A-GTGTAATTATACAC
1 ATGAACTTTAATTTAATGTGTAATTATACAC
*
58494661 GTGAA
1 ATGAA
58494666 ATTCTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
ATGAACTTTAATTTAATGTGTAATTATACAC
Found at i:58496974 original size:20 final size:19
Alignment explanation
Indices: 58496936--58497161 Score: 86
Period size: 19 Copynumber: 11.9 Consensus size: 19
58496926 ACAATAATAA
*
58496936 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACACGAAATT
58496955 TTTTTGAAAACACTGAAA--
1 TTTTTGAAAACAC-GAAATT
* * *
58496973 TTTTCG-ATACATGAGAATT
1 TTTTTGAAAACACGA-AATT
*
58496992 TTTTTG---ACACGAAA-A
1 TTTTTGAAAACACGAAATT
* *
58497007 ATTTTGAAAACACGAAA-A
1 TTTTTGAAAACACGAAATT
*
58497025 TTTTT-AAAACATGAATATT
1 TTTTTGAAAACACGAA-ATT
*
58497044 TTTTT-TAAACACG-AATT
1 TTTTTGAAAACACGAAATT
* *
58497061 TTTTTAAAAAAAAACATGAGAA-T
1 TTTTT----GAAAACACGA-AATT
*
58497084 TTTTTGAAAACACGAACACATGAAA
1 TTTTTGAAAACACG-A-A-AT---T
* *
58497109 ATTTTGAAAACACGAAA-A
1 TTTTTGAAAACACGAAATT
58497127 TTTTTG-AAACACGAGAA-T
1 TTTTTGAAAACACGA-AATT
58497145 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
58497162 ACACGAAAAT
Statistics
Matches: 161, Mismatches: 22, Indels: 49
0.69 0.09 0.21
Matches are distributed among these distances:
15 5 0.03
16 4 0.02
17 36 0.22
18 36 0.22
19 44 0.27
20 5 0.03
21 1 0.01
22 7 0.04
23 7 0.04
24 3 0.02
25 13 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:58496976 original size:18 final size:18
Alignment explanation
Indices: 58496934--58497046 Score: 60
Period size: 17 Copynumber: 6.4 Consensus size: 18
58496924 ATACAATAAT
*
58496934 AATTTTTGAAAACACGGA
1 AATTTTTGAAAACACTGA
*
58496952 ATTTTTTTGAAAACACTGA
1 A-ATTTTTGAAAACACTGA
* *
58496971 AATTTTCG-ATACA-TGA
1 AATTTTTGAAAACACTGA
***
58496987 GAATTTTT-TTGACAC-GAA
1 -AATTTTTGAAAACACTG-A
*
58497005 AAATTTTGAAAACAC-GAA
1 AATTTTTGAAAACACTG-A
58497023 AATTTTT-AAAACA-TGA
1 AATTTTTGAAAACACTGA
58497039 ATATTTTT
1 A-ATTTTT
58497047 TTTAAACACG
Statistics
Matches: 74, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.07
17 33 0.45
18 20 0.27
19 16 0.22
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (18 bp):
AATTTTTGAAAACACTGA
Found at i:58496976 original size:19 final size:18
Alignment explanation
Indices: 58496936--58497161 Score: 106
Period size: 18 Copynumber: 11.9 Consensus size: 18
58496926 ACAATAATAA
*
58496936 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACAC-GAAAT
58496955 TTTTTGAAAACACTGAAA-
1 TTTTTGAAAACAC-GAAAT
* * *
58496973 TTTTCG-ATACATGAGAATT
1 TTTTTGAAAACACGA-AA-T
*
58496992 TTTTTG---ACACGAAAA
1 TTTTTGAAAACACGAAAT
* *
58497007 ATTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAT
*
58497025 TTTTT-AAAACATGAATAT
1 TTTTTGAAAACACGAA-AT
** *
58497043 TTTTTTTAAACACGAATT
1 TTTTTGAAAACACGAAAT
* *
58497061 TTTTTAAAAAAAAACATGAGAAT
1 TTTTT----GAAAACACGA-AAT
58497084 TTTTTGAAAACACGAACACAT
1 TTTTTGAAAACACG-A-A-AT
* *
58497105 GAAAATTTTGAAAACACGAAAA
1 ----TTTTTGAAAACACGAAAT
58497127 TTTTTG-AAACACGAGAAT
1 TTTTTGAAAACACGA-AAT
58497145 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
58497162 ACACGAAAAT
Statistics
Matches: 160, Mismatches: 26, Indels: 43
0.70 0.11 0.19
Matches are distributed among these distances:
15 5 0.03
16 4 0.03
17 28 0.17
18 45 0.28
19 44 0.28
20 2 0.01
21 2 0.01
22 8 0.05
23 8 0.05
24 1 0.01
25 13 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:58497046 original size:17 final size:17
Alignment explanation
Indices: 58497007--58497069 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
58496997 GACACGAAAA
* *
58497007 ATTTTGAAAACACGAAA
1 ATTTTTAAAACACGAAT
*
58497024 ATTTTTAAAACATGAAT
1 ATTTTTAAAACACGAAT
*
58497041 ATTTTTTTTAAACACGAAT
1 A--TTTTTAAAACACGAAT
*
58497060 TTTTTTAAAA
1 ATTTTTAAAA
58497070 AAAAACATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 23 0.62
19 14 0.38
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTTTTAAAACACGAAT
Found at i:58497101 original size:25 final size:25
Alignment explanation
Indices: 58497056--58497124 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
58497046 TTTTAAACAC
* **
58497056 GAATTTTTTTAAAA-AAAAACATGA
1 GAATTTTTTGAAAACACGAACATGA
58497080 GAATTTTTTGAAAACACGAACACATGA
1 GAATTTTTTGAAAACACG-A-ACATGA
*
58497107 -AA-ATTTTGAAAACACGAA
1 GAATTTTTTGAAAACACGAA
58497125 AATTTTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.03
24 14 0.37
25 14 0.37
26 3 0.08
27 6 0.16
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.28
Consensus pattern (25 bp):
GAATTTTTTGAAAACACGAACATGA
Found at i:58497262 original size:23 final size:22
Alignment explanation
Indices: 58497232--58497279 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
58497222 TTCACGAGAG
*
58497232 TTTTTTTTTG-AAACATGAGAAA
1 TTTTTTTTTGAAAACACGA-AAA
58497254 TTTTTTTTTGAAAACACGAAAA
1 TTTTTTTTTGAAAACACGAAAA
58497276 TTTT
1 TTTT
58497280 CAAACACGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTTTTTTTGAAAACACGAAAA
Found at i:58497272 original size:105 final size:97
Alignment explanation
Indices: 58497158--58497507 Score: 486
Period size: 105 Copynumber: 3.5 Consensus size: 97
58497148 TTGAAAACAC
* * **
58497158 GAAAACACGAAAATTTGTCAAATACGGAATTTTTTTTTTGAAACACGATAACATCAAAAAAATAT
1 GAAAACACGAAAATTT-TCAAACACGGAA---ATTTTTAAAAACACGATAACATCAAAAAAATAT
*
58497223 TCACGAGAGTTTTTTTTTGAAACATGAGAAATTTTTTTTT
62 TCACGAGAG--TTTTTTTGAAACACGAG-AA-TTTTTTTT
58497263 GAAAACACGAAAATTTTCAAACACGGAAATTTTTAAAAACACGATAACATCAAAAAAATATTCAC
1 GAAAACACGAAAATTTTCAAACACGGAAATTTTTAAAAACACGATAACATCAAAAAAATATTCAC
58497328 GAGAGTTTTTTTGAAACACGAGAATTTTTTTT
66 GAGAGTTTTTTTGAAACACGAGAATTTTTTTT
58497360 GAAAACACGAAAACATGAAATTTTTCAAACACGGAAATTTTTAAAAACACGATAACATCAAAAAA
1 GAAAACACG-----A--AAA-TTTTCAAACACGGAAATTTTTAAAAACACGATAACATCAAAAAA
58497425 ATATTCACGAGAGTTTTTTTGAAACACGAGAA-TTTTTTT
58 ATATTCACGAGAGTTTTTTTGAAACACGAGAATTTTTTTT
* *
58497464 GAAAACACGAAAATTTTCAAACACGGGAATTTTTGAAAACACGA
1 GAAAACACGAAAATTTTCAAACACGGAAATTTTTAAAAACACGA
58497508 AAATTTTTTA
Statistics
Matches: 230, Mismatches: 7, Indels: 25
0.88 0.03 0.10
Matches are distributed among these distances:
96 29 0.13
97 20 0.09
98 2 0.01
99 17 0.07
101 39 0.17
102 1 0.00
104 30 0.13
105 92 0.40
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (97 bp):
GAAAACACGAAAATTTTCAAACACGGAAATTTTTAAAAACACGATAACATCAAAAAAATATTCAC
GAGAGTTTTTTTGAAACACGAGAATTTTTTTT
Found at i:58497296 original size:17 final size:16
Alignment explanation
Indices: 58497265--58497295 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58497255 TTTTTTTTGA
58497265 AAACACGAAAATTTTC
1 AAACACGAAAATTTTC
*
58497281 AAACACGGAAATTTT
1 AAACACGAAAATTTT
58497296 TAAAAACACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (16 bp):
AAACACGAAAATTTTC
Found at i:58497304 original size:18 final size:17
Alignment explanation
Indices: 58497258--58497305 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
58497248 GAGAAATTTT
58497258 TTTTTGAAAACAC-GAAA
1 TTTTT-AAAACACGGAAA
* *
58497275 ATTTTCAAACACGGAAA
1 TTTTTAAAACACGGAAA
58497292 TTTTTAAAAACACG
1 TTTTT-AAAACACG
58497306 ATAACATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 6 0.24
17 12 0.48
18 7 0.28
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (17 bp):
TTTTTAAAACACGGAAA
Found at i:58497349 original size:19 final size:21
Alignment explanation
Indices: 58497325--58497369 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
58497315 AAAAAATATT
58497325 CACGAG-AGTTTTTTTG-AAA
1 CACGAGAAGTTTTTTTGAAAA
*
58497344 CACGAGAATTTTTTTTGAAAA
1 CACGAGAAGTTTTTTTGAAAA
58497365 CACGA
1 CACGA
58497370 AAACATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (21 bp):
CACGAGAAGTTTTTTTGAAAA
Found at i:58497407 original size:18 final size:17
Alignment explanation
Indices: 58497376--58497410 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
58497366 ACGAAAACAT
*
58497376 GAAATTTTTCAAACACG
1 GAAATTTTTAAAACACG
58497393 GAAATTTTTAAAAACACG
1 GAAATTTTT-AAAACACG
58497411 ATAACATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (17 bp):
GAAATTTTTAAAACACG
Found at i:58497487 original size:16 final size:17
Alignment explanation
Indices: 58497460--58497586 Score: 69
Period size: 17 Copynumber: 7.2 Consensus size: 17
58497450 ACGAGAATTT
58497460 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* * *
58497477 TTTT-CAAACACGGGAAT
1 TTTTGAAAACAC-GAAAA
58497494 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
** ** *
58497511 TTTTTTATTCACGAGAAT
1 TTTTGAAAACACGA-AAA
* *
58497529 TTTTG-AAACATGAAGATT
1 TTTTGAAAACACGAA-A-A
* *
58497547 TTTTGAAAACATGGAAATT
1 TTTTGAAAACA-CGAAA-A
*
58497566 TTTTGAAAACACGGAAA
1 TTTTGAAAACACGAAAA
58497583 TTTT
1 TTTT
58497587 ATTATTATTT
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
16 7 0.08
17 34 0.40
18 21 0.25
19 19 0.23
20 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:58497581 original size:19 final size:19
Alignment explanation
Indices: 58497439--58497586 Score: 111
Period size: 19 Copynumber: 8.2 Consensus size: 19
58497429 TCACGAGAGT
*
58497439 TTTTTTG-AAACACGAGAAT
1 TTTTTTGAAAACACG-GAAA
58497458 TTTTTTGAAAACAC-GAAA
1 TTTTTTGAAAACACGGAAA
* * *
58497476 -ATTTT-CAAACACGGGAA
1 TTTTTTGAAAACACGGAAA
*
58497493 -TTTTTGAAAACACGAAAA
1 TTTTTTGAAAACACGGAAA
**
58497511 TTTTTT--ATTCAC-GAGAA
1 TTTTTTGAAAACACGGA-AA
*
58497528 -TTTTTG-AAACA-TGAAGA
1 TTTTTTGAAAACACGGAA-A
*
58497545 TTTTTTGAAAACATGGAAA
1 TTTTTTGAAAACACGGAAA
58497564 TTTTTTGAAAACACGGAAA
1 TTTTTTGAAAACACGGAAA
58497583 TTTT
1 TTTT
58497587 ATTATTATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
16 13 0.13
17 23 0.22
18 18 0.17
19 40 0.39
20 9 0.09
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
TTTTTTGAAAACACGGAAA
Found at i:58498204 original size:15 final size:15
Alignment explanation
Indices: 58498186--58498214 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58498176 GGCGTTAGGC
58498186 TGGGCAGTGGCCTGT
1 TGGGCAGTGGCCTGT
58498201 TGGGCAGTGGCCTG
1 TGGGCAGTGGCCTG
58498215 CTGCGGGTTG
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:0.07, C:0.21, G:0.48, T:0.24
Consensus pattern (15 bp):
TGGGCAGTGGCCTGT
Found at i:58498331 original size:11 final size:12
Alignment explanation
Indices: 58498317--58498372 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
58498307 TTTTTTTTTC
58498317 TTTTTC-TTCTA
1 TTTTTCTTTCTA
* *
58498328 TTTTTCTTTTTG
1 TTTTTCTTTCTA
58498340 TTTCTT-TTTCT-
1 TTT-TTCTTTCTA
58498351 TTTTTCTTTCTA
1 TTTTTCTTTCTA
58498363 -TTTTCTTTCT
1 TTTTTCTTTCT
58498373 TCCCCTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 2 0.05
11 24 0.63
12 10 0.26
13 2 0.05
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTCTA
Found at i:58498331 original size:17 final size:17
Alignment explanation
Indices: 58498311--58498370 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
58498301 TCTTTGTTTT
58498311 TTTTTCTTTTTCTTCTA
1 TTTTTCTTTTTCTTCTA
* *
58498328 TTTTTCTTTTTGTT-TC
1 TTTTTCTTTTTCTTCTA
58498344 TTTTTCTTTTTTCTTTCTA
1 TTTTTC-TTTTTC-TTCTA
58498363 -TTTTCTTT
1 TTTTTCTTT
58498371 CTTCCCCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.19
17 21 0.58
18 7 0.19
19 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTTCTTCTA
Found at i:58498344 original size:27 final size:27
Alignment explanation
Indices: 58498296--58498373 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
58498286 GCTGCTATTT
* *
58498296 TTTATTCTTTGTTTTTTTTTCTTTTTC
1 TTTATTCTTTCTTTTTCTTTCTTTTTC
*
58498323 TTCTATT-TTTCTTTTTGTTTCTTTTTC
1 TT-TATTCTTTCTTTTTCTTTCTTTTTC
*
58498350 TTTTTTCTTTCTATTTTCTTTCTT
1 TTTATTCTTTCT-TTTTCTTTCTT
58498374 CCCCTTCTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
26 3 0.07
27 27 0.61
28 14 0.32
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (27 bp):
TTTATTCTTTCTTTTTCTTTCTTTTTC
Found at i:58498348 original size:34 final size:34
Alignment explanation
Indices: 58498294--58498370 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
58498284 CTGCTGCTAT
*
58498294 TTTTTATTCTTTGTTTTTTTT-TCTTTTTC-TTCTA
1 TTTTTCTT-TTTGTTTTTTTTCT-TTTTTCTTTCTA
58498328 TTTTTCTTTTTGTTTCTTTTTCTTTTTTCTTTCTA
1 TTTTTCTTTTTGTTT-TTTTTCTTTTTTCTTTCTA
58498363 -TTTTCTTT
1 TTTTTCTTT
58498371 CTTCCCCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 7 0.18
34 26 0.67
35 6 0.15
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.81
Consensus pattern (34 bp):
TTTTTCTTTTTGTTTTTTTTCTTTTTTCTTTCTA
Found at i:58498354 original size:23 final size:22
Alignment explanation
Indices: 58498294--58498359 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
58498284 CTGCTGCTAT
* *
58498294 TTTTTATTCTTTGTTTTTTTTTC
1 TTTTTCTTCTTT-TTTCTTTTTC
*
58498317 TTTTTCTTCTATTTTTCTTTTTG
1 TTTTTCTTCT-TTTTTCTTTTTC
*
58498340 TTTCTTTTTCTTTTTTCTTT
1 TTT-TTCTTCTTTTTTCTTT
58498360 CTATTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 29 0.78
24 8 0.22
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTCTTTTTC
Found at i:58498517 original size:20 final size:21
Alignment explanation
Indices: 58498464--58498518 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
58498454 GGCCGGTATC
*
58498464 TCCTTTC-CTCTTT-TTTCTT
1 TCCTTTCTCTCTTTCCTTCTT
*
58498483 TTCTTTCTCTCCTTTCCTT-TT
1 TCCTTTCTCT-CTTTCCTTCTT
58498504 TCCTTTCTCTCTTTC
1 TCCTTTCTCTCTTTC
58498519 TCTCTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 15 0.50
22 2 0.07
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
TCCTTTCTCTCTTTCCTTCTT
Found at i:58498696 original size:22 final size:22
Alignment explanation
Indices: 58498670--58498717 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
58498660 ATGAGGGCCC
* * *
58498670 TTTTGCTGCTTTTTTTTTGATT
1 TTTTGCTGCTGTTTTCTTAATT
58498692 TTTTGCTGCTGTTTTCTTAATT
1 TTTTGCTGCTGTTTTCTTAATT
58498714 TTTT
1 TTTT
58498718 TCTTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (22 bp):
TTTTGCTGCTGTTTTCTTAATT
Found at i:58499044 original size:30 final size:30
Alignment explanation
Indices: 58499010--58499117 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 30
58499000 AAAAGCTAAG
58499010 GGGTTAAAATGTAATTTAAAGAAAA-TTTAA
1 GGGTTAAAATGTAATTTAAAGAAAAGTTT-A
** *
58499040 GGGTTTGAATGTAATTTATAGAAAAGTTTA
1 GGGTTAAAATGTAATTTAAAGAAAAGTTTA
* * **
58499070 GGGTCAAAATGTAAATTT-CA-AAAAGTACA
1 GGGTTAAAATGT-AATTTAAAGAAAAGTTTA
*
58499099 GGGGCTAAAATGTAATTTA
1 -GGGTTAAAATGTAATTTA
58499118 TATTTTTTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 12 0.19
30 43 0.68
31 8 0.13
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTAAAGAAAAGTTTA
Found at i:58499149 original size:18 final size:18
Alignment explanation
Indices: 58499114--58499152 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58499104 TAAAATGTAA
*
58499114 TTTATATTTTTTGTATTT
1 TTTATATTTTTTGGATTT
58499132 TTTAT-TTTTTTGAGATTT
1 TTTATATTTTTTG-GATTT
58499150 TTT
1 TTT
58499153 TACTACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTATATTTTTTGGATTT
Found at i:58499584 original size:79 final size:76
Alignment explanation
Indices: 58499481--58499980 Score: 496
Period size: 79 Copynumber: 6.3 Consensus size: 76
58499471 AGTTGAGCTC
* * *
58499481 TGAAAAATAGAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCACTTCTAGCATTATGAG
1 TGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGCATTATGAG
58499546 TTGATTTTTTTTT
66 TTGA--TTTTTTT
*
58499559 TGAAAAAACAGAAATTGAAATTACCTCAGCGTGACCCGAGGCTCAAAC-CA-TCTCTCGCATTAT
1 TG-AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTC-AACTCACT-TCTCGCATTAT
58499622 GAGTTGATTTTTTT
63 GAGTTGATTTTTTT
* *
58499636 TGAAAAA-AGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAA
1 TGAAAAACAGAAA-TT--GA-AAATACCTCAGCGT--GACCCGAGGCTCAACTCACTTCTCGCAT
58499700 TATGAGTTGA-TTTTTT
60 TATGAGTTGATTTTTTT
* *
58499716 TGAAAAACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCAC
1 TGAAAAAC--AG------AAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGC
58499781 ATTATGAGTTGA--TTTTT
58 ATTATGAGTTGATTTTTTT
* * * *
58499798 TG-AAAAGAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGGGGCTCAACTCACTTCTCGCAA
1 TGAAAAACAGAAA-TT--GA-AAATACCTCAGCGT--GACCCGAGGCTCAACTCACTTCTCGCAT
58499862 TATGAGTTGA-TTTTTT
60 TATGAGTTGATTTTTTT
** * *
58499878 TGAAAAACAGAGAAACATAAATTGAAAATACCTCAGCGTGATTCGAGACTCAACTCACTTTTCGC
1 TGAAAAAC--AG------AAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGC
58499943 ATTATGAGTTGA-TTTTTT
58 ATTATGAGTTGATTTTTTT
58499961 TGAAAAACAGAAATTGAAAA
1 TGAAAAACAGAAATTGAAAA
58499981 ATATTTCTTA
Statistics
Matches: 361, Mismatches: 25, Indels: 75
0.78 0.05 0.16
Matches are distributed among these distances:
73 3 0.01
74 2 0.01
75 15 0.04
76 8 0.02
77 23 0.06
78 4 0.01
79 106 0.29
80 26 0.07
81 41 0.11
82 8 0.02
83 85 0.24
85 28 0.08
86 2 0.01
88 4 0.01
89 6 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (76 bp):
TGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGCATTATGAG
TTGATTTTTTT
Found at i:58499847 original size:162 final size:163
Alignment explanation
Indices: 58499498--58499980 Score: 712
Period size: 162 Copynumber: 3.0 Consensus size: 163
58499488 TAGAAATTGA
* * * ***
58499498 AAATACCTCAGCGT--AACCCGAGGCTCAACTCACTTCTAGCATTATGAGTTGATTTTTTT-TTT
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
* * * *
58499560 GA-A-A-AAACAGAAATTGAAATTACCTCAGCGTGACCCGAGGCTCAAAC-CATCTCTCGCATTA
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTC-AACTCACCTCTCGCATTA
58499621 TGAGTTGATTTTTTTTGAAAAAAGAAATTTAAAAG
130 TGAGTTGA-TTTTTTTGAAAAAAGAAATTTAAAAG
58499656 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
*
58499721 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTAT
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
*
58499786 GAGTTGA-TTTTTTGAAAAGAGAAATTTAAAAG
131 GAGTTGATTTTTTTGAAAAAAGAAATTTAAAAG
*
58499818 AAATACCTCAGCGTGCGACCCGGGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
** * * *
58499883 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGATTCGAGACTCAACTCACTTTTCGCATTAT
66 AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
*
58499948 GAGTTGATTTTTTTGAAAAACAGAAATTGAAAA
131 GAGTTGATTTTTTTGAAAAA-AGAAATTTAAAA
58499981 ATATTTCTTA
Statistics
Matches: 295, Mismatches: 21, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
158 14 0.05
160 42 0.14
161 1 0.00
162 155 0.53
163 15 0.05
164 68 0.23
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (163 bp):
AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
AACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
GAGTTGATTTTTTTGAAAAAAGAAATTTAAAAG
Found at i:58500878 original size:15 final size:15
Alignment explanation
Indices: 58500841--58500891 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
58500831 TGATTTTTTC
* *
58500841 TTTTTCTTTGTTTTG
1 TTTTTTTTTGCTTTG
58500856 TGTTTTTTTTG--TTG
1 T-TTTTTTTTGCTTTG
58500870 TTTTTTTTTGCTTTG
1 TTTTTTTTTGCTTTG
58500885 TTTTTTT
1 TTTTTTT
58500892 CAGGCATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 11 0.34
16 8 0.25
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTGCTTTG
Found at i:58511768 original size:23 final size:23
Alignment explanation
Indices: 58511738--58511788 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
58511728 GTCGGTTACG
58511738 CGCGAGGAAGGTATTAGCACCCT
1 CGCGAGGAAGGTATTAGCACCCT
58511761 CGCGAGGAAGGTATTAGCACCCT
1 CGCGAGGAAGGTATTAGCACCCT
58511784 CGCGA
1 CGCGA
58511789 CGCCCAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.16
Consensus pattern (23 bp):
CGCGAGGAAGGTATTAGCACCCT
Found at i:58511976 original size:20 final size:19
Alignment explanation
Indices: 58511938--58512099 Score: 78
Period size: 17 Copynumber: 8.8 Consensus size: 19
58511928 ACAATAATAA
*
58511938 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACACGAAATT
58511957 TTTTTGAAAACACTGAAA--
1 TTTTTGAAAACAC-GAAATT
* * *
58511975 TTTTCG-ATACATGAGAATT
1 TTTTTGAAAACACGA-AATT
*
58511994 TTTTTG---ACACGAAA-A
1 TTTTTGAAAACACGAAATT
*
58512009 ATTTTGAAAACACGAAA--
1 TTTTTGAAAACACGAAATT
* *
58512026 ATTTTGAAAACATGAATATT
1 TTTTTGAAAACACGAA-ATT
* *
58512046 TTTTT-TAAACACG-GATT
1 TTTTTGAAAACACGAAATT
* *
58512063 TTTTTAAAAAAACATGAGAA-T
1 TTTTT--GAAAACACGA-AATT
58512084 TTTTTGAAAACACGAA
1 TTTTTGAAAACACGAA
58512100 CACATGAAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 31
0.69 0.11 0.19
Matches are distributed among these distances:
15 5 0.05
16 4 0.04
17 34 0.31
18 15 0.14
19 32 0.29
20 13 0.12
21 6 0.05
22 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:58511978 original size:17 final size:18
Alignment explanation
Indices: 58511908--58512037 Score: 51
Period size: 17 Copynumber: 7.3 Consensus size: 18
58511898 TTTTGTTTTT
58511908 AAACAC-GAGAATTTTGA
1 AAACACTGAGAATTTTGA
* * *
58511925 AATACAATAATAATTTTTGA
1 AA-ACACTGAGAA-TTTTGA
58511945 AAACAC-G-GAATTTTTTTGA
1 AAACACTGAGAA---TTTTGA
58511964 AAACACTGA-AATTTTCG-
1 AAACACTGAGAATTTT-GA
* **
58511981 ATACA-TGAGAATTTTTT
1 AAACACTGAGAATTTTGA
** *
58511998 TGACAC-GAAAAATTTTGA
1 AAACACTG-AGAATTTTGA
*
58512016 AAACAC-GAAAATTTTGA
1 AAACACTGAGAATTTTGA
58512033 AAACA
1 AAACA
58512038 TGAATATTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
16 3 0.03
17 37 0.43
18 16 0.19
19 19 0.22
20 11 0.13
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
AAACACTGAGAATTTTGA
Found at i:58511978 original size:19 final size:18
Alignment explanation
Indices: 58511938--58512161 Score: 93
Period size: 19 Copynumber: 11.9 Consensus size: 18
58511928 ACAATAATAA
*
58511938 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACAC-GAAAT
58511957 TTTTTGAAAACACTGAAA-
1 TTTTTGAAAACAC-GAAAT
* * *
58511975 TTTTCG-ATACATGAGAATT
1 TTTTTGAAAACACGA-AA-T
*
58511994 TTTTTG---ACACGAAAA
1 TTTTTGAAAACACGAAAT
*
58512009 ATTTTGAAAACACGAAA-
1 TTTTTGAAAACACGAAAT
* *
58512026 ATTTTGAAAACATGAATAT
1 TTTTTGAAAACACGAA-AT
** * *
58512045 TTTTTTTAAACACGGATT
1 TTTTTGAAAACACGAAAT
* *
58512063 TTTTTAAAAAAACATGAGAAT
1 TTTTT--GAAAACACGA-AAT
58512084 TTTTTGAAAACACGAACACAT
1 TTTTTGAAAACACG-A-A-AT
* * *
58512105 GAAAATTTTGAAAACATGAAAA
1 ----TTTTTGAAAACACGAAAT
*
58512127 TTTTTG-AAACACGGGAAT
1 TTTTTGAAAACAC-GAAAT
58512145 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
58512162 ACACGAAAAT
Statistics
Matches: 154, Mismatches: 32, Indels: 39
0.68 0.14 0.17
Matches are distributed among these distances:
15 5 0.03
16 4 0.03
17 31 0.20
18 37 0.24
19 45 0.29
20 8 0.05
21 9 0.06
22 1 0.01
23 1 0.01
24 1 0.01
25 12 0.08
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:58512133 original size:18 final size:18
Alignment explanation
Indices: 58512101--58512162 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
58512091 AAACACGAAC
58512101 ACATGAAAA-TTTTGAAA
1 ACATGAAAATTTTTGAAA
58512118 ACATGAAAATTTTTG-AA
1 ACATGAAAATTTTTGAAA
* * *
58512135 ACACGGGAATTTTTTGAAA
1 ACA-TGAAAATTTTTGAAA
*
58512154 ACACGAAAA
1 ACATGAAAA
58512163 CACGAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 14 0.39
18 17 0.47
19 5 0.14
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (18 bp):
ACATGAAAATTTTTGAAA
Found at i:58512162 original size:44 final size:45
Alignment explanation
Indices: 58512114--58512310 Score: 152
Period size: 44 Copynumber: 4.3 Consensus size: 45
58512104 TGAAAATTTT
*
58512114 GAAAACATGAAAATTTTTGAAACACGGGAA-TTTTTTGAAAACAC
1 GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
* * *
58512158 GAAAACACGAAAATTTGTCAAATACGGGAATTTTTTTTG-AAACAC
1 GAAAACATGAAAATTTTTCAAACACGGGAA-TTTTTTTGAAAACAC
* * * * *
58512203 GATAACATCAAAAAAATATTCAAGAAAACACGAGAATTTTTTTTTGAAAACAC
1 GAAAACAT--GAAAATTTTTC----AAACACGGGAA--TTTTTTTGAAAACAC
* * *
58512256 GAAAACAT-TAAATTTTTCAAACAC-GGAA-ATTTTTAAAAACAC
1 GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
* *
58512298 GATAACATCAAAA
1 GAAAACATGAAAA
58512311 AAATATTCAC
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
42 19 0.16
43 3 0.02
44 26 0.21
45 15 0.12
46 13 0.11
47 7 0.06
50 7 0.06
51 9 0.07
52 9 0.07
53 13 0.11
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (45 bp):
GAAAACATGAAAATTTTTCAAACACGGGAATTTTTTTGAAAACAC
Found at i:58512295 original size:18 final size:17
Alignment explanation
Indices: 58512265--58512298 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58512255 CGAAAACATT
*
58512265 AAATTTTTCAAACACGG
1 AAATTTTTAAAACACGG
58512282 AAATTTTTAAAAACACG
1 AAATTTTT-AAAACACG
58512299 ATAACATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (17 bp):
AAATTTTTAAAACACGG
Found at i:58512296 original size:95 final size:98
Alignment explanation
Indices: 58512144--58512319 Score: 268
Period size: 95 Copynumber: 1.8 Consensus size: 98
58512134 AACACGGGAA
* * **
58512144 TTTTTTGAAAACACGAAAACACGAAAATTTGTCAAATACGGGAATTTTTTTTGAAACACGATAAC
1 TTTTTTGAAAACACGAAAACACGAAAATTTGTCAAACACGGGAATATTTTTAAAAACACGATAAC
58512209 ATCAAAAAAATATTCAAGAAAACACGAGAATTT
66 ATCAAAAAAATATTCAAGAAAACACGAGAATTT
** *
58512242 TTTTTTGAAAACACGAAAACA-TTAAATTTTTCAAACAC-GGAA-ATTTTTAAAAACACGATAAC
1 TTTTTTGAAAACACGAAAACACGAAAATTTGTCAAACACGGGAATATTTTTAAAAACACGATAAC
58512304 ATCAAAAAAATATTCA
66 ATCAAAAAAATATTCA
58512320 CGAGAGTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
95 33 0.46
96 4 0.06
97 13 0.18
98 21 0.30
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (98 bp):
TTTTTTGAAAACACGAAAACACGAAAATTTGTCAAACACGGGAATATTTTTAAAAACACGATAAC
ATCAAAAAAATATTCAAGAAAACACGAGAATTT
Found at i:58512342 original size:19 final size:19
Alignment explanation
Indices: 58512318--58512354 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58512308 AAAAAATATT
*
58512318 CACGAGAGTTTTTTTGAAG
1 CACGAGAATTTTTTTGAAG
58512337 CACGAGAATTTTTTTGAA
1 CACGAGAATTTTTTTGAA
58512355 AACATGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
CACGAGAATTTTTTTGAAG
Found at i:58512446 original size:19 final size:21
Alignment explanation
Indices: 58512422--58512466 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
58512412 AAAAAATATT
58512422 CACGAG-AGTTTTTTTG-AAA
1 CACGAGAAGTTTTTTTGAAAA
*
58512441 CACGAGAATTTTTTTTGAAAA
1 CACGAGAAGTTTTTTTGAAAA
58512462 CACGA
1 CACGA
58512467 AAACACGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (21 bp):
CACGAGAAGTTTTTTTGAAAA
Found at i:58512489 original size:105 final size:105
Alignment explanation
Indices: 58512228--58512508 Score: 465
Period size: 104 Copynumber: 2.7 Consensus size: 105
58512218 ATATTCAAGA
*
58512228 AAACACGAGAATTTTTTTTTGAAAACACGAAAACATTAAATTTTTCAAACACGGAAATTTTTAAA
1 AAACACGAGAA-TTTTTTTTGAAAACACGAAAACATGAAATTTTTCAAACACGGAAATTTTTAAA
58512293 AACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
65 AACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
* * *
58512334 AAGCACGAGAA-TTTTTTTGAAAACATGGAAACATGAAATTTTTCAAACACGGAAATTTTTAAAA
1 AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAATTTTTCAAACACGGAAATTTTTAAAA
*
58512398 ATACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
66 ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
* * * *
58512438 AAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTCAAACACGGGAATTTTTGAAA
1 AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAATTTTTCAAACACGGAAATTTTTAAAA
58512503 ACACGA
66 ACACGA
58512509 AATTTTTTTA
Statistics
Matches: 161, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
104 99 0.61
105 52 0.32
106 10 0.06
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (105 bp):
AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAATTTTTCAAACACGGAAATTTTTAAAA
ACACGATAACATCAAAAAAATATTCACGAGAGTTTTTTTG
Found at i:58512512 original size:17 final size:17
Alignment explanation
Indices: 58512465--58512587 Score: 97
Period size: 17 Copynumber: 6.9 Consensus size: 17
58512455 TTGAAAACAC
*
58512465 GAAAACACGAAAATTTT
1 GAAAACACGAAATTTTT
* *
58512482 -CAAACACGGGAATTTTT
1 GAAAACAC-GAAATTTTT
58512499 GAAAACACGAAATTTTT
1 GAAAACACGAAATTTTT
** ** *
58512516 TTATTCGCGAGAATTTTT
1 GAAAACACGA-AATTTTT
58512534 G-AAACACGAAGATTTTTT
1 GAAAACACGAA-A-TTTTT
58512552 GAAAACACGGAAATTTTTT
1 GAAAACAC-GAAA-TTTTT
58512571 GAAAACACGGAAATTTT
1 GAAAACAC-GAAATTTT
58512588 ATTATTATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.08
17 26 0.31
18 23 0.27
19 26 0.31
20 3 0.04
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
GAAAACACGAAATTTTT
Found at i:58512551 original size:19 final size:18
Alignment explanation
Indices: 58512529--58512587 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 18
58512519 TTCGCGAGAA
58512529 TTTTTG-AAACACGAAGAT
1 TTTTTGAAAACACGAA-AT
58512547 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACAC-GAAAT
58512566 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACAC-GAAAT
58512585 TTT
1 TTT
58512588 ATTATTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 6 0.15
19 30 0.77
20 3 0.08
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:58513327 original size:11 final size:12
Alignment explanation
Indices: 58513311--58513366 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
58513301 TGTTTTTTTC
58513311 TTTTTC-TTCTA
1 TTTTTCTTTCTA
* *
58513322 TTTTTCTTTTTC
1 TTTTTCTTTCTA
58513334 TTTCTT-TTTCT-
1 TTT-TTCTTTCTA
58513345 TTTTTCTTTCTA
1 TTTTTCTTTCTA
58513357 -TTTTCTTTCT
1 TTTTTCTTTCT
58513367 TCTCCTTCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 2 0.05
11 24 0.63
12 10 0.26
13 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTCTA
Found at i:58513331 original size:23 final size:23
Alignment explanation
Indices: 58513296--58513353 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
58513286 CTATTTTTTA
*
58513296 TTCTTTGTT-TTTTTCTTT-TTC
1 TTCTTTTTTCTTTTTCTTTCTTC
*
58513317 TTCTATTTTTCTTTTTCTTTCTTT
1 TTCT-TTTTTCTTTTTCTTTCTTC
58513341 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
58513354 CTATTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 18 0.56
24 6 0.19
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (23 bp):
TTCTTTTTTCTTTTTCTTTCTTC
Found at i:58513342 original size:35 final size:35
Alignment explanation
Indices: 58513305--58513369 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
58513295 ATTCTTTGTT
58513305 TTTTTC-TTTTTC-TTCTATTTTTCTTT-TTCTTTC
1 TTTTTCTTTTTTCTTTCTA-TTTTCTTTCTTCTTTC
58513338 TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCT
1 TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCT
58513370 CCTTCCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 6 0.21
34 14 0.48
35 9 0.31
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTTCTTTTTTCTTTCTATTTTCTTTCTTCTTTC
Found at i:58513345 original size:27 final size:28
Alignment explanation
Indices: 58513303--58513367 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
58513293 TTATTCTTTG
58513303 TTTT-TTTCTTTTTCTTCTATT-TTTCT-
1 TTTTCTTTCTTTTTCTT-TATTCTTTCTA
*
58513329 TTTTCTTTCTTTTTCTTTTTTCTTTCTA
1 TTTTCTTTCTTTTTCTTTATTCTTTCTA
58513357 TTTTCTTTCTT
1 TTTTCTTTCTT
58513368 CTCCTTCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 7 0.20
27 17 0.49
28 11 0.31
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTCTTTCTTTTTCTTTATTCTTTCTA
Found at i:58513361 original size:18 final size:18
Alignment explanation
Indices: 58513306--58513369 Score: 82
Period size: 17 Copynumber: 3.7 Consensus size: 18
58513296 TTCTTTGTTT
58513306 TTTTC-TTTTTC-TTCTA
1 TTTTCTTTTTTCTTTCTA
58513322 TTTT-TCTTTTTCTTTCT-
1 TTTTCT-TTTTTCTTTCTA
58513339 TTTTCTTTTTTCTTTCTA
1 TTTTCTTTTTTCTTTCTA
*
58513357 TTTTCTTTCTTCT
1 TTTTCTTTTTTCT
58513370 CCTTCCTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 4 0.10
17 21 0.50
18 17 0.40
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTCTA
Found at i:58514024 original size:30 final size:30
Alignment explanation
Indices: 58513990--58514047 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
58513980 TAAGCGGTCA
58513990 AAATGTAATTTAAAGAAAA-TTTAGGGGTTT
1 AAATGTAATTTAAAGAAAAGTTT-GGGGTTT
*
58514020 AAATGTAATTTATAGAAAAGTTTGGGGT
1 AAATGTAATTTAAAGAAAAGTTTGGGGT
58514048 CAAAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.36
Consensus pattern (30 bp):
AAATGTAATTTAAAGAAAAGTTTGGGGTTT
Found at i:58518644 original size:304 final size:304
Alignment explanation
Indices: 58518095--58518705 Score: 990
Period size: 304 Copynumber: 2.0 Consensus size: 304
58518085 TTTCTCGTTG
*
58518095 AAACAAAAATCAGAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
1 AAACAAAAATCAAAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
* * * *
58518160 ATGCATGATTTAGATTTTAAGATTTAATAATGGTAAGGAGTACAATTCAAAAACCTTTAATAGGT
66 ATGCATGAATCAGATTTTAAGATCTAATAATGGCAAGGAGTACAATTCAAAAACCTTTAATAGGT
* * * *
58518225 TTTGTGAAGAGGATGAAATTGAGCATCAGTTGATGGTGCCATACACTCCACAATAAAATGGAGTC
131 TTTATGAAGAGGATGAAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
58518290 AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAAAAGAATC-TTC
196 AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAAAAGAATCTTTC
* * *
58518354 CAAAAAGCTTTTGGGGAGAAGCTGCAAACACTGCTGTGTTCTTGC
261 C-AAAAGATTTTGGGGAGAAGCTGCAAACACTACTGTGTTCTTAC
* * * * *
58518399 AAACAAAAATTAAAATTTGTTGGTGTGTTTTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
1 AAACAAAAATCAAAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
* * *
58518464 ATGCATGAATCAGATTTTAAGATCTGATAATGGCAAGGAGTACACTTCAGAAACCTTTAATAGGT
66 ATGCATGAATCAGATTTTAAGATCTAATAATGGCAAGGAGTACAATTCAAAAACCTTTAATAGGT
* *
58518529 TTTATGAAGAGGTTGGAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
131 TTTATGAAGAGGATGAAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
* *
58518594 AGTGAAAGGAGGAACAGATTCATAATGGAGATGACTCGATGTATGCTTCATGAGAAGAATCTTTC
196 AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAAAAGAATCTTTC
58518659 CAAAAGATTTTGGGGAGAAGCTGCAAACACTACTGTGTTCTTAC
261 CAAAAGATTTTGGGGAGAAGCTGCAAACACTACTGTGTTCTTAC
58518703 AAA
1 AAA
58518706 ATCAGATTTC
Statistics
Matches: 282, Mismatches: 24, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
304 278 0.99
305 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (304 bp):
AAACAAAAATCAAAAGTTGCTGGTGTCTTCTGGAAATTCAAAGCCAGAGTTGAGAATGAAAGTGG
ATGCATGAATCAGATTTTAAGATCTAATAATGGCAAGGAGTACAATTCAAAAACCTTTAATAGGT
TTTATGAAGAGGATGAAATTGAACATCAGTTGACGGTGCCATACACTCCACAACAAAATGGAGTC
AGTGAAAGGAGGAACAGATTCATAATAGAGATGACTCGATGTATGCTTCATGAAAAGAATCTTTC
CAAAAGATTTTGGGGAGAAGCTGCAAACACTACTGTGTTCTTAC
Found at i:58523909 original size:19 final size:19
Alignment explanation
Indices: 58523866--58523911 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
58523856 AATTTTATTT
*
58523866 AATTAT-TTAAAATTATAA
1 AATTATATTAAAATGATAA
58523884 AGA-TATATTAAAATGATAA
1 A-ATTATATTAAAATGATAA
58523903 AATTATATT
1 AATTATATT
58523912 TTTAGTATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
AATTATATTAAAATGATAA
Found at i:58524965 original size:16 final size:16
Alignment explanation
Indices: 58524919--58524968 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
58524909 AAGCCAAATT
58524919 AAAATAAGAGGAA-ATG
1 AAAATAAGAGGAAGA-G
58524935 AAAATAGAGAGGAAGAG
1 AAAATA-AGAGGAAGAG
58524952 AAAATAAGAGGAAGAG
1 AAAATAAGAGGAAGAG
58524968 A
1 A
58524969 GTGTACCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 17 0.53
17 14 0.44
18 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.08
Consensus pattern (16 bp):
AAAATAAGAGGAAGAG
Found at i:58532288 original size:19 final size:19
Alignment explanation
Indices: 58532244--58532314 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
58532234 TATTTTGATA
*
58532244 TTAACTTGTTTTGAAACAGTT
1 TTAACTTG-ATTGAAACA-TT
58532265 TTAACTTGATTGAAA-ATGT
1 TTAACTTGATTGAAACAT-T
**
58532284 TTAACTCAATTGAAACCATT
1 TTAACTTGATTGAAA-CATT
58532304 TTAACTTGATT
1 TTAACTTGATT
58532315 TTATCATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.02
19 15 0.36
20 16 0.38
21 10 0.24
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (19 bp):
TTAACTTGATTGAAACATT
Found at i:58541666 original size:29 final size:31
Alignment explanation
Indices: 58541608--58541666 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
58541598 ATATATAAAT
*
58541608 TTTAATTTAATGTATAATTATATACATGAAC
1 TTTAATTTAATGTATAATTATACACATGAAC
* *
58541639 TTTAATTT-A-GTGTAATTATACACGTGAA
1 TTTAATTTAATGTATAATTATACACATGAA
58541667 ATTCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 1 0.04
31 8 0.32
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (31 bp):
TTTAATTTAATGTATAATTATACACATGAAC
Found at i:58542637 original size:27 final size:29
Alignment explanation
Indices: 58542607--58542663 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
58542597 TAAGAATTGA
*
58542607 ATTAAAT-A-AATTAAAATTCATATACAC
1 ATTAAATCATAATTAAAATCCATATACAC
*
58542634 ATTAAATCATATTTAAAATCCATATACAC
1 ATTAAATCATAATTAAAATCCATATACAC
58542663 A
1 A
58542664 AAATTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 1 0.04
29 18 0.69
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (29 bp):
ATTAAATCATAATTAAAATCCATATACAC
Found at i:58545415 original size:30 final size:30
Alignment explanation
Indices: 58545382--58545507 Score: 150
Period size: 30 Copynumber: 4.2 Consensus size: 30
58545372 TTTTATTTTG
*
58545382 CATTTTGACCCCTAAACTTTTCTAAAATTG
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
58545412 CATTTTGACCCCTAAAC-TTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTTCT-AAAATTA
* *
58545442 TATTTAT-ACACCTAAACTTTTCT-AAATTA
1 CATTT-TGACCCCTAAACTTTTCTAAAATTA
* * * *
58545471 CATTTGGGCCCCTAAACTTTCCAAAAATTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
58545501 CATTTTG
1 CATTTTG
58545508 GCCTCATATT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
29 27 0.33
30 48 0.59
31 6 0.07
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTA
Found at i:58545485 original size:59 final size:60
Alignment explanation
Indices: 58545392--58545505 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 60
58545382 CATTTTGACC
* * *
58545392 CCTAAACTTTTCTAAAATTGCATTTTGACCCCTAAACTTTCTC-AAAATTATATTTATACA
1 CCTAAACTTTTCTAAAATTACATTTGGACCCCTAAACTTTC-CAAAAATTACATTTATACA
*
58545452 CCTAAACTTTTCT-AAATTACATTTGGGCCCCTAAACTTTCCAAAAATTACATTT
1 CCTAAACTTTTCTAAAATTACATTTGGACCCCTAAACTTTCCAAAAATTACATTT
58545506 TGGCCTCATA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 1 0.02
59 35 0.71
60 13 0.27
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (60 bp):
CCTAAACTTTTCTAAAATTACATTTGGACCCCTAAACTTTCCAAAAATTACATTTATACA
Found at i:58546090 original size:30 final size:29
Alignment explanation
Indices: 58546022--58546090 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
58546012 GGGCCGAACG
58546022 AAGAAG-AAAAGAAAAAATAAAAAAAAGA
1 AAGAAGAAAAAGAAAAAATAAAAAAAAGA
** *
58546050 GGGAAGGAAAAAG-AAAAATGAAAGAAAAGGA
1 AAGAA-GAAAAAGAAAAAAT-AAA-AAAAAGA
58546081 AAGAAGAAAA
1 AAGAAGAAAA
58546091 TTTTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.09
29 7 0.22
30 13 0.41
31 9 0.28
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (29 bp):
AAGAAGAAAAAGAAAAAATAAAAAAAAGA
Found at i:58546575 original size:17 final size:17
Alignment explanation
Indices: 58546550--58546600 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
58546540 ATCGCATATT
58546550 TTTAAGTTTTT-TTTGTA
1 TTTAAGTTTTTATTT-TA
*
58546567 TTTATGTTTTTATTTTA
1 TTTAAGTTTTTATTTTA
*
58546584 TTTTA--TTTTATTTTA
1 TTTAAGTTTTTATTTTA
58546599 TT
1 TT
58546601 CGTTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 12 0.40
17 15 0.50
18 3 0.10
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTAAGTTTTTATTTTA
Found at i:58546584 original size:5 final size:5
Alignment explanation
Indices: 58546574--58546600 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
58546564 GTATTTATGT
58546574 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
58546601 CGTTAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:58546926 original size:18 final size:18
Alignment explanation
Indices: 58546903--58546948 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
58546893 AAACTAATTG
58546903 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
58546920 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
58546938 TGTTTCAAAAA
1 TGTTTCAAAAA
58546949 AATAATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:58547155 original size:37 final size:36
Alignment explanation
Indices: 58547005--58547231 Score: 144
Period size: 37 Copynumber: 6.2 Consensus size: 36
58546995 TTCGTATTTC
* *
58547005 AAAAATTTCCGTGTTTTTAAAAATTTCCGTGTTTT--A
1 AAAAATTTCC-TG-TTTTATAAATTTTCGTGTTTTCAA
* * * *
58547041 AAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTC--
1 AAAAATTTCCTGTTTT--ATAAATTT-TCGTGTTTTCAA
* * ** * *
58547078 AAAAATTCTCGTATTTCGT-AACTTTCTTGTTTTCAGA
1 AAAAATT-TCCTGTTTTATAAATTTTCGTGTTTTCA-A
58547115 AAAAATTTCCATGTTTTATAAATTTTCGTGTTTTCAA
1 AAAAATTTCC-TGTTTTATAAATTTTCGTGTTTTCAA
* *
58547152 AAAAA-TTCCTGTCTTTTAAAAATTTTTGTGTTTTCAA
1 AAAAATTTCCTG--TTTTATAAATTTTCGTGTTTTCAA
* * *
58547189 AAAAATTGACCGTGTTTCATAAATTTCCGTG-TTTCAA
1 AAAAATT-TCC-TGTTTTATAAATTTTCGTGTTTTCAA
58547226 AAAAAT
1 AAAAAT
58547232 CCTCGTGTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
34 12 0.08
35 8 0.05
36 22 0.14
37 72 0.47
38 35 0.23
39 2 0.01
40 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (36 bp):
AAAAATTTCCTGTTTTATAAATTTTCGTGTTTTCAA
Found at i:58547190 original size:18 final size:18
Alignment explanation
Indices: 58547001--58547228 Score: 157
Period size: 17 Copynumber: 12.5 Consensus size: 18
58546991 AAACTTCGTA
58547001 TTTCAAAAATTTCCGTGT
1 TTTCAAAAATTTCCGTGT
*
58547019 TTTTAAAAATTTCCGTGT
1 TTTCAAAAATTTCCGTGT
*
58547037 TTT-AAAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGT
58547054 TTTCAAAAAATTTCCCGTGT
1 TTTC-AAAAATTT-CCGTGT
*
58547074 TTTCAAAAA-TTCTCGT-A
1 TTTCAAAAATTTC-CGTGT
** * *
58547091 TTTCGTAACTTT-CTTGT
1 TTTCAAAAATTTCCGTGT
*
58547108 TTTCAGAAAAAATTTCCATGT
1 TTTC---AAAAATTTCCGTGT
* *
58547129 TTT-ATAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGT
*
58547146 TTTCAAAAAAATTCC-TGT
1 TTTC-AAAAATTTCCGTGT
* **
58547164 CTTTTAAAAATTTTTGTGT
1 -TTTCAAAAATTTCCGTGT
*
58547183 TTTCAAAAAAATTGACCGTG-
1 TTTC--AAAAATT-TCCGTGT
*
58547203 TTTCATAAATTTCCGTG-
1 TTTCAAAAATTTCCGTGT
58547220 TTTCAAAAA
1 TTTCAAAAA
58547229 AATCCTCGTG
Statistics
Matches: 163, Mismatches: 30, Indels: 35
0.71 0.13 0.15
Matches are distributed among these distances:
16 2 0.01
17 54 0.33
18 46 0.28
19 26 0.16
20 25 0.15
21 10 0.06
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTCAAAAATTTCCGTGT
Found at i:58547316 original size:20 final size:21
Alignment explanation
Indices: 58547253--58547317 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 21
58547243 ATAATTTATC
* * *
58547253 AAAATTTTTGTGTTCTCAAAA
1 AAAATTATCGTGTTTTCAAAA
*
58547274 TAAAATTATTGTGTTTT--AAA
1 -AAAATTATCGTGTTTTCAAAA
58547294 AAAATT-TCGTGTTTTCAAAA
1 AAAATTATCGTGTTTTCAAAA
58547314 AAAA
1 AAAA
58547318 AAGTTGTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.21
19 6 0.16
20 10 0.26
22 14 0.37
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (21 bp):
AAAATTATCGTGTTTTCAAAA
Found at i:58555049 original size:83 final size:74
Alignment explanation
Indices: 58554769--58555140 Score: 453
Period size: 77 Copynumber: 4.8 Consensus size: 74
58554759 NNNNNNNTTC
*
58554769 TTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCA
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CA
58554833 CGCTGAGGTA-
64 CGCTGAGGTAT
* * * *
58554843 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCATTGGGTCACG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
58554907 CTGAGGTAT
66 CTGAGGTAT
* * * * * *
58554916 TTTTAATTTATATCTTTTTAAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTAAATT-TCTGTTTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
58554981 ACGCTGAGGTATTT
63 ACGCTGAGGTA--T
58554995 CTTTTAAATTTCTGTTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 -TTTTAAATTTCTG----TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
**
58555060 GACCACGCTGAGGTATTTT
59 GGTCACGCTGAGGTA---T
58555079 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
58555141 GCATGCCGAG
Statistics
Matches: 261, Mismatches: 21, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
72 12 0.05
73 8 0.03
74 39 0.15
75 22 0.08
76 19 0.07
77 73 0.28
79 9 0.03
80 8 0.03
83 68 0.26
84 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (74 bp):
TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
CTGAGGTAT
Found at i:58555104 original size:160 final size:149
Alignment explanation
Indices: 58554769--58555140 Score: 464
Period size: 160 Copynumber: 2.4 Consensus size: 149
58554759 NNNNNNNTTC
*
58554769 TTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCA
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CA
58554833 CGCTGAGGTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCAT
64 CGCTGAGGTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCAT
* **
58554898 TGGGTCACGCTGAGGTATTTT
129 CGGACCACGCTGAGGTATTTT
* ** * *
58554919 TAATTT--ATATCT-TTTTAAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
1 T--TTTAAATTTCTGTTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
58554981 ACGCTGAGGTATTTCTTTTAAATTTCTGTTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGG
63 ACGCTGAGGTA----TTTTAAATTTCTG----TTTTTC--AAAAATCAACTCATAATAC-AGAGG
*
58555046 TGAGTTGAGCCTCGGACCACGCTGAGGTATTTT
117 TGAGTTGAGCATCGGACCACGCTGAGGTATTTT
58555079 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
58555141 GCATGCCGAG
Statistics
Matches: 187, Mismatches: 17, Indels: 26
0.81 0.07 0.11
Matches are distributed among these distances:
149 12 0.06
150 9 0.05
151 39 0.21
152 3 0.02
153 13 0.07
157 6 0.03
158 3 0.02
159 17 0.09
160 81 0.43
161 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
CTGAGGTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCATCG
GACCACGCTGAGGTATTTT
Found at i:58555366 original size:30 final size:30
Alignment explanation
Indices: 58555335--58555460 Score: 134
Period size: 30 Copynumber: 4.2 Consensus size: 30
58555325 TTTATTTTTG
*
58555335 CATTTTGACCCCTAAACTTTTCTAAAATTG
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
*
58555365 CATTTTGACCCTTAAAC-TTTCTTAAAATTA
1 CATTTTGACCCCTAAACTTTTC-TAAAATTA
58555395 CATTTAT-ACCCCTAAACTTTTCT-AAATTA
1 CATTT-TGACCCCTAAACTTTTCTAAAATTA
* * * * *
58555424 CATCTGGGCCCTTAAAC-TTTCCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAA-TTA
58555454 CATTTTG
1 CATTTTG
58555461 GCCTCATATT
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.05
29 25 0.31
30 46 0.57
31 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTA
Found at i:58555455 original size:59 final size:60
Alignment explanation
Indices: 58555342--58555458 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
58555332 TTGCATTTTG
* * * *
58555342 ACCCCTAAACTTTTCTAAAATTGCATTTTGACCCTTAAACTTTCTTAAAATTACATTTAT
1 ACCCCTAAACTTTTCTAAAATTACATCTGGACCCTTAAACTTTCTCAAAATTACATTTAT
*
58555402 ACCCCTAAACTTTTCT-AAATTACATCTGGGCCCTTAAACTTTC-CAAAATTTACATTT
1 ACCCCTAAACTTTTCTAAAATTACATCTGGACCCTTAAACTTTCTCAAAA-TTACATTT
58555459 TGGCCTCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
58 4 0.08
59 31 0.61
60 16 0.31
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (60 bp):
ACCCCTAAACTTTTCTAAAATTACATCTGGACCCTTAAACTTTCTCAAAATTACATTTAT
Found at i:58555860 original size:24 final size:23
Alignment explanation
Indices: 58555822--58555871 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
58555812 AAGCAAGCAT
58555822 AAACAAAAAAAACAGCAAACAAG
1 AAACAAAAAAAACAGCAAACAAG
*
58555845 AAACAACAAAAAACAGCAAAGAAG
1 AAACAA-AAAAAACAGCAAACAAG
58555869 AAA
1 AAA
58555872 AAGGAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (23 bp):
AAACAAAAAAAACAGCAAACAAG
Found at i:58556036 original size:23 final size:21
Alignment explanation
Indices: 58555995--58556063 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 21
58555985 CCGAACGAAG
* *
58555995 AAGAAAAGAAAAAATAAAAAA
1 AAGAAAAGGAAAAAGAAAAAA
*
58556016 AAGAGGGAAGGAAAAAGAAAAATGA
1 AAGA--AAAGGAAAAAGAAAAA--A
58556041 AAGAAAAGGAAAGAAGAAAAAA
1 AAGAAAAGGAAA-AAGAAAAAA
58556063 A
1 A
58556064 TTTAAAACAG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.10
22 2 0.05
23 20 0.51
24 8 0.21
25 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (21 bp):
AAGAAAAGGAAAAAGAAAAAA
Found at i:58556060 original size:30 final size:29
Alignment explanation
Indices: 58555992--58556061 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
58555982 GGGCCGAACG
58555992 AAGAAG-AAAAGAAAAAATAAAAAAAAGA
1 AAGAAGAAAAAGAAAAAATAAAAAAAAGA
** *
58556020 GGGAAGGAAAAAG-AAAAATGAAAGAAAAGGA
1 AAGAA-GAAAAAGAAAAAAT-AAA-AAAAAGA
58556051 AAGAAGAAAAA
1 AAGAAGAAAAA
58556062 AATTTAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
28 3 0.09
29 7 0.21
30 14 0.42
31 9 0.27
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (29 bp):
AAGAAGAAAAAGAAAAAATAAAAAAAAGA
Found at i:58556609 original size:18 final size:17
Alignment explanation
Indices: 58556583--58556634 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
58556573 GTCTATTATT
*
58556583 TTTAAGTTTTTTTTTGTA
1 TTTAAGTTTTTATTT-TA
*
58556601 TTTATGTTTTTATTTTA
1 TTTAAGTTTTTATTTTA
*
58556618 TTTTA--TTTTATTTTA
1 TTTAAGTTTTTATTTTA
58556633 TT
1 TT
58556635 CGTTAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.40
17 5 0.17
18 13 0.43
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTAAGTTTTTATTTTA
Found at i:58556616 original size:5 final size:5
Alignment explanation
Indices: 58556608--58556634 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
58556598 GTATTTATGT
58556608 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
58556635 CGTTAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:58556959 original size:18 final size:18
Alignment explanation
Indices: 58556936--58556981 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
58556926 AAACTAATTG
58556936 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
58556953 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
58556971 TGTTTCAAAAA
1 TGTTTCAAAAA
58556982 AATAATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:58557050 original size:17 final size:17
Alignment explanation
Indices: 58557030--58557242 Score: 106
Period size: 17 Copynumber: 11.8 Consensus size: 17
58557020 AAAAAAACTT
58557030 CGTGTTTCAAAAATTTC
1 CGTGTTTCAAAAATTTC
* *
58557047 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTC
58557064 CGTGTTTTCAAAAAATTTCC
1 CGTG-TTTC-AAAAATTT-C
58557084 CGTGTTTTCAAAAA-TTC
1 CGTG-TTTCAAAAATTTC
* ** *
58557101 TCGTATTTC-GTAATTTT
1 -CGTGTTTCAAAAATTTC
*
58557118 CTTGTTTTCAGAAAAATTTC
1 CGTG-TTTC--AAAAATTTC
* * *
58557138 CATGTTTTATAAATTTC
1 CGTGTTTCAAAAATTTC
*
58557155 CGTGTTTTCAAAAAAATTC
1 CGTG-TTTC-AAAAATTTC
* * * *
58557174 TTGTCTTTTAAAAATTTT
1 -CGTGTTTCAAAAATTTC
* * *
58557192 TGTGTTTTAAAAAAAATTGAC
1 CGTG-TTT--CAAAAATT-TC
*
58557213 CGTGTTTCATAAATTTC
1 CGTGTTTCAAAAATTTC
58557230 CGTGTTTCAAAAA
1 CGTGTTTCAAAAA
58557243 AATCCTCGTG
Statistics
Matches: 146, Mismatches: 34, Indels: 32
0.69 0.16 0.15
Matches are distributed among these distances:
16 4 0.03
17 57 0.39
18 27 0.18
19 26 0.18
20 29 0.20
21 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTC
Found at i:58557088 original size:54 final size:54
Alignment explanation
Indices: 58557022--58557168 Score: 149
Period size: 54 Copynumber: 2.7 Consensus size: 54
58557012 TCTGTTTAAA
*
58557022 AAAAACTT-CGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTCA-
1 AAAAATTTCCGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTCAG
* *** *
58557074 AAAAATTTCCCGTGTTTTCAAAAA-TTCTCGT-ATTTCGTAATTTTCTTGTTTTCAG
1 AAAAATTT-CCGTG-TTTCAAAAATTTC-CGTGTTTTAAAAATTTTCGTGTTTTCAG
* * *
58557129 AAAAATTTCCATGTTTTATAAATTTCCGTGTTTTCAAAAA
1 AAAAATTTCCGTGTTTCAAAAATTTCCGTGTTTT-AAAAA
58557169 AATTCTTGTC
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
52 7 0.09
53 10 0.14
54 35 0.47
55 22 0.30
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (54 bp):
AAAAATTTCCGTGTTTCAAAAATTTCCGTGTTTTAAAAATTTTCGTGTTTTCAG
Found at i:58557258 original size:36 final size:37
Alignment explanation
Indices: 58557020--58557260 Score: 187
Period size: 37 Copynumber: 6.6 Consensus size: 37
58557010 ATTCTGTTTA
* *
58557020 AAAAAAACT-TCGTGTTTCAAAAATTTCCGTGTTTT-
1 AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
* *
58557055 --AAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTC
1 AAAAAAATTCTCGTG-TTTC-ATAAATTT-CCGTGTTTTC
* * * *
58557093 --AAAAATTCTCGTATTTCGT-AATTTTCTTGTTTTC
1 AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
* * *
58557127 AGAAAAATT-TCCATGTTTTATAAATTTCCGTGTTTTC
1 AAAAAAATTCT-CGTGTTTCATAAATTTCCGTGTTTTC
* * * * ** *
58557164 AAAAAAATTCTTGTCTTTTAAAAATTTTTGTGTTTTA
1 AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
58557201 AAAAAAATTGAC-CGTGTTTCATAAATTTCCGTG-TTTC
1 AAAAAAATT--CTCGTGTTTCATAAATTTCCGTGTTTTC
*
58557238 AAAAAAATCCTCGTGTTTCATAA
1 AAAAAAATTCTCGTGTTTCATAA
58557261 TTTATCAAAA
Statistics
Matches: 164, Mismatches: 29, Indels: 25
0.75 0.13 0.11
Matches are distributed among these distances:
33 6 0.04
34 13 0.08
35 11 0.07
36 33 0.20
37 73 0.45
38 27 0.16
39 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (37 bp):
AAAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
Found at i:58557328 original size:17 final size:17
Alignment explanation
Indices: 58557308--58557366 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 17
58557298 TATTTTTAAA
58557308 AAAAAAATCGTGTTTTT
1 AAAAAAATCGTGTTTTT
** *
58557325 AAAATTATTGTG-TTTT
1 AAAAAAATCGTGTTTTT
*
58557341 AAAAAAATTTCGTGTTTTC
1 AAAAAAA--TCGTGTTTTT
58557360 AAAAAAA
1 AAAAAAA
58557367 AAAAGTTGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 9 0.28
17 9 0.28
18 4 0.12
19 10 0.31
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (17 bp):
AAAAAAATCGTGTTTTT
Found at i:58557380 original size:21 final size:23
Alignment explanation
Indices: 58557341--58557384 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
58557331 ATTGTGTTTT
*
58557341 AAAAAAATTTCGTGTTTTCAAAA
1 AAAAAAAGTTCGTGTTTTCAAAA
58557364 AAAAAAAGTT-GTG-TTTCAAAA
1 AAAAAAAGTTCGTGTTTTCAAAA
58557385 TTATCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (23 bp):
AAAAAAAGTTCGTGTTTTCAAAA
Found at i:58557388 original size:56 final size:56
Alignment explanation
Indices: 58557265--58557398 Score: 146
Period size: 56 Copynumber: 2.4 Consensus size: 56
58557255 TCATAATTTA
* * * *
58557265 TCAAAATTTTTGTGTTCTCAAAATAAAATTTTGTATTTTTAAAAAAAAAATCGTGTTT
1 TCAAAATTATTGTGTT-T-TAAATAAAATTTCGTATTTTAAAAAAAAAAATCGTGTTT
* * *
58557323 TTAAAATTATTGTGTTTTAAA-AAAATTTCGTGTTTTCAAAAAAAAAAAGTTGTG-TT
1 TCAAAATTATTGTGTTTTAAATAAAATTTCGTATTTT-AAAAAAAAAAA-TCGTGTTT
*
58557379 TCAAAATTATCGTGTTTTAA
1 TCAAAATTATTGTGTTTTAA
58557399 CTGGATCAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
55 13 0.20
56 33 0.51
57 5 0.08
58 14 0.22
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (56 bp):
TCAAAATTATTGTGTTTTAAATAAAATTTCGTATTTTAAAAAAAAAAATCGTGTTT
Found at i:58558476 original size:2 final size:2
Alignment explanation
Indices: 58558469--58558502 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58558459 NNNNNNNNNN
58558469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58558503 CACTTGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58558762 original size:21 final size:20
Alignment explanation
Indices: 58558733--58558771 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58558723 AATGATAAAG
* *
58558733 TAAATAAACATAATAAAAGAA
1 TAAAGAAAC-TAAAAAAAGAA
58558754 TAAAGAAACTAAAAAAAG
1 TAAAGAAACTAAAAAAAG
58558772 TTAAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (20 bp):
TAAAGAAACTAAAAAAAGAA
Found at i:58559837 original size:28 final size:29
Alignment explanation
Indices: 58559792--58559848 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
58559782 ACTACTGTTA
58559792 CTGTTACCGATTCAGCACTTTGTGTGTCG
1 CTGTTACCGATTCAGCACTTTGTGTGTCG
*
58559821 CTGTTA-CGATTCGGCACTTTGTGTGTCG
1 CTGTTACCGATTCAGCACTTTGTGTGTCG
58559849 AATACTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.39
Consensus pattern (29 bp):
CTGTTACCGATTCAGCACTTTGTGTGTCG
Found at i:58561016 original size:27 final size:27
Alignment explanation
Indices: 58560986--58561052 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
58560976 CCTATCAGGT
58560986 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
58561013 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
58561040 AGGCGCCAATGAA
1 AGGCGCCAATGAA
58561053 ATTTATGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:58561260 original size:19 final size:19
Alignment explanation
Indices: 58561233--58561314 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 19
58561223 ATATCCCGAC
*
58561233 ATTACAATATTCATACAAA
1 ATTATAATATTCATACAAA
*
58561252 ATTATAATA-T--TACAAT
1 ATTATAATATTCATACAAA
* *
58561268 ATTAT--TCATACA-AAAAA
1 ATTATAAT-ATTCATACAAA
**
58561285 ATTGCAATATTCATACAAA
1 ATTATAATATTCATACAAA
58561304 ATTATAATATT
1 ATTATAATATT
58561315 ANNNNNNNNN
Statistics
Matches: 45, Mismatches: 11, Indels: 14
0.64 0.16 0.20
Matches are distributed among these distances:
14 1 0.02
15 1 0.02
16 10 0.22
17 6 0.13
18 5 0.11
19 22 0.49
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (19 bp):
ATTATAATATTCATACAAA
Found at i:58561276 original size:30 final size:27
Alignment explanation
Indices: 58561233--58561315 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 27
58561223 ATATCCCGAC
58561233 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTATAAT
58561260 ATTACAATATTATTCATAC-AAA--A-AA-
1 ATTAC-A-A-TATTCATACAAAATTATAAT
*
58561285 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTATAAT
58561312 ATTA
1 ATTA
58561316 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
22 9 0.20
23 4 0.09
24 1 0.02
25 5 0.11
26 4 0.09
27 9 0.20
28 1 0.02
29 4 0.09
30 9 0.20
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTATAAT
Found at i:58561672 original size:19 final size:19
Alignment explanation
Indices: 58561648--58561688 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
58561638 ACAAACACAA
*
58561648 AAATTTATAACATAATCCT
1 AAATTTATAACATAACCCT
58561667 AAATTTATAACATAACCCT
1 AAATTTATAACATAACCCT
58561686 AAA
1 AAA
58561689 CCCGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTTATAACATAACCCT
Found at i:58561743 original size:27 final size:27
Alignment explanation
Indices: 58561705--58561779 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
58561695 AAAATCAGAG
58561705 CATTGGCGCCTCCCAGATAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
*
58561732 CATTGGCGCCTCCTAGATAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
*
58561759 CATTGGCGCCTCCCAAATAGG
1 CATTGGCGCCTCCCAGATAGG
58561780 TGCCAATACT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.17
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGATAGGCACCAC
Found at i:58567161 original size:41 final size:41
Alignment explanation
Indices: 58567104--58567186 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
58567094 TAACACAGTG
58567104 ATTAATTTATTCAATGGCTAATCATGATATGATCCATGCAC
1 ATTAATTTATTCAATGGCTAATCATGATATGATCCATGCAC
58567145 ATTAATTTATTCAATGGCTAATCATGATATGATCCATGCAC
1 ATTAATTTATTCAATGGCTAATCATGATATGATCCATGCAC
58567186 A
1 A
58567187 AAGCCACAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (41 bp):
ATTAATTTATTCAATGGCTAATCATGATATGATCCATGCAC
Found at i:58569195 original size:106 final size:105
Alignment explanation
Indices: 58569000--58569307 Score: 418
Period size: 106 Copynumber: 2.9 Consensus size: 105
58568990 AGCATAGATT
* *
58569000 AAAATTCAAGAGGATATTTGGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCAC
1 AAAATT-AAAAGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCAC
*
58569065 GTTCCTCAAATTTCCAAACGCAAAACATTACCTTATTTTGTA
65 GTTCCTCAAATTTCCAAACGCAAAACATTACCTTATTTT-AA
*** * * *
58569107 ATTTTTGAAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACG
1 AAAATTAAAAGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACG
* * *
58569172 TTCCTCGAATTTCCAAACACAAAACATTGCCTTATTTTAA
66 TTCCTCAAATTTCCAAACGCAAAACATTACCTTATTTTAA
* * *
58569212 AAAATTAAAAGGATATTAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCA
1 AAAATTAAAAGGATATTTAGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCA
* *
58569277 CATTTTCTCAAATTTCCAAACGCAAAACATT
64 C-GTTCCTCAAATTTCCAAACGCAAAACATT
58569308 GCCTCAATTA
Statistics
Matches: 174, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
105 31 0.18
106 89 0.51
107 29 0.17
108 25 0.14
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (105 bp):
AAAATTAAAAGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACG
TTCCTCAAATTTCCAAACGCAAAACATTACCTTATTTTAA
Found at i:58574424 original size:26 final size:26
Alignment explanation
Indices: 58574388--58574448 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
58574378 ACAGCTCTTA
* * *
58574388 TGAGCGTCCCG-TTATATGGCTTTTTG
1 TGAGCTTCCCGATTA-AAGGCTCTTTG
58574414 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTTG
58574440 TGAGCTTCC
1 TGAGCTTCC
58574449 TGTTGTGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTTG
Found at i:58574549 original size:25 final size:24
Alignment explanation
Indices: 58574490--58574551 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
58574480 GCTATCCGGT
58574490 GCTACCCGTTA-AGTGCTCTTCGAA
1 GCTACCCGTTATAG-GCTCTTCGAA
*
58574514 GCTACCCGTTATAGGCTCTTTGTAA
1 GCTACCCGTTATAGGCTCTTCG-AA
* *
58574539 GCTTCCTGTTATA
1 GCTACCCGTTATA
58574552 TTGCCTGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (24 bp):
GCTACCCGTTATAGGCTCTTCGAA
Found at i:58574606 original size:24 final size:24
Alignment explanation
Indices: 58574536--58574606 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
58574526 AGGCTCTTTG
* **
58574536 TAAGCTTCCTGTTATATTGCCTGGA
1 TAAGCTTCCTGTTATAGTG-CTTAA
* *
58574561 TAAGCTTCCCGTTACAAG-GCTTAA
1 TAAGCTTCCTGTTA-TAGTGCTTAA
*
58574585 TGAGCTTCCTGTTATAGTGCTT
1 TAAGCTTCCTGTTATAGTGCTT
58574607 GAGAGAGAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
23 2 0.06
24 19 0.53
25 14 0.39
26 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (24 bp):
TAAGCTTCCTGTTATAGTGCTTAA
Found at i:58575744 original size:20 final size:20
Alignment explanation
Indices: 58575716--58575761 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
58575706 AAAGGGACGA
*
58575716 AATGATTAATTTCTAATATT
1 AATGTTTAATTTCTAATATT
58575736 AATGTTTAATTTCTAATATT
1 AATGTTTAATTTCTAATATT
58575756 AATGTT
1 AATGTT
58575762 AAGTAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (20 bp):
AATGTTTAATTTCTAATATT
Found at i:58576586 original size:18 final size:19
Alignment explanation
Indices: 58576540--58576591 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
58576530 TCCAAGTCAG
*
58576540 ATAAAAAAAATTAAAATAT
1 ATAAATAAAATTAAAATAT
*
58576559 ATAACTAAAA-TAAAATA-
1 ATAAATAAAATTAAAATAT
58576576 ATAAATCAAAAATTAA
1 ATAAAT--AAAATTAA
58576592 GGAAGCGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 12 0.44
20 3 0.11
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAAATAAAATTAAAATAT
Found at i:58581937 original size:21 final size:21
Alignment explanation
Indices: 58581913--58581954 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58581903 GTTGAGAAAA
*
58581913 TTATTTAATGAAAAAAATAAT
1 TTATCTAATGAAAAAAATAAT
* *
58581934 TTATCTAATTAAATAAATAAT
1 TTATCTAATGAAAAAAATAAT
58581955 AGAAAACATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTATCTAATGAAAAAAATAAT
Found at i:58584423 original size:2 final size:2
Alignment explanation
Indices: 58584416--58584449 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58584406 CTTCATCCGC
58584416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58584450 TAACTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58586637 original size:30 final size:31
Alignment explanation
Indices: 58586603--58586667 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
58586593 GCAAAGAGTT
* * *
58586603 AATTTGATCATCAACCTTTTAAAAA-AGTCA
1 AATTTGACCATCAACCTTTCAAAAACAATCA
* *
58586633 AATTTGACCATTAATCTTTCAAAAACAATCA
1 AATTTGACCATCAACCTTTCAAAAACAATCA
58586664 AATT
1 AATT
58586668 GTTGTTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.34
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTCAAAAACAATCA
Found at i:58586901 original size:19 final size:19
Alignment explanation
Indices: 58586877--58586930 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
58586867 CTTGAAAAAG
*
58586877 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
58586896 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
*
58586915 GATATACAATCTTAGA
1 GATATGCAATCTTAGA
58586931 AGATAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:58587827 original size:24 final size:24
Alignment explanation
Indices: 58587796--58588045 Score: 148
Period size: 24 Copynumber: 10.7 Consensus size: 24
58587786 GTGTATTGTA
*
58587796 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* *
58587820 TTTTATTATTTGT-AATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
*
58587843 TATTATTATTTTAAATTCAT--TG
1 TATTATTATTTTAAATTTATCATG
**
58587865 TTAACATTATTTTAAATTTATCATG
1 -TATTATTATTTTAAATTTATCATG
* *
58587890 TA-TATCTATTTCAATTTTATCAT-
1 TATTAT-TATTTTAAATTTATCATG
* * *
58587913 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* **
58587935 TACTATTATTTTGGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* *
58587959 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * *
58587982 CA-AAAT-TTTTAAATTTTAT-ATG
1 TATTATTATTTTAAA-TTTATCATG
* * *
58588004 TATTATTATTTCAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
58588028 TATTATTTATTGTAAATT
1 TATTA-TTATTTTAAATT
58588046 GTCCAATTCA
Statistics
Matches: 171, Mismatches: 36, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
20 2 0.01
21 18 0.11
22 13 0.08
23 46 0.27
24 78 0.46
25 14 0.08
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:58587877 original size:70 final size:69
Alignment explanation
Indices: 58587794--58587968 Score: 178
Period size: 70 Copynumber: 2.5 Consensus size: 69
58587784 AAGTGTATTG
* * *
58587794 TATATTATTATTTTAGATTTATCATGTTTTATTATTTGTAA-TTTATCAATATTATTATTTTAAA
1 TATACTATTATTTTAGATTTATCATGTTTTATTATTT-CAATTTTATCAATAATA-T-TTTTAAA
*
58587858 TTCATTG
63 TTCATTA
* * *
58587865 T-TAAC-ATTATTTTAAATTTATCATG-TATATCTATTTCAATTTTATCATTAATATTTTTAAAT
1 TAT-ACTATTATTTTAGATTTATCATGTTTTAT-TATTTCAATTTTATCAATAATATTTTTAAAT
*
58587927 TTATTA
64 TCATTA
* * *
58587933 TATACTATTATTTTGGATTTATCATGTATGATTATT
1 TATACTATTATTTTAGATTTATCATGTTTTATTATT
58587969 CTAGAATTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
68 15 0.18
69 30 0.35
70 38 0.45
71 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (69 bp):
TATACTATTATTTTAGATTTATCATGTTTTATTATTTCAATTTTATCAATAATATTTTTAAATTC
ATTA
Found at i:58587979 original size:69 final size:67
Alignment explanation
Indices: 58587755--58588036 Score: 195
Period size: 69 Copynumber: 4.1 Consensus size: 67
58587745 TTATACTTAT
* * * * *
58587755 TATTA-TTA-AATTAGTCATTAATATTATCTAAGTGTATTGTATATTATTATTTTAGATTTATCA
1 TATTATTTAGAATTA-TCATTAATATT-TTTAAATTTATTATATACTATTATTTTAGATTTATCA
*
58587818 TGTTT
64 TG-TA
* * * * *
58587823 TATTATTT-GTAATTTATCAATATTATTATTTTAAATTCATTGT-TAAC-ATTATTTTAAATTTA
1 TATTATTTAG-AA-TTATCATTAATA-T-TTTTAAATTTATTATAT-ACTATTATTTTAGATTTA
58587885 TCATGTA
61 TCATGTA
* *
58587892 TATCTATTTCA-ATTTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTGGATTTATC
1 TAT-TATTT-AGA-ATTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAGATTTATC
58587956 ATGTA
63 ATGTA
* * * * * *
58587961 TGATTATTCTAGAATTATCATCAAAATTTTTAAATTT-TATATGTATTATTATTTCAAATTTAT-
1 T-ATTATT-TAGAATTATCATTAATATTTTTAAATTTAT-TATATACTATTATTTTAGATTTATC
*
58588024 -TATA
63 ATGTA
58588028 TATTATTTA
1 TATTATTTA
58588037 TTGTAAATTG
Statistics
Matches: 172, Mismatches: 25, Indels: 37
0.74 0.11 0.16
Matches are distributed among these distances:
65 2 0.01
66 6 0.03
67 4 0.02
68 21 0.12
69 74 0.43
70 49 0.28
71 15 0.09
72 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (67 bp):
TATTATTTAGAATTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAGATTTATCATG
TA
Found at i:58598111 original size:2 final size:2
Alignment explanation
Indices: 58598101--58598135 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
58598091 TTATGGATAA
58598101 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58598136 TCATTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58598702 original size:31 final size:31
Alignment explanation
Indices: 58598665--58598728 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
58598655 TAAAATGGTT
58598665 ATTGAACTATTCAAAAGTTCTCATTTAAGTC
1 ATTGAACTATTCAAAAGTTCTCATTTAAGTC
* * * *
58598696 ATTGAACTATTCGAATGTTTTTATTTAAGTC
1 ATTGAACTATTCAAAAGTTCTCATTTAAGTC
58598727 AT
1 AT
58598729 CGGATCAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTCTCATTTAAGTC
Found at i:58599282 original size:27 final size:28
Alignment explanation
Indices: 58599224--58599283 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
58599214 CACTCATCCA
* *
58599224 TATTTAATATATATTTTCTAATCCAATC
1 TATTTAACATATATTCTCTAATCCAATC
* *
58599252 TATTTAACATAT-TTCTCTAATTCAATT
1 TATTTAACATATATTCTCTAATCCAATC
58599279 TATTT
1 TATTT
58599284 TTAGTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (28 bp):
TATTTAACATATATTCTCTAATCCAATC
Found at i:58610232 original size:2 final size:2
Alignment explanation
Indices: 58610225--58610257 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58610215 TGGCTTATGG
58610225 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 A
58610258 CATGTTCACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58611998 original size:2 final size:2
Alignment explanation
Indices: 58611991--58612031 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
58611981 CATCCAGGTA
58611991 AT AT 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 AT AT A
58612032 ATAGGACCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58616972 original size:31 final size:31
Alignment explanation
Indices: 58616934--58616999 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
58616924 TAAAATGGTT
** *
58616934 ATTGAACTATTTGAAAGTTTTCATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTCAAGTC
* *
58616965 ATTGAACTATTCAAAAGTTTTTATTCAAGTT
1 ATTGAACTATTCAAAAGTTTTCATTCAAGTC
58616996 ATTG
1 ATTG
58617000 GATTAAGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTTTCATTCAAGTC
Found at i:58618455 original size:2 final size:2
Alignment explanation
Indices: 58618442--58618490 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
58618432 TTTGAGCCTT
*
58618442 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58618484 TA TA TA T
1 TA TA TA T
58618491 TCTCTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58627322 original size:18 final size:18
Alignment explanation
Indices: 58627301--58627384 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
58627291 ATTTTCTTTT
58627301 ACACGAAAATTTTTGAAA
1 ACACGAAAATTTTTGAAA
*
58627319 ACACGAAAATTTGTGAAA
1 ACACGAAAATTTTTGAAA
**
58627337 ACACGAATTTTTTTTTG-AA
1 ACACGAA--AATTTTTGAAA
*
58627356 ACACG--AATTGTTGAAA
1 ACACGAAAATTTTTGAAA
58627372 ACAC-AAAATTTTT
1 ACACGAAAATTTTT
58627385 TCTTAAGGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.09
16 6 0.11
17 6 0.11
18 24 0.45
19 7 0.13
20 5 0.09
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (18 bp):
ACACGAAAATTTTTGAAA
Found at i:58627385 original size:37 final size:37
Alignment explanation
Indices: 58627310--58627385 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 37
58627300 TACACGAAAA
*
58627310 TTTTTGAAAACACGAAAATTTGTGAAAACACGAATTTT
1 TTTTTGAAAACACG-AAATTTGTGAAAACACAAATTTT
*
58627348 TTTTTG-AAACACG-AA-TTGTTGAAAACACAAAATTT
1 TTTTTGAAAACACGAAATTTG-TGAAAACACAAATTTT
58627383 TTT
1 TTT
58627386 CTTAAGGACG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 3 0.09
35 19 0.54
37 7 0.20
38 6 0.17
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (37 bp):
TTTTTGAAAACACGAAATTTGTGAAAACACAAATTTT
Found at i:58627902 original size:12 final size:10
Alignment explanation
Indices: 58627877--58627927 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
58627867 GCTCCTCTTC
58627877 TTCTTTTTTT
1 TTCTTTTTTT
58627887 TTCTTTTTCCTT
1 TTCTTTTT--TT
58627899 TTC-TTTTTT
1 TTCTTTTTTT
58627908 TTCTTTCTTCTT
1 TTCTTT-TT-TT
58627920 TT-TTTTTT
1 TTCTTTTTT
58627928 CTGGTTGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.17
10 12 0.33
11 9 0.25
12 9 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:58627907 original size:21 final size:20
Alignment explanation
Indices: 58627872--58627927 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
58627862 CTCGAGCTCC
*
58627872 TCTTCTTCTTTTTTTTTCTT
1 TCTTCTTTTTTTTTTTTCTT
58627892 T-TTCCTTTTCTTTTTTTTCTT
1 TCTT-CTTTT-TTTTTTTTCTT
58627913 TCTTCTTTTTTTTTT
1 TCTTCTTTTTTTTTT
58627928 CTGGTTGGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.06
20 11 0.34
21 17 0.53
22 2 0.06
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TCTTCTTTTTTTTTTTTCTT
Found at i:58627918 original size:16 final size:15
Alignment explanation
Indices: 58627877--58627925 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
58627867 GCTCCTCTTC
*
58627877 TTCTTTTTTTTTCTTT
1 TTCTTTTTCTTT-TTT
*
58627893 TTCCTTTTCTTTTTT
1 TTCTTTTTCTTTTTT
58627908 TTCTTTCTTCTTTTTT
1 TTCTTT-TTCTTTTTT
58627924 TT
1 TT
58627926 TTCTGGTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTTCTTTTTT
Found at i:58627925 original size:25 final size:25
Alignment explanation
Indices: 58627869--58627916 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
58627859 CGACTCGAGC
*
58627869 TCCTCTTCTTCTTTTTTTTTCTTTT
1 TCCTTTTCTTCTTTTTTTTTCTTTT
58627894 TCCTTTTCTT-TTTTTTCTTTCTT
1 TCCTTTTCTTCTTTTTT-TTTCTT
58627917 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (25 bp):
TCCTTTTCTTCTTTTTTTTTCTTTT
Found at i:58628236 original size:5 final size:6
Alignment explanation
Indices: 58628221--58628314 Score: 68
Period size: 7 Copynumber: 14.8 Consensus size: 6
58628211 AAAAAATTTA
* * *
58628221 TTTTCTT TTTTCT TTTTCT TTTTC- TTTTCT TCTTTCT TCTTCCC CTTTCT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT T-TTTCT TTTTCT
58628271 TCTTTC- -TTTCT TCTTTCT TTTTCT TCTTTCT TTCTTCT TCTTTC
1 T-TTTCT TTTTCT T-TTTCT TTTTCT T-TTTCT TT-TTCT T-TTTC
58628315 CTTCTTTTCT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.06
5 5 0.07
6 23 0.32
7 39 0.54
8 1 0.01
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTCT
Found at i:58628258 original size:31 final size:31
Alignment explanation
Indices: 58628222--58628322 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
58628212 AAAAATTTAT
58628222 TTTCTTTTTTCTTTTTCTTTTTCTTTTCTTC
1 TTTCTTTTTTCTTTTTCTTTTTCTTTTCTTC
* * **
58628253 TTTCTTCTTCCCCTTTCTTCTTTC-TTTCTTC
1 TTTCTTTTTTCTTTTTCTT-TTTCTTTTCTTC
*
58628284 TTTC-TTTTTCTTCTTTCTTTCTTCTTCT-TTC
1 TTTCTTTTTTCTT-TTTCTTT-TTCTTTTCTTC
*
58628315 CTTCTTTT
1 TTTCTTTT
58628323 CTTTCTTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
30 5 0.09
31 41 0.75
32 9 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTCTTTTTTCTTTTTCTTTTTCTTTTCTTC
Found at i:58628327 original size:27 final size:25
Alignment explanation
Indices: 58628221--58628331 Score: 117
Period size: 24 Copynumber: 4.5 Consensus size: 25
58628211 AAAAAATTTA
*
58628221 TTTTCTTT-TTTCTTTTTCTTTTTC
1 TTTTCTTTCTTTCTTCTTCTTTTTC
**
58628245 TTTTC-TTCTTTCTTCTTCCCCTTTC
1 TTTTCTTTCTTTCTTCTT-CTTTTTC
58628270 --TTCTTTCTTTCTTCTTTCTTTTTC
1 TTTTCTTTCTTTCTTC-TTCTTTTTC
58628294 --TTCTTTCTTTCTTCTTCTTTCCTTC
1 TTTTCTTTCTTTCTTCTTCTTT--TTC
58628319 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
58628332 CCGATCAGCC
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
23 11 0.15
24 42 0.57
25 10 0.14
27 11 0.15
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTCTTTCTTTCTTCTTCTTTTTC
Found at i:58628433 original size:15 final size:16
Alignment explanation
Indices: 58628408--58628447 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
58628398 CTCTCCCCTA
*
58628408 TTTTC-TTCTTT-TTC
1 TTTTCTTTCTTTGCTC
58628422 TTTTCTTTCTTTGCTC
1 TTTTCTTTCTTTGCTC
58628438 TTTT-TTTCTT
1 TTTTCTTTCTT
58628448 CTTTGTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTCTTTCTTTGCTC
Found at i:58628442 original size:22 final size:21
Alignment explanation
Indices: 58628414--58628468 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
58628404 CCTATTTTCT
58628414 TCTTTTTCTTTTCTTTCTTTGC
1 TCTTTTT-TTTTCTTTCTTTGC
*
58628436 TCTTTTTTTCTTCTTTGTTTGC
1 TCTTTTTTT-TTCTTTCTTTGC
*
58628458 TGTTTTTTTTT
1 TCTTTTTTTTT
58628469 TTACTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.76
Consensus pattern (21 bp):
TCTTTTTTTTTCTTTCTTTGC
Found at i:58628840 original size:29 final size:28
Alignment explanation
Indices: 58628758--58628841 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 28
58628748 CAATTTTAAG
58628758 AAAATTTT-GGGGTCAAAATGTAAATTTA
1 AAAATTTTAGGGGTCAAAATGT-AATTTA
* * * * *
58628786 AAAAGTTGAGGGGTTAAAGTGAAATTTCA
1 AAAATTTTAGGGGTCAAAATGTAATTT-A
58628815 AAAATTTTAGGGGTCAAAATGTAATTT
1 AAAATTTTAGGGGTCAAAATGTAATTT
58628842 TTTTTTATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 11 0.25
29 33 0.75
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (28 bp):
AAAATTTTAGGGGTCAAAATGTAATTTA
Found at i:58629454 original size:78 final size:79
Alignment explanation
Indices: 58629027--58630267 Score: 1662
Period size: 78 Copynumber: 16.0 Consensus size: 79
58629017 CAAAAATTGA
* * * *
58629027 AAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
58629092 CAGAAATTTAAAAG
66 CAGAAATTTAAAAG
* * * *
58629106 AAATACCTCGGCATAG-G--CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTT-AAAA
1 AAATACCTCAGCGT-GCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
*
58629165 A-AAACAATTT---A-
65 ACAGA-AATTTAAAAG
*
58629176 AAATACCTCAGCGT--GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAA
* *
58629239 AATAGAAATTTAAAAA
64 AACAGAAATTTAAAAG
* * * *
58629255 AAAAACCTCAGTGTGCGACCCGAGGCTCAACTCACCACTCGCAATATGAGTTGATTTTCGAAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
*
58629320 CAGAAA-TT-GAA-
66 CAGAAATTTAAAAG
* * * *
58629331 AAATACCTC-GACGT--GACTCGAGGCTTAACTCACCTCTCACAATATGAGTTTATTTTTG-AAA
1 AAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
*
58629392 ACGGAAATTTAAAAG
65 ACAGAAATTTAAAAG
* * * * *
58629407 AAACACCTCAGCGTGCGACCCAAGGTTCAACTTACCTCTCGCAATATGAGTTGCTTTTTTGAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTGAAAA
58629472 ACAGAAATTTAAAAG
65 ACAGAAATTTAAAAG
*
58629487 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAA
58629552 AACAAGAAAATTTAAAAG
64 AAC-AG-AAATTTAAAAG
*
58629570 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTG-AAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
58629634 CAGAAATTTAAAAG
66 CAGAAATTTAAAAG
*
58629648 AAATACCTCAGCGTGCGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
*
58629713 ATAGAAATTTAAAAG
65 ACAGAAATTTAAAAG
* *
58629728 AAGTACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
58629793 ACAGAAATTT--AA-
65 ACAGAAATTTAAAAG
58629805 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
58629870 ACAGAAATTT--AA-
65 ACAGAAATTTAAAAG
58629882 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
58629947 ACAGAAATTT--AA-
65 ACAGAAATTTAAAAG
*
58629959 AAATACCTC-GACGT--GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAA
1 AAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
58630020 ACAGAAATTTAAAAG
65 ACAGAAATTTAAAAG
58630035 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
58630099 CAGAAATTTAAAAG
66 CAGAAATTTAAAAG
*
58630113 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
*
58630178 CAGAAA-TT-GAA-
66 CAGAAATTTAAAAG
* * * * *
58630189 AAATACATCAACGT--GACTCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAA
1 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAA
*
58630252 AAACAGAAATTGAAAA
63 AAACAGAAATTTAAAA
58630268 ATGTAATTCT
Statistics
Matches: 1050, Mismatches: 67, Indels: 90
0.87 0.06 0.07
Matches are distributed among these distances:
68 1 0.00
70 44 0.04
71 1 0.00
72 3 0.00
73 24 0.02
74 84 0.08
75 61 0.06
76 54 0.05
77 212 0.20
78 221 0.21
79 62 0.06
80 159 0.15
81 59 0.06
82 2 0.00
83 63 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (79 bp):
AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
CAGAAATTTAAAAG
Found at i:58629661 original size:241 final size:235
Alignment explanation
Indices: 58629026--58630267 Score: 1670
Period size: 241 Copynumber: 5.3 Consensus size: 235
58629016 ACAAAAATTG
* * * *
58629026 AAAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * * *
58629091 ACAGAAATTTAAAAGAAATACCTCGGCATAG-G--CTGAGGCTCAACTCACTTCTCGCAATATGA
66 ACAGAAATTTAAAAGAAATACCTCAGCGT-GCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
* * *
58629153 GTTGA--TTT-AAAAAAAACAATTT---A-AAATACCTCAGCGT--GACTCGAGGCTCAACTCAC
130 GTTGATTTTTGAAAACAGA-AATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCAC
*
58629209 CTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAA
194 CTCTCGCAATATGAGTTGATTTTTG--AAAAACAGAAATTT-AAA
* * * *
58629254 AAAAAACCTCAGTGTGCGACCCGAGGCTCAACTCACCACTCGCAATATGAGTTGATTTTCGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * * *
58629319 ACAGAAA-TT-GAA-AAATACCTC-GACGT--GACTCGAGGCTTAACTCACCTCTCACAATATGA
66 ACAGAAATTTAAAAGAAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
* * * * * *
58629378 GTTTATTTTTGAAAACGGAAATTTAAAAGAAACACCTCAGCGTGCGACCCAAGGTTCAACTTACC
130 GTTGATTTTTGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACC
*
58629443 TCTCGCAATATGAGTTGCTTTTTTGAAAAACAGAAATTTAAA
195 TCTCGCAATATGAGTTG-ATTTTTGAAAAACAGAAATTTAAA
*
58629485 AGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTTTGA
1 A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGA
*
58629550 AAAACAAGAAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACATCTCGCAAT
63 AAAAC-AG-AAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
*
58629615 ATGAGTTGATTTTTGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCAAGGCTCAACT
126 ATGAGTTGATTTTTGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACT
*
58629680 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTTAAA
191 CACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAA
* *
58629726 AGAAGTACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAA
1 A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA
58629791 AAACAGAAATTT--AA-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
64 AAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATG
58629853 AGTTGATTTTTTGAAAAACAGAAATTT--AA-AAATACCTCAGCGTGCGACCCGAGGCTCAACTC
129 AGTTGA-TTTTTG-AAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTC
58629915 ACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTT--A
192 ACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTTAAA
*
58629958 AAAATACCTC-GACGT--GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AA
1 AAAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
58630019 AACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
65 AACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
58630084 GTTGATTTTTGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACC
130 GTTGATTTTTGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACC
* *
58630149 TCTTGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-GA
195 TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAA
* * * * *
58630188 AAAATACATCAACGT--GACTCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGA
*
58630251 AAAACAGAAATTGAAAA
63 AAAACAGAAATTTAAAA
58630268 ATGTAATTCT
Statistics
Matches: 915, Mismatches: 58, Indels: 76
0.87 0.06 0.07
Matches are distributed among these distances:
223 1 0.00
224 1 0.00
225 40 0.04
226 2 0.00
227 23 0.03
228 88 0.10
229 46 0.05
230 118 0.13
231 87 0.10
232 65 0.07
233 45 0.05
234 99 0.11
235 57 0.06
236 11 0.01
237 15 0.02
238 8 0.01
239 14 0.02
240 14 0.02
241 181 0.20
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (235 bp):
AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
ACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAA
Done.