Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008550.1 Hibiscus syriacus cultivar Beakdansim tig00111445_pilon, whole genome shotgun sequence
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: 1154708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 6
Found at i:835 original size:27 final size:27
Alignment explanation
Indices: 797--851 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
787 GATGTTTTAT
797 AATGATAGCAGTACTTGGTTGTAATGA
1 AATGATAGCAGTACTTGGTTGTAATGA
*
824 AATGATAGCAGTAGTTGGTTGTAATGA
1 AATGATAGCAGTACTTGGTTGTAATGA
851 A
1 A
852 TTTTGAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (27 bp):
AATGATAGCAGTACTTGGTTGTAATGA
Found at i:1652 original size:18 final size:20
Alignment explanation
Indices: 1612--1653 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1602 TTATTACTAT
*
1612 TTTATAATATGTAATGATCA
1 TTTATAATATGTAATGATAA
*
1632 TTTATAATA-GT-TTGATAA
1 TTTATAATATGTAATGATAA
1650 TTTA
1 TTTA
1654 ATGATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTATAATATGTAATGATAA
Found at i:4305 original size:18 final size:18
Alignment explanation
Indices: 4263--4305 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4253 AACCGGTCAT
*
4263 GACCCGACCCGTTGACCT
1 GACCCGACCCGTTGACCC
*
4281 GATCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
4299 GACCCGA
1 GACCCGA
4306 ATGTTGACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:4397 original size:29 final size:29
Alignment explanation
Indices: 4364--4483 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 29
4354 GTTATTCTAA
*
4364 GAATTAATTCCAAATGAATGCTATTTTGG
1 GAATTAATTCGAAATGAATGCTATTTTGG
* * * *
4393 TAATTATTTCGAAA--AATGATATTCTGG
1 GAATTAATTCGAAATGAATGCTATTTTGG
* * * *
4420 GGATTAATTTGAAAGTG-GTGCTACTTTGG
1 GAATTAATTCGAAA-TGAATGCTATTTTGG
* **
4449 GAATTAATTCGAAAAGGGTGCTATTTTGG
1 GAATTAATTCGAAATGAATGCTATTTTGG
*
4478 TAATTA
1 GAATTA
4484 TTTAAAAAGG
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
27 21 0.30
28 1 0.01
29 47 0.68
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (29 bp):
GAATTAATTCGAAATGAATGCTATTTTGG
Found at i:4450 original size:28 final size:29
Alignment explanation
Indices: 4417--4503 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 29
4407 AATGATATTC
* *
4417 TGGGGATTAATTTG-AAAGTGGTGCTACTT
1 TGGGAATTAATTCGAAAAG-GGTGCTACTT
*
4446 TGGGAATTAATTCGAAAAGGGTGCTATTT
1 TGGGAATTAATTCGAAAAGGGTGCTACTT
* **
4475 TGGTAATT-ATTTAAAAAGGGTGCTA-TT
1 TGGGAATTAATTCGAAAAGGGTGCTACTT
4502 TG
1 TG
4504 TGTAAAATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
27 4 0.08
28 15 0.29
29 28 0.55
30 4 0.08
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.38
Consensus pattern (29 bp):
TGGGAATTAATTCGAAAAGGGTGCTACTT
Found at i:11526 original size:29 final size:29
Alignment explanation
Indices: 11494--11584 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
11484 ATTCAGTTTT
11494 GGTGCTATTCTGGGAATTAATTTGAAATA
1 GGTGCTATTCTGGGAATTAATTTGAAATA
* * * * * *
11523 GGTGTTATT-TTGGTATT-TTTTAAAAAA
1 GGTGCTATTCTGGGAATTAATTTGAAATA
* * * *
11550 AGTGATATTCTGGGAATTAATTCGAAATT
1 GGTGCTATTCTGGGAATTAATTTGAAATA
11579 GGTGCT
1 GGTGCT
11585 TTTTTATAAT
Statistics
Matches: 43, Mismatches: 17, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
27 14 0.33
28 12 0.28
29 17 0.40
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTTGAAATA
Found at i:11610 original size:28 final size:29
Alignment explanation
Indices: 11564--11644 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 29
11554 ATATTCTGGG
**
11564 AATTAATTCGAAATTGGTGCT-TTTT-TAT
1 AATTAATTCGAAAAGGGTGCTATTTTGT-T
11592 AATTAATTCGAAAAGGGTGCTATTTTGTT
1 AATTAATTCGAAAAGGGTGCTATTTTGTT
** *
11621 AATT-ATTTTAAAAAGGTGCTATTT
1 AATTAATTCGAAAAGGGTGCTATTT
11645 GTGTAAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 36 0.78
29 9 0.20
30 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (29 bp):
AATTAATTCGAAAAGGGTGCTATTTTGTT
Found at i:20692 original size:12 final size:12
Alignment explanation
Indices: 20677--20722 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
20667 CGGTTTTTTT
*
20677 ACCGGATAAAAA
1 ACCGGTTAAAAA
20689 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
20704 ACCGGTTAAAAA
1 ACCGGTTAAAAA
20716 ACCGGTT
1 ACCGGTT
20723 TTATCCGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:20704 original size:15 final size:13
Alignment explanation
Indices: 20683--20723 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
20673 TTTTACCGGA
20683 TAAAAAACCGGTT
1 TAAAAAACCGGTT
20696 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
20710 TAAAAAACCGGTT
1 TAAAAAACCGGTT
20723 T
1 T
20724 TATCCGGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:23250 original size:21 final size:21
Alignment explanation
Indices: 23226--23265 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23216 TTTATTTTAT
23226 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
23247 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
23266 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:23313 original size:33 final size:33
Alignment explanation
Indices: 23260--23358 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
23250 TTTGTTTCAA
*
23260 TTATCGAACTT-GAAGTTTTTAAGTATTTAAAT
1 TTATCAAACTTGGAAGTTTTTAAGTATTTAAAT
*
23292 TTATCAAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCAAACTTGGAAGTTTTTAAGTATTTAAAT
* * *
23325 TTATCAAACTTGAAAGTATTTAAGTATTTCAAT
1 TTATCAAACTTGGAAGTTTTTAAGTATTTAAAT
23358 T
1 T
23359 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 10 0.16
33 51 0.84
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (33 bp):
TTATCAAACTTGGAAGTTTTTAAGTATTTAAAT
Found at i:23387 original size:13 final size:13
Alignment explanation
Indices: 23344--23398 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
23334 TTGAAAGTAT
23344 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
23357 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
23371 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
23384 TTAAGTATTTGAA
1 TTAAGTATTTCAA
23397 TT
1 TT
23399 TTATCGAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:23621 original size:21 final size:21
Alignment explanation
Indices: 23595--23651 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
23585 TGGAGCGTGG
*
23595 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
23616 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
23637 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
23652 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:23855 original size:17 final size:18
Alignment explanation
Indices: 23835--23868 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23825 GTTTTTTTAT
23835 AACCG-GTTTTTTAAAAA
1 AACCGAGTTTTTTAAAAA
*
23852 AACCGATTTTTTTAAAA
1 AACCGAGTTTTTTAAAA
23869 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGAGTTTTTTAAAAA
Found at i:23868 original size:15 final size:15
Alignment explanation
Indices: 23814--23872 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
23804 CAATCTGGAA
* *
23814 TTTTAAAATCGGTTT
1 TTTTAAAACCGATTT
* *
23829 TTTTATAACCGGTTT
1 TTTTAAAACCGATTT
*
23844 TTTAAAAAAACCGATTT
1 TTT--TAAAACCGATTT
23861 TTTTAAAACCGA
1 TTTTAAAACCGA
23873 AACCGGTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 24 0.67
17 12 0.33
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (15 bp):
TTTTAAAACCGATTT
Found at i:23988 original size:15 final size:17
Alignment explanation
Indices: 23962--23993 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23952 TTCTATGGGA
23962 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
23978 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
23994 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:37659 original size:2 final size:2
Alignment explanation
Indices: 37654--37689 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
37644 TTTTTATAGT
37654 TA TA TA TA TA TA TA TA -A GTA 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
37690 AAGTCGGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38905 original size:29 final size:29
Alignment explanation
Indices: 38833--38915 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
38823 AATATATAAT
*
38833 TTTCAAAAATTATAATTTTGATCC-CTAAAC
1 TTTCAAAAATTATAA-TTT-AGCCACTAAAC
**
38863 TTATCAAAGTTTATAATTTAGCCACTAAAC
1 TT-TCAAAAATTATAATTTAGCCACTAAAC
* *
38893 TTTCAAAACTTATATTTTAGCCA
1 TTTCAAAAATTATAATTTAGCCA
38916 GTAGACAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 21 0.47
30 13 0.29
31 11 0.24
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTCAAAAATTATAATTTAGCCACTAAAC
Found at i:42840 original size:24 final size:25
Alignment explanation
Indices: 42813--42967 Score: 126
Period size: 24 Copynumber: 6.5 Consensus size: 25
42803 ATGTTTTATA
* *
42813 TGATTTTC-GATTTGAATTTTGTTC
1 TGATTTTCTGATCTGAATTCTGTTC
* * *
42837 TGA-TTTCTGATATGAATTATGTTA
1 TGATTTTCTGATCTGAATTCTGTTC
* *
42861 T-AATTTATGATCTGAATTCTGTTC
1 TGATTTTCTGATCTGAATTCTGTTC
* * *
42885 TTA-TTTCTGATCTAAATTTTGTTC
1 TGATTTTCTGATCTGAATTCTGTTC
* * *
42909 TGA-TTTCTGATTTGGATTCTGTTA
1 TGATTTTCTGATCTGAATTCTGTTC
* *
42933 TGATATT-TGATCTGAATTCTGTTT
1 TGATTTTCTGATCTGAATTCTGTTC
42957 TGA-TTTCTGAT
1 TGATTTTCTGAT
42968 ATCTCCATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
23 7 0.07
24 95 0.90
25 3 0.03
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.54
Consensus pattern (25 bp):
TGATTTTCTGATCTGAATTCTGTTC
Found at i:42917 original size:72 final size:72
Alignment explanation
Indices: 42827--42967 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
42817 TTTCGATTTG
42827 AATTTTGTTCTGATTTCTGATATGAATTATGTTATAAT-TTATGATCTGAATTCTGTTCTT-ATT
1 AATTTTGTTCTGATTTCTGATATGAATTATGTTATAATATT-TGATCTGAATTCTGTT-TTGATT
42890 TCTGATCTA
64 TCTGATCTA
* * * *
42899 AATTTTGTTCTGATTTCTGATTTGGATTCTGTTATGATATTTGATCTGAATTCTGTTTTGATTTC
1 AATTTTGTTCTGATTTCTGATATGAATTATGTTATAATATTTGATCTGAATTCTGTTTTGATTTC
42964 TGAT
66 TGAT
42968 ATCTCCATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
71 2 0.03
72 59 0.94
73 2 0.03
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (72 bp):
AATTTTGTTCTGATTTCTGATATGAATTATGTTATAATATTTGATCTGAATTCTGTTTTGATTTC
TGATCTA
Found at i:42928 original size:48 final size:48
Alignment explanation
Indices: 42811--42967 Score: 165
Period size: 48 Copynumber: 3.3 Consensus size: 48
42801 AAATGTTTTA
* *
42811 TATGATTT-TCGATTTGAATTTTGTTCTGATTTCTGATATGAATTATGT
1 TATGATTTCT-GATTTGAATTCTGTTCTGATTTCTGATCTGAATTATGT
* * * * * *
42859 TATAATTTATGATCTGAATTCTGTTCTTATTTCTGATCTAAATTTTGT
1 TATGATTTCTGATTTGAATTCTGTTCTGATTTCTGATCTGAATTATGT
* * * *
42907 TCTGATTTCTGATTTGGATTCTGTTATGATATT-TGATCTGAATTCTGT
1 TATGATTTCTGATTTGAATTCTGTTCTGAT-TTCTGATCTGAATTATGT
*
42955 TTTGATTTCTGAT
1 TATGATTTCTGAT
42968 ATCTCCATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
48 87 0.97
49 3 0.03
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (48 bp):
TATGATTTCTGATTTGAATTCTGTTCTGATTTCTGATCTGAATTATGT
Found at i:42965 original size:36 final size:36
Alignment explanation
Indices: 42862--42967 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 36
42852 ATTATGTTAT
42862 AATTTATGATCTGAATTCTGTTCTT-ATTTCTGATCTA
1 AATTT-TGATCTGAATTCTGTT-TTGATTTCTGATCTA
* * *
42899 AATTTTGTTCTGATTTCTGATTTGGA-TTCTG-T-TA
1 AATTTTGATCTGAATTCTG-TTTTGATTTCTGATCTA
*
42933 TGATATTTGATCTGAATTCTGTTTTGATTTCTGAT
1 -AAT-TTTGATCTGAATTCTGTTTTGATTTCTGAT
42968 ATCTCCATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
34 2 0.04
35 8 0.14
36 37 0.66
37 9 0.16
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (36 bp):
AATTTTGATCTGAATTCTGTTTTGATTTCTGATCTA
Found at i:44626 original size:19 final size:19
Alignment explanation
Indices: 44574--44618 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
44564 TCGGTCTAAC
44574 CCATTGACCTTGACCCAAA
1 CCATTGACCTTGACCCAAA
44593 CCATTGACCTTGACCCAAA
1 CCATTGACCTTGACCCAAA
44612 CCATTGA
1 CCATTGA
44619 TTTTGACCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.36, G:0.11, T:0.22
Consensus pattern (19 bp):
CCATTGACCTTGACCCAAA
Found at i:48783 original size:21 final size:21
Alignment explanation
Indices: 48758--48797 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48748 AAGACTTTAT
48758 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
48779 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
48798 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:53448 original size:75 final size:75
Alignment explanation
Indices: 53325--53471 Score: 294
Period size: 75 Copynumber: 2.0 Consensus size: 75
53315 CAAACTCACC
53325 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
1 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
53390 TTAATTCGTG
66 TTAATTCGTG
53400 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
1 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
53465 TTAATTC
66 TTAATTC
53472 ATGCTTCAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.32
Consensus pattern (75 bp):
TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
TTAATTCGTG
Found at i:56900 original size:75 final size:75
Alignment explanation
Indices: 56777--56928 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
56767 TGAACCGAAT
* *
56777 TCTTTTTATTTGTATAATTGAAATGCAATCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
1 TCTTTTTATTTGTACAATTGAAATGCAACCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
*
56842 GAATTGCTAC
66 GAACTGCTAC
*
56852 TCTTTTTATTTGTACAATTGAAATGCAACCAAACTACAAAAGTTGTATGATATGAGTCAACAACG
1 TCTTTTTATTTGTACAATTGAAATGCAACCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
56917 GAACTGCTAC
66 GAACTGCTAC
56927 TC
1 TC
56929 CTTACGTTAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (75 bp):
TCTTTTTATTTGTACAATTGAAATGCAACCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
GAACTGCTAC
Found at i:60850 original size:42 final size:42
Alignment explanation
Indices: 60739--60852 Score: 183
Period size: 42 Copynumber: 2.7 Consensus size: 42
60729 TGAATTCTTG
* * *
60739 TGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTCCCG
1 TGTTTGTTTAACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
*
60781 TGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
1 TGTTTGTTTAACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
*
60823 TGTTTGTTTAACGTAATTGGTTTTCCGGAA
1 TGTTTGTTTAACGTAATTCGTTTTCCGGAA
60853 TGTAATTGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.46
Consensus pattern (42 bp):
TGTTTGTTTAACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
Found at i:60859 original size:19 final size:19
Alignment explanation
Indices: 60835--60878 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
60825 TTTGTTTAAC
60835 GTAATTGGTTTTCCGGAAT
1 GTAATTGGTTTTCCGGAAT
60854 GTAATTGGTTTTCCGGAAT
1 GTAATTGGTTTTCCGGAAT
60873 GTAATT
1 GTAATT
60879 CATTTTCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (19 bp):
GTAATTGGTTTTCCGGAAT
Found at i:60884 original size:19 final size:19
Alignment explanation
Indices: 60843--60886 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
60833 ACGTAATTGG
**
60843 TTTTCCGGAATGTAATTGG
1 TTTTCCGGAATGTAATTCA
60862 TTTTCCGGAATGTAATTCA
1 TTTTCCGGAATGTAATTCA
60881 TTTTCC
1 TTTTCC
60887 TAGTAACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (19 bp):
TTTTCCGGAATGTAATTCA
Found at i:61090 original size:22 final size:22
Alignment explanation
Indices: 61065--61145 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
61055 ATTTATTTAT
61065 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
61087 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
* *
61111 TAATCAATTAT-ATTATAATAATA
1 TAAT-ATTTATAATAAT-ATAATA
*
61134 TAAGATATTATA
1 TAATAT-TTATA
61146 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 16 0.36
23 12 0.27
24 13 0.29
25 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:61179 original size:52 final size:51
Alignment explanation
Indices: 61069--61179 Score: 120
Period size: 52 Copynumber: 2.1 Consensus size: 51
61059 ATTTATTAAT
**
61069 ATTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATCAATT
1 ATTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATCAAAA
* *
61120 ATATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAAT-AAAA
1 AT-TTATAATAATAT-A-ATATAATATTTTTAATATTATATAA-A-ATAATCAAAA
61173 ATTTATA
1 ATTTATA
61180 TATTTAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
51 2 0.04
52 21 0.41
53 11 0.22
54 17 0.33
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATCAAAA
Found at i:61185 original size:29 final size:29
Alignment explanation
Indices: 61051--61230 Score: 91
Period size: 29 Copynumber: 6.0 Consensus size: 29
61041 TCAAAATATT
* *
61051 ATTTATTTATTTATTAATATTTATAATAATATA
1 ATTTATATATTTAATAATA--TATAATAA-A-A
* * * *
61084 ATATAATATTTTTAATATTATATAA-AATA
1 AT-TTATATATTTAATAATATATAATAAAA
** * *
61113 ATCAATTATATTATAATAATATA-AGATATTAT
1 ATTTA-TATATT-TAATAATATATA-ATA-AAA
*
61145 ATTTTTAT-TTTAATAATATATAATAAAA
1 ATTTATATATTTAATAATATATAATAAAA
**
61173 ATTTATATATTTAATAATGA-ATAAT-ATT
1 ATTTATATATTTAATAAT-ATATAATAAAA
*
61201 ATTTATATATTTAAATAATATTTTAATAAA
1 ATTTATATATTT-AATAATA-TATAATAAA
61231 GATATTTAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
28 24 0.21
29 42 0.38
30 18 0.16
31 7 0.06
32 7 0.06
33 2 0.02
34 12 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
ATTTATATATTTAATAATATATAATAAAA
Found at i:61199 original size:19 final size:19
Alignment explanation
Indices: 61156--61229 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
61146 TTTTTATTTT
61156 AATAATATA--TAATAA-A
1 AATAATATATTTAATAATA
* *
61172 AATTTATATATTTAATAATG
1 AA-TAATATATTTAATAATA
*
61192 AATAATATTATTTATATATTTA
1 AATAATA-TATTTA-ATA-ATA
61214 AATAATAT-TTTAATAA
1 AATAATATATTTAATAA
61230 AGATATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.04
17 6 0.13
19 13 0.29
20 12 0.27
21 4 0.09
22 8 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
AATAATATATTTAATAATA
Found at i:61250 original size:23 final size:23
Alignment explanation
Indices: 61224--61268 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61214 AATAATATTT
61224 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
61247 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
61269 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:61649 original size:15 final size:15
Alignment explanation
Indices: 61629--61673 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
61619 TTCATTTTCT
61629 AGTTCCAGTAATTCA
1 AGTTCCAGTAATTCA
61644 AGTTCCAGTAATTCA
1 AGTTCCAGTAATTCA
*
61659 AATTCCAGTAATTCA
1 AGTTCCAGTAATTCA
61674 TTTTCCGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (15 bp):
AGTTCCAGTAATTCA
Found at i:61679 original size:15 final size:15
Alignment explanation
Indices: 61631--61679 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
61621 CATTTTCTAG
*
61631 TTCCAGTAATTCAAG
1 TTCCAGTAATTCAAT
*
61646 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAT
*
61661 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAT
61676 TTCC
1 TTCC
61680 GGAAAACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (15 bp):
TTCCAGTAATTCAAT
Found at i:65352 original size:21 final size:20
Alignment explanation
Indices: 65315--65354 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
65305 TTTGGTTGGA
*
65315 GAAAAATAACTATGGTCAAT
1 GAAAAATAACTACGGTCAAT
*
65335 GAAAAATCAATTACGGTCAA
1 GAAAAAT-AACTACGGTCAA
65355 AGGAAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (20 bp):
GAAAAATAACTACGGTCAAT
Found at i:69655 original size:31 final size:31
Alignment explanation
Indices: 69617--69675 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
69607 CGAGGGTTAA
69617 CTATGTTCTACGGAACATATGGACAGTTTAC
1 CTATGTTCTACGGAACATATGGACAGTTTAC
*
69648 CTATGTTCTTCGGAACATATGGACAGTT
1 CTATGTTCTACGGAACATATGGACAGTT
69676 ACATAGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
CTATGTTCTACGGAACATATGGACAGTTTAC
Found at i:69692 original size:30 final size:31
Alignment explanation
Indices: 69618--69694 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
69608 GAGGGTTAAC
* * *
69618 TATGTTCTACGGAACATATGGACAGTTTACC
1 TATGGTCTTCGGAACATATGGACAGTTTACA
*
69649 TATGTTCTTCGGAACATATGGACAG-TTACA
1 TATGGTCTTCGGAACATATGGACAGTTTACA
69679 TA-GGTCATTCGGAACA
1 TATGGTC-TTCGGAACA
69695 AATTTTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.07
30 15 0.36
31 24 0.57
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (31 bp):
TATGGTCTTCGGAACATATGGACAGTTTACA
Found at i:80095 original size:20 final size:20
Alignment explanation
Indices: 80046--80088 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
80036 AATTTTGTGG
80046 AAGCTTTTGCTGAAAATTGA
1 AAGCTTTTGCTGAAAATTGA
80066 AAGCTTTTGCTGAAAATTGA
1 AAGCTTTTGCTGAAAATTGA
80086 AAG
1 AAG
80089 TATTTGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (20 bp):
AAGCTTTTGCTGAAAATTGA
Found at i:86201 original size:30 final size:30
Alignment explanation
Indices: 86160--86240 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
86150 AATTGAAAGA
*
86160 TAAGTGGTCAAAATAGAATCTCCCAATAAT
1 TAAGTGGTCAAAATAGAATCTCCCAACAAT
* *
86190 TAAGTGATCAAAATAAAATCTCCCAACAAT
1 TAAGTGGTCAAAATAGAATCTCCCAACAAT
*
86220 TAAGTGGTAAAAATAGAATCT
1 TAAGTGGTCAAAATAGAATCT
86241 ATTAATAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (30 bp):
TAAGTGGTCAAAATAGAATCTCCCAACAAT
Found at i:86420 original size:42 final size:42
Alignment explanation
Indices: 86362--86455 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
86352 CCTTCCTCTA
*
86362 TCTAAAACCCCATTTTTCATTTTATAGTTCTAATCTAGGCAC
1 TCTAAAACCCCATTTTTCATTTTATAGTTCCAATCTAGGCAC
*
86404 TCTAAAACCCCATTTTTCATTTTATATTTCCAATCTAGGCAC
1 TCTAAAACCCCATTTTTCATTTTATAGTTCCAATCTAGGCAC
86446 TCTAAAACCC
1 TCTAAAACCC
86456 TAAACCTCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (42 bp):
TCTAAAACCCCATTTTTCATTTTATAGTTCCAATCTAGGCAC
Found at i:90723 original size:21 final size:21
Alignment explanation
Indices: 90681--90723 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
90671 TTTATGGGTT
*
90681 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
90702 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
90723 A
1 A
90724 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:90796 original size:23 final size:22
Alignment explanation
Indices: 90752--90796 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
90742 AATCTCATAG
*
90752 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
90774 GGGAACCGATTACCCCTAAAGGA
1 GGGAACCGATT-CCCCCAAAGGA
90797 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:92307 original size:103 final size:103
Alignment explanation
Indices: 92082--92299 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
92072 GTCGAGGGTC
* *
92082 TATGTGGTCCTTCGGGATATATATGTATTCTTTGAAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTATGGTGAGACACATAC
* *
92147 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
92185 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTATGGTGAGACACATAC
*
92250 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
92288 TATGTGGTCCTT
1 TATGTGGTCCTT
92300 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTATGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:92349 original size:23 final size:23
Alignment explanation
Indices: 92316--92383 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
92306 ATTATTATAT
92316 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
92339 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
92362 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
92384 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:94383 original size:31 final size:31
Alignment explanation
Indices: 94355--94468 Score: 103
Period size: 31 Copynumber: 3.7 Consensus size: 31
94345 CCATTATAGG
94355 ATAAT-TATTAAATTTATCGAAATGTTATAA
1 ATAATATATTAAATTTATCGAAATGTTATAA
** *
94385 ATTTTATATTAAATTTATCGAACTGTTATAA
1 ATAATATATTAAATTTATCGAAATGTTATAA
** *
94416 ATTTTATATTAAATTTTATC-AAATTATTAT-A
1 ATAATATATTAAA-TTTATCGAAA-TGTTATAA
*
94447 A-AATATCA-TAAATTTATAGAAA
1 ATAATAT-ATTAAATTTATCGAAA
94469 CATCGCAGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.07
30 13 0.18
31 42 0.59
32 11 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (31 bp):
ATAATATATTAAATTTATCGAAATGTTATAA
Found at i:94450 original size:21 final size:20
Alignment explanation
Indices: 94410--94461 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
94400 TATCGAACTG
94410 TTATAAATTTTATATTAAATT
1 TTATAAATTTTATA-TAAATT
*
94431 TTATCAAATTATTATA-AAATA
1 TTAT-AAATT-TTATATAAATT
*
94452 TCATAAATTT
1 TTATAAATTT
94462 ATAGAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 11 0.41
22 5 0.19
23 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATAAATTTTATATAAATT
Found at i:97046 original size:22 final size:23
Alignment explanation
Indices: 97019--97071 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
97009 CATTCCACTC
97019 CCCTAAATTCTCAAAC-TT-AAAT
1 CCCTAAATT-TCAAACATTCAAAT
97041 CCCTAAAATTTCAAACATTCAAAT
1 CCCT-AAATTTCAAACATTCAAAT
*
97065 CTCTAAA
1 CCCTAAA
97072 AATCTCCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (23 bp):
CCCTAAATTTCAAACATTCAAAT
Found at i:97070 original size:24 final size:23
Alignment explanation
Indices: 97019--97077 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
97009 CATTCCACTC
97019 CCCT-AAATTCTCAAACTTAAAT
1 CCCTAAAATTCTCAAACTTAAAT
97041 CCCTAAAATT-TCAAACATTCAAAT
1 CCCTAAAATTCTCAAAC-TT-AAAT
* *
97065 CTCTAAAAATCTC
1 CCCTAAAATTCTC
97078 CTTAATCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 10 0.32
23 7 0.23
24 12 0.39
25 2 0.06
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (23 bp):
CCCTAAAATTCTCAAACTTAAAT
Found at i:98076 original size:42 final size:42
Alignment explanation
Indices: 98012--98291 Score: 400
Period size: 42 Copynumber: 6.7 Consensus size: 42
98002 GGCATCGTCC
* * *
98012 GGGATTTCAGCACTCGGTGAGGAACTTCCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* * *
98054 GGGGTTTCAGCACCCGACGAGGAGCTTTCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* *
98096 GGGATTTCAGCA-CCGGCGAGGAGCTTTCAATGTTTAGGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
*
98137 GGGATTTCAGCATCCGGCGAGGAACTTTCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* * *
98179 GGGATTTCAGCACCTGGCGAGGAATTTTCAATGTTTACGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* * *
98221 GGGATTTCAGCGCACAGCGAGGAACTTTCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* *
98263 GGGATTTCAGCACACAGCGAGGAACTTTC
1 GGGATTTCAGCACCCGGCGAGGAACTTTC
98292 GTCTTCACCG
Statistics
Matches: 215, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 39 0.18
42 176 0.82
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (42 bp):
GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
Found at i:102594 original size:18 final size:18
Alignment explanation
Indices: 102573--102625 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
102563 GAGAGAAGAA
102573 AAAATTAATATATAATAT
1 AAAATTAATATATAATAT
*
102591 AAAATT-ATGA-AT-ACAT
1 AAAATTAAT-ATATAATAT
102607 AAAA-TAATATATATATAT
1 AAAATTAATATATA-ATAT
102625 A
1 A
102626 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 4 0.14
18 11 0.39
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATTAATATATAATAT
Found at i:102620 original size:2 final size:2
Alignment explanation
Indices: 102613--102639 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
102603 ACATAAAATA
102613 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 A
102640 ATGGACGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103113 original size:2 final size:2
Alignment explanation
Indices: 103106--103146 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
103096 CTATTTTACC
103106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
103147 TCACCTTAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:125825 original size:12 final size:12
Alignment explanation
Indices: 125808--125833 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
125798 GACCACCACC
125808 GTCAAAAGCAGT
1 GTCAAAAGCAGT
125820 GTCAAAAGCAGT
1 GTCAAAAGCAGT
125832 GT
1 GT
125834 ACTGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (12 bp):
GTCAAAAGCAGT
Found at i:129926 original size:21 final size:20
Alignment explanation
Indices: 129899--129997 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
129889 AATCAGTTTC
129899 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
129920 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
129941 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
129961 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
129982 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
129998 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:130026 original size:20 final size:20
Alignment explanation
Indices: 129965--130193 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
129955 GATTTTCAAG
* ** *
129965 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
129985 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
130005 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
130025 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
130045 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
130065 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
130085 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
130105 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
130125 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
130145 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
130165 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
130185 AATCACAAC
1 AATCGCAAC
130194 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:130924 original size:24 final size:24
Alignment explanation
Indices: 130885--130931 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
130875 AAATTTGGTC
130885 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
130909 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
130932 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:131123 original size:12 final size:12
Alignment explanation
Indices: 131106--131130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
131096 ATATAATCCT
131106 GAAGAAGAAAAA
1 GAAGAAGAAAAA
131118 GAAGAAGAAAAA
1 GAAGAAGAAAAA
131130 G
1 G
131131 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:133518 original size:72 final size:72
Alignment explanation
Indices: 133425--133658 Score: 279
Period size: 72 Copynumber: 3.3 Consensus size: 72
133415 GCAACGAGAG
133425 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
133490 AAATGAA
66 AAATGAA
* * *
133497 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCACAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
133561 GAAATGAA
65 GAAATGAA
* * * * * *
133569 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATTGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
133629 CG--A-GAG
64 CGAAATGAA
133635 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
133659 GCAATGCGAA
Statistics
Matches: 139, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.12
72 90 0.65
73 9 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:133546 original size:53 final size:52
Alignment explanation
Indices: 133411--133680 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
133401 CGGAAATTAC
*
133411 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
133458 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
133516 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
133569 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
133621 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
133674 AATCGCA
1 AATCGCA
133681 TTGCGATTCT
Statistics
Matches: 203, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 64 0.32
53 113 0.56
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:133686 original size:72 final size:68
Alignment explanation
Indices: 133392--133685 Score: 258
Period size: 72 Copynumber: 4.2 Consensus size: 68
133382 GCATTTGACT
** * * *
133392 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
133456 AAA
66 AAA
*
133459 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
133524 CGA-GAGA
61 CGATGAAA
* * * * * *
133531 ATCGCAATGCGGAAATGAAAATCACAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
133593 CGAAATGAAA
61 CG--ATGAAA
*
133603 ATTGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
133667 AAATGAAA
63 --ATGAAA
*
133675 ATCGCATTGCG
1 ATCGCAATGCG
133686 ATTCTCTCGT
Statistics
Matches: 185, Mismatches: 23, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.18
69 4 0.02
70 1 0.01
71 20 0.11
72 104 0.56
73 4 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
AAA
Found at i:133700 original size:105 final size:105
Alignment explanation
Indices: 133411--133680 Score: 408
Period size: 105 Copynumber: 2.6 Consensus size: 105
133401 CGGAAATTAC
*
133411 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCAA--C-
*
133470 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
133516 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCAACGAG
*
133581 AGAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
133621 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCA
133681 TTGCGATTCT
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 123 0.79
106 16 0.10
108 2 0.01
109 1 0.01
111 13 0.08
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:133759 original size:54 final size:52
Alignment explanation
Indices: 133676--133793 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 52
133666 GAAATGAAAA
133676 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTACGATTTTCATT
*
133729 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
133782 TCGCATTGCGAT
1 TCGCATTGCGAT
133794 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
52 11 0.17
53 19 0.30
54 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
Found at i:133801 original size:19 final size:19
Alignment explanation
Indices: 133695--133793 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
133685 GATTCTCTCG
133695 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
133715 TTACGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
133735 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
133749 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
133768 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
133787 TTGCGAT
1 TTGCGAT
133794 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 5 0.07
17 6 0.09
18 3 0.04
19 26 0.37
20 24 0.34
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:133919 original size:14 final size:14
Alignment explanation
Indices: 133900--133936 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
133890 CATCAATTAC
133900 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
133914 ACAAATCATCTTTT
1 ACAAATCAACTTTT
133928 ACAAATCAA
1 ACAAATCAA
133937 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:134053 original size:12 final size:12
Alignment explanation
Indices: 134033--134062 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
134023 AAATCAATTA
*
134033 AACTATTGAATC
1 AACTTTTGAATC
134045 AACTTTTGAATC
1 AACTTTTGAATC
134057 AACTTT
1 AACTTT
134063 GCAGCCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (12 bp):
AACTTTTGAATC
Found at i:135904 original size:19 final size:19
Alignment explanation
Indices: 135862--136034 Score: 132
Period size: 19 Copynumber: 9.6 Consensus size: 19
135852 TAGTTTACTT
* *
135862 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-GAAAA
* * *
135882 TCGCAGCGCGAAATGAGAA
1 TCGCAACGCGAAACGAAAA
* *
135901 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
135920 TCGCAACGCGAAACAAAAA
1 TCGCAACGCGAAACGAAAA
*
135939 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
135958 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACGAAAA
* *
135972 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
135991 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAACGAAAA
*
136005 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
136024 TCGCAATGCGA
1 TCGCAACGCGA
136035 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
14 19 0.16
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 80 0.66
20 11 0.09
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACGAAAA
Found at i:135975 original size:14 final size:14
Alignment explanation
Indices: 135956--136012 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
135946 GCGAAATGAA
*
135956 AATCGCAACGACAG
1 AATCGCAACGAAAG
135970 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
135987 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
136003 AATCGCAACG
1 AATCGCAACG
136013 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:135983 original size:33 final size:33
Alignment explanation
Indices: 135937--136029 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
135927 GCGAAACAAA
135937 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
135970 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
136003 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
136030 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:136026 original size:52 final size:52
Alignment explanation
Indices: 135896--136034 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
135886 AGCGCGAAAT
* * * *
135896 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACAAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACAAAAATCGCAACGA
* ** * **
135948 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACAAAAATCGCAACGA
*
136000 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
136035 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACAAAAATCGCAACGA
Found at i:136065 original size:14 final size:14
Alignment explanation
Indices: 136046--136104 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
136036 TTTGGTTTCG
136046 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
136060 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
136077 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
136093 CGTTGCGATTTT
1 CGTTGCGATTTT
136105 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:136072 original size:33 final size:33
Alignment explanation
Indices: 136030--136153 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
136020 AAAATCGCAA
*
136030 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
136063 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
136096 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
136129 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
136154 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:136084 original size:19 final size:18
Alignment explanation
Indices: 136030--136121 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
136020 AAAATCGCAA
136030 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
136049 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
136063 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
136082 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
136096 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
136115 TGCGATT
1 TGCGATT
136122 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:136131 original size:14 final size:14
Alignment explanation
Indices: 136079--136135 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
136069 TTTGGTTTCG
*
136079 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
136093 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
136112 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
136126 CGTTGCGATT
1 CGTTGCGATT
136136 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:136410 original size:93 final size:93
Alignment explanation
Indices: 136251--136566 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
136241 TCAGGGTATT
136251 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
136316 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
136344 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
136409 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
136437 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
136502 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
136530 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
136567 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:138305 original size:21 final size:21
Alignment explanation
Indices: 138251--138307 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
138241 TCTTTTGGTT
138251 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
138272 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
138292 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
138308 TGCGATTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:138333 original size:19 final size:19
Alignment explanation
Indices: 138308--138429 Score: 75
Period size: 21 Copynumber: 6.7 Consensus size: 19
138298 AAAATCGCAA
138308 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
138327 TGTGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
138341 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
138360 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
138374 TGCGATTTTCATTTTTCTCGT
1 TGCGATTTTCA--TTTCGCGT
** *
138395 TGCAGATAGTCATTTTCACGT
1 TGC-GATTTTCA-TTTCGCGT
138416 TGCGATTTTCATTT
1 TGCGATTTTCATTT
138430 ATCTCGTTGC
Statistics
Matches: 80, Mismatches: 10, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.24
16 6 0.08
17 6 0.08
19 17 0.21
20 6 0.08
21 20 0.25
22 6 0.08
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:138347 original size:14 final size:14
Alignment explanation
Indices: 138324--138380 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
138314 TTTCATTTCG
*
138324 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
138338 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
138357 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
138371 CGTTGCGATT
1 CGTTGCGATT
138381 TTCATTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:138350 original size:33 final size:33
Alignment explanation
Indices: 138308--138387 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
138298 AAAATCGCAA
*
138308 TGCGATTTTCATTTCGCGTTGTGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
138341 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
138374 TGCGATTTTCATTT
1 TGCGATTTTCATTT
138388 TTCTCGTTGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.10, C:0.21, G:0.20, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:138393 original size:21 final size:21
Alignment explanation
Indices: 138368--138441 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
138358 GTTGCGATTC
138368 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
138389 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
138410 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
138431 TCTCGTTGCGA
1 TCTCGTTGCGA
138442 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:138563 original size:33 final size:33
Alignment explanation
Indices: 138521--138591 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
138511 AATACTAACT
138521 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
138554 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
138587 TGAAA
1 TGAAA
138592 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:139159 original size:20 final size:20
Alignment explanation
Indices: 138971--139144 Score: 244
Period size: 20 Copynumber: 8.7 Consensus size: 20
138961 CTTTAAAAAT
138971 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
138991 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
139011 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
139032 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
139052 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
139072 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
139092 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
139112 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
139132 CGCGTTGCGATTT
1 CGCGTTGCGATTT
139145 TCATATTCGC
Statistics
Matches: 138, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
20 120 0.87
21 18 0.13
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:140032 original size:29 final size:30
Alignment explanation
Indices: 139978--140036 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
139968 ATTGCAATTA
139978 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
140008 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
140037 TTATAGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:141245 original size:3 final size:3
Alignment explanation
Indices: 141237--141283 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
141227 ATTAATTATT
*
141237 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
141281 TAA
1 TAA
141284 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:141260 original size:13 final size:13
Alignment explanation
Indices: 141224--141287 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
141214 TGTATTAAAA
*
141224 ATAAT-TAATTAT
1 ATAATATAATAAT
*
141236 TTAATAATAATAAT
1 ATAAT-ATAATAAT
141250 ATAATATAATAAT
1 ATAATATAATAAT
* * *
141263 AAAACAAAATAAT
1 ATAATATAATAAT
141276 AATAATA-AATAA
1 -ATAATATAATAA
141288 AACAAATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 4 0.10
13 23 0.56
14 14 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:141260 original size:16 final size:15
Alignment explanation
Indices: 141239--141286 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
141229 TAATTATTTA
141239 ATAATAATAATATAAT
1 ATAATAATAATA-AAT
* *
141255 ATAATAATAAAACAAA
1 ATAATAATAATA-AAT
141271 ATAATAATAATAAAT
1 ATAATAATAATAAAT
141286 A
1 A
141287 AAACAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:141295 original size:19 final size:18
Alignment explanation
Indices: 141238--141302 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
141228 TTAATTATTT
*
141238 AATAATAAT-AAT-ATAA
1 AATAATAATAAATAAAAA
*
141254 TATAATAATAAA-ACAAAA
1 AATAATAATAAATA-AAAA
141272 TAATAATAATAAATAAAACA
1 -AATAATAATAAATAAAA-A
141292 AATAA-AATAAA
1 AATAATAATAAA
141303 AACTAGTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.20
17 2 0.05
18 9 0.22
19 19 0.47
20 2 0.05
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAATAATAAATAAAAA
Found at i:141296 original size:32 final size:32
Alignment explanation
Indices: 141238--141303 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
141228 TTAATTATTT
* *
141238 AATAATAATAATATAATATAATAATAAAACAA
1 AATAATAATAATATAATAAAAAAATAAAACAA
*
141270 AATAATAATAATA-AATAAAACAAATAAAATAA
1 AATAATAATAATATAATAAAA-AAATAAAACAA
141302 AA
1 AA
141304 ACTAGTGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (32 bp):
AATAATAATAATATAATAAAAAAATAAAACAA
Found at i:141719 original size:113 final size:113
Alignment explanation
Indices: 141536--142316 Score: 1251
Period size: 113 Copynumber: 6.9 Consensus size: 113
141526 AGAATCATGC
*
141536 AAAAGATTGAACAAGTTCTTCTCATTCTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * * * *
141601 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATGCGAGCA
65 TATGAACTCGAC-CTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
* *
141650 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
141715 ATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATAAATTCAAGTG
66 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
*
141763 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
141828 ATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
141876 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
141941 ATGAACTCGACCTGGTAATGTTGATCCATCAAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
*
141989 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
142054 ATGAACTCGACCTGGTAATGATGATCCATCAAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
142102 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
142167 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
* * *
142215 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * **
142280 ATGAACTCGACCT-GAAATGTTGATCCATTGAATGATG
66 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATG
142317 GATTTGAACT
Statistics
Matches: 634, Mismatches: 32, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
112 20 0.03
113 608 0.96
114 6 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
Found at i:142748 original size:22 final size:22
Alignment explanation
Indices: 142723--142765 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
142713 GATAAAGCTT
*
142723 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTG
*
142745 TCATCTTTAAAAAGGGAATCT
1 TCATCTTTAAAAAGAGAATCT
142766 ATCACCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTG
Found at i:143226 original size:54 final size:54
Alignment explanation
Indices: 143144--143407 Score: 375
Period size: 54 Copynumber: 4.9 Consensus size: 54
143134 AGAATAGCAG
*
143144 GTTCGTAAAACATTTGACAGCACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
143198 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
143252 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * * * *
143306 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTTAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * * **
143360 GTTCGTAAAGCGTTTGACAACATATTCATCCTTTTTTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
143408 CAAGATTTCT
Statistics
Matches: 184, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 184 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:143333 original size:108 final size:108
Alignment explanation
Indices: 143144--143407 Score: 438
Period size: 108 Copynumber: 2.4 Consensus size: 108
143134 AGAATAGCAG
* * * *
143144 GTTCGTAAAACATTTGACAGCACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
1 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
* *
143209 ATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAA
66 ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTCAGAA
143252 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
1 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
* *
143317 ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTTAGAC
66 ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTCAGAA
* *
143360 GTTCGTAAAGCGTTTGACAACATATTCATCCTTTTTTGTGGCTTCTGC
1 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
143408 CAAGATTTCT
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 146 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (108 bp):
GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTCAGAA
Found at i:145799 original size:114 final size:114
Alignment explanation
Indices: 145599--145813 Score: 378
Period size: 114 Copynumber: 1.9 Consensus size: 114
145589 TGCAGTTCAT
* *
145599 CTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAAACAGATCAGATAACTCAAAGAACACT
1 CTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCGAAACAGATCAGATAACTCAAAGAACACT
145664 TCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAACAAATTAAG
66 TCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAACAAATTAAG
*
145713 CTTTCAAATCCAATGATTGGTTTTGGGGTTCATACC-AAATCAGATCAGATAACTCAAAGAACAC
1 CTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCGAAA-CAGATCAGATAACTCAAAGAACAC
*
145777 TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
65 TTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTA
145814 CGAGAATGTG
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 3 0.03
114 93 0.97
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
CTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCGAAACAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAACAAATTAAG
Found at i:147448 original size:24 final size:23
Alignment explanation
Indices: 147420--147483 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
147410 AGATATCAAA
* *
147420 AATCAAAACATAATTCATATCAG
1 AATCAGAACAAAATTCATATCAG
* * *
147443 ATATCAGATCAGAATCCATATCAG
1 A-ATCAGAACAAAATTCATATCAG
147467 AATCAGAACAAAATTCA
1 AATCAGAACAAAATTCA
147484 GGTAACGTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (23 bp):
AATCAGAACAAAATTCATATCAG
Found at i:148437 original size:18 final size:18
Alignment explanation
Indices: 148416--148451 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
148406 CTTCCATCCG
*
148416 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
148434 ATCTTATCATTTATTTCA
1 ATCTTATCATTTAATTCA
148452 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:151962 original size:8 final size:8
Alignment explanation
Indices: 151949--152035 Score: 93
Period size: 8 Copynumber: 10.4 Consensus size: 8
151939 TTGATTCAAT
151949 TTTTTTTC
1 TTTTTTTC
151957 TTTTTTTC
1 TTTTTTTC
*
151965 TTTTTTTT
1 TTTTTTTC
*
151973 TTCTTTTTA
1 TT-TTTTTC
*
151982 TTTCTTTCC
1 TTT-TTTTC
151991 TTTTATTTC
1 TTTT-TTTC
152000 TTTTTTTC
1 TTTTTTTC
*
152008 TTTTTTCC
1 TTTTTTTC
152016 TCTTTTTTC
1 T-TTTTTTC
*
152025 TTTTTTCC
1 TTTTTTTC
152033 TTT
1 TTT
152036 CTTTGCTGGA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
8 40 0.60
9 27 0.40
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:151963 original size:10 final size:10
Alignment explanation
Indices: 151948--152030 Score: 71
Period size: 10 Copynumber: 8.5 Consensus size: 10
151938 CTTGATTCAA
151948 TTTTTTTTCT
1 TTTTTTTTCT
*
151958 TTTTTTCT-T
1 TTTTTTTTCT
151967 TTTTTTTTCT
1 TTTTTTTTCT
*
151977 TTTTATTTCT
1 TTTTTTTTCT
** *
151987 TTCCTTTTAT
1 TTTTTTTTCT
*
151997 TTCTTTTT-T
1 TTTTTTTTCT
* *
152006 TCTTTTTTCC
1 TTTTTTTTCT
*
152016 TCTTTTTTCT
1 TTTTTTTTCT
152026 TTTTT
1 TTTTT
152031 CCTTTCTTTG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
9 15 0.26
10 43 0.74
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:151989 original size:25 final size:24
Alignment explanation
Indices: 151948--152039 Score: 70
Period size: 25 Copynumber: 3.9 Consensus size: 24
151938 CTTGATTCAA
*
151948 TTTTT-TTTCTTTT-TTTCTTTTT
1 TTTTTCTTTTTTTTCTTTCTTTTT
*
151970 TTTTTCTTTTTATTTCTTTC-CTTT
1 TTTTTCTTTTT-TTTCTTTCTTTTT
*
151994 TATTTC-TTTTTTTCTTT-TTTCCTCT
1 TTTTTCTTTTTTTTCTTTCTTT--T-T
*
152019 TTTTTC-TTTTTTCCTTTCTTT
1 TTTTTCTTTTTTTTCTTTCTTT
152040 GCTGGATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
22 13 0.23
23 8 0.14
24 12 0.21
25 20 0.36
26 3 0.05
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTCTTTTTTTTCTTTCTTTTT
Found at i:152023 original size:43 final size:42
Alignment explanation
Indices: 151948--152035 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 42
151938 CTTGATTCAA
* * *
151948 TTTTTTTTCTTTTTTTCTTTTTTTTTTCTTTTTATTTCTTTCC
1 TTTTATTTCTTTTTTTCTTTTTTCTCTCTTTTTATTT-TTTCC
*
151991 TTTTATTTCTTTTTTTCTTTTTTC-CTCTTTTTTCTTTTTTCC
1 TTTTATTTCTTTTTTTCTTTTTTCTCTC-TTTTTATTTTTTCC
152033 TTT
1 TTT
152036 CTTTGCTGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 10 0.25
43 30 0.75
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (42 bp):
TTTTATTTCTTTTTTTCTTTTTTCTCTCTTTTTATTTTTTCC
Found at i:152051 original size:15 final size:15
Alignment explanation
Indices: 152033--152079 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
152023 TCTTTTTTCC
152033 TTTCTTTGCTGGATT
1 TTTCTTTGCTGGATT
*
152048 TTTCTTT--T---TC
1 TTTCTTTGCTGGATT
152058 TTTCTTTGCTGGATT
1 TTTCTTTGCTGGATT
152073 TTTCTTT
1 TTTCTTT
152080 TTCTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 8 0.32
12 1 0.04
13 1 0.04
15 15 0.60
ACGTcount: A:0.04, C:0.15, G:0.13, T:0.68
Consensus pattern (15 bp):
TTTCTTTGCTGGATT
Found at i:152055 original size:25 final size:25
Alignment explanation
Indices: 152019--152096 Score: 138
Period size: 25 Copynumber: 3.0 Consensus size: 25
152009 TTTTTCCTCT
152019 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTC-TTTTT-CTTTCTTTGCTGGA
152046 TTTTTCTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTCTTTCTTTGCTGGA
152071 TTTTTCTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTCTTTCTTTGCTGGA
152096 T
1 T
152097 GAGTATAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 40 0.78
26 5 0.10
27 6 0.12
ACGTcount: A:0.04, C:0.17, G:0.12, T:0.68
Consensus pattern (25 bp):
TTTTTCTTTTTCTTTCTTTGCTGGA
Found at i:152056 original size:50 final size:50
Alignment explanation
Indices: 151970--152096 Score: 134
Period size: 50 Copynumber: 2.5 Consensus size: 50
151960 TTTTCTTTTT
* * ** *
151970 TTTTTCTTTTTATTTCTTTCCTTTTATTTCTT-TTTTTCTTT-TTTCCT-CT
1 TTTTTCTTTTTCTTTCTTTGC-TGGATTT-TTCTTTTTCTTTCTTTCCTGCA
* *
152019 TTTTTCTTTTTTCCTTTCTTTGCTGGATTTTTCTTTTTCTTTCTTTGCTGGA
1 TTTTTC-TTTTT-CTTTCTTTGCTGGATTTTTCTTTTTCTTTCTTTCCTGCA
152071 TTTTTCTTTTTCTTTCTTTGCTGGAT
1 TTTTTCTTTTTCTTTCTTTGCTGGAT
152097 GAGTATAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
49 8 0.12
50 34 0.52
51 18 0.27
52 6 0.09
ACGTcount: A:0.04, C:0.17, G:0.07, T:0.72
Consensus pattern (50 bp):
TTTTTCTTTTTCTTTCTTTGCTGGATTTTTCTTTTTCTTTCTTTCCTGCA
Found at i:152988 original size:2 final size:2
Alignment explanation
Indices: 152981--153045 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
152971 CAATGCTTCC
152981 TA TA TA 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
153023 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
153046 TAAAGGATAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:155457 original size:32 final size:31
Alignment explanation
Indices: 155405--155522 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 31
155395 GTTCCTTAGA
*
155405 ACATAGGTATACTGTCCATATGTCTCAAAAG
1 ACATAGGTATTCTGTCCATATGTCTCAAAAG
* **
155436 ACATAGGTAATTCTGTCCATATGTTTC-GTAG
1 ACATAGGT-ATTCTGTCCATATGTCTCAAAAG
155467 AACATAGGTATAT-TGTCCATATGTCTCAAAAG
1 -ACATAGGTAT-TCTGTCCATATGTCTCAAAAG
155499 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATTCTGTCCATATGT
155523 TCCGTAGAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
31 34 0.46
32 40 0.54
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (31 bp):
ACATAGGTATTCTGTCCATATGTCTCAAAAG
Found at i:155468 original size:63 final size:63
Alignment explanation
Indices: 155388--155542 Score: 283
Period size: 63 Copynumber: 2.5 Consensus size: 63
155378 AGGTAAACTA
*
155388 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
* *
155451 TCCATATGTTTCGTAGAACATAGGTATATTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
155514 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
155543 CCTCGACTCT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
Found at i:155535 original size:32 final size:32
Alignment explanation
Indices: 155354--155539 Score: 161
Period size: 31 Copynumber: 5.9 Consensus size: 32
155344 TCATCGGTAA
* * * *
155354 CTGTCTATAGGTTCCG-ATGAACCTAGGTAA-A
1 CTGTCCATATGTTCCGTA-GAACATAGGTAATT
* * *
155385 CTATCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTTCCGTAGAACATAGGTAATT
***
155416 CTGTCCATATGTCTCAAAAG-ACATAGGTAATT
1 CTGTCCATATGT-TCCGTAGAACATAGGTAATT
*
155448 CTGTCCATATGTTTCGTAGAACATAGGT-ATAT
1 CTGTCCATATGTTCCGTAGAACATAGGTAAT-T
***
155480 -TGTCCATATGTCTCAAAAG-ACATAGGTAATT
1 CTGTCCATATGT-TCCGTAGAACATAGGTAATT
155511 CTGTCCATATGTTCCGTAGAACATAGGTA
1 CTGTCCATATGTTCCGTAGAACATAGGTA
155540 TACCCTCGAC
Statistics
Matches: 124, Mismatches: 21, Indels: 19
0.76 0.13 0.12
Matches are distributed among these distances:
30 1 0.01
31 70 0.56
32 53 0.43
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (32 bp):
CTGTCCATATGTTCCGTAGAACATAGGTAATT
Found at i:159489 original size:14 final size:15
Alignment explanation
Indices: 159472--159504 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
159462 ACAGAAACAT
159472 AAATA-ATGAAAATA
1 AAATACATGAAAATA
*
159486 AAATACTTGAAAATA
1 AAATACATGAAAATA
159501 AAAT
1 AAAT
159505 GAAACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (15 bp):
AAATACATGAAAATA
Found at i:159571 original size:28 final size:26
Alignment explanation
Indices: 159516--159573 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
159506 AAACATTAAT
*
159516 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
159542 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
159570 AAAA
1 AAAA
159574 GAAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:160201 original size:20 final size:20
Alignment explanation
Indices: 160170--160230 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
160160 ATAAATATTA
*
160170 ATAAAAAATTTATTAAAAAT
1 ATAAATAATTTATTAAAAAT
*
160190 ATATATAATTTA-TAAAAAGT
1 ATAAATAATTTATTAAAAA-T
160210 A-AAAT-ATTTATTTAAAAAT
1 ATAAATAATTTA-TTAAAAAT
160229 AT
1 AT
160231 CAGAAAATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 5 0.15
19 11 0.32
20 18 0.53
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATAAATAATTTATTAAAAAT
Found at i:160614 original size:29 final size:30
Alignment explanation
Indices: 160560--160618 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
160550 ATTGCAATTA
160560 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
160590 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
160619 TTATAGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:161281 original size:3 final size:3
Alignment explanation
Indices: 161273--161319 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
161263 ATTAATTATT
*
161273 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
161317 TAA
1 TAA
161320 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:161296 original size:13 final size:13
Alignment explanation
Indices: 161260--161323 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
161250 TGTATTAAAA
*
161260 ATAAT-TAATTAT
1 ATAATATAATAAT
*
161272 TTAATAATAATAAT
1 ATAAT-ATAATAAT
161286 ATAATATAATAAT
1 ATAATATAATAAT
* * *
161299 AAAACAAAATAAT
1 ATAATATAATAAT
161312 AATAATA-AATAA
1 -ATAATATAATAA
161324 AACAAATGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 4 0.10
13 23 0.56
14 14 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:161296 original size:16 final size:15
Alignment explanation
Indices: 161275--161322 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
161265 TAATTATTTA
161275 ATAATAATAATATAAT
1 ATAATAATAATA-AAT
* *
161291 ATAATAATAAAACAAA
1 ATAATAATAATA-AAT
161307 ATAATAATAATAAAT
1 ATAATAATAATAAAT
161322 A
1 A
161323 AAACAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:166927 original size:9 final size:9
Alignment explanation
Indices: 166908--166941 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
166898 TATTTAAAAT
166908 TTAATTTCGG
1 TTAA-TTCGG
166918 TTAATTCGG
1 TTAATTCGG
*
166927 TTAATTCGC
1 TTAATTCGG
166936 TTAATT
1 TTAATT
166942 AACCGAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:168440 original size:125 final size:125
Alignment explanation
Indices: 168184--168426 Score: 405
Period size: 125 Copynumber: 1.9 Consensus size: 125
168174 GTCACGGAAA
* * * * * *
168184 AAAGATGTCATGTCATCGTTCCGTTAACGGATTAACGGTGGAGTGGCAAAATTGCAGTGAAACAT
1 AAAGATGCCATGTCATCGTCCCGTTAACAGATTAACGGCGGAGTGGCAAAATTACAATGAAACAT
* *
168249 AAACGTCGGTGCTAAAATTGGCAAAATTGAAACGTTAATGGCATTTTCGAGCCTAAGCTT
66 AAACGTCAGTGCTAAAATTGGCAAAATTGAAACGTCAATGGCATTTTCGAGCCTAAGCTT
168309 AAAGATGCCATGTCATCGTCCCGTTAACAGATTAACGGCGGAGTGGCAAAATTACAATGAAACAT
1 AAAGATGCCATGTCATCGTCCCGTTAACAGATTAACGGCGGAGTGGCAAAATTACAATGAAACAT
*
168374 AAACGTCAGTGCTAAAATTGGCAAAATTGAAACGTCGATGGCATTTTCGAGCC
66 AAACGTCAGTGCTAAAATTGGCAAAATTGAAACGTCAATGGCATTTTCGAGCC
168427 CGGTCTTAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 109 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (125 bp):
AAAGATGCCATGTCATCGTCCCGTTAACAGATTAACGGCGGAGTGGCAAAATTACAATGAAACAT
AAACGTCAGTGCTAAAATTGGCAAAATTGAAACGTCAATGGCATTTTCGAGCCTAAGCTT
Found at i:171760 original size:22 final size:21
Alignment explanation
Indices: 171730--171774 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
171720 TTAGGTACGA
* *
171730 ACTTTTAAAATTTTAAGGACAG
1 ACTTGTAAAATTTGAAGGA-AG
171752 ACTTGTAAAATTTGAAGGAAG
1 ACTTGTAAAATTTGAAGGAAG
171773 AC
1 AC
171775 GAAAACAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (21 bp):
ACTTGTAAAATTTGAAGGAAG
Found at i:172610 original size:20 final size:22
Alignment explanation
Indices: 172587--172627 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
172577 GAAATATGCT
*
172587 ATATTT-TT-AATTAAAAAATA
1 ATATTTGTTGAATGAAAAAATA
172607 ATATTTGTTGAATGAAAAAAT
1 ATATTTGTTGAATGAAAAAAT
172628 TGATGTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
ATATTTGTTGAATGAAAAAATA
Found at i:178460 original size:12 final size:12
Alignment explanation
Indices: 178439--178472 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
178429 ACCACATTTC
*
178439 CAATACCAAACA
1 CAATATCAAACA
178451 CAATATCAAACA
1 CAATATCAAACA
178463 CAATATCAAA
1 CAATATCAAA
178473 ATCCACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:178649 original size:24 final size:24
Alignment explanation
Indices: 178598--178651 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
178588 GTATTCGAAA
*
178598 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* * *
178622 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
178646 TTTGAT
1 TTTGAT
178652 GATGTGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Done.