Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 99 of 144
Found at i:23204200 original size:38 final size:38
Alignment explanation
Indices: 23204158--23204252 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
23204148 TGTTCTCACA
* * *
23204158 AGCCAATATTGCTCTTACGAGCCAGTATTACTTTTTCG
1 AGCCAGTATTGCTCTTACGAGACAGTATTACTCTTTCG
* * *
23204196 AGCCAGTATTGCTCTTATGAGATAGTATTTCTCTTTCG
1 AGCCAGTATTGCTCTTACGAGACAGTATTACTCTTTCG
23204234 AGCCAGTATTGCTCTTACG
1 AGCCAGTATTGCTCTTACG
23204253 TATTGCTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (38 bp):
AGCCAGTATTGCTCTTACGAGACAGTATTACTCTTTCG
Found at i:23206490 original size:58 final size:58
Alignment explanation
Indices: 23206422--23206542 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
23206412 TTTTCTTGTT
* *
23206422 GTTGTAGGGTCTTT-AGAATATGGTATTTATACCCCCTAATTGATTTCCAACCATTGAG
1 GTTGTAGGGTCTTTGA-AAGATGGTATTTATACCCCCTAATTGATTTCCAACCATTGAA
* *
23206480 GTTGTAGGGTCTTTGAAAGATGGTATTTATACTCCCTAATTGATTTCTAACCATTGAA
1 GTTGTAGGGTCTTTGAAAGATGGTATTTATACCCCCTAATTGATTTCCAACCATTGAA
23206538 GTTGT
1 GTTGT
23206543 TGGTGTCATG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (58 bp):
GTTGTAGGGTCTTTGAAAGATGGTATTTATACCCCCTAATTGATTTCCAACCATTGAA
Found at i:23207022 original size:20 final size:19
Alignment explanation
Indices: 23206972--23207022 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
23206962 AACTTGTTTG
* *
23206972 AAAATCATTTTGTTTTGTT
1 AAAATCATTTTGCTTGGTT
*
23206991 AAAATGATTTTTGACTTGGTT
1 AAAATCA-TTTTG-CTTGGTT
23207012 AAAATCATTTT
1 AAAATCATTTT
23207023 AAATTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
21 11 0.42
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (19 bp):
AAAATCATTTTGCTTGGTT
Found at i:23216780 original size:14 final size:14
Alignment explanation
Indices: 23216757--23216793 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
23216747 TTTTAAATTG
*
23216757 AAGAATTTTAAAAA
1 AAGAAATTTAAAAA
23216771 AAGAAATTT--AAA
1 AAGAAATTTAAAAA
23216783 AAGAAATTTAA
1 AAGAAATTTAA
23216794 TATAAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (14 bp):
AAGAAATTTAAAAA
Found at i:23216785 original size:12 final size:12
Alignment explanation
Indices: 23216768--23216793 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23216758 AGAATTTTAA
23216768 AAAAAGAAATTT
1 AAAAAGAAATTT
23216780 AAAAAGAAATTT
1 AAAAAGAAATTT
23216792 AA
1 AA
23216794 TATAAATATC
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:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAAGAAATTT
Found at i:23220347 original size:17 final size:19
Alignment explanation
Indices: 23220325--23220374 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
23220315 TGACAATATA
23220325 TTTCTTTTCTTTT-TTT-T
1 TTTCTTTTCTTTTCTTTCT
23220342 TTTCTTTTCTTCTTCTTTCT
1 TTTCTTTTCTT-TTCTTTCT
23220362 TTT-TCTTTCTTTT
1 TTTCT-TTTCTTTT
23220375 GTGATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 11 0.38
18 2 0.07
19 6 0.21
20 10 0.34
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTCTTTTCTTTTCTTTCT
Found at i:23220349 original size:10 final size:10
Alignment explanation
Indices: 23220325--23220374 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
23220315 TGACAATATA
*
23220325 TTTCTTTTCTT
1 TTTCTTTT-TC
*
23220336 TTTTTTTTTC
1 TTTCTTTTTC
*
23220346 TTTTCTTCTTC
1 -TTTCTTTTTC
23220357 TTTCTTTTTC
1 TTTCTTTTTC
23220367 TTTCTTTT
1 TTTCTTTT
23220375 GTGATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 18 0.55
11 15 0.45
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:23220372 original size:20 final size:20
Alignment explanation
Indices: 23220331--23220369 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
23220321 TATATTTCTT
*
23220331 TTCTTTTTTTTTTTCTTTTC
1 TTCTTTTTCTTTTTCTTTTC
23220351 TTCTTCTTTCTTTTTCTTT
1 TTCTT-TTTCTTTTTCTTT
23220370 CTTTTGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTCTTTTTCTTTTTCTTTTC
Found at i:23221152 original size:21 final size:21
Alignment explanation
Indices: 23221126--23221166 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
23221116 CTCGCCTTCT
23221126 TCTTTGTGC-TTCTTCTTCTTA
1 TCTTTGTGCTTTC-TCTTCTTA
23221147 TCTTTGTGCTTTCTCTTCTT
1 TCTTTGTGCTTTCTCTTCTT
23221167 GTCCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.02, C:0.24, G:0.10, T:0.63
Consensus pattern (21 bp):
TCTTTGTGCTTTCTCTTCTTA
Found at i:23221166 original size:16 final size:19
Alignment explanation
Indices: 23221121--23221166 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
23221111 GGGCGCTCGC
23221121 CTTCTTCTTTGTGCTTCTT
1 CTTCTTCTTTGTGCTTCTT
23221140 CTTCTTATCTTTGTGCTT-TCT
1 CTTC-T-TCTTTGTGCTTCT-T
23221161 CTTCTT
1 CTTCTT
23221167 GTCCTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 5 0.21
20 3 0.12
21 16 0.67
ACGTcount: A:0.02, C:0.26, G:0.09, T:0.63
Consensus pattern (19 bp):
CTTCTTCTTTGTGCTTCTT
Found at i:23223881 original size:14 final size:15
Alignment explanation
Indices: 23223846--23223881 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
23223836 CTACTGATTG
23223846 TTGT-TATAACTCCC
1 TTGTCTATAACTCCC
23223860 TTGTCTATAACTCCC
1 TTGTCTATAACTCCC
23223875 TTG-CTAT
1 TTGTCTAT
23223882 GAGGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.19, C:0.28, G:0.08, T:0.44
Consensus pattern (15 bp):
TTGTCTATAACTCCC
Found at i:23238512 original size:15 final size:16
Alignment explanation
Indices: 23238481--23238514 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
23238471 TCCACAGATA
23238481 TTAAGTTTTCATATAT
1 TTAAGTTTTCATATAT
*
23238497 TTAAGTTTTTAT-TAT
1 TTAAGTTTTCATATAT
23238512 TTA
1 TTA
23238515 CTGTAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAAGTTTTCATATAT
Found at i:23239387 original size:15 final size:15
Alignment explanation
Indices: 23239369--23239398 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23239359 CCAGAAACAG
23239369 AAAGAAAAAGAGAGA
1 AAAGAAAAAGAGAGA
*
23239384 AAAGAAAGAGAGAGA
1 AAAGAAAAAGAGAGA
23239399 GAGAGAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAGAGA
Found at i:23239389 original size:19 final size:20
Alignment explanation
Indices: 23239361--23239402 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
23239351 CAGAAAACCC
23239361 AGAAACAGAAAGAAAAAGAG
1 AGAAACAGAAAGAAAAAGAG
* *
23239381 AGAAA-AGAAAGAGAGAGAG
1 AGAAACAGAAAGAAAAAGAG
23239400 AGA
1 AGA
23239403 GAATCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAACAGAAAGAAAAAGAG
Found at i:23242772 original size:23 final size:23
Alignment explanation
Indices: 23242729--23242772 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
23242719 TTTTAAGTAA
* * *
23242729 CAATAAAATGAGTTTATTTAGAT
1 CAATAAAATAAGTTGACTTAGAT
23242752 CAATAAAATAAGTTGACTTAG
1 CAATAAAATAAGTTGACTTAG
23242773 CTGACATACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (23 bp):
CAATAAAATAAGTTGACTTAGAT
Found at i:23247566 original size:24 final size:25
Alignment explanation
Indices: 23247539--23247616 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 25
23247529 AGTTTTATAT
23247539 TATA-TTA-TTTTTAATAATTTAAAA
1 TATATTTATTTTTTAAT-ATTTAAAA
*
23247563 TATATTTATTTTTGTAATATATAATGAA
1 TATATTTATTTTT-TAATATTTAA--AA
23247591 TATATTTATTTTTTAATTATTTAAAA
1 TATATTTATTTTTTAA-TATTTAAAA
23247617 CTTGATTTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
24 4 0.09
25 3 0.07
26 11 0.24
27 7 0.15
28 21 0.46
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TATATTTATTTTTTAATATTTAAAA
Found at i:23250246 original size:12 final size:12
Alignment explanation
Indices: 23250229--23250254 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23250219 AAGTTAGTAT
23250229 TGTTTTTATCTA
1 TGTTTTTATCTA
23250241 TGTTTTTATCTA
1 TGTTTTTATCTA
23250253 TG
1 TG
23250255 CTTTGCGTTG
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:0.15, C:0.08, G:0.12, T:0.65
Consensus pattern (12 bp):
TGTTTTTATCTA
Found at i:23255581 original size:30 final size:29
Alignment explanation
Indices: 23255547--23255660 Score: 97
Period size: 30 Copynumber: 3.9 Consensus size: 29
23255537 TTCAAGGAAC
*
23255547 TTGGGGTCAAAATTGAAATTTTTGGAAAAT
1 TTGGGGTCAAAA-TGAAACTTTTGGAAAAT
* * * *
23255577 TTGGGATTAAAAATCAAACTTTTAGAAAAT
1 TTGGG-GTCAAAATGAAACTTTTGGAAAAT
* **
23255607 TTGAGGTCGAAAATGCGACTTTTGG-AAAT
1 TTGGGGTC-AAAATGAAACTTTTGGAAAAT
*
23255636 TTGGGG-CAAAATGATAATTTTTGGA
1 TTGGGGTCAAAATGA-AACTTTTGGA
23255661 TGTTCGAGGG
Statistics
Matches: 64, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
27 6 0.09
28 8 0.12
29 10 0.16
30 35 0.55
31 5 0.08
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (29 bp):
TTGGGGTCAAAATGAAACTTTTGGAAAAT
Found at i:23255682 original size:29 final size:30
Alignment explanation
Indices: 23255638--23255780 Score: 92
Period size: 28 Copynumber: 5.0 Consensus size: 30
23255628 TTGGAAATTT
*
23255638 GGGG-CAAAATGATAATTTTTGGAT-GTTC
1 GGGGTCAAAATGGTAATTTTTGGATAGTTC
*
23255666 GAGGGT-AAAATGGTAA-TTTTGGATGAGTTT
1 G-GGGTCAAAATGGTAATTTTTGGAT-AGTTC
* *
23255696 GGGGTCAAAAT-GTAATTTTTATGA-AGTTTA
1 GGGGTCAAAATGGTAATTTTT-GGATAG-TTC
* *
23255726 GGGGTTAAAAT-GTAA-TTTTGTGA-AGTTA
1 GGGGTCAAAATGGTAATTTTTG-GATAGTTC
* *
23255754 GGGGTTAAAAT-GTAA-TTTTGGAAAGTT
1 GGGGTCAAAATGGTAATTTTTGGATAGTT
23255781 TATGGGTATA
Statistics
Matches: 99, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
27 2 0.02
28 36 0.36
29 30 0.30
30 29 0.29
31 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATGGTAATTTTTGGATAGTTC
Found at i:23255713 original size:58 final size:58
Alignment explanation
Indices: 23255626--23255802 Score: 156
Period size: 58 Copynumber: 3.1 Consensus size: 58
23255616 AAAATGCGAC
* *
23255626 TTTTG-GAAATTTGGGG-CAAAATGATAATTTTT-GGATGTTCGA-GGG-TAAAATGGTAA
1 TTTTGTGAAGTTTGGGGTCAAAATG-TAATTTTTAGGAAGTT-GAGGGGTTAAAAT-GTAA
* *
23255682 TTTTG-GATGAGTTTGGGGTCAAAATGTAATTTTTATGAAGTTTAGGGGTTAAAATGTAA
1 TTTTGTGA--AGTTTGGGGTCAAAATGTAATTTTTAGGAAGTTGAGGGGTTAAAATGTAA
* * * *
23255741 TTTTGTGAAGTTAGGGGTTAAAATGTAA-TTTT-GGAAAGTTTATGGG-TATAAATGTAA
1 TTTTGTGAAGTTTGGGGTCAAAATGTAATTTTTAGG-AAGTTGAGGGGTTA-AAATGTAA
23255798 TTTTG
1 TTTTG
23255803 GAAAAGTTTA
Statistics
Matches: 104, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
56 10 0.10
57 27 0.26
58 35 0.34
59 24 0.23
60 8 0.08
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (58 bp):
TTTTGTGAAGTTTGGGGTCAAAATGTAATTTTTAGGAAGTTGAGGGGTTAAAATGTAA
Found at i:23255763 original size:28 final size:28
Alignment explanation
Indices: 23255671--23255821 Score: 155
Period size: 29 Copynumber: 5.1 Consensus size: 28
23255661 TGTTCGAGGG
23255671 TAAAATGGTAATTTTGGATGAGTTT-GGGGT
1 TAAAAT-GTAATTTTGGA--AGTTTAGGGGT
* *
23255701 CAAAATGTAATTTTTATGAAGTTTAGGGGT
1 TAAAATGTAA-TTTT-GGAAGTTTAGGGGT
23255731 TAAAATGTAATTTTGTGAAG-TTAGGGGT
1 TAAAATGTAATTTTG-GAAGTTTAGGGGT
*
23255759 TAAAATGTAATTTTGGAAAGTTTATGGG-
1 TAAAATGTAATTTTGG-AAGTTTAGGGGT
*
23255787 TATAAATGTAATTTTGGAAAAGTTTAAGGGT
1 TA-AAATGTAATTTTGG--AAGTTTAGGGGT
23255818 TAAA
1 TAAA
23255822 CATAATTTTA
Statistics
Matches: 106, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
27 1 0.01
28 28 0.26
29 37 0.35
30 36 0.34
31 4 0.04
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.39
Consensus pattern (28 bp):
TAAAATGTAATTTTGGAAGTTTAGGGGT
Found at i:23255797 original size:29 final size:28
Alignment explanation
Indices: 23255668--23255842 Score: 142
Period size: 29 Copynumber: 6.0 Consensus size: 28
23255658 GGATGTTCGA
* *
23255668 GGGTAAAATGGTAATTTTGGATGAGTTT-G
1 GGGTTAAAT-GTAATTTTGGA-AAGTTTAG
* *
23255697 GGGTCAAAATGTAATTTT-TATGAAGTTTAG
1 GGGT-TAAATGTAATTTTGGA--AAGTTTAG
23255727 GGGTTAAAATGTAATTTTGTG-AAG-TTAG
1 GGGTT-AAATGTAATTTTG-GAAAGTTTAG
*
23255755 GGGTTAAAATGTAATTTTGGAAAGTTTAT
1 GGGTT-AAATGTAATTTTGGAAAGTTTAG
*
23255784 GGGTATAAATGTAATTTTGGAAAAGTTTAA
1 GGGT-TAAATGTAATTTTGG-AAAGTTTAG
** *
23255814 GGGTTAAACATAATTTTAGAAAAGTTTAG
1 GGGTTAAATGTAATTTT-GGAAAGTTTAG
23255843 AGTAAGTTTA
Statistics
Matches: 124, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.01
28 27 0.22
29 60 0.48
30 36 0.29
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38
Consensus pattern (28 bp):
GGGTTAAATGTAATTTTGGAAAGTTTAG
Found at i:23255839 original size:87 final size:87
Alignment explanation
Indices: 23255671--23255839 Score: 186
Period size: 87 Copynumber: 1.9 Consensus size: 87
23255661 TGTTCGAGGG
* * * *
23255671 TAAAATGGTAATTTTGGATGAGTTTGGGGTCAAAATGTAATTTTTATGAAGTTTAGGGGTTAAAA
1 TAAAATGGTAATTTTGGATAAGTTTGGGGTCAAAATGTAATTTTGATAAAGTTTAAGGGTTAAAA
**
23255736 TGTAATTTTGTGAAGTTAGGGGT
66 -GTAATTTTGAAAAGTTAGGGGT
*
23255759 TAAAAT-GTAATTTTGGA-AAGTTTATGGGT-ATAAATGTAATTTTGGA-AAAGTTTAAGGGTTA
1 TAAAATGGTAATTTTGGATAAGTTT-GGGGTCA-AAATGTAATTTT-GATAAAGTTTAAGGGTTA
23255820 AACA-TAATTTTAGAAAAGTT
63 AA-AGTAATTTT-GAAAAGTT
23255840 TAGAGTAAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
86 13 0.19
87 48 0.70
88 8 0.12
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (87 bp):
TAAAATGGTAATTTTGGATAAGTTTGGGGTCAAAATGTAATTTTGATAAAGTTTAAGGGTTAAAA
GTAATTTTGAAAAGTTAGGGGT
Found at i:23257429 original size:6 final size:6
Alignment explanation
Indices: 23257418--23257480 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
23257408 GACTTTATTT
* *
23257418 ATTTAA ATTTAA A-TTAA A-TTAA ATTTAA A-ATAA ATTTAA ACTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
23257463 A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
23257481 ATGGGGTTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 18 0.37
6 31 0.63
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:23257436 original size:11 final size:12
Alignment explanation
Indices: 23257418--23257480 Score: 71
Period size: 11 Copynumber: 5.6 Consensus size: 12
23257408 GACTTTATTT
23257418 ATTTAAATTTAA
1 ATTTAAATTTAA
23257430 A-TTAAA-TTAA
1 ATTTAAATTTAA
*
23257440 ATTTAAA-ATAA
1 ATTTAAATTTAA
*
23257451 ATTTAAACTTAA
1 ATTTAAATTTAA
*
23257463 A-ATAAATTTAA
1 ATTTAAATTTAA
23257474 ATTTAAA
1 ATTTAAA
23257481 ATGGGGTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
10 5 0.12
11 29 0.67
12 9 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:23257456 original size:17 final size:17
Alignment explanation
Indices: 23257418--23257482 Score: 105
Period size: 17 Copynumber: 3.9 Consensus size: 17
23257408 GACTTTATTT
*
23257418 ATTTAAATTTAAATTAA
1 ATTTAAATTTAAAATAA
23257435 A-TTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
23257451 ATTTAAACTTAAAATAA
1 ATTTAAATTTAAAATAA
23257468 ATTTAAATTTAAAAT
1 ATTTAAATTTAAAAT
23257483 GGGGTTCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
16 15 0.34
17 29 0.66
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:23258113 original size:78 final size:77
Alignment explanation
Indices: 23257975--23258448 Score: 479
Period size: 78 Copynumber: 6.1 Consensus size: 77
23257965 AAGAGATTGG
* * * * * * *
23257975 ATGGTTGCAATCTACCCCTGGCGCAGGGTAAGAGATTGGTTGACGGTGATCTGTCCCAGGCTTTG
1 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGGCTTGG
23258040 GGTAAAAGATCGA
65 GGTAAAAGATCGA
** * * * * *
23258053 ATGGCTGCAATCTGCCCCAAACTCAGGGTAAGAGATTGGCTGATGGTGATTTGCCTCAGGCTCGA
1 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCC-CAGGCTTGG
*
23258118 GGTAAAAGGTCGA
65 GGTAAAAGATCGA
* * * * * * *
23258131 ATGGATGCAATCTGCCCTAGGCTCGAGATAAAAGATTGGTTGATGGTAATCTGCCCCAGGCTCGG
1 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGGCTTGG
23258196 GGTAAAAGATC-A
65 GGTAAAAGATCGA
* *
23258208 GATGGCTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTAGTTGATGGTGATCTGACCCAGGCTTG
1 -ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGGCTTG
*
23258273 GGGTAAAAGAT-TA
64 GGGTAAAAGATCGA
* *
23258286 GATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGG-TTC
1 -ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGGCTT-
*** * *
23258350 AACGTAAAAGATTGG
63 GGGGTAAAAGATCGA
* * ** * *
23258365 ATGGCTGCAATCTGTCCCAAGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAGGCTCGA
1 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCC-AGGCTTGG
*
23258430 GATAAAAGATC-A
65 GGTAAAAGATCGA
23258442 GATGGCT
1 -ATGGCT
23258449 TTAATCCGCC
Statistics
Matches: 329, Mismatches: 58, Indels: 18
0.81 0.14 0.04
Matches are distributed among these distances:
77 8 0.02
78 318 0.97
79 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCAGGCTTGGG
GTAAAAGATCGA
Found at i:23258261 original size:39 final size:38
Alignment explanation
Indices: 23258000--23258439 Score: 202
Period size: 39 Copynumber: 11.3 Consensus size: 38
23257990 CCCTGGCGCA
* * * **
23258000 GGGTAAGAGATTGGTTGACGGTGATCTGTCCCAGGCTTT
1 GGGTAAAAGATTAGTTGATGGTGATCTG-CCCAGGCTCG
* * ** *
23258039 GGGTAAAAGA-TCG--AATGGCTGCAATCTGCCCCAAACTCA
1 GGGTAAAAGATTAGTTGATGG-TG--ATCTG-CCCAGGCTCG
* * * *
23258078 GGGTAAGAGATTGGCTGATGGTGATTTGCCTCAGGCTCG
1 GGGTAAAAGATTAGTTGATGGTGATCTGCC-CAGGCTCG
* * * * * **
23258117 AGGTAAAAGGTCGAATGGAT-GCAATCTGCCCTAGGCTCG
1 GGGTAAAAGAT-TAGTTGATGGTGATCTGCCC-AGGCTCG
* * * *
23258156 AGATAAAAGATTGGTTGATGGTAATCTGCCCCAGGCTCG
1 GGGTAAAAGATTAGTTGATGGTGATCTG-CCCAGGCTCG
*
23258195 GGGTAAAAGATCA---GATGGCTGCAATCTGCCTCAGGCTCG
1 GGGTAAAAGATTAGTTGATGG-TG--ATCTGCC-CAGGCTCG
* *
23258234 GGGTAAGAGATTAGTTGATGGTGATCTGACCCAGGCTTG
1 GGGTAAAAGATTAGTTGATGGTGATCTG-CCCAGGCTCG
* ** *
23258273 GGGTAAAAGATTAGATGACT-GCAATCTACCCCAGGCTCG
1 GGGTAAAAGATTAGTTGA-TGGTGATCT-GCCCAGGCTCG
* * * *
23258312 GGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGTTCA
1 GGGTAAAAGATTAGTTGATGGTGATCTG-CCCAGGCTCG
** *
23258351 ACGTAAAAGATT-G--GATGGCTGCAATCTGTCCCAAGCTCG
1 GGGTAAAAGATTAGTTGATGG-TG--ATCTG-CCCAGGCTCG
* *
23258390 GGGTAAGAGATT-GACTGATGGTGATCTGCCCTAGGCTCG
1 GGGTAAAAGATTAG-TTGATGGTGATCTGCCC-AGGCTCG
* *
23258429 AGATAAAAGAT
1 GGGTAAAAGAT
23258440 CAGATGGCTT
Statistics
Matches: 301, Mismatches: 70, Indels: 60
0.70 0.16 0.14
Matches are distributed among these distances:
36 13 0.04
37 5 0.02
38 16 0.05
39 236 0.78
40 11 0.04
41 6 0.02
42 14 0.05
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (38 bp):
GGGTAAAAGATTAGTTGATGGTGATCTGCCCAGGCTCG
Found at i:23270597 original size:30 final size:29
Alignment explanation
Indices: 23270485--23270789 Score: 153
Period size: 29 Copynumber: 10.3 Consensus size: 29
23270475 GAATGGGCAG
* * *
23270485 TTTTGGA-AAATTTGAGGTCGAAAATGTGAC
1 TTTTGGATAAGTTTGGGGTC-AAAATGT-AA
* *
23270515 TTTTGGA-AATTTTGAGG-CAAAATGGTAA
1 TTTTGGATAAGTTTGGGGTCAAAAT-GTAA
* *
23270543 TTTTTGGAT--GTTCGGGGGCAAAATGGTAA
1 -TTTTGGATAAGTTTGGGGTCAAAAT-GTAA
*
23270572 TTTTGGATGAGTTTGGGGTCAAAATGTAA
1 TTTTGGATAAGTTTGGGGTCAAAATGTAA
* * * *
23270601 TCTTGGGA-AAGTTTGGGAGTTAAAAAAGCAA
1 T-TTTGGATAAGTTTGGG-G-TCAAAATGTAA
* *
23270632 TTTTGGAAAAGTTTGGGGTTAAAATGTAA
1 TTTTGGATAAGTTTGGGGTCAAAATGTAA
* * * *
23270661 TTTT-TACGAAGCTTGAGGGTCAAAATGTGA
1 TTTTGGA-TAAGTTTG-GGGTCAAAATGTAA
*** *
23270691 TTTTGGA-AAGTTTAACAGTTAAAATGTAA
1 TTTTGGATAAGTTT-GGGGTCAAAATGTAA
*** *
23270720 TTTTGGA-AAGTTTAACAGTTAAAATGTAA
1 TTTTGGATAAGTTT-GGGGTCAAAATGTAA
* *
23270749 TTTTGGAAAAGTTTAGGGAGTAAAAATGTAAA
1 TTTTGGATAAGTTT-GGG-GTCAAAATGT-AA
23270781 TTTT-GATAA
1 TTTTGGATAA
23270790 ATTTAGGGAC
Statistics
Matches: 225, Mismatches: 33, Indels: 33
0.77 0.11 0.11
Matches are distributed among these distances:
28 20 0.09
29 103 0.46
30 64 0.28
31 32 0.14
32 6 0.03
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
TTTTGGATAAGTTTGGGGTCAAAATGTAA
Found at i:23272393 original size:17 final size:17
Alignment explanation
Indices: 23272373--23272407 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
23272363 GGACTTTATT
23272373 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
*
23272390 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
23272407 T
1 T
23272408 TGGGTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:23275020 original size:11 final size:11
Alignment explanation
Indices: 23275004--23275053 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
23274994 CGATCATGTG
23275004 ATTATATTTGA
1 ATTATATTTGA
* *
23275015 ATTATATTAGG
1 ATTATATTTGA
23275026 ATTATATTTGA
1 ATTATATTTGA
* * *
23275037 ACTATGTTTGG
1 ATTATATTTGA
23275048 ATTATA
1 ATTATA
23275054 AATTTATTAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (11 bp):
ATTATATTTGA
Found at i:23275031 original size:22 final size:22
Alignment explanation
Indices: 23275003--23275053 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
23274993 ACGATCATGT
*
23275003 GATTATATTTGAATTATATTAG
1 GATTATATTTGAACTATATTAG
* *
23275025 GATTATATTTGAACTATGTTTG
1 GATTATATTTGAACTATATTAG
23275047 GATTATA
1 GATTATA
23275054 AATTTATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
GATTATATTTGAACTATATTAG
Found at i:23278241 original size:9 final size:9
Alignment explanation
Indices: 23278227--23278259 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
23278217 CTTCATGTTT
23278227 TTTTTTTAA
1 TTTTTTTAA
23278236 -TTTTTTAA
1 TTTTTTTAA
*
23278244 TTTTTTAAA
1 TTTTTTTAA
23278253 TTTTTTT
1 TTTTTTT
23278260 TATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:23278247 original size:7 final size:8
Alignment explanation
Indices: 23278228--23278258 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
23278218 TTCATGTTTT
23278228 TTTTTTAA
1 TTTTTTAA
23278236 TTTTTTAA
1 TTTTTTAA
23278244 TTTTTTAAA
1 TTTTTT-AA
23278253 TTTTTT
1 TTTTTT
23278259 TTATAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTAA
Found at i:23280855 original size:9 final size:9
Alignment explanation
Indices: 23280843--23280880 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
23280833 TTTATTCGGT
23280843 TTATTCGAA
1 TTATTCGAA
23280852 TTATTCGAA
1 TTATTCGAA
*
23280861 TAATTCGAA
1 TTATTCGAA
*
23280870 TAATTCGAA
1 TTATTCGAA
23280879 TT
1 TT
23280881 CGAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (9 bp):
TTATTCGAA
Found at i:23288501 original size:26 final size:26
Alignment explanation
Indices: 23288472--23288554 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
23288462 GCTGTGTCGA
* *
23288472 CGAGCCCTCATTGCAAGTTATGTTTG
1 CGAGCCCTCATTGCAAGCTATGTCTG
* * ***
23288498 CGAGCCTTCCTTATGAGCTATGTCTG
1 CGAGCCCTCATTGCAAGCTATGTCTG
* * *
23288524 CGAGCCCTCATTGCGAGCTATGCCTA
1 CGAGCCCTCATTGCAAGCTATGTCTG
23288550 CGAGC
1 CGAGC
23288555 TCTCCTTGTG
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (26 bp):
CGAGCCCTCATTGCAAGCTATGTCTG
Found at i:23288554 original size:52 final size:52
Alignment explanation
Indices: 23288447--23288574 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 52
23288437 ATCCCCTTAT
* * * * ** *
23288447 GAGCTCTCCTTGTAAGCTGTGTC-GACGAGCCCTCATTGCAAGTTATGTTTGC
1 GAGCTCTCCTTATGAGCTATGTCTG-CGAGCCCTCATTGCAAGCTATGCCTAC
*
23288499 GAGC-CTTCCTTATGAGCTATGTCTGCGAGCCCTCATTGCGAGCTATGCCTAC
1 GAGCTC-TCCTTATGAGCTATGTCTGCGAGCCCTCATTGCAAGCTATGCCTAC
* *
23288551 GAGCTCTCCTTGTGAGCTGTGTCT
1 GAGCTCTCCTTATGAGCTATGTCT
23288575 TTAAGTGGGG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
51 1 0.02
52 60 0.95
53 2 0.03
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.32
Consensus pattern (52 bp):
GAGCTCTCCTTATGAGCTATGTCTGCGAGCCCTCATTGCAAGCTATGCCTAC
Found at i:23288567 original size:26 final size:26
Alignment explanation
Indices: 23288498--23288568 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
23288488 GTTATGTTTG
* * * *
23288498 CGAGCCTTCCTTATGAGCTATGTCTG
1 CGAGCCCTCCTTGTGAGCTATGCCTA
* *
23288524 CGAGCCCTCATTGCGAGCTATGCCTA
1 CGAGCCCTCCTTGTGAGCTATGCCTA
*
23288550 CGAGCTCTCCTTGTGAGCT
1 CGAGCCCTCCTTGTGAGCT
23288569 GTGTCTTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.15, C:0.31, G:0.24, T:0.30
Consensus pattern (26 bp):
CGAGCCCTCCTTGTGAGCTATGCCTA
Found at i:23289275 original size:14 final size:15
Alignment explanation
Indices: 23289248--23289277 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
23289238 CCTACTTCCT
23289248 TAAAATACATTAAAA
1 TAAAATACATTAAAA
23289263 TAAAATA-ATTAAAA
1 TAAAATACATTAAAA
23289277 T
1 T
23289278 TTCACAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAATACATTAAAA
Found at i:23289539 original size:13 final size:14
Alignment explanation
Indices: 23289520--23289555 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
23289510 AAGACTTCTA
23289520 AAGAGAAAAATT-G
1 AAGAGAAAAATTGG
*
23289533 CAGAGAAAAATTGG
1 AAGAGAAAAATTGG
23289547 AAGAGAAAA
1 AAGAGAAAA
23289556 TAAGATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.61, C:0.03, G:0.25, T:0.11
Consensus pattern (14 bp):
AAGAGAAAAATTGG
Found at i:23291870 original size:22 final size:22
Alignment explanation
Indices: 23291845--23291888 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
23291835 TATTTTGAAG
*
23291845 ATAGGCAACAATATTGATTGCT
1 ATAGACAACAATATTGATTGCT
*
23291867 ATAGACAACAATGTTGATTGCT
1 ATAGACAACAATATTGATTGCT
23291889 TCAGCCTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
ATAGACAACAATATTGATTGCT
Found at i:23293967 original size:13 final size:14
Alignment explanation
Indices: 23293948--23293983 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
23293938 AAGACTTTTA
23293948 AAGAGAAAAATT-G
1 AAGAGAAAAATTGG
*
23293961 CAGAGAAAAATTGG
1 AAGAGAAAAATTGG
23293975 AAGAGAAAA
1 AAGAGAAAA
23293984 TAAGATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.61, C:0.03, G:0.25, T:0.11
Consensus pattern (14 bp):
AAGAGAAAAATTGG
Found at i:23297198 original size:16 final size:17
Alignment explanation
Indices: 23297177--23297209 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23297167 AACCCTTGTA
23297177 ATCATC-CATAATTCAT
1 ATCATCACATAATTCAT
*
23297193 ATCATCACATATTTCAT
1 ATCATCACATAATTCAT
23297210 TTACTTATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
ATCATCACATAATTCAT
Found at i:23297541 original size:19 final size:19
Alignment explanation
Indices: 23297519--23297556 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23297509 TATTGTCATC
23297519 CACCGTAATCAAATTTGTT
1 CACCGTAATCAAATTTGTT
23297538 CACCGTAATCAAATTTGTT
1 CACCGTAATCAAATTTGTT
23297557 ATTAACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
CACCGTAATCAAATTTGTT
Found at i:23298292 original size:26 final size:26
Alignment explanation
Indices: 23298262--23298311 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
23298252 TGGGATGAAA
23298262 GAGGAGTAAAAGTTTTGGAGGAAAGT
1 GAGGAGTAAAAGTTTTGGAGGAAAGT
*
23298288 GAGGAGTAAAAGTTTTGGTGGAAA
1 GAGGAGTAAAAGTTTTGGAGGAAA
23298312 AGTAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (26 bp):
GAGGAGTAAAAGTTTTGGAGGAAAGT
Found at i:23311894 original size:30 final size:29
Alignment explanation
Indices: 23311858--23311914 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
23311848 TTTGGATCAC
* *
23311858 AATTAAAGTTTCATGTGTATAATTACACCA
1 AATTAAAG-TTCATGTATACAATTACACCA
23311888 AATTAAAGTTCATGTATACAATTACAC
1 AATTAAAGTTCATGTATACAATTACAC
23311915 ATTAAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (29 bp):
AATTAAAGTTCATGTATACAATTACACCA
Found at i:23311910 original size:29 final size:30
Alignment explanation
Indices: 23311826--23311914 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 30
23311816 GACTAAATCA
* * * ** *
23311826 AAATTAAAATTTCAAGTATACATTTGGATC
1 AAATTAAAGTTTCATGTATACAATTACACC
* *
23311856 ACAATTAAAGTTTCATGTGTATAATTACACC
1 A-AATTAAAGTTTCATGTATACAATTACACC
23311887 AAATTAAAG-TTCATGTATACAATTACAC
1 AAATTAAAGTTTCATGTATACAATTACAC
23311915 ATTAAATCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 17 0.35
30 9 0.19
31 22 0.46
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTACACC
Found at i:23311939 original size:29 final size:27
Alignment explanation
Indices: 23311872--23311939 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 27
23311862 AAAGTTTCAT
*
23311872 GTGTATAATTACACCAAATTAAAGTTC
1 GTGTATAATTACACCAAATCAAAGTTC
* *
23311899 ATGTATACAATTACACATTAAATCAAAGTTC
1 GTGTAT--AATTACAC--CAAATCAAAGTTC
23311930 GTGTATAATT
1 GTGTATAATT
23311940 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.36
31 16 0.48
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (27 bp):
GTGTATAATTACACCAAATCAAAGTTC
Found at i:23314630 original size:25 final size:26
Alignment explanation
Indices: 23314599--23314670 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
23314589 TATTCTAAAT
23314599 TCTGGCTCGTAAGAGCAATATTTCAT-
1 TCTGGCTCGTAAGAGCAATATTTC-TG
* *
23314625 T-TGGCTCGTAAAAGCGATA-TTCTG
1 TCTGGCTCGTAAGAGCAATATTTCTG
*
23314649 TCTGGCTCGTAAGAGCACTATT
1 TCTGGCTCGTAAGAGCAATATT
23314671 CTGCTTGTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 31 0.82
26 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (26 bp):
TCTGGCTCGTAAGAGCAATATTTCTG
Found at i:23318049 original size:24 final size:24
Alignment explanation
Indices: 23318017--23318066 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
23318007 GAACGAGTTA
23318017 GGTTGTGTACTAATAATATAAGCT
1 GGTTGTGTACTAATAATATAAGCT
23318041 GGTTGTGTACTAATAATATAAGCT
1 GGTTGTGTACTAATAATATAAGCT
23318065 GG
1 GG
23318067 GAAAGTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (24 bp):
GGTTGTGTACTAATAATATAAGCT
Found at i:23320623 original size:25 final size:25
Alignment explanation
Indices: 23320533--23320648 Score: 126
Period size: 25 Copynumber: 4.6 Consensus size: 25
23320523 TGTTATAAAT
* * *
23320533 TCTGGCTCGTAAGAGTAACATTCTA
1 TCTGGCTCGTAAGAGCAATATTCTG
* *
23320558 TTTGGCTCGTAAGAGAAATATTCTG
1 TCTGGCTCGTAAGAGCAATATTCTG
* * *
23320583 TCTGGCTCATAAGAGCGATATTATG
1 TCTGGCTCGTAAGAGCAATATTCTG
*
23320608 TCTGGCTCGTAAGAGC-GTATTCTG
1 TCTGGCTCGTAAGAGCAATATTCTG
*
23320632 TCTGGACTCGAAAGAGC
1 TCTGG-CTCGTAAGAGC
23320649 TAATTTTGGA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 11 0.14
25 66 0.86
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCAATATTCTG
Found at i:23321529 original size:21 final size:21
Alignment explanation
Indices: 23321500--23321552 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
23321490 TTTTAGTATT
23321500 GGTAAAAGTATGAC-TTGTTTC
1 GGTAAAAGTAT-ACATTGTTTC
*
23321521 GGTAGAAGT-TACAATTGTTTC
1 GGTAAAAGTATAC-ATTGTTTC
23321542 GGTAAAAGTAT
1 GGTAAAAGTAT
23321553 TTCAAGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
21 23 0.85
22 1 0.04
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (21 bp):
GGTAAAAGTATACATTGTTTC
Found at i:23324398 original size:28 final size:27
Alignment explanation
Indices: 23324347--23324400 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
23324337 TAAACAACAT
23324347 CAAAACAAATAAATGCAAATTAAATACC
1 CAAAACAAATAAAT-CAAATTAAATACC
23324375 CAAAACAAATAAAAT-AAATATAAATA
1 CAAAACAAAT-AAATCAAAT-TAAATA
23324401 AATATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.17
28 16 0.67
29 4 0.17
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.19
Consensus pattern (27 bp):
CAAAACAAATAAATCAAATTAAATACC
Found at i:23324401 original size:10 final size:10
Alignment explanation
Indices: 23324381--23324412 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
23324371 TACCCAAAAC
23324381 AAATA-AAAT
1 AAATATAAAT
23324390 AAATATAAAT
1 AAATATAAAT
23324400 AAATATAAA-
1 AAATATAAAT
23324409 AAAT
1 AAAT
23324413 TTAAGAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAATATAAAT
Found at i:23332956 original size:2 final size:2
Alignment explanation
Indices: 23332949--23332973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23332939 GTTTTGCAGC
23332949 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
23332974 AGGAAGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23338659 original size:29 final size:29
Alignment explanation
Indices: 23338627--23338777 Score: 135
Period size: 29 Copynumber: 5.2 Consensus size: 29
23338617 ATTTAAGGGC
*
23338627 AAAATGGTAGTTTTTGGATGTTCGGGGGT
1 AAAATGGTAATTTTTGGATGTTCGGGGGT
* *
23338656 AAAATGGTAATTTCTGAATGTTCGGGGGT
1 AAAATGGTAATTTTTGGATGTTCGGGGGT
* * * *
23338685 AAAATGATAATCTTTAGATGTTCGGGGGA
1 AAAATGGTAATTTTTGGATGTTCGGGGGT
* *** *
23338714 AAAAT-GTAA-TTTTGGAAAAGTTTAAGGTT
1 AAAATGGTAATTTTTGG--ATGTTCGGGGGT
* * *
23338743 AAAATGATAATTTTTGGATGTTCGAGGAT
1 AAAATGGTAATTTTTGGATGTTCGGGGGT
23338772 AAAATG
1 AAAATG
23338778 CAATTTTGGA
Statistics
Matches: 95, Mismatches: 23, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
27 4 0.04
28 3 0.03
29 79 0.83
30 3 0.03
31 6 0.06
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCGGGGGT
Found at i:23338804 original size:29 final size:30
Alignment explanation
Indices: 23338713--23339071 Score: 281
Period size: 30 Copynumber: 12.1 Consensus size: 30
23338703 TGTTCGGGGG
*
23338713 AAAAATGTAATTTTGGAAAAGTTT-AAGGT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
* * * *
23338742 TAAAATGATAATTTTTGG--ATGTTCGAGGAT
1 AAAAATG-TAA-TTTTGGAAAAGTTTGAGGGT
*
23338772 -AAAATGCAATTTTGGAAAAGTTT-AGGGT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
* * **
23338800 GAAAATGTGATTTTGGAAAAGTTCAAGGG-
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
* * *
23338829 CAAAATGTAATTTT-AAAGAAGTTCGAGGGT
1 AAAAATGTAATTTTGGAA-AAGTTTGAGGGT
* *
23338859 CAATATGTAATTTTTGG-AAAGTTTGAGGGT
1 AAAAATGTAA-TTTTGGAAAAGTTTGAGGGT
* *
23338889 AAAAATGTGATTTTTGG--AAGTTTGAGGGC
1 AAAAATGT-AATTTTGGAAAAGTTTGAGGGT
* *
23338918 AAAAATGTAATTTTTGAGAAGTTTGAGGGT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
* * * *
23338948 AAAAATGTAATTTTTGAGAAGTTTTAGGAT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
** * *
23338978 -AAAATGTAACGTTGGAAAAATTTAAGGGT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
* * * *
23339007 TAAAATATAATTTGGGAAAAGTTTAAGGGT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGGT
* * *
23339037 TAAAATATAATTTTGAAAAAGTTTGAGGGCT
1 AAAAATGTAATTTTGGAAAAGTTTGAGGG-T
23339068 AAAA
1 AAAA
23339072 TATGATTTTT
Statistics
Matches: 270, Mismatches: 44, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
27 6 0.02
28 14 0.05
29 103 0.38
30 131 0.49
31 16 0.06
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
AAAAATGTAATTTTGGAAAAGTTTGAGGGT
Found at i:23338909 original size:59 final size:60
Alignment explanation
Indices: 23338571--23338970 Score: 215
Period size: 58 Copynumber: 6.8 Consensus size: 60
23338561 CTGGGATGAG
* * * **
23338571 AATGTAATTTTTGAGAAATTTGA-GGTCAAAAT-TAAAATTTTTG-GAAATTTAAGGGC-AA
1 AATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGT--AATTTTTGAGAAGTTCGAGGGCAAA
* * * * * * **
23338629 AATGGTAGTTTTTG-GATGTTCGGGGGT-AAAATGGTAATTTCTGA-ATGTTCG-GGGGTAA
1 AAT-GTAATTTTTGAGAAGTTTGAGGGTAAAAAT-GTAATTTTTGAGAAGTTCGAGGGCAAA
* * * * * * * * **
23338687 AATGATAATCTTT-AGATGTTCG-GGGGAAAAATGTAATTTTGGAAAAGTT-TAAGGTTAA
1 AATG-TAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGCAAA
* * * * * * * **
23338745 AATGATAATTTTTG-GATGTTCGAGGAT-AAAATGCAATTTTGGAAAAGTT-TAGGGTGAA
1 AATG-TAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGCAAA
* * * ** * **
23338803 AATGTGATTTTGGAAAAGTTCAAGGG-CAAAATGTAATTTTAAAGAAGTTCGAGGGTC-AA
1 AATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGG-CAAA
* * *
23338862 TATGTAATTTTTG-GAAAGTTTGAGGGTAAAAATGTGATTTTTG-GAAGTTTGAGGGCAAA
1 AATGTAATTTTTGAG-AAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGCAAA
23338921 AATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTT
1 AATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTT
23338971 TTAGGATAAA
Statistics
Matches: 269, Mismatches: 51, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
57 23 0.09
58 135 0.50
59 91 0.34
60 20 0.07
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (60 bp):
AATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGCAAA
Found at i:23338929 original size:89 final size:87
Alignment explanation
Indices: 23338713--23338981 Score: 260
Period size: 89 Copynumber: 3.0 Consensus size: 87
23338703 TGTTCGGGGG
* * ** ** * *
23338713 AAAAATGTAATTTTGGAAAAGTTTAAGGTTAAAATGATAATTTT-TGGATGTTCGAGGAT-AAAA
1 AAAAATGTGATTTTGG-AAAGTTCAAGGGCAAAATG-TAATTTTAAAGAAGTTCGAGGGTAAAAA
*
23338776 TGCAA-TTTTGGAAAAGTTTAGGGT
64 TGTAATTTTTGG-AAAGTTTAGGGT
* * *
23338800 GAAAATGTGATTTTGGAAAAGTTCAAGGGCAAAATGTAATTTTAAAGAAGTTCGAGGGTCAATAT
1 AAAAATGTGATTTTGG-AAAGTTCAAGGGCAAAATGTAATTTTAAAGAAGTTCGAGGGTAAAAAT
23338865 GTAATTTTTGGAAAGTTTGAGGGT
65 GTAATTTTTGGAAAGTTT-AGGGT
** ** *
23338889 AAAAATGTGATTTTTGG-AAGTTTGAGGGCAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAA
1 AAAAATGTGA-TTTTGGAAAGTTCAAGGGC-AAAATGTAATTTTAAAGAAGTTCGAGGGTAAAAA
*
23338953 TGTAATTTTT-GAGAAGTTTTAGGAT
64 TGTAATTTTTGGA-AAG-TTTAGGGT
23338978 AAAA
1 AAAA
23338982 TGTAACGTTG
Statistics
Matches: 154, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
86 7 0.05
87 42 0.27
88 26 0.17
89 70 0.45
90 9 0.06
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (87 bp):
AAAAATGTGATTTTGGAAAGTTCAAGGGCAAAATGTAATTTTAAAGAAGTTCGAGGGTAAAAATG
TAATTTTTGGAAAGTTTAGGGT
Found at i:23339071 original size:30 final size:28
Alignment explanation
Indices: 23338652--23339086 Score: 241
Period size: 29 Copynumber: 14.8 Consensus size: 28
23338642 GGATGTTCGG
* * *
23338652 GGGTAAAATGGTAATTTCTG-AATGTTCGG
1 GGGTAAAAT-GTAATTT-TGAAAAGTTTGA
* * * *
23338681 GGGTAAAATGATAATCTTT-AGATGTTCGG
1 GGGTAAAATG-TAAT-TTTGAAAAGTTTGA
* *
23338710 GGGAAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTAAAATGTAATTTT-GAAAAGTTTGA
* * * *
23338739 GGTTAAAATGATAATTTTTG-GATGTTCGA
1 GGGTAAAATG-TAA-TTTTGAAAAGTTTGA
* *
23338768 GGATAAAATGCAATTTTGGAAAAGTTT-A
1 GGGTAAAATGTAATTTT-GAAAAGTTTGA
* **
23338796 GGGTGAAAATGTGATTTTGGAAAAGTTCAA
1 GGGT-AAAATGTAATTTT-GAAAAGTTTGA
* * *
23338826 GGGCAAAATGTAATTTTAAAGAAGTTCGA
1 GGGTAAAATGTAATTTTGAA-AAGTTTGA
* *
23338855 GGGTCAATATGTAATTTTTGGAAAGTTTGA
1 GGGT-AAAATGTAA-TTTTGAAAAGTTTGA
* *
23338885 GGGTAAAAATGTGATTTTTG-GAAGTTTGA
1 GGGT-AAAATGT-AATTTTGAAAAGTTTGA
* *
23338914 GGGCAAAAATGTAATTTTTGAGAAGTTTGA
1 GGG-TAAAATGTAA-TTTTGAAAAGTTTGA
* *
23338944 GGGTAAAAATGTAATTTTTGAGAAGTTTTA
1 GGGT-AAAATGTAA-TTTTGAAAAGTTTGA
* * * * *
23338974 GGATAAAATGTAACGTTGGAAAAATTTAA
1 GGGTAAAATGTAA-TTTTGAAAAGTTTGA
* * *
23339003 GGGTTAAAATATAATTTGGGAAAAGTTTAA
1 GGG-TAAAATGTAATTT-TGAAAAGTTTGA
*
23339033 GGGTTAAAATATAATTTTGAAAAAGTTTGA
1 GGG-TAAAATGTAATTTTG-AAAAGTTTGA
* *
23339063 GGGCTAAAATATGATTTTTGAAAA
1 GGG-TAAAATGT-AATTTTGAAAA
23339087 ATTCAGGGAC
Statistics
Matches: 329, Mismatches: 54, Indels: 45
0.77 0.13 0.11
Matches are distributed among these distances:
27 7 0.02
28 15 0.05
29 151 0.46
30 140 0.43
31 16 0.05
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTGAAAAGTTTGA
Found at i:23340351 original size:14 final size:14
Alignment explanation
Indices: 23340334--23340365 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
23340324 CAACTTACTG
23340334 GTGGCGGTGCTAAC
1 GTGGCGGTGCTAAC
*
23340348 GTGGCGGTGCTGAC
1 GTGGCGGTGCTAAC
23340362 GTGG
1 GTGG
23340366 TAACTTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.19, G:0.50, T:0.22
Consensus pattern (14 bp):
GTGGCGGTGCTAAC
Found at i:23340540 original size:6 final size:6
Alignment explanation
Indices: 23340531--23340641 Score: 65
Period size: 6 Copynumber: 19.5 Consensus size: 6
23340521 TGGACTTTTA
* * *
23340531 AAATTT AAATTT AAA-TT AAA-AT AAATTT AAATTT AAA-AT AAATTC
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * * *
23340576 AAACTC AAA-AT AAGTTT AAATTT AAA-AT AAATTT AAACTT AAA--T
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
**
23340620 AAATAA AAATTT AAAATTT AAA
1 AAATTT AAATTT -AAATTT AAA
23340642 ATCAGGTTCC
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
4 4 0.05
5 19 0.23
6 52 0.64
7 6 0.07
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (6 bp):
AAATTT
Found at i:23340568 original size:17 final size:17
Alignment explanation
Indices: 23340536--23340636 Score: 125
Period size: 17 Copynumber: 6.1 Consensus size: 17
23340526 TTTTAAAATT
23340536 TAAATTTAAA-TTAAAA
1 TAAATTTAAATTTAAAA
23340552 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
23340569 TAAATTCAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
23340586 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
23340603 TAAATTTAAACTT-AAA
1 TAAATTTAAATTTAAAA
**
23340619 TAAATAAAAATTTAAAA
1 TAAATTTAAATTTAAAA
23340636 T
1 T
23340637 TTAAAATCAG
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
16 23 0.32
17 48 0.68
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:23341157 original size:39 final size:38
Alignment explanation
Indices: 23341098--23341629 Score: 261
Period size: 39 Copynumber: 13.7 Consensus size: 38
23341088 GATGGTTGTA
23341098 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
1 ATCTG-CCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * * * * * *
23341137 ATCTGTCCCAGGCTCAGGGTAAGAGATCGGATGGCT-GTA
1 ATCTG-CCCAAGCTCGGGGTAAAAGATTGGCT-GATGGTG
* * * *
23341176 ATCTGCCTCAGGCTTGGGGTAAGAGATTGGCTGATGATG
1 ATCTGCC-CAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* *
23341215 ATCTGCCCCAGGCTCGGGGTAAAAGA-T--C-GAAGGTTG
1 ATCTG-CCCAAGCTCGGGGTAAAAGATTGGCTGATGG-TG
* * *
23341251 CCATCTGCTCCAAGCTCGGGGTGAGAGATTGGCTGATAGTG
1 --ATCTGC-CCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* *
23341292 ATCTGCCCCAGGCTCGGGGTAAAAGA-T--C-GAATGGCTACA
1 ATCTG-CCCAAGCTCGGGGTAAAAGATTGGCTG-ATGG-T--G
* * * ** * *
23341331 ATCTGCCCTAGGCTCAGGGTAAAAGATCGAATAGCT-GTA
1 ATCTGCCC-AAGCTCGGGGTAAAAGATTGGCT-GATGGTG
* *
23341370 ATCTGTCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTG
1 ATCTG-CCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * * *
23341409 ATATGTCTCAAGCTCGGGGTAAGAGATTGGCTGATAGTG
1 ATCTG-CCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
*
23341448 ATCTGCCTCAAGCTCGGGGTAAAAGATT-G--AATGGCTG
1 ATCTGCC-CAAGCTCGGGGTAAAAGATTGGCTGATGG-TG
* * * * *
23341485 CAATCTGCCCAAGGTTCCGGGTAAGAGATTAGCTTATGGTG
1 --ATCTGCCCAA-GCTCGGGGTAAAAGATTGGCTGATGGTG
* * * * *
23341526 ATCTGCCTAGGCTCGAGGTAAAATA-T--C-GAATGGCTACA
1 ATCTGCCCAAGCTCGGGGTAAAAGATTGGCTG-ATGG-T--G
* * *
23341564 ATCTGCCTCAAGCTCGGGGTAAGAGATTGACTGATAGTG
1 ATCTGCC-CAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* *
23341603 ATTTGCCCCAGGCTCGGGGTAAAAGAT
1 ATCTG-CCCAAGCTCGGGGTAAAAGAT
23341630 CGAATGGCTG
Statistics
Matches: 379, Mismatches: 71, Indels: 86
0.71 0.13 0.16
Matches are distributed among these distances:
35 9 0.02
36 11 0.03
37 5 0.01
38 54 0.14
39 266 0.70
40 12 0.03
41 7 0.02
42 12 0.03
43 2 0.01
44 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (38 bp):
ATCTGCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
Found at i:23341424 original size:117 final size:116
Alignment explanation
Indices: 23341215--23341590 Score: 402
Period size: 117 Copynumber: 3.2 Consensus size: 116
23341205 GCTGATGATG
* * * *
23341215 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAA-GGTTGCCATCTGCTCCAAGCTCGGGGTGAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGGCTGCAATCTGC-CCAAGCTCGGGGTAAGAGA
*
23341279 TTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTACA
65 TTGGCTGATAGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * *
23341331 ATCTGCCCTAGGCTCAGGGTAAAAGATCGAATAGCTGTAATCTGTCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGGCTGCAATCTG-CCCAAGCTCGGGGTAAGAGA
* * * * * ** * **
23341396 TTGGCTGATAGTGATATGTCTCAAGCTCGGGGTAAGAGATTGGCT-GATAGTG
65 TTGGCTGATAGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTA-CA
* * * *
23341448 ATCTG-CCTCAAGCTCGGGGTAAAAGATTGAATGGCTGCAATCTGCCCAAGGTTCCGGGTAAGAG
1 ATCTGCCCT-AGGCTCGGGGTAAAAGATCGAATGGCTGCAATCTGCCCAA-GCTCGGGGTAAGAG
* * * * *
23341512 ATTAGCTTATGGTGATCTGCCT-AGGCTCGAGGTAAAATATCGAATGGCTACA
64 ATTGGCTGATAGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* *
23341564 ATCTG-CCTCAAGCTCGGGGTAAGAGAT
1 ATCTGCCCT-AGGCTCGGGGTAAAAGAT
23341591 TGACTGATAG
Statistics
Matches: 213, Mismatches: 41, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
116 82 0.38
117 130 0.61
118 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (116 bp):
ATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGGCTGCAATCTGCCCAAGCTCGGGGTAAGAGAT
TGGCTGATAGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
Found at i:23341540 original size:233 final size:233
Alignment explanation
Indices: 23341137--23341570 Score: 588
Period size: 233 Copynumber: 1.9 Consensus size: 233
23341127 GCTGATGGTG
* * * * *
23341137 ATCTGTCCCAGGCTCAGGGTAAGAGATCGGATGGCTGTAATCTGCCTCAGGCTTGGGGTAAGAGA
1 ATCTGTCCCAAGCTCAGGGTAAGAGATCGGATGGATGTAATATGCCTCAAGCTCGGGGTAAGAGA
* * *
23341202 TTGGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAAGGTTGCCATCTGCTCCAAGCT
66 TTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAAGGCTGCAATCTGCTCCAAGCT
* * * *
23341267 CGGGGTGAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTACAA
131 CCGGGTAAGAGATTAGCTGATAGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGGCTACAA
23341332 TCTGCCCTAGGCTCAGGGTAAAAGATCGAATAGCTGTA
196 TCTGCCCTAGGCTCAGGGTAAAAGATCGAATAGCTGTA
* * * * *
23341370 ATCTGTCCCAAGCTCGGGGTAAGAGATTGGCT-GATAGTGATATGTCTCAAGCTCGGGGTAAGAG
1 ATCTGTCCCAAGCTCAGGGTAAGAGATCGGATGGAT-GTAATATGCCTCAAGCTCGGGGTAAGAG
* *
23341434 ATTGGCTGAT-AGTGATCTGCCTCAAGCTCGGGGTAAAAGATTGAATGGCTGCAATCTGC-CCAA
65 ATTGGCTGATGA-TGATCTGCCCCAAGCTCGGGGTAAAAGATCGAA-GGCTGCAATCTGCTCCAA
* * * * *
23341497 GGTTCCGGGTAAGAGATTAGCTTATGGTGATCTG-CCTAGGCTCGAGGTAAAATATCGAATGGCT
128 -GCTCCGGGTAAGAGATTAGCTGATAGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGGCT
23341561 ACAATCTGCC
192 ACAATCTGCC
23341571 TCAAGCTCGG
Statistics
Matches: 173, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
232 3 0.02
233 132 0.76
234 38 0.22
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (233 bp):
ATCTGTCCCAAGCTCAGGGTAAGAGATCGGATGGATGTAATATGCCTCAAGCTCGGGGTAAGAGA
TTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAAGGCTGCAATCTGCTCCAAGCT
CCGGGTAAGAGATTAGCTGATAGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGGCTACAA
TCTGCCCTAGGCTCAGGGTAAAAGATCGAATAGCTGTA
Found at i:23341663 original size:78 final size:77
Alignment explanation
Indices: 23341097--23341652 Score: 564
Period size: 78 Copynumber: 7.1 Consensus size: 77
23341087 GGATGGTTGT
* * * * *
23341097 AATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGTCCCAGGCTCAGGGTAAGAG
1 AATCTG-CCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAG
* *
23341162 ATCGGATGGCTGT
65 ATCGAATGGCTGC
* *
23341175 AATCTGCCTCAGGCTTGGGGTAAGAGATTGGCTGAT-GATGATCTGCCCCAGGCTCGGGGTAAAA
1 AATCTGCC-CAAGCTCGGGGTAAGAGATTGGCTGATAG-TGATCTGCCCCAGGCTCGGGGTAAAA
*
23341239 GATCGAA-GGTTGC
64 GATCGAATGGCTGC
* *
23341252 CATCTGCTCCAAGCTCGGGGTGAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAG
1 AATCTGC-CCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAG
*
23341317 ATCGAATGGCTAC
65 ATCGAATGGCTGC
* * * * ** * * * * *
23341330 AATCTGCCCTAGGCTCAGGGTAAAAGATCGAATAGCT-GTAATCTGTCCCAAGCTCGGGGTAAGA
1 AATCTGCCC-AAGCTCGGGGTAAGAGATTGGCT-GATAGTGATCTGCCCCAGGCTCGGGGTAAAA
* ** * *
23341394 GATTGGCT-GATAGT
64 GATCGAATGGCT-GC
* * * * *
23341408 GATATGTCTCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCTCAAGCTCGGGGTAAAAG
1 AATCTG-CCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAG
*
23341473 ATTGAATGGCTGC
65 ATCGAATGGCTGC
* * * * * * * *
23341486 AATCTGCCCAAGGTTCCGGGTAAGAGATTAGCTTATGGTGATCTG-CCTAGGCTCGAGGTAAAAT
1 AATCTGCCCAA-GCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAG
*
23341550 ATCGAATGGCTAC
65 ATCGAATGGCTGC
* *
23341563 AATCTGCCTCAAGCTCGGGGTAAGAGATTGACTGATAGTGATTTGCCCCAGGCTCGGGGTAAAAG
1 AATCTGCC-CAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAG
23341628 ATCGAATGGCTGC
65 ATCGAATGGCTGC
23341641 AATCTGTCCCAA
1 AATCTG-CCCAA
23341653 ACTAGAGGTA
Statistics
Matches: 385, Mismatches: 78, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
77 139 0.36
78 238 0.62
79 8 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (77 bp):
AATCTGCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTCGGGGTAAAAGA
TCGAATGGCTGC
Found at i:23341666 original size:194 final size:193
Alignment explanation
Indices: 23341097--23341707 Score: 589
Period size: 194 Copynumber: 3.1 Consensus size: 193
23341087 GGATGGTTGT
* *
23341097 AATCTGCCCCAA-GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGTCCC-AGGCTCAGGGTAAG
1 AATCTG-CCCAAGGCTCGGGGTAAAAGATT-GCTAATGGTGATCTG-CCCTAGGCTCAGGGTAAA
* * * *
23341160 AGATCGGATGGCTGTAATCTGCCTCAGGCTTGGGGTAAGAGATTGGCTGAT-GATGATCTGCCCC
63 AGATCGAATGGCTGTAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATAG-TGATATGCCCC
* * * * ** *
23341224 AGGCTCGGGGTAAAAGATCGAA-GGTTGCCATCTGCTCCAAGCTCGGGGTGAGAGATTGGCT-GA
127 AGGCTCGGGGTAAAAGATCGAATGGATGCAATCTGC-CCAAGCTCGGGGTAAAAGATTGAATGGC
*
23341287 TAGT
191 T-GC
* * * *
23341291 GATCTGCCCCAGGCTCGGGGTAAAAGA-T-CGAATGGCTACAATCTGCCCTAGGCTCAGGGTAAA
1 AATCTGCCCAAGGCTCGGGGTAAAAGATTGCTAATGG-T--GATCTGCCCTAGGCTCAGGGTAAA
* * *
23341354 AGATCGAATAGCTGTAATCTGTCC-CAAGCTCGGGGTAAGAGATTGGCTGATAGTGATATGTCTC
63 AGATCGAATGGCTGTAATCTG-CCTCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATATGCCCC
* * * ** **
23341418 AAGCTCGGGGTAAGAGATTGGCT-GATAGTGATCTGCCTCAAGCTCGGGGTAAAAGATTGAATGG
127 AGGCTCGGGGTAAAAGATCGAATGGAT-GCAATCTGCC-CAAGCTCGGGGTAAAAGATTGAATGG
23341482 CTGC
190 CTGC
* * * *
23341486 AATCTGCCCAAGGTTCCGGGTAAGAGATTAGCTTATGGTGATCTG-CCTAGGCTC-GAGGTAAAA
1 AATCTGCCCAAGGCTCGGGGTAAAAGATT-GCTAATGGTGATCTGCCCTAGGCTCAG-GGTAAAA
* ** * *
23341549 TATCGAATGGCTACAATCTGCCTCAAGCTCGGGGTAAGAGATTGACTGATAGTGATTTGCCCCAG
64 GATCGAATGGCTGTAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATATGCCCCAG
* * * * * *
23341614 GCTCGGGGTAAAAGATCGAATGGCTGCAATCTGTCCCAAACTAGAGGTAAAAGATCGAATGGCTA
129 GCTCGGGGTAAAAGATCGAATGGATGCAATCTG-CCCAAGCTCGGGGTAAAAGATTGAATGGCTG
23341679 C
193 C
* *
23341680 AATCTACCTC-AGGCTCGGGGTAAGAGAT
1 AATCTGCC-CAAGGCTCGGGGTAAAAGAT
23341708 CGGAATCTTT
Statistics
Matches: 339, Mismatches: 59, Indels: 38
0.78 0.14 0.09
Matches are distributed among these distances:
191 5 0.01
192 1 0.00
193 11 0.03
194 250 0.74
195 63 0.19
196 3 0.01
197 1 0.00
198 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (193 bp):
AATCTGCCCAAGGCTCGGGGTAAAAGATTGCTAATGGTGATCTGCCCTAGGCTCAGGGTAAAAGA
TCGAATGGCTGTAATCTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATATGCCCCAGGC
TCGGGGTAAAAGATCGAATGGATGCAATCTGCCCAAGCTCGGGGTAAAAGATTGAATGGCTGC
Found at i:23341702 original size:39 final size:39
Alignment explanation
Indices: 23341137--23341709 Score: 224
Period size: 39 Copynumber: 14.7 Consensus size: 39
23341127 GCTGATGGTG
* * * **
23341137 ATCTGTCC-CAGGCTCAGGGTAAGAGATCGGATGGCTGTA
1 ATCTG-CCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * * ** * **
23341176 ATCTGCCTCAGGCTTGGGGTAAGAGATTGGCT-GATGATG
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCT-ACA
* * * *
23341215 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAA-GGTTGCC
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * * * ** * **
23341253 ATCTG-CTCCAAGCTCGGGGTGAGAGATTGGCT-GATAGTG
1 ATCTGCCT-CAGGCTCGGGGTAAAAGATCGAATGGCTA-CA
*
23341292 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTACA
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * **
23341331 ATCTGCC-CTAGGCTCAGGGTAAAAGATCGAATAGCTGTA
1 ATCTGCCTC-AGGCTCGGGGTAAAAGATCGAATGGCTACA
* * * ** * **
23341370 ATCTGTCC-CAAGCTCGGGGTAAGAGATTGGCT-GATAGTG
1 ATCTG-CCTCAGGCTCGGGGTAAAAGATCGAATGGCTA-CA
* * * * * ** * **
23341409 ATATGTCTCAAGCTCGGGGTAAGAGATTGGCT-GATAGTG
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTA-CA
* * *
23341448 ATCTGCCTCAAGCTCGGGGTAAAAGATTGAATGGCTGCA
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * * ** *
23341487 ATCTGCC-CAAGGTTCCGGGTAAGAGATTAGCTTATGG-T--G
1 ATCTGCCTC-AGGCTCGGGGTAAAAGA-T--CGAATGGCTACA
* *
23341526 ATCTGCCT-AGGCTCGAGGTAAAATATCGAATGGCTACA
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * * * * **
23341564 ATCTGCCTCAAGCTCGGGGTAAGAGATTGACT-GATAGTG
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTA-CA
* * *
23341603 ATTTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
** * *
23341642 ATCTGTCC-CAAACTAGAGGTAAAAGATCGAATGGCTACA
1 ATCTG-CCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* *
23341681 ATCTACCTCAGGCTCGGGGTAAGAGATCG
1 ATCTGCCTCAGGCTCGGGGTAAAAGATCG
23341710 GAATCTTTAA
Statistics
Matches: 399, Mismatches: 109, Indels: 52
0.71 0.19 0.09
Matches are distributed among these distances:
35 5 0.01
36 1 0.00
37 2 0.01
38 58 0.15
39 314 0.79
40 14 0.04
41 1 0.00
42 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
ATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGGCTACA
Found at i:23353766 original size:29 final size:29
Alignment explanation
Indices: 23353734--23354101 Score: 245
Period size: 30 Copynumber: 12.5 Consensus size: 29
23353724 AATTTAGGAT
* * *
23353734 TAAAATTGAAATTTTTAGAAATTTGAGGG
1 TAAAAATGTAATTTTTAGAAGTTTGAGGG
* * *
23353763 T-AAAATGGTAATTTTTGGATGTTCGAGGG
1 TAAAAAT-GTAATTTTTAGAAGTTTGAGGG
*
23353792 T-AAAATGGTAATTTTTA-AA-TGTTCAGGGG
1 TAAAAAT-GTAATTTTTAGAAGT-TTGA-GGG
*
23353821 T-AAAATGGTAATCTTT-GAATGTTTGAGGG
1 TAAAAAT-GTAATTTTTAGAA-GTTTGAGGG
* * *
23353850 TAAAAATATAATTTTGGAAAAGTTT-AGGG
1 TAAAAATGTAATTTT-TAGAAGTTTGAGGG
* * * *
23353879 TTAAAATGGTAATTTTT-TATGTTCGAGGG
1 TAAAAAT-GTAATTTTTAGAAGTTTGAGGG
* * *
23353908 TAAAAATGTAATTTTGGAAAAATTT-AGGG
1 TAAAAATGTAATTTT-TAGAAGTTTGAGGG
* * *
23353937 TAAAAATGTGA-TTTTAGAAATATTTACGGG
1 TAAAAATGTAATTTTTAGAAGT-TTGA-GGG
* * *
23353967 TTAAAATGTAATTTTGAAGAAGTTTAAGGG
1 TAAAAATGTAATTTT-TAGAAGTTTGAGGG
*
23353997 TTAAAATGTAATTTTTGAGAAGTTT-AGGGG
1 TAAAAATGTAATTTTT-AGAAGTTTGA-GGG
23354027 TAAAAATGTAATTTTTGAGAAGTTTGAGGG
1 TAAAAATGTAATTTTT-AGAAGTTTGAGGG
* * *
23354057 TAAAAATGTAATTTTGAAAAAGTTTAAGGG
1 TAAAAATGTAATTTT-TAGAAGTTTGAGGG
* *
23354087 TCAAAATATAATTTT
1 TAAAAATGTAATTTT
23354102 GAAAAAGTGT
Statistics
Matches: 274, Mismatches: 43, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.02
28 24 0.09
29 100 0.36
30 129 0.47
31 10 0.04
32 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (29 bp):
TAAAAATGTAATTTTTAGAAGTTTGAGGG
Found at i:23353805 original size:58 final size:56
Alignment explanation
Indices: 23353734--23354071 Score: 240
Period size: 58 Copynumber: 5.8 Consensus size: 56
23353724 AATTTAGGAT
* * *
23353734 TAAAATTGAAATTTTTAGAAATTTGAGGGTAAAATGGTAATTTTTGGATGTTCGAGGG
1 TAAAAATGTAATTTTTAGAAATTT-AGGGTAAAAT-GTAATTTTTGAATGTTCGAGGG
* *
23353792 T-AAAATGGTAATTTTT--AAATGTTCAGGGGTAAAATGGTAATCTTTGAATGTTTGAGGG
1 TAAAAAT-GTAATTTTTAGAAAT-TT-A-GGGTAAAAT-GTAATTTTTGAATGTTCGAGGG
* * *
23353850 TAAAAATATAA-TTTTGGAAAAGTTTAGGGTTAAAATGGTAATTTTT-TATGTTCGAGGG
1 TAAAAATGTAATTTTTAG-AAA-TTTAGGG-TAAAAT-GTAATTTTTGAATGTTCGAGGG
* * * * * *
23353908 TAAAAATGTAATTTTGGAAAAATTTAGGGTAAAAATGTGATTTTAGAAATATT-TACGGG
1 TAAAAATGTAATTTT-TAGAAATTTAGGGT-AAAATGTAATTTTTG-AATGTTCGA-GGG
* * * * *
23353967 TTAAAATGTAATTTTGAAGAAGTTTAAGGGTTAAAATGTAATTTTTGAGAAGTT-TAGGGG
1 TAAAAATGTAATTTT-TAGAAATTT-AGGG-TAAAATGTAATTTTTGA-ATGTTCGA-GGG
*
23354027 TAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTT
1 TAAAAATGTAATTTTT-AGAAATTT-AGGGT-AAAATGTAATTTT
23354072 GAAAAAGTTT
Statistics
Matches: 229, Mismatches: 31, Indels: 38
0.77 0.10 0.13
Matches are distributed among these distances:
56 4 0.02
57 19 0.08
58 78 0.34
59 57 0.25
60 69 0.30
61 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.38
Consensus pattern (56 bp):
TAAAAATGTAATTTTTAGAAATTTAGGGTAAAATGTAATTTTTGAATGTTCGAGGG
Found at i:23353884 original size:30 final size:29
Alignment explanation
Indices: 23353841--23354137 Score: 253
Period size: 30 Copynumber: 10.0 Consensus size: 29
23353831 ATCTTTGAAT
*
23353841 GTTTGAGGGTAAAAATATAATTTTGGAAAA
1 GTTT-AGGGTAAAAATGTAATTTTGGAAAA
* ** *
23353871 GTTTAGGGTTAAAATGGTAATTTT--TTAT
1 GTTTAGGGTAAAAAT-GTAATTTTGGAAAA
*
23353899 GTTCGAGGGTAAAAATGTAATTTTGGAAAA
1 GTT-TAGGGTAAAAATGTAATTTTGGAAAA
* * *
23353929 ATTTAGGGTAAAAATGTGATTTTAGAAATA
1 GTTTAGGGTAAAAATGTAATTTTGGAAA-A
*
23353959 -TTTACGGGTTAAAATGTAATTTT-GAAGAA
1 GTTTA-GGGTAAAAATGTAATTTTGGAA-AA
* * *
23353988 GTTTAAGGGTTAAAATGTAATTTTTGAGAA
1 GTTT-AGGGTAAAAATGTAATTTTGGAAAA
* *
23354018 GTTTAGGGGTAAAAATGTAATTTTTGAGAA
1 GTTTA-GGGTAAAAATGTAATTTTGGAAAA
*
23354048 GTTTGAGGGTAAAAATGTAATTTTGAAAAA
1 GTTT-AGGGTAAAAATGTAATTTTGGAAAA
* * *
23354078 GTTTAAGGGTCAAAATATAATTTTGAAAAA
1 GTTT-AGGGTAAAAATGTAATTTTGGAAAA
* *
23354108 GTGTAGGGATCAAAATATG-ATTTTTGGAAA
1 GTTTAGGG-T-AAAA-ATGTAATTTTGGAAA
23354138 GCTCAAGGAC
Statistics
Matches: 223, Mismatches: 29, Indels: 29
0.79 0.10 0.10
Matches are distributed among these distances:
28 12 0.05
29 55 0.25
30 138 0.62
31 16 0.07
32 2 0.01
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.36
Consensus pattern (29 bp):
GTTTAGGGTAAAAATGTAATTTTGGAAAA
Found at i:23354115 original size:90 final size:89
Alignment explanation
Indices: 23353847--23354133 Score: 280
Period size: 90 Copynumber: 3.2 Consensus size: 89
23353837 GAATGTTTGA
* * ** * **
23353847 GGGTAAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATGGTAATTTT--TTATGTTCGAGGGTA
1 GGGTAAAAATATAATTTTTGAGAAGTTTAGGGTTAAAAT-GTAATTTTGAAAAAGTTTAAGGGTA
23353910 AAAATGTAATTTTGGAAAAA-TTTA-
65 AAAATGTAATTTT-GAAAAAGTTTAG
* * * * *
23353934 GGGTAAAAATGTGATTTTAGA-AATATTTACGGGTTAAAATGTAATTTTGAAGAAGTTTAAGGGT
1 GGGTAAAAATATAATTTTTGAGAA-GTTTA-GGGTTAAAATGTAATTTTGAAAAAGTTTAAGGGT
* *
23353998 TAAAATGTAATTTTTG-AGAAGTTTAG
64 AAAAATGTAA-TTTTGAAAAAGTTTAG
* * *
23354024 GGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTAATTTTGAAAAAGTTTAAGGGTC
1 GGGTAAAAATATAATTTTTGAGAAGTTT-AGGGTTAAAATGTAATTTTGAAAAAGTTTAAGGGTA
* *
23354089 AAAATATAATTTTGAAAAAGTGTAG
65 AAAATGTAATTTTGAAAAAGTTTAG
* * *
23354114 GGATCAAAATATGATTTTTG
1 GGGTAAAAATATAATTTTTG
23354134 GAAAGCTCAA
Statistics
Matches: 166, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
86 2 0.01
87 30 0.18
88 13 0.08
89 28 0.17
90 90 0.54
91 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (89 bp):
GGGTAAAAATATAATTTTTGAGAAGTTTAGGGTTAAAATGTAATTTTGAAAAAGTTTAAGGGTAA
AAATGTAATTTTGAAAAAGTTTAG
Found at i:23355028 original size:13 final size:13
Alignment explanation
Indices: 23355006--23355038 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
23354996 AAAAATATTT
*
23355006 AATAATTGACAGC
1 AATAAATGACAGC
23355019 AATAAATGACAGC
1 AATAAATGACAGC
23355032 AATAAAT
1 AATAAAT
23355039 ATATTAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (13 bp):
AATAAATGACAGC
Found at i:23355545 original size:22 final size:22
Alignment explanation
Indices: 23355520--23355562 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23355510 TGTAAAATTT
*
23355520 GAATTTTGGATTTGGACTTTTG
1 GAATTTTGGATTTGCACTTTTG
*
23355542 GAATTTTGTATTTGCACTTTT
1 GAATTTTGGATTTGCACTTTT
23355563 AAAATTTAAA
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:0.19, C:0.07, G:0.21, T:0.53
Consensus pattern (22 bp):
GAATTTTGGATTTGCACTTTTG
Found at i:23355568 original size:22 final size:22
Alignment explanation
Indices: 23355521--23355569 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23355511 GTAAAATTTG
* **
23355521 AATTTTGGATTTGGACTTTTGG
1 AATTTTGGATTTGCACTTTTAA
*
23355543 AATTTTGTATTTGCACTTTTAA
1 AATTTTGGATTTGCACTTTTAA
23355565 AATTT
1 AATTT
23355570 AAATTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (22 bp):
AATTTTGGATTTGCACTTTTAA
Found at i:23355606 original size:17 final size:16
Alignment explanation
Indices: 23355569--23355639 Score: 72
Period size: 17 Copynumber: 4.3 Consensus size: 16
23355559 TTTTAAAATT
*
23355569 TAAATTT-AATTTAAAA
1 TAAATTTAAACTT-AAA
* *
23355585 TAAATTCAAACTCAAGA
1 TAAATTTAAACTTAA-A
*
23355602 TAAATTTAAATTTAAAA
1 TAAATTTAAACTT-AAA
23355619 TAAATTTAAACTTAAA
1 TAAATTTAAACTTAAA
23355635 TAAAT
1 TAAAT
23355640 AAAAATTTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 16 0.36
17 27 0.60
18 2 0.04
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (16 bp):
TAAATTTAAACTTAAA
Found at i:23355618 original size:34 final size:32
Alignment explanation
Indices: 23355569--23355639 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 32
23355559 TTTTAAAATT
23355569 TAAATTTAATTTAAAATAAATTCAAACTCAAGA
1 TAAATTTAATTTAAAATAAATTCAAACTCAA-A
* *
23355602 TAAATTTAAATTTAAAATAAATTTAAACTTAAA
1 TAAATTT-AATTTAAAATAAATTCAAACTCAAA
23355635 TAAAT
1 TAAAT
23355640 AAAAATTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (32 bp):
TAAATTTAATTTAAAATAAATTCAAACTCAAA
Found at i:23358973 original size:24 final size:26
Alignment explanation
Indices: 23358935--23358983 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
23358925 GAGTCTTTCA
*
23358935 AAAATTTAGCTCATACGA-CCCAGAC
1 AAAATTTAACTCATACGAGCCCAGAC
23358960 AAAA-TTAACTCATACGAGCCCAGA
1 AAAATTTAACTCATACGAGCCCAGA
23358984 AAGGTTAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (26 bp):
AAAATTTAACTCATACGAGCCCAGAC
Found at i:23359104 original size:24 final size:24
Alignment explanation
Indices: 23358972--23359104 Score: 171
Period size: 24 Copynumber: 5.6 Consensus size: 24
23358962 AATTAACTCA
* *
23358972 TACGAGCCCAGAAAGGTTAGCTGT
1 TACGAGCCCAGAATGGTTAGCTCT
**
23358996 TATAAGCCCAGAAT-GTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
23359019 TACGAGCCCAGAATGGTGAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
* *
23359043 TACAAGCTCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
23359067 TACGAGCCTC-GAATGGTTAGCTCT
1 TACGAGCC-CAGAATGGTTAGCTCT
*
23359091 TACGAGCCTAGAAT
1 TACGAGCCCAGAAT
23359105 TAGAATAACG
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
23 20 0.22
24 72 0.77
25 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:23359155 original size:26 final size:27
Alignment explanation
Indices: 23359086--23359157 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
23359076 CGAATGGTTA
* *
23359086 GCTCTTACGAGCCTAGAATTAGAATAAC
1 GCTCTTACGAGCC-AAAATCAGAATAAC
* *
23359114 GCTATTTCGAGCCAAAATCAGAATAAC
1 GCTCTTACGAGCCAAAATCAGAATAAC
23359141 G-TCTTACGAGCCAAAAT
1 GCTCTTACGAGCCAAAAT
23359158 TAGATTACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 14 0.37
27 13 0.34
28 11 0.29
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (27 bp):
GCTCTTACGAGCCAAAATCAGAATAAC
Found at i:23360894 original size:15 final size:15
Alignment explanation
Indices: 23360876--23360909 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
23360866 TCTCAAAACC
23360876 ACTGTTTTCAACACT
1 ACTGTTTTCAACACT
*
23360891 ACTGTTTTCGACACT
1 ACTGTTTTCAACACT
23360906 ACTG
1 ACTG
23360910 AAAAATGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (15 bp):
ACTGTTTTCAACACT
Found at i:23364473 original size:54 final size:54
Alignment explanation
Indices: 23364386--23364501 Score: 180
Period size: 54 Copynumber: 2.1 Consensus size: 54
23364376 CTACTTACTC
*
23364386 TTTTCAAATGAAAAATAATGAAAGAAACAATTATTTTAATAA-CCATAATATGATG
1 TTTT-AAATGAAAAATAATGAAAGAAACAATTATTTTAA-AATCCATAATATGATA
* *
23364441 TTTTAAATGAAAAATAGTGAAAGAAACAATTATTTTAAAATCCATAATGTGATA
1 TTTTAAATGAAAAATAATGAAAGAAACAATTATTTTAAAATCCATAATATGATA
23364495 TTTTAAA
1 TTTTAAA
23364502 AATAAGTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
53 2 0.04
54 51 0.89
55 4 0.07
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (54 bp):
TTTTAAATGAAAAATAATGAAAGAAACAATTATTTTAAAATCCATAATATGATA
Found at i:23365410 original size:22 final size:22
Alignment explanation
Indices: 23365384--23365428 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
23365374 CTAATGGTTA
* *
23365384 AAATATTTAATTTAAAAAAATT
1 AAATAATTAATTCAAAAAAATT
*
23365406 AAATAATTAATTCGAAAAAATT
1 AAATAATTAATTCAAAAAAATT
23365428 A
1 A
23365429 GTAATTAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATAATTAATTCAAAAAAATT
Found at i:23374277 original size:251 final size:253
Alignment explanation
Indices: 23373722--23374338 Score: 680
Period size: 251 Copynumber: 2.4 Consensus size: 253
23373712 TGTTGGCGAG
* * *
23373722 AGCGT-AAAAAAAATACT-AACATAGAGAGCTT-ATTGA-ATTTTTAATTATTTTAAAATAATTT
1 AGCGTAAAAAAAAATACTGAA-ATAAAGAGCTTAATTGATTTTTTTAATTATTTTATAATAATTT
*
23373783 AATTGTTTTTGGCTTATATGTATAAAAAAAACTCTTTAAAAATAAAAAAATCATTAATTTTTATT
65 AATTGTTTTTGGCTTATATGTAT-AAAAAAAC-CTTTAAAAATAAAAAAATCATTAAGTTTTATT
* **
23373848 TGGAATATGTTGTTTAACTAGGCTACATATGGATTCACAATGACAACCTTATAAAAAAAAACCAT
128 TGGAATA-----TTTAACTAGACTACATATGGATTCACAATGACAACCGAATAAAAAAAAACCAT
* * * ** * *
23373913 ATCTTTGGCTTATATGCATAAAAAAAATCATATCTTTGACAATGGCATGGTACAATATTAGGGAG
188 ATCATTGACTTATATG-ATAAAAAAAATCATATATTTGACAATGAAATAGTAAAATATTAGGGAG
*
23373978 AT
252 AC
* * * * * *
23373980 AGC-TAGGGTAGAAAAATA-TCGACATAAAGAGTTTAATTGATTTTTTTAATTATTTTATAGTAG
1 AGCGTA---AAAAAAAATACT-GAAATAAAGAGCTTAATTGATTTTTTTAATTATTTTATAATAA
* *
23374043 TTTAATTGTTTTTGCCTTATATGTATAAAAAAACCTTTAAAAAT-AAAAAATCGTTAAGTTTTAT
62 TTTAATTGTTTTTGGCTTATATGTATAAAAAAACCTTTAAAAATAAAAAAATCATTAAGTTTTAT
* * * * * **
23374107 TTGGAATA-TTAACTCGATTATATATGGATTGACAATGATAACCGAAT-AAAAAAAATTATATCA
127 TTGGAATATTTAACTAGACTACATATGGATTCACAATGACAACCGAATAAAAAAAAACCATATCA
** * *
23374170 TTGACTTATATG-TGTAAAAAATCATATATTTGACAATGAAATAGTAAAATGTTAGTGAGAC
192 TTGACTTATATGATAAAAAAAATCATATATTTGACAATGAAATAGTAAAATATTAGGGAGAC
23374231 AGCGTAAAAAAAAACTACTGAAATAAAGAGCTTAATTGATTTTTTTTAATTATTTTATAATAATT
1 AGCGTAAAAAAAAA-TACTGAAATAAAGAGCTTAATTGA-TTTTTTTAATTATTTTATAATAATT
*
23374296 TAATT-TCTTTTGGCTTATATGTATATTAGAAAACCTTTAAAAA
64 TAATTGT-TTTTGGCTTATATGTATA--AAAAAACCTTTAAAAA
23374339 AATCATTTAA
Statistics
Matches: 302, Mismatches: 42, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
249 6 0.02
250 21 0.07
251 88 0.29
252 2 0.01
253 39 0.13
254 31 0.10
257 1 0.00
258 3 0.01
260 27 0.09
261 27 0.09
262 14 0.05
263 43 0.14
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (253 bp):
AGCGTAAAAAAAAATACTGAAATAAAGAGCTTAATTGATTTTTTTAATTATTTTATAATAATTTA
ATTGTTTTTGGCTTATATGTATAAAAAAACCTTTAAAAATAAAAAAATCATTAAGTTTTATTTGG
AATATTTAACTAGACTACATATGGATTCACAATGACAACCGAATAAAAAAAAACCATATCATTGA
CTTATATGATAAAAAAAATCATATATTTGACAATGAAATAGTAAAATATTAGGGAGAC
Found at i:23375002 original size:41 final size:41
Alignment explanation
Indices: 23374945--23375174 Score: 325
Period size: 41 Copynumber: 5.6 Consensus size: 41
23374935 AACGTTCGCA
* * **
23374945 AAAGGTCAGAGCAATAGCGGTGCTTATGGGCAAGCGTAGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* *
23374986 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* * * * *
23375027 AAAGATCAGAGTAATAGCGACGCTTATGGTAAAGCGCCTCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
*
23375068 AAAGGTAAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* *
23375109 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCAGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
*
23375150 AAAGGTCAAAGCAATAGCGGCGCTT
1 AAAGGTCAGAGCAATAGCGGCGCTT
23375175 GAGCAATAGT
Statistics
Matches: 169, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 169 1.00
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
Found at i:23375181 original size:17 final size:17
Alignment explanation
Indices: 23375159--23375191 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23375149 TAAAGGTCAA
23375159 AGCAATAGCGGCGCTTG
1 AGCAATAGCGGCGCTTG
*
23375176 AGCAATAGTGGCGCTT
1 AGCAATAGCGGCGCTT
23375192 ATGGGCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.21
Consensus pattern (17 bp):
AGCAATAGCGGCGCTTG
Found at i:23375192 original size:58 final size:58
Alignment explanation
Indices: 23375117--23375232 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
23375107 CTAAAGGTCA
*
23375117 GAGCAATAGCGGTGCTTATGGGAAAGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
* * * * *
23375175 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGGTGCTT
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
23375233 ATGGGAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (58 bp):
GAGCAATAGCGGCGCTTATGGGAAAGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
Found at i:23375233 original size:41 final size:41
Alignment explanation
Indices: 23375175--23375273 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
23375165 AGCGGCGCTT
* * **
23375175 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCA
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCAACTAAAGGTCA
*
23375216 GAGCAATAGCGGTGCTTATGGGAAAGCGCAACTAAAGGTCA
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCAACTAAAGGTCA
*
23375257 AAGCAATAGCGGCGCTT
1 GAGCAATAGCGGCGCTT
23375274 GAGCAATAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.18
Consensus pattern (41 bp):
GAGCAATAGCGGCGCTTATGGGAAAGCGCAACTAAAGGTCA
Found at i:23375251 original size:99 final size:99
Alignment explanation
Indices: 23375076--23375364 Score: 524
Period size: 99 Copynumber: 2.9 Consensus size: 99
23375066 CTAAAGGTAA
* * *
23375076 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAA
1 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAA
23375141 AGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
66 AGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
23375175 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAA
1 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAA
*
23375240 AGCGCAACTAAAGGTCAAAGCAATAGCGGCGCTT
66 AGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
* *
23375274 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGATGCTTATGGGCA
1 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAA
23375339 AGCGCAGCTAAAGGTCAAAGCAATAG
66 AGCGCAGCTAAAGGTCAAAGCAATAG
23375365 TGACGCTGAT
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 183 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.17
Consensus pattern (99 bp):
GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAA
AGCGCAGCTAAAGGTCAAAGCAATAGCGGCGCTT
Found at i:23375280 original size:17 final size:17
Alignment explanation
Indices: 23375258--23375290 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23375248 TAAAGGTCAA
23375258 AGCAATAGCGGCGCTTG
1 AGCAATAGCGGCGCTTG
*
23375275 AGCAATAGTGGCGCTT
1 AGCAATAGCGGCGCTT
23375291 ATGGGCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.21
Consensus pattern (17 bp):
AGCAATAGCGGCGCTTG
Found at i:23375280 original size:58 final size:58
Alignment explanation
Indices: 23375216--23375325 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 58
23375206 CTAAAGGTCA
*
23375216 GAGCAATAGCGGTGCTTATGGGAAAGCGCAACTAAAGGTCAAAGCAATAGCGGCGCTT
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCAACTAAAGGTCAAAGCAATAGCGGCGCTT
* * ** *
23375274 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCAACTAAAGGTCAAAGCAATAGCG
23375326 ATGCTTATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.17
Consensus pattern (58 bp):
GAGCAATAGCGGCGCTTATGGGAAAGCGCAACTAAAGGTCAAAGCAATAGCGGCGCTT
Found at i:23375332 original size:41 final size:41
Alignment explanation
Indices: 23375274--23375431 Score: 208
Period size: 41 Copynumber: 3.9 Consensus size: 41
23375264 AGCGGCGCTT
* * *
23375274 GAGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCA
1 GAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCA
* *
23375315 GAGCAATAGCGATGCTTATGGGCAAGCGCAGCTAAAGGTCA
1 GAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCA
* * * *
23375356 AAGCAATAGTGACGCTGATGGGCAAGCACCGCTAAAGGTCA
1 GAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCA
* * *
23375397 GAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAA
1 GAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAA
23375432 TTTATTTAAA
Statistics
Matches: 100, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.31, C:0.21, G:0.32, T:0.16
Consensus pattern (41 bp):
GAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCA
Found at i:23375414 original size:82 final size:82
Alignment explanation
Indices: 23375275--23375431 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 82
23375265 GCGGCGCTTG
* * * * * * *
23375275 AGCAATAGTGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAGCGATGCTTATGGGCAA
1 AGCAATAGTGACGCTGATGGGCAAGCACCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGAAA
23375340 GCGCAGCTAAAGGTCAA
66 GCGCAGCTAAAGGTCAA
*
23375357 AGCAATAGTGACGCTGATGGGCAAGCACCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGAAA
1 AGCAATAGTGACGCTGATGGGCAAGCACCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGAAA
*
23375422 GCGCCGCTAA
66 GCGCAGCTAA
23375432 TTTATTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (82 bp):
AGCAATAGTGACGCTGATGGGCAAGCACCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGAAA
GCGCAGCTAAAGGTCAA
Found at i:23380548 original size:96 final size:96
Alignment explanation
Indices: 23380364--23380555 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
23380354 AAATTTGAAG
* ** * *
23380364 AAGGATATTTGATTATCTCGATTTGAAGAAATGTTGCACCTAGTGAGTTAAGGCGCTAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCTAAGTTTCA
* *
23380429 TAACCGAAGATAAGGAAACATTGCCTCGATT
66 TAACCGAAAATAAAGAAACATTGCCTCGATT
* *
23380460 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCG-TAAAGTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCT-AAGTTTC
*
23380524 GA-AACTC-AAAATAAA-AGAATATTGCCTCGATT
65 -ATAAC-CGAAAATAAAGA-AACATTGCCTCGATT
23380556 TTAAAGCTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 78 0.95
97 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCTAAGTTTCA
TAACCGAAAATAAAGAAACATTGCCTCGATT
Found at i:23380866 original size:30 final size:30
Alignment explanation
Indices: 23380831--23381142 Score: 303
Period size: 30 Copynumber: 10.5 Consensus size: 30
23380821 AAAATAGTAA
* * *
23380831 TTTTGGGGTTGAAAATGAAATTTTTGGAAT
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
*
23380861 TTTTGGGGTTAAAAATGGAATTTTTGGAAT
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
* *
23380891 TTTTGAGTTTAAAAATGGAATTTTTTGGAAG
1 TTTTGGGGTTAAAAATGGAA-TTTTTGGAAG
* **
23380922 -TTCGAGGG-TAAAAATATAATTTTTGGAAG
1 TTTTG-GGGTTAAAAATGGAATTTTTGGAAG
* *
23380951 TTTCGGGGTTAAAAATGGAATTTTTGGAAA
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
* * *
23380981 TTTAGGGG-AAAAAATGGAATTTTTGGATG
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
* * *
23381010 -TTCGAGGG-TAAAAATGTAATTTTTGAAAAG
1 TTTTG-GGGTTAAAAATGGAATTTTTG-GAAG
* *
23381040 TTTTAGGGTCAAAAATGGAATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
* *
23381070 TTTTGGGGTCAAAAATGTAATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
** * * **
23381100 TTTAAGGG-CAAAAATGTAATTTTTAAAAG
1 TTTTGGGGTTAAAAATGGAATTTTTGGAAG
23381129 TTTTGGGGTTAAAA
1 TTTTGGGGTTAAAA
23381143 TGTAATTATG
Statistics
Matches: 237, Mismatches: 36, Indels: 18
0.81 0.12 0.06
Matches are distributed among these distances:
28 3 0.01
29 74 0.31
30 133 0.56
31 27 0.11
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.38
Consensus pattern (30 bp):
TTTTGGGGTTAAAAATGGAATTTTTGGAAG
Found at i:23381143 original size:119 final size:119
Alignment explanation
Indices: 23380831--23381171 Score: 357
Period size: 119 Copynumber: 2.9 Consensus size: 119
23380821 AAAATAGTAA
* * * * *
23380831 TTTTGGGGTTGAAAATGAAATTTTTGGAATTTTTGGGGTTAAAAATGGAATTTTTGGAATTTTTG
1 TTTTGGGGTTAAAAATGAAATTTTTGGAAATTTAGGGG-AAAAAATGGAATTTTTGGAAGTTTTG
* * * ** *
23380896 AGTTTAAAAATGGAATTTTTTG-GAAGTTCGAGGGT-AAAAATATAATTTTTGGAAG
65 GGGTT-AAAATGTAA-TTTTTGAGAAGTTTTAGGGTCAAAAATAGAATTTTTGGAAG
* * * *
23380951 TTTCGGGGTTAAAAATGGAATTTTTGGAAATTTAGGGGAAAAAATGGAATTTTTGGATG-TTCGA
1 TTTTGGGGTTAAAAATGAAATTTTTGGAAATTTAGGGGAAAAAATGGAATTTTTGGAAGTTTTG-
* * *
23381015 GGGTAAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAG
65 GGGTTAAAATGTAATTTTTGAGAAGTTTTAGGGTCAAAAATAGAATTTTTGGAAG
* * * * * * **
23381070 TTTTGGGGTCAAAAATGTAATTTTTGGAAGTTTAAGGGCAAAAATGTAATTTTTAAAAGTTTTGG
1 TTTTGGGGTTAAAAATGAAATTTTTGGAAATTTAGGGGAAAAAATGGAATTTTTGGAAGTTTTGG
* * *
23381135 GGTTAAAATGTAATTATGGAGAAG-TTTGGGGTCAAAA
66 GGTTAAAATGTAATTTTTGAGAAGTTTTAGGGTCAAAA
23381172 TATGATTTCT
Statistics
Matches: 183, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
117 6 0.03
118 33 0.18
119 108 0.59
120 36 0.20
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (119 bp):
TTTTGGGGTTAAAAATGAAATTTTTGGAAATTTAGGGGAAAAAATGGAATTTTTGGAAGTTTTGG
GGTTAAAATGTAATTTTTGAGAAGTTTTAGGGTCAAAAATAGAATTTTTGGAAG
Found at i:23381190 original size:59 final size:57
Alignment explanation
Indices: 23380831--23381190 Score: 232
Period size: 60 Copynumber: 6.1 Consensus size: 57
23380821 AAAATAGTAA
* * * * * *
23380831 TTTTGGGGTTGAAAATGAAATTTTTG-GAATTTTTGGGGTTAAAAATGGAATTTTTGGAAT
1 TTTTGGGG-TAAAAATGTAATTTTTGAGAA-GTTTAGGGTCAAAAAT-GAA-TTTTGGAAG
** * * *
23380891 TTTTGAGTTTAAAAATGGAATTTTTTG-GAAGTTCGAGGGT-AAAAATATAATTTTTGGAAG
1 TTTTG-GGGTAAAAATGTAA-TTTTTGAGAAGTT-TAGGGTCAAAAAT-GAA-TTTTGGAAG
* * * ** *
23380951 TTTCGGGGTTAAAAATGGAATTTTTG-GAAATTTAGGGGAAAAAATGGAATTTTTGGATG
1 TTTTGGGG-TAAAAATGTAATTTTTGAGAAGTTTAGGGTCAAAAAT-GAA-TTTTGGAAG
* *
23381010 -TTCGAGGGTAAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAG
1 TTTTG-GGGTAAAAATGTAATTTTTGAGAAG-TTTAGGGTCAAAAAT-GAA-TTTTGGAAG
**
23381070 TTTTGGGGTCAAAAATGTAATTTTTG-GAAGTTTAAGGG-CAAAAATGTAATTTTTAAAAG
1 TTTTGGGGT-AAAAATGTAATTTTTGAGAAGTTT-AGGGTCAAAAATG-AA-TTTTGGAAG
* * * *
23381129 TTTTGGGGTTAAAATGTAATTATGGAGAAGTTTGGGGTCAAAATATG-ATTTCTGGACAG
1 TTTTGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGTCAAAA-ATGAATTT-TGGA-AG
23381188 TTT
1 TTT
23381191 AAGGACCTCT
Statistics
Matches: 248, Mismatches: 35, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
57 3 0.01
58 44 0.18
59 80 0.32
60 88 0.35
61 33 0.13
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.38
Consensus pattern (57 bp):
TTTTGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGTCAAAAATGAATTTTGGAAG
Found at i:23383164 original size:12 final size:12
Alignment explanation
Indices: 23383144--23383190 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
23383134 TTATATTTGG
23383144 ATATT-AATTTA
1 ATATTAAATTTA
*
23383155 ATTTTAAATTTA
1 ATATTAAATTTA
23383167 A-ACTTAAATTT-
1 ATA-TTAAATTTA
23383178 ATATTAAATTTA
1 ATATTAAATTTA
23383190 A
1 A
23383191 ACTTTATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 13 0.43
12 17 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATTAAATTTA
Found at i:23383166 original size:6 final size:6
Alignment explanation
Indices: 23383149--23383223 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
23383139 TTTGGATATT
* * *
23383149 AATTTA ATTTTA AATTTA AACTTA AATTTA TA-TTA AATTTA AACTTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA
* *
23383196 -ATGTA AATTTA AATTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA
23383224 GTTTTAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
4 2 0.04
5 9 0.17
6 40 0.74
7 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:23383173 original size:23 final size:23
Alignment explanation
Indices: 23383147--23383231 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
23383137 TATTTGGATA
23383147 TTAATTTAATTTTAAATTTAAAC
1 TTAATTTAATTTTAAATTTAAAC
*
23383170 TTAAATTT-ATATTAAATTTAAAC
1 TT-AATTTAATTTTAAATTTAAAC
* * * *
23383193 TTTATGTAAATTTAAATTTAAAA
1 TTAATTTAATTTTAAATTTAAAC
* *
23383216 TAAATTTAGTTTTAAA
1 TTAATTTAATTTTAAA
23383232 ATAAAATTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 3 0.06
23 41 0.84
24 5 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAATTTAATTTTAAATTTAAAC
Found at i:23383229 original size:17 final size:17
Alignment explanation
Indices: 23383149--23383244 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
23383139 TTTGGATATT
* *
23383149 AATTTAATTTTAAATTTA
1 AATTTAAATTTAAA-ATA
* * *
23383167 AACTTAAATTTATATTA
1 AATTTAAATTTAAAATA
**
23383184 AATTTAAACTTT-ATGTA
1 AATTTAAA-TTTAAAATA
23383201 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
**
23383218 AATTTAGTTTTAAAATA
1 AATTTAAATTTAAAATA
*
23383235 AAATTAAATT
1 AATTTAAATT
23383245 CTGTTGGGCA
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
16 3 0.05
17 45 0.73
18 14 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:23384906 original size:43 final size:43
Alignment explanation
Indices: 23384834--23385260 Score: 513
Period size: 43 Copynumber: 10.0 Consensus size: 43
23384824 ATCTGTTAAT
23384834 TTTAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGTTC
* * * *
23384876 TTTAGTGGTGTTTGTGTTGAAAGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGTTC
** *
23384919 TTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
1 TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGTTC
* * * *
23384962 TTTAGCGACGTTTGTG-GTTAAAGCGTCGCTAATGACCATGTTC
1 TTTAGCGGCGTTTGTGTG-GAAAGCGCCGCTAAAGACCATGTTC
* * *
23385005 TTTAGCGGTGTTTGTGTTGAAAGCGCCGCTAATGACCATGTTC
1 TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGTTC
** *
23385048 TTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
1 TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGTTC
* * * *
23385091 TTTAGTGACGTTTGTG-GGTAAAGCGTCGCTAAATACCATGTTC
1 TTTAGCGGCGTTTGTGTGG-AAAGCGCCGCTAAAGACCATGTTC
* * *
23385134 TTTAGCGGCGTTTATG-GTAAAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGTG-GAAAGCGCCGCTAAAGACCATGTTC
* * *
23385177 TTTAGCTGCGTTTGT-TGTAAAAGCGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGTG-GAAAGCGCCGCTAAAGACCATGTTC
* * *
23385220 TTTAGTGGCGTTTGTGAGGAAAGCGCCGCTAAAGAACATGT
1 TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGT
23385261 GGGGAAAGCG
Statistics
Matches: 327, Mismatches: 51, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
42 17 0.05
43 309 0.94
44 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGACCATGTTC
Found at i:23385002 original size:129 final size:128
Alignment explanation
Indices: 23384834--23385260 Score: 581
Period size: 129 Copynumber: 3.3 Consensus size: 128
23384824 ATCTGTTAAT
* * * * *
23384834 TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGTGTTTGTGTTGAAAG
1 TTTAGCGACGTTTGTGGTAAAGCGTCGCTAATGACCATGTTCTTTAGCGGTGTTTGTGTTGAAAG
*
23384899 TGCCGCTAAAGACCATGTTCTTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
66 CGCCGCTAAAGACCATGTTCTTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
23384962 TTTAGCGACGTTTGTGGTTAAAGCGTCGCTAATGACCATGTTCTTTAGCGGTGTTTGTGTTGAAA
1 TTTAGCGACGTTTGTGG-TAAAGCGTCGCTAATGACCATGTTCTTTAGCGGTGTTTGTGTTGAAA
*
23385027 GCGCCGCTAATGACCATGTTCTTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
65 GCGCCGCTAAAGACCATGTTCTTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
* * * * *
23385091 TTTAGTGACGTTTGTGGGTAAAGCGTCGCTAAAT-ACCATGTTCTTTAGCGGCGTTTATGGTAAA
1 TTTAGCGACGTTTGT-GGTAAAGCGTCGCT-AATGACCATGTTCTTTAGCGGTGTTTGTGTTGAA
* * * *
23385155 AGCACCGCTAAAGACCATGTTCTTTAGC-TGCGTTTGT-TGTAAAAGCGTCGCTAAAGACCATGT
64 AGCGCCGCTAAAGACCATGTTCTTTAGCAT-CGTTTGTGTG-GAAAGCGCCGCTAGAGACCATGT
23385218 TC
127 TC
* * * * * *
23385220 TTTAGTGGCGTTTGTGAGGAAAGCGCCGCTAAAGAACATGT
1 TTTAGCGACGTTTGTG-GTAAAGCGTCGCTAATGACCATGT
23385261 GGGGAAAGCG
Statistics
Matches: 270, Mismatches: 22, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
128 22 0.08
129 243 0.90
130 5 0.02
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (128 bp):
TTTAGCGACGTTTGTGGTAAAGCGTCGCTAATGACCATGTTCTTTAGCGGTGTTTGTGTTGAAAG
CGCCGCTAAAGACCATGTTCTTTAGCATCGTTTGTGTGGAAAGCGCCGCTAGAGACCATGTTC
Found at i:23385268 original size:26 final size:26
Alignment explanation
Indices: 23385232--23385286 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
23385222 TAGTGGCGTT
23385232 TGTGAGGAAAGCGCCGCTAAAGAACA
1 TGTGAGGAAAGCGCCGCTAAAGAACA
* ** *
23385258 TGTGGGGAAAGCGTTGCTAAAGACCA
1 TGTGAGGAAAGCGCCGCTAAAGAACA
23385284 TGT
1 TGT
23385287 TCTTTAGCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (26 bp):
TGTGAGGAAAGCGCCGCTAAAGAACA
Found at i:23385325 original size:42 final size:42
Alignment explanation
Indices: 23385263--23385384 Score: 190
Period size: 42 Copynumber: 2.9 Consensus size: 42
23385253 GAACATGTGG
* *
23385263 GGAAAGCGTTGCTAAAGACCATGTTCTTTAGCGGCGTTTATA
1 GGAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCGTTTATA
* * *
23385305 GGTAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCTTTTGTA
1 GGAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCGTTTATA
*
23385347 GGAAAGCGTCGCTAAAGACCATGTTCTTTAGCTGCGTT
1 GGAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCGTT
23385385 CTTCCTCATA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
GGAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCGTTTATA
Found at i:23396996 original size:21 final size:19
Alignment explanation
Indices: 23396972--23397016 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
23396962 ACAATGATTT
23396972 TATATTTAAAAAATTAATAAA
1 TATATTTAAAAAA-T-ATAAA
*
23396993 TATA-TTATAAAATATAAA
1 TATATTTAAAAAATATAAA
23397011 TATATT
1 TATATT
23397017 AAATAGTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 7 0.32
21 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATTTAAAAAATATAAA
Found at i:23397012 original size:22 final size:21
Alignment explanation
Indices: 23396972--23397012 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
23396962 ACAATGATTT
*
23396972 TATATTTAAAAAATTAATAAA
1 TATATTTAAAAAATAAATAAA
*
23396993 TATATTATAAAATATAAATA
1 TATATT-TAAAAAATAAATA
23397013 TATTAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATATTTAAAAAATAAATAAA
Found at i:23399655 original size:15 final size:16
Alignment explanation
Indices: 23399625--23399663 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
23399615 TAGTAAAAAT
23399625 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
23399642 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
23399657 ATAATTT
1 ATAATTT
23399664 TTAAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:23399775 original size:82 final size:82
Alignment explanation
Indices: 23399620--23399776 Score: 181
Period size: 81 Copynumber: 1.9 Consensus size: 82
23399610 TATGATAGTA
* * * * * * * **
23399620 AAAATATAATTTTATTATTTTAATAATTTATATTTTTATAATTTTTAAAGAATTAAATTAAATTT
1 AAAATATAATTTTATTA-TATAATAATTTAAAATTTTATAAATTATAAAAAACTAAATTAAAAAT
*
23399685 TTATTATTTTTTATGGTC
65 TTACTATTTTTTATGGTC
* *
23399703 AAAATATAATTTTATTA-ATACTCATTTAAAATTTTATAAATTATAAAAAACCTAAATTAAAAAT
1 AAAATATAATTTTATTATATAATAATTTAAAATTTTATAAATTATAAAAAA-CTAAATTAAAAAT
23399767 TTACTATTTT
65 TTACTATTTT
23399777 AAAAATTACT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
81 25 0.41
82 19 0.31
83 17 0.28
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (82 bp):
AAAATATAATTTTATTATATAATAATTTAAAATTTTATAAATTATAAAAAACTAAATTAAAAATT
TACTATTTTTTATGGTC
Found at i:23403987 original size:27 final size:27
Alignment explanation
Indices: 23403942--23404013 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
23403932 TCCTTGTACT
*
23403942 ATTATTAAT-ATTTTA--TTTAA-TTA
1 ATTATAAATAATTTTATTTTTAATTTA
23403965 ATTACTAAATAATTTTATTTTTAATTTA
1 ATTA-TAAATAATTTTATTTTTAATTTA
* *
23403993 ATTATTAATATTTTTATTTTT
1 ATTATAAATAATTTTATTTTT
23404014 TAATCTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.10
24 4 0.10
25 6 0.15
27 20 0.49
28 7 0.17
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTATAAATAATTTTATTTTTAATTTA
Found at i:23404700 original size:14 final size:14
Alignment explanation
Indices: 23404681--23404723 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
23404671 TTTTATGATA
23404681 TTTTTATTTATAAT
1 TTTTTATTTATAAT
23404695 TTTTTATCATGT-TAAT
1 TTTTTAT--T-TATAAT
23404711 TTTTTATTTATAA
1 TTTTTATTTATAA
23404724 ATTAAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.04
14 11 0.44
16 12 0.48
17 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTTATTTATAAT
Found at i:23405630 original size:3 final size:3
Alignment explanation
Indices: 23405622--23405664 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
23405612 AAAAGTATAG
23405622 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
23405665 AGTATTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23411228 original size:29 final size:29
Alignment explanation
Indices: 23411189--23411248 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
23411179 CTTTTTAATA
*
23411189 TTTTAATATTT-AATTTTATAGTTTTCTATT
1 TTTTAATATTTAAATTTAAT-GTTTT-TATT
23411219 TTTTAA-ATTTAAATTTAATGTTTTTATT
1 TTTTAATATTTAAATTTAATGTTTTTATT
23411247 TT
1 TT
23411249 AATTGCCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
29 9 0.32
30 13 0.46
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTAATATTTAAATTTAATGTTTTTATT
Found at i:23411234 original size:30 final size:28
Alignment explanation
Indices: 23411180--23411248 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
23411170 AAAAATGTAC
* *
23411180 TTTTTAATATTTTAATATTTAATTTTATAG
1 TTTTT-ATTTTTTAATATTTAATTTAAT-G
23411210 TTTTCTATTTTTTAA-ATTTAAATTTAATG
1 TTTT-TATTTTTTAATATTT-AATTTAATG
23411239 TTTTTATTTT
1 TTTTTATTTT
23411249 AATTGCCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 6 0.17
29 9 0.26
30 19 0.54
31 1 0.03
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTATTTTTTAATATTTAATTTAATG
Found at i:23414580 original size:25 final size:23
Alignment explanation
Indices: 23414552--23414597 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
23414542 GTTGGATCCA
23414552 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
23414577 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
23414598 CCCTGATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:23416495 original size:13 final size:13
Alignment explanation
Indices: 23416477--23416502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23416467 TTTTTCGAAA
23416477 AAAGTCAACGGTC
1 AAAGTCAACGGTC
23416490 AAAGTCAACGGTC
1 AAAGTCAACGGTC
23416503 GGTCAATGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:23416518 original size:21 final size:21
Alignment explanation
Indices: 23416493--23416539 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
23416483 AACGGTCAAA
* * *
23416493 GTCAACGGTCGGTCAATGTCG
1 GTCAACGATCGGTCAACGCCG
23416514 GTCAACGATCGGTCAACGCCG
1 GTCAACGATCGGTCAACGCCG
23416535 GTCAA
1 GTCAA
23416540 TGGTTTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (21 bp):
GTCAACGATCGGTCAACGCCG
Found at i:23416525 original size:11 final size:10
Alignment explanation
Indices: 23416493--23416539 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
23416483 AACGGTCAAA
23416493 GTCAACGGTCG
1 GTCAAC-GTCG
*
23416504 GTCAATGTCG
1 GTCAACGTCG
23416514 GTCAACGATCG
1 GTCAACG-TCG
*
23416525 GTCAACGCCG
1 GTCAACGTCG
23416535 GTCAA
1 GTCAA
23416540 TGGTTTGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (10 bp):
GTCAACGTCG
Found at i:23416596 original size:15 final size:15
Alignment explanation
Indices: 23416576--23416605 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23416566 TGGTTCATTT
23416576 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
23416591 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
23416606 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Done.