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 102 of 144
Found at i:23870245 original size:24 final size:24
Alignment explanation
Indices: 23870216--23870263 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23870206 GGCATAATTT
*
23870216 ATTTTTTAAAATATTGTAATATATG
1 ATTTTATAAAATA-TGTAATATATG
* *
23870241 ATTTTATATATTATGTAATATAT
1 ATTTTATAAAATATGTAATATAT
23870264 TATATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTTTATAAAATATGTAATATATG
Found at i:23873149 original size:29 final size:29
Alignment explanation
Indices: 23873093--23873149 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
23873083 AAGTTTATGT
*
23873093 GAATTTAATTTTTATATTTTTACTTTTAG
1 GAATTTAATTTTTATATTTTTACATTTAG
*
23873122 GAATTTAATTTTTTTATTTTCTA-ATTTA
1 GAATTTAATTTTTATATTTT-TACATTTA
23873150 AATATTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (29 bp):
GAATTTAATTTTTATATTTTTACATTTAG
Found at i:23881188 original size:18 final size:19
Alignment explanation
Indices: 23881172--23881223 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
23881162 AAAAATATAA
23881172 AATTTGGAATTTTTATAAAT
1 AATTT-GAATTTTTATAAAT
*
23881192 AATTTGAA-TTTTAAAAATT
1 AATTTGAATTTTTATAAA-T
*
23881211 AGTTTGAATTTTT
1 AATTTGAATTTTT
23881224 GAAAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.29
19 11 0.39
20 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTTGAATTTTTATAAAT
Found at i:23881202 original size:19 final size:20
Alignment explanation
Indices: 23881172--23881237 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
23881162 AAAAATATAA
*
23881172 AATTTGGAATTTTTATAAA-T
1 AATTT-GAATTTTTAAAAATT
23881192 AATTTGAA-TTTTAAAAATT
1 AATTTGAATTTTTAAAAATT
* *
23881211 AGTTTGAATTTTTGAAAATT
1 AATTTGAATTTTTAAAAATT
*
23881231 ATTTTGA
1 AATTTGA
23881238 TTTATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.20
19 11 0.28
20 21 0.52
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
AATTTGAATTTTTAAAAATT
Found at i:23881499 original size:24 final size:24
Alignment explanation
Indices: 23881466--23881516 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
23881456 AGAAATAATA
*
23881466 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
23881490 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
23881514 TTT
1 TTT
23881517 GAGTAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:23881525 original size:24 final size:24
Alignment explanation
Indices: 23881474--23881528 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
23881464 TATTTCAGTT
*
23881474 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATA
* *
23881498 AAACTCTGTTTATTTGTTTGAGTA
1 AAACTCTGTTTATTTGTTTCAATA
23881522 AAACTCT
1 AAACTCT
23881529 TATTAGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATA
Found at i:23885692 original size:22 final size:24
Alignment explanation
Indices: 23885657--23885702 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
23885647 TTGAGAATTT
* *
23885657 AGAATTTAGTTCTTTTA-TTTTTA
1 AGAATTTAGATCTTCTACTTTTTA
23885680 AGAATTTA-ATCTTCTACTTTTTA
1 AGAATTTAGATCTTCTACTTTTTA
23885703 GACATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.57
Consensus pattern (24 bp):
AGAATTTAGATCTTCTACTTTTTA
Found at i:23887251 original size:29 final size:29
Alignment explanation
Indices: 23887204--23887281 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 29
23887194 ATTCCAATTT
23887204 AAATTTCATATATATAATTAC-ACTAAATCA
1 AAATTT-ATATATA-AATTACAACTAAATCA
*
23887234 AAATTTATATATTAAATTACATATTAAATCA
1 AAATTTATATA-TAAATTACA-ACTAAATCA
23887265 AAATTTATATATAAATT
1 AAATTTATATATAAATT
23887282 TAATATTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 11 0.25
30 14 0.32
31 19 0.43
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTTATATATAAATTACAACTAAATCA
Found at i:23887967 original size:24 final size:24
Alignment explanation
Indices: 23887940--23887994 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
23887930 GAATAATAAG
* *
23887940 AGTTTGACTCAAACAAATAAACAA
1 AGTTTAACTAAAACAAATAAACAA
* *
23887964 AGTTTAATTAAAACAAATAAACAG
1 AGTTTAACTAAAACAAATAAACAA
23887988 AGTTTAA
1 AGTTTAA
23887995 TTTAAAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (24 bp):
AGTTTAACTAAAACAAATAAACAA
Found at i:23887995 original size:24 final size:24
Alignment explanation
Indices: 23887950--23887996 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
23887940 AGTTTGACTC
23887950 AAACAAATAAACAAAGTTTAATTA
1 AAACAAATAAACAAAGTTTAATTA
*
23887974 AAACAAATAAACAGAGTTTAATT
1 AAACAAATAAACAAAGTTTAATT
23887997 TAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTA
Found at i:23891236 original size:1 final size:1
Alignment explanation
Indices: 23891230--23891261 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
23891220 GGTCTCTTAA
23891230 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
23891262 GAGCTGTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:23893056 original size:15 final size:16
Alignment explanation
Indices: 23893024--23893056 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23893014 AATCTAAATC
*
23893024 AAACTCTCAAATATAA
1 AAACTCTCAAATAAAA
23893040 AAACTCT-AAATAAAA
1 AAACTCTCAAATAAAA
23893055 AA
1 AA
23893057 GTCTTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACTCTCAAATAAAA
Found at i:23897533 original size:73 final size:73
Alignment explanation
Indices: 23897442--23897635 Score: 307
Period size: 73 Copynumber: 2.7 Consensus size: 73
23897432 TCAACAAAAG
* **
23897442 ACACAATACATAACCAAATATTTTAACTGATTTAAGCACTCGGACGTATATTTCAACTGCTTTAA
1 ACACAATACATAATCAAATATTTTAACTGATTTAAGCACTCGGACACATATTTCAACTGCTTTAA
23897507 CCATTCTA
66 CCATTCTA
*
23897515 ACACAATACATAATCAAATATTTTAACTGATTTAAGTACTCGGACACATATTTCAACTGCTTTAA
1 ACACAATACATAATCAAATATTTTAACTGATTTAAGCACTCGGACACATATTTCAACTGCTTTAA
*
23897580 CCATTCTG
66 CCATTCTA
* * * *
23897588 ACACAATACATAATCAAATATTTTAATTGCTTTAACCACTCGAACACA
1 ACACAATACATAATCAAATATTTTAACTGATTTAAGCACTCGGACACA
23897636 ATACATAAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (73 bp):
ACACAATACATAATCAAATATTTTAACTGATTTAAGCACTCGGACACATATTTCAACTGCTTTAA
CCATTCTA
Found at i:23897610 original size:43 final size:43
Alignment explanation
Indices: 23897562--23897643 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
23897552 ACTCGGACAC
*
23897562 ATATTTCAACTGCTTTAACCATTCTG-ACACAATACATAATCAA
1 ATATTTCAACTGCTTTAACCACTC-GAACACAATACATAATCAA
* *
23897605 ATATTTTAATTGCTTTAACCACTCGAACACAATACATAA
1 ATATTTCAACTGCTTTAACCACTCGAACACAATACATAA
23897644 AAGTCCTGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (43 bp):
ATATTTCAACTGCTTTAACCACTCGAACACAATACATAATCAA
Found at i:23899780 original size:28 final size:28
Alignment explanation
Indices: 23899739--23899794 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
23899729 GTTAATTATC
23899739 TTAACGTTGATCATAATGATTGCTCATG
1 TTAACGTTGATCATAATGATTGCTCATG
*
23899767 TTAACGTTGCTCATAATGATTGCTCATG
1 TTAACGTTGATCATAATGATTGCTCATG
23899795 GATTATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (28 bp):
TTAACGTTGATCATAATGATTGCTCATG
Found at i:23911687 original size:20 final size:20
Alignment explanation
Indices: 23911662--23911700 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23911652 TAAACAATCA
23911662 ATTTTT-AAAGAAAATTTTTT
1 ATTTTTCAAA-AAAATTTTTT
*
23911682 ATTTTTCAAAAGAATTTTT
1 ATTTTTCAAAAAAATTTTT
23911701 CTTGAGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTTCAAAAAAATTTTTT
Found at i:23914699 original size:17 final size:17
Alignment explanation
Indices: 23914674--23914746 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
23914664 TTTTAATTTT
* *
23914674 ATTTTAATTGAAAATAA
1 ATTTAAATTTAAAATAA
*
23914691 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
**
23914708 ATTTAAACTCAAAAAATAA
1 ATTTAAA-T-TTAAAATAA
23914727 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
23914744 ATT
1 ATT
23914747 CAAACTTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 31 0.67
18 2 0.04
19 13 0.28
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:23914729 original size:36 final size:36
Alignment explanation
Indices: 23914684--23914752 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
23914674 ATTTTAATTG
* *
23914684 AAAATAAATTTAAATTTAAAGTAAATTTAAACTCAA
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTCAA
23914720 AAAATAAATTTAAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
23914753 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.33
Consensus pattern (36 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTCAA
Found at i:23914750 original size:30 final size:30
Alignment explanation
Indices: 23914694--23914750 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
23914684 AAAATAAATT
*
23914694 TAAATTTAAAGTAAATTTAAACTCAAAAAA
1 TAAATTTAAAGTAAATATAAACTCAAAAAA
* *
23914724 TAAATTTAAATTTAAA-ATAAATTCAAA
1 TAAATTTAAA-GTAAATATAAACTCAAA
23914751 CTTATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (30 bp):
TAAATTTAAAGTAAATATAAACTCAAAAAA
Found at i:23915078 original size:13 final size:13
Alignment explanation
Indices: 23915060--23915109 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
23915050 TAAATCAAGC
23915060 TTTCAAAAGTATT
1 TTTCAAAAGTATT
23915073 TTTCAAAA-TCATTT
1 TTTCAAAAGT-A-TT
* *
23915087 TTTC-AAAGCACT
1 TTTCAAAAGTATT
23915099 TTTCAAAAGTA
1 TTTCAAAAGTA
23915110 CTGCTAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.20
13 18 0.60
14 6 0.20
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTCAAAAGTATT
Found at i:23915290 original size:16 final size:16
Alignment explanation
Indices: 23915269--23915299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23915259 CATGTTGGAG
23915269 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
23915285 CATATATATTTGAAA
1 CATATAAATTTGAAA
23915300 AAAATTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:23915876 original size:24 final size:24
Alignment explanation
Indices: 23915844--23915895 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
23915834 AAGTTATTTA
23915844 AATTGTAAAATTTAACTCGATTCG
1 AATTGTAAAATTTAACTCGATTCG
*
23915868 AATTGTAAAATTTAACTCTATTCG
1 AATTGTAAAATTTAACTCGATTCG
23915892 AATT
1 AATT
23915896 ATTTATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (24 bp):
AATTGTAAAATTTAACTCGATTCG
Found at i:23918308 original size:11 final size:11
Alignment explanation
Indices: 23918292--23918317 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23918282 TAATAGCATT
23918292 AAAAAGAAAAA
1 AAAAAGAAAAA
23918303 AAAAAGAAAAA
1 AAAAAGAAAAA
23918314 AAAA
1 AAAA
23918318 GATTGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:23924164 original size:20 final size:20
Alignment explanation
Indices: 23924139--23924178 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
23924129 TTAAATATTT
23924139 TAAATACT-TAATTTAAAAAA
1 TAAATACTATAA-TTAAAAAA
23924159 TAAATACTATAATTAAAAAA
1 TAAATACTATAATTAAAAAA
23924179 AACTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATACTATAATTAAAAAA
Found at i:23924177 original size:21 final size:20
Alignment explanation
Indices: 23924139--23924179 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
23924129 TTAAATATTT
*
23924139 TAAATACTTAATTTAAAAAA
1 TAAATACTTAATTAAAAAAA
23924159 TAAATACTATAATTAAAAAAA
1 TAAATACT-TAATTAAAAAAA
23924180 ACTATATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATACTTAATTAAAAAAA
Found at i:23924849 original size:29 final size:29
Alignment explanation
Indices: 23924768--23924848 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
23924758 AATCTCAAAA
23924768 CTATACATGAACTTT-AGTTTAATGTGCAATT
1 CTATACATGAACTTTGA-TTT--TGTGCAATT
*
23924799 CTATACATGTACTTTGATTTTGTGCAATT
1 CTATACATGAACTTTGATTTTGTGCAATT
*
23924828 CTATACATGAAATTTTGATTT
1 CTATACATG-AACTTTGATTT
23924849 GACCAAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 18 0.40
30 9 0.20
31 17 0.38
32 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (29 bp):
CTATACATGAACTTTGATTTTGTGCAATT
Found at i:23925019 original size:31 final size:31
Alignment explanation
Indices: 23924980--23925067 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
23924970 AATGTTCATG
23924980 ATTGAATCAAAATTAAAATTTCATGTATATA
1 ATTGAATCAAAATTAAAATTTCATGTATATA
* * * * *
23925011 TTTGAATCACAATCAAAGTTTCATGTGTATA
1 ATTGAATCAAAATTAAAATTTCATGTATATA
*
23925042 ATTGCATC-AAATTAAAA-TTCATGTAT
1 ATTGAATCAAAATTAAAATTTCATGTAT
23925068 CAAATTTCAT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 8 0.17
30 6 0.13
31 32 0.70
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (31 bp):
ATTGAATCAAAATTAAAATTTCATGTATATA
Found at i:23926947 original size:23 final size:23
Alignment explanation
Indices: 23926912--23926966 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
23926902 ATCAGTAAAT
* *
23926912 TATATTTAT-CAATGCTTGTATA
1 TATAATTATACAATGCTTATATA
* * *
23926934 TCTTATTATACAATGTTTATATA
1 TATAATTATACAATGCTTATATA
23926957 TATAATTATA
1 TATAATTATA
23926967 ATTGTTTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (23 bp):
TATAATTATACAATGCTTATATA
Found at i:23927564 original size:33 final size:33
Alignment explanation
Indices: 23927527--23927599 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
23927517 ACAAAAAAAT
**
23927527 TTATTATTTTCTTGTTGTTTTGCTACTATTTTC-
1 TTATTATTTTCTCATTGTTTTGCTACTA-TTTCA
*
23927560 TTATTGTTTTCTCATTGTTTTGCTACTATTTCA
1 TTATTATTTTCTCATTGTTTTGCTACTATTTCA
23927593 TTATTAT
1 TTATTAT
23927600 ATTACTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.15, C:0.12, G:0.08, T:0.64
Consensus pattern (33 bp):
TTATTATTTTCTCATTGTTTTGCTACTATTTCA
Found at i:23927614 original size:33 final size:33
Alignment explanation
Indices: 23927544--23927614 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
23927534 TTTCTTGTTG
* * *
23927544 TTTTGCTACTATTTTCTTATTGTTTTCTCATTG
1 TTTTGCTACTATTTTCTTATTATTTACTCATTA
23927577 TTTTGCTACTA-TTTCATTATTATATTACT-ATTA
1 TTTTGCTACTATTTTC-TTATTAT-TTACTCATTA
23927610 TTTTG
1 TTTTG
23927615 TTGTTATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.12
33 25 0.76
34 4 0.12
ACGTcount: A:0.18, C:0.13, G:0.07, T:0.62
Consensus pattern (33 bp):
TTTTGCTACTATTTTCTTATTATTTACTCATTA
Found at i:23933590 original size:18 final size:19
Alignment explanation
Indices: 23933545--23933590 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
23933535 TAAAAATATT
*
23933545 TATTTTAT-TTTATTTTAA
1 TATTTTATATTTATTATAA
*
23933563 TATTTAATATTT-TTATAA
1 TATTTTATATTTATTATAA
*
23933581 TTTTTTATAT
1 TATTTTATAT
23933591 AGTCATCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTATATTTATTATAA
Found at i:23936596 original size:58 final size:58
Alignment explanation
Indices: 23936487--23936595 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
23936477 ATTTTTTTTA
* **
23936487 AATTTGGTATCTAAACTTTGATACTTTTCTTTAAGTTGGTATTTAATTTTTTGAGTTC
1 AATTTGGTATCTAAACTTTAATACTTTTCTTTAAGTTGGTACATAATTTTTTGAGTTC
* *
23936545 AATTTGGTATCTAAA-TTTAACTATTTTTC-TTAATTTGGTACATAATTTTTT
1 AATTTGGTATCTAAACTTTAA-TACTTTTCTTTAAGTTGGTACATAATTTTTT
23936596 TAATATTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 23 0.51
58 22 0.49
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (58 bp):
AATTTGGTATCTAAACTTTAATACTTTTCTTTAAGTTGGTACATAATTTTTTGAGTTC
Found at i:23936825 original size:59 final size:58
Alignment explanation
Indices: 23936730--23936894 Score: 192
Period size: 59 Copynumber: 2.8 Consensus size: 58
23936720 AATATTTAAT
* *
23936730 AAATTTA-GTATCAAATTAG-GAAAAAATGCTAGGTTCAAGTACCAAATTGAGTCCAAAAA
1 AAATTTAGGTATCAAATTAGAAAAAAAAT-C-AAGTTCAAGTACCAAATTGAGT-CAAAAA
** *
23936789 AAATTTAGGTATCAAATTAGAAAAAAAATCAAGTTC-AGATAATAAATTGGGTCAAAAA
1 AAATTTAGGTATCAAATTAGAAAAAAAATCAAGTTCAAG-TACCAAATTGAGTCAAAAA
* * *
23936847 AAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAAT
1 AAATTTAGGTATCAAATT-AGAAAAAAAATCAAGTTCAAGTACCAAAT
23936895 ATTATGTTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
58 24 0.26
59 45 0.49
60 15 0.16
61 7 0.08
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.25
Consensus pattern (58 bp):
AAATTTAGGTATCAAATTAGAAAAAAAATCAAGTTCAAGTACCAAATTGAGTCAAAAA
Found at i:23940311 original size:29 final size:29
Alignment explanation
Indices: 23940273--23940361 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
23940263 GTAAGTTAGC
23940273 TCACTCTATACTTATTTTCCAATGTCTCA
1 TCACTCTATACTTATTTTCCAATGTCTCA
23940302 TCACTCTATACTTATTTTCCAATGTCTCA
1 TCACTCTATACTTATTTTCCAATGTCTCA
23940331 TCACTCTATACTTATTTTCCAATGTCTCA
1 TCACTCTATACTTATTTTCCAATGTCTCA
23940360 TC
1 TC
23940362 CTTTCAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.24, C:0.28, G:0.03, T:0.45
Consensus pattern (29 bp):
TCACTCTATACTTATTTTCCAATGTCTCA
Found at i:23948879 original size:11 final size:11
Alignment explanation
Indices: 23948865--23948905 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
23948855 AAATAAATAT
*
23948865 AAGATAAGAAA
1 AAGAAAAGAAA
23948876 AAGAAAAG-AA
1 AAGAAAAGAAA
23948886 AAGAAAAG-AA
1 AAGAAAAGAAA
23948896 AAGAAAAGAA
1 AAGAAAAGAA
23948906 GGGAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:23948882 original size:5 final size:5
Alignment explanation
Indices: 23948874--23948905 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
23948864 TAAGATAAGA
23948874 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
23948906 GGGAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:23952872 original size:22 final size:23
Alignment explanation
Indices: 23952820--23952872 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
23952810 TATGTTTTGT
*
23952820 TTCTATTTCCACAGGGTAGGTTAG
1 TTCTA-TTCCACAAGGTAGGTTAG
*
23952844 TTC-ATTCCACAAGGTAGTTTA-
1 TTCTATTCCACAAGGTAGGTTAG
23952865 TTCTATTC
1 TTCTATTC
23952873 TGTGACTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.73
23 1 0.04
24 3 0.12
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
TTCTATTCCACAAGGTAGGTTAG
Found at i:23953029 original size:2 final size:2
Alignment explanation
Indices: 23953022--23953077 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
23953012 TCTTATTTTA
23953022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23953064 AT -T AT AT GAT AT AT
1 AT AT AT AT -AT AT AT
23953078 GATAGTATGT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23953864 original size:22 final size:24
Alignment explanation
Indices: 23953829--23953873 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
23953819 ATAAAGTATA
*
23953829 ATATTACAATTTTTAAA-GGGGTT
1 ATATTACAAATTTTAAACGGGGTT
23953852 ATATTA-AAATTTTAAACGGGGT
1 ATATTACAAATTTTAAACGGGGT
23953874 CAGCGTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (24 bp):
ATATTACAAATTTTAAACGGGGTT
Found at i:23954499 original size:20 final size:19
Alignment explanation
Indices: 23954476--23954520 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
23954466 CGATTTAAGT
23954476 AATAATGAATCAATTCAAAC
1 AATAAT-AATCAATTCAAAC
*
23954496 AATAAATAATCAATTCAAAT
1 AAT-AATAATCAATTCAAAC
23954516 AATAA
1 AATAA
23954521 AAAAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (19 bp):
AATAATAATCAATTCAAAC
Found at i:23954529 original size:21 final size:21
Alignment explanation
Indices: 23954483--23954559 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
23954473 AGTAATAATG
*
23954483 AATCAATTCAAACAAT-AAAT
1 AATCAATTCAAATAATAAAAT
*
23954503 AATCAATTCAAATAATAAAAA
1 AATCAATTCAAATAATAAAAT
*
23954524 AATCAAGTC-AATCAATAAAAT
1 AATCAATTCAAAT-AATAAAAT
* *
23954545 AATCGATCCAAATAA
1 AATCAATTCAAATAA
23954560 GCAAAGAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 18 0.38
21 26 0.55
22 3 0.06
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (21 bp):
AATCAATTCAAATAATAAAAT
Found at i:23961853 original size:18 final size:18
Alignment explanation
Indices: 23961830--23961865 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23961820 ATAACCCCAA
23961830 CATTACTCAGACAGATGT
1 CATTACTCAGACAGATGT
23961848 CATTACTCAGACAGATGT
1 CATTACTCAGACAGATGT
23961866 TCAGTTTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
CATTACTCAGACAGATGT
Found at i:23968928 original size:6 final size:6
Alignment explanation
Indices: 23968902--23968994 Score: 70
Period size: 6 Copynumber: 16.2 Consensus size: 6
23968892 CAAGCCCAAT
* * *
23968902 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
* * * * *
23968948 TTT-AT TTTGAA TTTAAA TTT-AT TTTAAA TTTGAA TTTAAA TTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
23968994 T
1 T
23968995 ATCTAAAATG
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
4 3 0.04
5 13 0.19
6 50 0.72
7 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:23968964 original size:23 final size:24
Alignment explanation
Indices: 23968902--23968994 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 24
23968892 CAAGCCCAAT
* * *
23968902 TTTAAATTTTAATTT-ATTTTAAG
1 TTTAAATTTGAATTTAAATTTAAA
23968925 TTTAAATTT--ATTATAAATTTAAA
1 TTTAAATTTGAATT-TAAATTTAAA
* *
23968948 TTT-ATTTTGAATTTAAATTT-AT
1 TTTAAATTTGAATTTAAATTTAAA
*
23968970 TTTAAATTTGAATTTAAATTAAAA
1 TTTAAATTTGAATTTAAATTTAAA
23968994 T
1 T
23968995 ATCTAAAATG
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.05
22 9 0.16
23 40 0.70
24 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
TTTAAATTTGAATTTAAATTTAAA
Found at i:23968992 original size:17 final size:17
Alignment explanation
Indices: 23968900--23968985 Score: 127
Period size: 17 Copynumber: 5.1 Consensus size: 17
23968890 ATCAAGCCCA
*
23968900 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
23968917 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
23968934 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
23968951 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
23968968 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
23968985 A
1 A
23968986 AATTAAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:23970568 original size:30 final size:30
Alignment explanation
Indices: 23970529--23970930 Score: 323
Period size: 30 Copynumber: 13.7 Consensus size: 30
23970519 AAGGTCCCTG
* *
23970529 AACTGTCCAAAAATCACATTTTGACCCTTA
1 AACTTTCCAAAAATTACATTTTGACCCTTA
*
23970559 AACTTTCCAAAAATTACATTTTGACCCCTA
1 AACTTTCCAAAAATTACATTTTGACCCTTA
* *
23970589 AAC-TTCTC-AAAA-TACATTTTAACCCCTA
1 AACTTTC-CAAAAATTACATTTTGACCCTTA
* * *
23970617 AACTTTCTAAAAAGTACATTTTGACCCCTCA
1 AACTTTCCAAAAATTACATTTTGA-CCCTTA
* * *
23970648 AAC-TTCTC-AAAATTGCATTTTAAACCTTA
1 AACTTTC-CAAAAATTACATTTTGACCCTTA
* *
23970677 AACTTTCCAAAAGTTACATTTTAATCCC-TA
1 AACTTTCCAAAAATTACATTTTGA-CCCTTA
* *
23970707 AACTTTCCAAAAATTACCTTTTGACCCTCA
1 AACTTTCCAAAAATTACATTTTGACCCTTA
* *
23970737 AACTTTCCAAAAATTACATTTTGACCTTTG
1 AACTTTCCAAAAATTACATTTTGACCCTTA
* * * **
23970767 AACTTTCTAAAAATTATATTTTTACCCTCG
1 AACTTTCCAAAAATTACATTTTGACCCTTA
* * * *
23970797 AAC-TTCCAAAGATCACATTTT-TCTCC-AA
1 AACTTTCCAAAAATTACATTTTGAC-CCTTA
*
23970825 AAC-TTCCAAAAATCACATTTT-A-CCTTA
1 AACTTTCCAAAAATTACATTTTGACCCTTA
* * * *
23970852 AA-TTTCCCAAAATGACATTTTTACCGCTAA
1 AACTTTCCAAAAATTACATTTTGACC-CTTA
* *
23970882 AACTTTCC-AAAATTACATTTTAACCCCT-
1 AACTTTCCAAAAATTACATTTTGACCCTTA
* *
23970910 AACTCTCCAAAACTT-CATTTT
1 AACTTTCCAAAAATTACATTTT
23970931 CGTCCTCGAT
Statistics
Matches: 305, Mismatches: 49, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.01
27 19 0.06
28 53 0.17
29 48 0.16
30 169 0.55
31 14 0.05
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTGACCCTTA
Found at i:23982149 original size:208 final size:207
Alignment explanation
Indices: 23981791--23982469 Score: 928
Period size: 208 Copynumber: 3.3 Consensus size: 207
23981781 ATCCAAAACA
* * * *
23981791 AATAAAGTGGTTGTCTTCCTGATGAGATATAGAGAAATGGATCAAATCCGTCTTCCTGATGAGAT
1 AATAAAGTGGTCGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGAT
* * * *
23981856 ACAGAGAAGCGAATTGAAACAGTGATGTGACTATCTTCCTGATGAGATACAGAGAAGTATGCCAA
66 ACAGAGAAGCGGATTGAAAAAGTGATGCGACCATCTTCCTGATGAGATACAGAGAAGTATGCCAA
* * * * *
23981921 ATTAATGAAACAAAGCTCAATGTGAGCAAAACTTCGAATCCCAACTTTCTAATGAGATACTGAGG
131 ATTAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAA-CCCAGCTTCCTGATGAGATACTGAGA
*
23981986 AGCAAGTCGAAGC
195 AGCAGGTCGAAGC
* * * * *
23981999 AATAAAGTGGTTGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCATATTTCTGATGAGAT
1 AATAAAGTGGTCGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGAT
*
23982064 ACAGAGAAGCGGATTGAAATAGTGATGCGACCATCTTCCTGATGAGATACAGAGAAGTATGCCAA
66 ACAGAGAAGCGGATTGAAAAAGTGATGCGACCATCTTCCTGATGAGATACAGAGAAGTATGCCAA
* * *
23982129 ATCAATGAAACAAAGCTCAATCTGAGCGAAACTTCGAACTCTAGCTTCCTGATGAGATACTGAGA
131 ATTAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAAC-CCAGCTTCCTGATGAGATACTGAGA
*
23982194 AACAGGTCGAAGC
195 AGCAGGTCGAAGC
* * * * *
23982207 AATAAAGCGGTCGTCTTCTTGATGAGATATAGAGAAGTGAAACAAATCCGTCTTCCTGATGAGAT
1 AATAAAGTGGTCGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGAT
* * * * * *
23982272 ACAGAGAAGCAGA-TCAAACAAGTGAGGCGATCATCTTCCTGATCAGATACAGAGAAGTATACCA
66 ACAGAGAAGCGGATTGAAA-AAGTGATGCGACCATCTTCCTGATGAGATACAGAGAAGTATGCCA
** *
23982336 AATTAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGGCACTGAC
130 AATTAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAA-CCCAGCTTCCTGATGAGATACTGAG
23982401 AAGCAGGTCGAAGC
194 AAGCAGGTCGAAGC
* ** * *
23982415 AATAAAATGGTCACCTTCCTGATGAGATACAAAGAAGTGGACCTAATCCGTCTTC
1 AATAAAGTGGTCGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTC
23982470 TTAGTGAAAT
Statistics
Matches: 415, Mismatches: 53, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
207 5 0.01
208 409 0.99
209 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (207 bp):
AATAAAGTGGTCGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGAT
ACAGAGAAGCGGATTGAAAAAGTGATGCGACCATCTTCCTGATGAGATACAGAGAAGTATGCCAA
ATTAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAA
GCAGGTCGAAGC
Found at i:23982338 original size:85 final size:85
Alignment explanation
Indices: 23982173--23982329 Score: 199
Period size: 85 Copynumber: 1.8 Consensus size: 85
23982163 CGAACTCTAG
* * * * * * * *
23982173 CTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAATAAAGCGGTCGTCTTCTTGATGAGATATA
1 CTTCCTGATGAGATACAGAGAAACAGATCGAAACAATAAAGCGATCATCTTCCTGATCAGATACA
23982238 GAGAAGTGAAACAAATCCGT
66 GAGAAGTGAAACAAATCCGT
* * *
23982258 CTTCCTGATGAGATACAGAGAAGCAGATC-AAACAAGTGAGGCGATCATCTTCCTGATCAGATAC
1 CTTCCTGATGAGATACAGAGAAACAGATCGAAACAA-TAAAGCGATCATCTTCCTGATCAGATAC
23982322 AGAGAAGT
65 AGAGAAGT
23982330 ATACCAAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 5 0.08
85 55 0.92
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAACAGATCGAAACAATAAAGCGATCATCTTCCTGATCAGATACA
GAGAAGTGAAACAAATCCGT
Found at i:23982836 original size:17 final size:17
Alignment explanation
Indices: 23982804--23982889 Score: 109
Period size: 17 Copynumber: 5.1 Consensus size: 17
23982794 ATCAAGCCCA
* *
23982804 ATTTTTAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
23982821 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
23982838 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
23982855 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
23982872 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
23982889 A
1 A
23982890 AATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:23982848 original size:34 final size:34
Alignment explanation
Indices: 23982810--23982889 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
23982800 CCCAATTTTT
*
23982810 AATTTTAATTTATTTTAAGTTTAAATTTATTATA
1 AATTTAAATTTATTTTAAGTTTAAATTTATTATA
* *
23982844 AATTTAAATTTATTTTGAGTTTAAATTTATTTTA
1 AATTTAAATTTATTTTAAGTTTAAATTTATTATA
*
23982878 AATTTGAATTTA
1 AATTTAAATTTA
23982890 AATTAAAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (34 bp):
AATTTAAATTTATTTTAAGTTTAAATTTATTATA
Found at i:23982868 original size:23 final size:24
Alignment explanation
Indices: 23982810--23982898 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 24
23982800 CCCAATTTTT
* * *
23982810 AATTTTAATTT-ATTTTAAGTTTA
1 AATTTGAATTTAAATTTAAATTTA
23982833 AATTT--ATTATAAATTTAAATTT-
1 AATTTGAATT-TAAATTTAAATTTA
* * *
23982855 ATTTTGAGTTTAAATTT-ATTTTA
1 AATTTGAATTTAAATTTAAATTTA
*
23982878 AATTTGAATTTAAATTAAAAT
1 AATTTGAATTTAAATTTAAAT
23982899 GTCCAAAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
21 3 0.06
22 9 0.18
23 35 0.69
24 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
AATTTGAATTTAAATTTAAATTTA
Found at i:23983993 original size:30 final size:29
Alignment explanation
Indices: 23983952--23984277 Score: 227
Period size: 30 Copynumber: 11.1 Consensus size: 29
23983942 AAGGTCCTTG
* *
23983952 AACTGTCCAAAAATCATATTTTCACCCCCA
1 AACTTTCCAAAAATCACATTTT-ACCCCCA
*
23983982 AACTTTCCAAAAAGT-ACATTTTGACCCCTA
1 AACTTTCCAAAAA-TCACATTTT-ACCCCCA
* ** *
23984012 AACTTCCCAAAAATCATGTTTTAACCCCTA
1 AACTTTCCAAAAATCACATTTT-ACCCCCA
* **
23984042 AACTTTCC-AAAATTACATTTTTACCCTTA
1 AACTTTCCAAAAATCACA-TTTTACCCCCA
* * *
23984071 AACTTTCCAAAAATTACCTTTTAACCCTCA
1 AACTTTCCAAAAATCACATTTT-ACCCCCA
**
23984101 AACTTTCCAAAAAAT-ACATTTTAACCCTTA
1 AACTTTCC-AAAAATCACATTTT-ACCCCCA
* * *
23984131 AACTTTCCAAAAATTACATTTTACCCTCG
1 AACTTTCCAAAAATCACATTTTACCCCCA
* * *
23984160 AAC-TTCCAAAGATCACATTTTTTCCCTCA
1 AACTTTCCAAAAATCACA-TTTTACCCCCA
* *
23984189 AACTTT-CAAAAATCACGTTTTA-CCCTA
1 AACTTTCCAAAAATCACATTTTACCCCCA
* * *
23984216 AA-TTTCCCAAAATGACATTTTTACCCCTAA
1 AACTTTCCAAAAATCACA-TTTTACCCC-CA
* * * *
23984246 AACTTT-CTAAAATTATATTTTAACCCCA
1 AACTTTCCAAAAATCACATTTTACCCCCA
23984274 AACT
1 AACT
23984278 CTCTGAAACT
Statistics
Matches: 245, Mismatches: 37, Indels: 30
0.79 0.12 0.10
Matches are distributed among these distances:
26 3 0.01
27 13 0.05
28 26 0.11
29 71 0.29
30 122 0.50
31 10 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
AACTTTCCAAAAATCACATTTTACCCCCA
Found at i:23984093 original size:59 final size:58
Alignment explanation
Indices: 23983947--23984277 Score: 296
Period size: 60 Copynumber: 5.7 Consensus size: 58
23983937 TCTAGAAGGT
* * * * * * *
23983947 CCTTGAACTGTCCAAAAATCATATTTTCACCCCCAAACTTTCCAAAAAGTACATTTTGAC
1 CCTTAAACTTTCCAAAAATCACATTTT-AACCCTAAACTTTCC-AAAATTACATTTTTAC
* * **
23984007 CCCTAAACTTCCCAAAAATCATGTTTTAACCCCTAAACTTTCCAAAATTACATTTTTAC
1 CCTTAAACTTTCCAAAAATCACATTTTAA-CCCTAAACTTTCCAAAATTACATTTTTAC
* * * *
23984066 CCTTAAACTTTCCAAAAATTACCTTTTAACCCTCAAACTTTCCAAAAAATACATTTTAAC
1 CCTTAAACTTTCCAAAAATCACATTTTAACCCT-AAACTTTCC-AAAATTACATTTTTAC
* * * *
23984126 CCTTAAACTTTCCAAAAATTACATTTT-ACCCTCGAAC-TTCCAAAGATCACATTTTTTC
1 CCTTAAACTTTCCAAAAATCACATTTTAACCCT-AAACTTTCCAAA-ATTACATTTTTAC
* * *
23984184 CCTCAAACTTT-CAAAAATCACGTTTT-ACCCTAAA-TTTCCCAAAATGACATTTTTACC
1 CCTTAAACTTTCCAAAAATCACATTTTAACCCTAAACTTT-CCAAAATTACATTTTTA-C
* * * * *
23984241 CCTAAAACTTT-CTAAAATTATATTTTAACCCCAAACT
1 CCTTAAACTTTCCAAAAATCACATTTTAACCCTAAACT
23984278 CTCTGAAACT
Statistics
Matches: 228, Mismatches: 34, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
56 14 0.06
57 48 0.21
58 34 0.15
59 58 0.25
60 74 0.32
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
CCTTAAACTTTCCAAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTTAC
Found at i:23984708 original size:97 final size:97
Alignment explanation
Indices: 23984540--23984727 Score: 295
Period size: 97 Copynumber: 1.9 Consensus size: 97
23984530 TTTAAAATCG
* * * *
23984540 AGGCAATATTTCTTTATTTCGGGTTATGAAAATTTGTGCTTTAACTTACTAGGCGTGATTTTTCT
1 AGGCAATATTCCTTTATTTCGGGTTATGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTTCT
* *
23984605 TCAAACCGAAATAATTGAGTACCCTTAAGCCA
66 TCAAACCGAAATAATCGAATACCCTTAAGCCA
*
23984637 AGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTTCT
1 AGGCAATATTCCTTTATTTCGGGTTATGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTTCT
* *
23984702 TTAAACCGGAATAATCGAATACCCTT
66 TCAAACCGAAATAATCGAATACCCTT
23984728 TTTCAAGATT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (97 bp):
AGGCAATATTCCTTTATTTCGGGTTATGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTTCT
TCAAACCGAAATAATCGAATACCCTTAAGCCA
Found at i:23989403 original size:31 final size:31
Alignment explanation
Indices: 23989362--23989425 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
23989352 AAATTAGCAT
*
23989362 TAAATTATTTGAAAATTT-CTATTTAAGTCAC
1 TAAACTATTTGAAAATTTGC-ATTTAAGTCAC
* *
23989393 TAAACTATTTGAAAGTTTGCGTTTAAGTCAC
1 TAAACTATTTGAAAATTTGCATTTAAGTCAC
23989424 TA
1 TA
23989426 GATAGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (31 bp):
TAAACTATTTGAAAATTTGCATTTAAGTCAC
Found at i:23996123 original size:159 final size:158
Alignment explanation
Indices: 23995832--23996130 Score: 365
Period size: 159 Copynumber: 1.9 Consensus size: 158
23995822 ATGAAATTCG
* * *
23995832 ATCAGTTCTCGATACATGTATTCAACTCAGCCTCAACACATATTTATAATGAAATTTTATTGTCT
1 ATCAGTTCACGATACATGCATTCAACTCAGCCTCAACACATATTTAT-ATGAAATTTTATTATCT
* * *
23995897 TTATGCAGACGTTGATGTTGTCAAGCCTTCTTCCATCTTCCATCCAACCATGGTTGATCACGGAT
65 TTATGCAGACATTAATGTTGTCAAGCCTTCTTCCATCTTCCATCCAACCATGGTTGATCACGCAT
23995962 TTGATTTCCGCACACAAGGGAACATATCC
130 TTGATTTCCGCACACAAGGGAACATATCC
* * *
23995991 ATCAGTTCACGATACATGCATTCAGCTCAGCCTCAGCACATATTTGT-TGTAAATGTTT-TTCAT
1 ATCAGTTCACGATACATGCATTCAACTCAGCCTCAACACATATTTATATG-AAAT-TTTATT-AT
* * ** **
23996054 CTTTATGCA-ACCATTAATGTTGTCGATCCTTC-TCTCA-CTTCCAGTCTGACCATGGTTGATTG
63 CTTTATGCAGA-CATTAATGTTGTCAAGCCTTCTTC-CATCTTCCA-TCCAACCATGGTTGATCA
23996116 CGCATTTGATTTCCG
125 CGCATTTGATTTCCG
23996131 TGAGCACATA
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
157 2 0.02
158 15 0.13
159 102 0.86
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (158 bp):
ATCAGTTCACGATACATGCATTCAACTCAGCCTCAACACATATTTATATGAAATTTTATTATCTT
TATGCAGACATTAATGTTGTCAAGCCTTCTTCCATCTTCCATCCAACCATGGTTGATCACGCATT
TGATTTCCGCACACAAGGGAACATATCC
Found at i:23998797 original size:14 final size:14
Alignment explanation
Indices: 23998778--23998805 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23998768 ATCAACATAA
23998778 ATATTATAAAATTT
1 ATATTATAAAATTT
23998792 ATATTATAAAATTT
1 ATATTATAAAATTT
23998806 GAAGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTATAAAATTT
Found at i:24013535 original size:23 final size:23
Alignment explanation
Indices: 24013509--24013696 Score: 169
Period size: 23 Copynumber: 8.4 Consensus size: 23
24013499 AGTGCTGGGC
24013509 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
24013532 AACATAGAGTACATAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
24013551 -AC-TA-AGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
24013571 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
24013594 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
24013617 ATCAGAGAGCAC-CGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
*
24013640 TAACAGAGAGCACACACAA-AGCTA
1 -AACAGAGAGCACACA-AAGTGCTA
* *
24013664 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
24013687 AACAGAGAGC
1 AACAGAGAGC
24013697 GCGCTAGTGT
Statistics
Matches: 138, Mismatches: 15, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.06
17 2 0.01
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 11 0.08
23 92 0.67
24 12 0.09
25 4 0.03
26 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:24013674 original size:70 final size:68
Alignment explanation
Indices: 24013563--24013696 Score: 173
Period size: 70 Copynumber: 1.9 Consensus size: 68
24013553 TAAGCACACA
** * * *
24013563 AAGTGCTAATCAGAGAGCACACGAAGTGCTAATCAGAGAGCACACGA-AGTGCTAATCAGAGAGC
1 AAGTGCTAATCAGAGAGCACACGAAAAGCTAAACAAAGAGCACAC-ACAGTGCTAAACAGAGAGC
24013627 ACCG
65 ACCG
24013631 AAGTGCTAATAACAGAGAGCACAC-ACAAAGCTAAACAAAGAGCACACACAGTGCTAAACAGAGA
1 AAGTGCTAAT--CAGAGAGCACACGA-AAAGCTAAACAAAGAGCACACACAGTGCTAAACAGAGA
24013695 GC
63 GC
24013697 GCGCTAGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
68 10 0.18
69 2 0.04
70 45 0.79
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.11
Consensus pattern (68 bp):
AAGTGCTAATCAGAGAGCACACGAAAAGCTAAACAAAGAGCACACACAGTGCTAAACAGAGAGCA
CCG
Found at i:24022351 original size:11 final size:11
Alignment explanation
Indices: 24022283--24022351 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
24022273 CCATATGAGC
*
24022283 AAATGATTTTA
1 AAATTATTTTA
*
24022294 AAATTAATTTA
1 AAATTATTTTA
24022305 AAATTATTTTTTA
1 AAATTA--TTTTA
24022318 AAA-TA---TA
1 AAATTATTTTA
24022325 AAATTA--TTA
1 AAATTATTTTA
24022334 AAATTATTTTA
1 AAATTATTTTA
24022345 AAATTAT
1 AAATTAT
24022352 AATCATCATC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 8 0.16
11 25 0.51
12 2 0.04
13 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:24024257 original size:17 final size:17
Alignment explanation
Indices: 24024235--24024267 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
24024225 TTTTATTAAA
24024235 AATATATCAAAACTTTG
1 AATATATCAAAACTTTG
24024252 AATATATCAAAACTTT
1 AATATATCAAAACTTT
24024268 AAATGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
AATATATCAAAACTTTG
Found at i:24035334 original size:18 final size:17
Alignment explanation
Indices: 24035303--24035352 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
24035293 GATTATTTAG
*
24035303 TAATAATAATAATAATAA
1 TAATAACAA-AATAATAA
* *
24035321 TCATAACAACAATAATAG
1 TAATAACAA-AATAATAA
24035339 TAATAACAAAATAA
1 TAATAACAAAATAA
24035353 CAGAATCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (17 bp):
TAATAACAAAATAATAA
Found at i:24035363 original size:17 final size:17
Alignment explanation
Indices: 24035323--24035365 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
24035313 AATAATAATC
*
24035323 ATAACAACAATAATAGTA
1 ATAACAA-AATAACAGTA
24035341 ATAACAAAATAACAG-A
1 ATAACAAAATAACAGTA
24035357 ATCAACAAA
1 AT-AACAAA
24035366 GTATCCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 13 0.57
18 7 0.30
ACGTcount: A:0.65, C:0.14, G:0.05, T:0.16
Consensus pattern (17 bp):
ATAACAAAATAACAGTA
Found at i:24043483 original size:17 final size:17
Alignment explanation
Indices: 24043458--24043519 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
24043448 TCAACAAAGT
24043458 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
24043475 TTAAGTTTATTTTGAAAA
1 TTAAATTTATTTT-AAAA
* *
24043493 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
24043511 TTAAATTTA
1 TTAAATTTA
24043520 AAATATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 21 0.54
18 7 0.18
19 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:24043529 original size:17 final size:17
Alignment explanation
Indices: 24043490--24043531 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
24043480 TTTATTTTGA
**
24043490 AAATTTAAATTTATTAT
1 AAATTTAAATTTAAAAT
24043507 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
*
24043524 ATATTTAA
1 AAATTTAA
24043532 TAAATGTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:24054572 original size:15 final size:15
Alignment explanation
Indices: 24054540--24054579 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
24054530 TATAATTAAC
24054540 CACATA-ATATTTCA
1 CACATATATATTTCA
* *
24054554 CACATATATTTTTCT
1 CACATATATATTTCA
24054569 CACATATATAT
1 CACATATATAT
24054580 CATTATATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:24057592 original size:16 final size:15
Alignment explanation
Indices: 24057555--24057594 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
24057545 CAGTAAAAAA
*
24057555 AGAAAGAAAGGAAGG
1 AGAAAGGAAGGAAGG
24057570 AGAAAGGAAGGAAGGG
1 AGAAAGGAAGGAA-GG
*
24057586 AGTAAGGAA
1 AGAAAGGAA
24057595 AAAAAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (15 bp):
AGAAAGGAAGGAAGG
Found at i:24057975 original size:140 final size:140
Alignment explanation
Indices: 24057723--24058002 Score: 551
Period size: 140 Copynumber: 2.0 Consensus size: 140
24057713 ATTATTTTAA
24057723 AATGTTGTTTGTTAGTTTACAGTGTTTATATTTTTTTTGAATATACTGATGTGATTATATGATAA
1 AATGTTGTTTGTTAGTTTACAGTGTTTATATTTTTTTTGAATATACTGATGTGATTATATGATAA
24057788 TATTTATTCATACTCTCTTAACCCCTTTGAGAGGGCACACACACCTTGCACACACAAACGCTCGA
66 TATTTATTCATACTCTCTTAACCCCTTTGAGAGGGCACACACACCTTGCACACACAAACGCTCGA
24057853 ACTCGGAACC
131 ACTCGGAACC
24057863 AATGTTGTTTGTTAGTTTACAGTGTTTATATTTTTTTTGAATATACTGATGTGATTATATGATAA
1 AATGTTGTTTGTTAGTTTACAGTGTTTATATTTTTTTTGAATATACTGATGTGATTATATGATAA
*
24057928 TATTTATTCATACTCTCTTAACCCCTTTGAGAGGGCACACACACCTTGCACACACAAGCGCTCGA
66 TATTTATTCATACTCTCTTAACCCCTTTGAGAGGGCACACACACCTTGCACACACAAACGCTCGA
24057993 ACTCGGAACC
131 ACTCGGAACC
24058003 CTTAAGATGA
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (140 bp):
AATGTTGTTTGTTAGTTTACAGTGTTTATATTTTTTTTGAATATACTGATGTGATTATATGATAA
TATTTATTCATACTCTCTTAACCCCTTTGAGAGGGCACACACACCTTGCACACACAAACGCTCGA
ACTCGGAACC
Found at i:24058552 original size:34 final size:34
Alignment explanation
Indices: 24058484--24058559 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
24058474 AATCCTATTA
*
24058484 TTTAAACACAACTAAACAAATAATAAAAATTACC
1 TTTAAACACAACTAAACAAACAATAAAAATTACC
* *
24058518 TTTAAACAC-ACTAAAGTAAACACATAAACA-TACC
1 TTTAAACACAACTAAA-CAAACA-ATAAAAATTACC
*
24058552 TTTCAACA
1 TTTAAACA
24058560 AATCTTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 6 0.17
34 24 0.67
35 6 0.17
ACGTcount: A:0.54, C:0.21, G:0.01, T:0.24
Consensus pattern (34 bp):
TTTAAACACAACTAAACAAACAATAAAAATTACC
Found at i:24058858 original size:22 final size:20
Alignment explanation
Indices: 24058814--24058858 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
24058804 AATTAATTAG
*
24058814 AAAATTTATAAAATAAATAA
1 AAAATTTATAAAACAAATAA
*
24058834 AAAATATTATAATAACATATAA
1 AAAAT-TTATAA-AACAAATAA
24058856 AAA
1 AAA
24058859 TATAAACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATTTATAAAACAAATAA
Found at i:24060523 original size:24 final size:25
Alignment explanation
Indices: 24060489--24060539 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
24060479 GTTCAAGTTC
*
24060489 TTCTTTGTTCTGG-CTATT-CGGGTT
1 TTCTTTATTCTGGTC-ATTACGGGTT
24060513 TTCTTTATTCTGGTCATTACGGGTT
1 TTCTTTATTCTGGTCATTACGGGTT
24060538 TT
1 TT
24060540 AGTCACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.08, C:0.16, G:0.22, T:0.55
Consensus pattern (25 bp):
TTCTTTATTCTGGTCATTACGGGTT
Found at i:24064618 original size:24 final size:24
Alignment explanation
Indices: 24064591--24064662 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
24064581 TCCCTCCCGA
*
24064591 TGTTCCTGGACTCGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
** * *
24064615 TGTTGGAGGAGTTGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
** * *
24064639 TGTTGGAGGAGTTGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
24064663 AGTTGGAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.07, C:0.18, G:0.38, T:0.38
Consensus pattern (24 bp):
TGTTCCAGGACTCGTGGTTGTCCC
Found at i:24064667 original size:24 final size:24
Alignment explanation
Indices: 24064604--24064674 Score: 133
Period size: 24 Copynumber: 3.0 Consensus size: 24
24064594 TCCTGGACTC
24064604 GTGGTTGTCCCTGTTGGAGGAGTT
1 GTGGTTGTCCCTGTTGGAGGAGTT
24064628 GTGGTTGTCCCTGTTGGAGGAGTT
1 GTGGTTGTCCCTGTTGGAGGAGTT
*
24064652 GTGGTTGTCCCAGTTGGAGGAGT
1 GTGGTTGTCCCTGTTGGAGGAGT
24064675 CATGGTAGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.10, C:0.13, G:0.42, T:0.35
Consensus pattern (24 bp):
GTGGTTGTCCCTGTTGGAGGAGTT
Found at i:24064680 original size:24 final size:24
Alignment explanation
Indices: 24064605--24064704 Score: 110
Period size: 24 Copynumber: 4.2 Consensus size: 24
24064595 CCTGGACTCG
* **
24064605 TGGTTGTCCCTGTTGGAGGAGTTG
1 TGGTTGTCCCAGTTGGAGGAGTCA
* **
24064629 TGGTTGTCCCTGTTGGAGGAGTTG
1 TGGTTGTCCCAGTTGGAGGAGTCA
24064653 TGGTTGTCCCAGTTGGAGGAGTCA
1 TGGTTGTCCCAGTTGGAGGAGTCA
* ** *
24064677 TGGTAGGGCCAGTCGGAGGAGTCA
1 TGGTTGTCCCAGTTGGAGGAGTCA
24064701 TGGT
1 TGGT
24064705 AGGACCGGTG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.13, C:0.14, G:0.42, T:0.31
Consensus pattern (24 bp):
TGGTTGTCCCAGTTGGAGGAGTCA
Found at i:24064718 original size:24 final size:24
Alignment explanation
Indices: 24064661--24064710 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
24064651 TGTGGTTGTC
* *
24064661 CCAGTTGGAGGAGTCATGGTAGGG
1 CCAGTCGGAGGAGTCATGGTAGGA
24064685 CCAGTCGGAGGAGTCATGGTAGGA
1 CCAGTCGGAGGAGTCATGGTAGGA
24064709 CC
1 CC
24064711 GGTGGGAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.42, T:0.18
Consensus pattern (24 bp):
CCAGTCGGAGGAGTCATGGTAGGA
Found at i:24064748 original size:27 final size:27
Alignment explanation
Indices: 24064715--24064770 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
24064705 AGGACCGGTG
* *
24064715 GGAGTCGGATTTGTGTCTGGTAATGTT
1 GGAGTCGGATTAGTGTCCGGTAATGTT
*
24064742 GGAGTCGGATTAGTGTCCGGTGATGTT
1 GGAGTCGGATTAGTGTCCGGTAATGTT
24064769 GG
1 GG
24064771 GGTAGTAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.09, G:0.41, T:0.36
Consensus pattern (27 bp):
GGAGTCGGATTAGTGTCCGGTAATGTT
Found at i:24065202 original size:4 final size:4
Alignment explanation
Indices: 24065193--24065246 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
24065183 ATTATGAGCA
24065193 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
24065241 ATCT AT
1 ATCT AT
24065247 ATGTGTGTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:24069849 original size:19 final size:20
Alignment explanation
Indices: 24069827--24069869 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
24069817 CATTTTAACC
24069827 TTTATAGTAATTTT-TTATT
1 TTTATAGTAATTTTATTATT
*
24069846 TTTATATTAATTTTAATTATT
1 TTTATAGTAATTTT-ATTATT
24069867 TTT
1 TTT
24069870 CTTATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATAGTAATTTTATTATT
Found at i:24072278 original size:42 final size:42
Alignment explanation
Indices: 24072216--24072300 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
24072206 TGACTTGATT
* *
24072216 AACTTAAACCTACATTATTTTACGTGTAAACAATCAGATCAA
1 AACTTAAACCTACATGATTTTACATGTAAACAATCAGATCAA
*
24072258 AACTTAAATCTACATGATTTTACATGTAAACAATCAGATCAA
1 AACTTAAACCTACATGATTTTACATGTAAACAATCAGATCAA
24072300 A
1 A
24072301 CAAAATGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.31
Consensus pattern (42 bp):
AACTTAAACCTACATGATTTTACATGTAAACAATCAGATCAA
Found at i:24076199 original size:4 final size:4
Alignment explanation
Indices: 24076182--24076215 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
24076172 TGCTATATTT
* *
24076182 TACA TGCA TGCA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
24076216 TATATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:24078215 original size:20 final size:20
Alignment explanation
Indices: 24078192--24078233 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
24078182 AAAACGCATA
24078192 AAAAATAACACTC-AAACAAC
1 AAAAATAACA-TCAAAACAAC
24078212 AAAAATAACATCAAAACAAC
1 AAAAATAACATCAAAACAAC
24078232 AA
1 AA
24078234 CAAAAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:24078236 original size:23 final size:24
Alignment explanation
Indices: 24078206--24078261 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 24
24078196 ATAACACTCA
*
24078206 AACAACAAAAATAACAT-CAAAAC
1 AACAACAAAAATAACATGAAAAAC
*
24078229 AACAACAAAAATAGCATGAAAAAC
1 AACAACAAAAATAACATGAAAAAC
24078253 AACAACAAA
1 AACAACAAA
24078262 TAGCAGCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACATGAAAAAC
Found at i:24078851 original size:24 final size:23
Alignment explanation
Indices: 24078824--24078875 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
24078814 TCTTCTCTAG
* *
24078824 TTTTTATTTGCCTTTGTGGCATGC
1 TTTTTATCTGCC-TTGTGGCACGC
**
24078848 TTTTCCTCTGCCTTGTGGCACGC
1 TTTTTATCTGCCTTGTGGCACGC
24078871 TTTTT
1 TTTTT
24078876 CCTTATGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.06, C:0.23, G:0.19, T:0.52
Consensus pattern (23 bp):
TTTTTATCTGCCTTGTGGCACGC
Found at i:24078884 original size:18 final size:17
Alignment explanation
Indices: 24078858--24078891 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24078848 TTTTCCTCTG
*
24078858 CCTTGTGGCACGCTTTTT
1 CCTTATGGCACG-TTTTT
24078876 CCTTATGGCACGTTTT
1 CCTTATGGCACGTTTT
24078892 CGTCTACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (17 bp):
CCTTATGGCACGTTTTT
Found at i:24079999 original size:19 final size:19
Alignment explanation
Indices: 24079977--24080020 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
24079967 AGAAGAGAAT
*
24079977 GAAAAATAAAGAAATAAAA
1 GAAAAATAAAAAAATAAAA
**
24079996 GAAAGTTAAAAAAATAAAA
1 GAAAAATAAAAAAATAAAA
24080015 GAAAAA
1 GAAAAA
24080021 AATTAAATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
GAAAAATAAAAAAATAAAA
Found at i:24080466 original size:5 final size:5
Alignment explanation
Indices: 24080449--24080490 Score: 68
Period size: 5 Copynumber: 8.4 Consensus size: 5
24080439 TATGTCCCTA
24080449 TTCTT TT-TT TTCTT TTCTT TTCTT TTCTT TTCTTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTC-TT TTCTT TT
24080491 TATAATTGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
6 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTCTT
Found at i:24085156 original size:30 final size:31
Alignment explanation
Indices: 24085116--24085173 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
24085106 TAGATTTGTT
* *
24085116 TTATTGTCATGTTGTATT-ATGCTTTTATTA
1 TTATTGTCATGTTATATTCATGCATTTATTA
*
24085146 TTATTTTCATGTTATATTCATGCATTTA
1 TTATTGTCATGTTATATTCATGCATTTA
24085174 GGGAGTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (31 bp):
TTATTGTCATGTTATATTCATGCATTTATTA
Found at i:24092756 original size:26 final size:26
Alignment explanation
Indices: 24092696--24092756 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
24092686 CATATGGTAT
* * *
24092696 TTTGGATAGTAAATGTTATTATGGTG
1 TTTGGTTAGTAAATGTAATTATGATG
*
24092722 CTTGTGTTAGT-AATGATAATTATGATG
1 TTTG-GTTAGTAAATG-TAATTATGATG
24092749 TTTGGTTA
1 TTTGGTTA
24092757 AAATGATTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.48
Consensus pattern (26 bp):
TTTGGTTAGTAAATGTAATTATGATG
Found at i:24093683 original size:18 final size:19
Alignment explanation
Indices: 24093660--24093699 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
24093650 TTTACTACTT
*
24093660 TTATAT-TTTTGTTAGATA
1 TTATATATTTGGTTAGATA
24093678 TTATATCATTTGGTTAGATA
1 TTATAT-ATTTGGTTAGATA
24093698 TT
1 TT
24093700 CCAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (19 bp):
TTATATATTTGGTTAGATA
Found at i:24094645 original size:11 final size:12
Alignment explanation
Indices: 24094629--24094661 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
24094619 AAAATAATTT
24094629 TATTTTTAT-AA
1 TATTTTTATAAA
24094640 TATTTTTATAAA
1 TATTTTTATAAA
24094652 TATTGTTTAT
1 TATT-TTTAT
24094662 TATCTATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 6 0.30
13 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
TATTTTTATAAA
Found at i:24104438 original size:118 final size:117
Alignment explanation
Indices: 24104316--24104544 Score: 354
Period size: 118 Copynumber: 1.9 Consensus size: 117
24104306 CAATTTATTT
* ** * *
24104316 GTCTCTTTCTCCTCTTTTAC-GTATTTGGAGAGTCCTCGGAGGACATATCCTCATACCCATATCT
1 GTCTCTTTCTCATCTTTT-CTGTATTCCGAGAATCCTCAGAGGACATATCCTCATACCCATATCT
*
24104380 GGATACAGGTTAGATATACTTGTTCAATG-CTAAATTCCTATCACATTTGTTCGA
65 GGATAC-GGTCAGATATACTTGTTCAATGAC-AAATTCCTATCACATTTGTTCGA
24104434 GTCTCTTTCTCATCTTTTCTGTATTCCGAGAATCCTCAGAGGACATATCCTCATACCCATATCTG
1 GTCTCTTTCTCATCTTTTCTGTATTCCGAGAATCCTCAGAGGACATATCCTCATACCCATATCTG
*
24104499 GATACGGTCAGATATACTTGTTCAATGACAAGTTCCTATCACATTT
66 GATACGGTCAGATATACTTGTTCAATGACAAATTCCTATCACATTT
24104545 CTTTCTCCTC
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
117 38 0.37
118 64 0.63
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (117 bp):
GTCTCTTTCTCATCTTTTCTGTATTCCGAGAATCCTCAGAGGACATATCCTCATACCCATATCTG
GATACGGTCAGATATACTTGTTCAATGACAAATTCCTATCACATTTGTTCGA
Found at i:24105215 original size:59 final size:59
Alignment explanation
Indices: 24105124--24105275 Score: 150
Period size: 59 Copynumber: 2.6 Consensus size: 59
24105114 TTAATATAAT
* *
24105124 ATTTGATATTTGAACTTTACATGTTTTCTTAATTTAATATCTAAATTTTATTTT-ATTCA
1 ATTTGATATTTGAACTTTACATATTTTCTTAATTTAATATCTAAATTTT-TTTTAATCCA
* * * **
24105183 ATTTGGTATTTGAA-TTTGATATATTTTTTTAATTTGGTATCTAAATTTTTTTTAATCCA
1 ATTTGATATTTGAACTTT-ACATATTTTCTTAATTTAATATCTAAATTTTTTTTAATCCA
* * * *
24105242 ATTTAATACTTAAACTTGT-CAT-TTTTTTTAATTT
1 ATTTGATATTTGAACTT-TACATATTTTCTTAATTT
24105276 GGTATTTAAG
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
58 19 0.25
59 55 0.71
60 2 0.03
61 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (59 bp):
ATTTGATATTTGAACTTTACATATTTTCTTAATTTAATATCTAAATTTTTTTTAATCCA
Found at i:24105230 original size:31 final size:28
Alignment explanation
Indices: 24105147--24105235 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 28
24105137 ACTTTACATG
* **
24105147 TTTTCTTAATTTAATATCTAAATTTTAT
1 TTTTTTTAATTTGGTATCTAAATTTTAT
* * * *
24105175 TTTATTCAATTTGGTATTTGAATTTGATAT
1 TTTTTTTAATTTGGTATCTAAATTT--TAT
24105205 ATTTTTTTAATTTGGTATCTAAATTTT-T
1 -TTTTTTTAATTTGGTATCTAAATTTTAT
24105233 TTT
1 TTT
24105236 AATCCAATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
27 3 0.06
28 19 0.40
29 1 0.02
30 3 0.06
31 21 0.45
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (28 bp):
TTTTTTTAATTTGGTATCTAAATTTTAT
Found at i:24105555 original size:29 final size:30
Alignment explanation
Indices: 24105522--24105595 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 30
24105512 CCCAAAAAGT
* *
24105522 TTTAAATATCAACTTA-AAAAAGTGTCAAA
1 TTTAAATATCAAATTAGAAAAAATGTCAAA
* *
24105551 TTTAAGTATTAAATTAGGAAAAAATGTCAAA
1 TTTAAATATCAAATTA-GAAAAAATGTCAAA
* *
24105582 TTTATATACCAAAT
1 TTTAAATATCAAAT
24105596 ATTATATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 13 0.37
31 22 0.63
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
TTTAAATATCAAATTAGAAAAAATGTCAAA
Found at i:24106941 original size:19 final size:19
Alignment explanation
Indices: 24106917--24106953 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24106907 TATTGTTAAT
*
24106917 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
24106936 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
24106954 TCAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:24112682 original size:21 final size:21
Alignment explanation
Indices: 24112658--24112710 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
24112648 TTGTTGTTAT
24112658 CTTTGAATCAACTTGAGTCAC
1 CTTTGAATCAACTTGAGTCAC
24112679 CTTTGAATCAACTTGAGTCAC
1 CTTTGAATCAACTTGAGTCAC
24112700 CTTTGAATCAA
1 CTTTGAATCAA
24112711 TTCGCTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (21 bp):
CTTTGAATCAACTTGAGTCAC
Found at i:24119406 original size:2 final size:2
Alignment explanation
Indices: 24119401--24119452 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
24119391 TATTCCAACA
24119401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24119443 AT AT AT AT AT
1 AT AT AT AT AT
24119453 TAAATAAAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24120110 original size:21 final size:21
Alignment explanation
Indices: 24120071--24120112 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24120061 CTTCTCCAAA
*
24120071 AATTATATATTTTTTAATATT
1 AATTATATATTTTTAAATATT
24120092 AATT-TATATTTTTAAAATATT
1 AATTATATATTTTT-AAATATT
24120113 TTTACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTATATATTTTTAAATATT
Found at i:24120116 original size:19 final size:20
Alignment explanation
Indices: 24120076--24120125 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
24120066 CCAAAAATTA
*
24120076 TATATTTTT-TAATATTAATT
1 TATATTTTTAAAATATT-ATT
24120096 TATATTTTTAAAATATT-TT
1 TATATTTTTAAAATATTATT
24120115 TACT-TTTTTAA
1 TA-TATTTTTAA
24120126 TTTATGCCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 11 0.41
20 10 0.37
21 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTTTTAAAATATTATT
Found at i:24124180 original size:2 final size:2
Alignment explanation
Indices: 24124173--24124198 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24124163 ACATTAAATA
24124173 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24124199 GATTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24125848 original size:6 final size:6
Alignment explanation
Indices: 24125837--24125861 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24125827 AGAGTGTGTG
24125837 AGAGGT AGAGGT AGAGGT AGAGGT A
1 AGAGGT AGAGGT AGAGGT AGAGGT A
24125862 AAGAAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
AGAGGT
Found at i:24127144 original size:17 final size:17
Alignment explanation
Indices: 24127112--24127144 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24127102 TAATAAAAAT
24127112 ATAATTTTATTATTTAA
1 ATAATTTTATTATTTAA
24127129 ATAATCTTTATT-TTTA
1 ATAAT-TTTATTATTTA
24127145 TATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTTATTATTTAA
Found at i:24127204 original size:31 final size:29
Alignment explanation
Indices: 24127137--24127214 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 29
24127127 AAATAATCTT
*
24127137 TATTTTTA-TATTTTTTAAAAATTAAATTA
1 TATTTTTATTA-TTTTTAAAAATTAAAGTA
* *
24127166 AAATTTTATTATTTTTAAGGAAATTAAAGTA
1 TATTTTTATTATTTTTAA--AAATTAAAGTA
24127197 TATTTTTATT-TTTATTAA
1 TATTTTTATTATTT-TTAA
24127215 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.32
30 5 0.12
31 22 0.55
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (29 bp):
TATTTTTATTATTTTTAAAAATTAAAGTA
Found at i:24127225 original size:16 final size:17
Alignment explanation
Indices: 24127206--24127238 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24127196 ATATTTTTAT
*
24127206 TTTTATTAA-TTTAAAA
1 TTTTAATAATTTTAAAA
24127222 TTTTAATAATTTTAAAA
1 TTTTAATAATTTTAAAA
24127239 ACATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATAATTTTAAAA
Found at i:24129093 original size:158 final size:158
Alignment explanation
Indices: 24128800--24129117 Score: 487
Period size: 158 Copynumber: 2.0 Consensus size: 158
24128790 TTGTTAAACC
*
24128800 TTGAAATTCAATGTAATTTGGCTTCTCTTCGTCAACTAGTGAATCTAAAATCTATTTCTCTCTGT
1 TTGAAATTCAATGTAATTTGGCTTCTCTTCGTCAACTAGTGAATCTAAAATCCATTTCTCTCTGT
* * * *
24128865 CCATTTGCATCAAATCATGAAGAATTTGAGTTTGTAAAGTTTTCTGTTTGTTTTTCGGGAAAATA
66 CCATTTGCATCAAATCATGAAGAATCTGAGTTAGTAAAGTTTTCTGTTTATTTCTCGGGAAAATA
*
24128930 TTAAACCCATCTAATTTTGCTTTACCTT
131 CTAAACCCATCTAATTTTGCTTTACCTT
* * *
24128958 TTGAAATTCAATGTAATTTGGCTTCTCTTCTTCAACTGGTGAAT-TCAAAATCCATTTCTCTTTG
1 TTGAAATTCAATGTAATTTGGCTTCTCTTCGTCAACTAGTGAATCT-AAAATCCATTTCTCTCTG
* * *
24129022 TCCGTTTGCATCAAATCATGAATAATCTGAGTTAGTGAAA-TTTTTTGTTTATTTCTCGGGAAAA
65 TCCATTTGCATCAAATCATGAAGAATCTGAGTTAGT-AAAGTTTTCTGTTTATTTCTCGGGAAAA
*
24129086 TACTAAACCCGTCTAATTTTGCTTTACCTT
129 TACTAAACCCATCTAATTTTGCTTTACCTT
24129116 TT
1 TT
24129118 TCTTGAACGA
Statistics
Matches: 145, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
157 1 0.01
158 141 0.97
159 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (158 bp):
TTGAAATTCAATGTAATTTGGCTTCTCTTCGTCAACTAGTGAATCTAAAATCCATTTCTCTCTGT
CCATTTGCATCAAATCATGAAGAATCTGAGTTAGTAAAGTTTTCTGTTTATTTCTCGGGAAAATA
CTAAACCCATCTAATTTTGCTTTACCTT
Found at i:24135545 original size:27 final size:27
Alignment explanation
Indices: 24135519--24135621 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
24135509 AATCTGTTTT
*
24135519 TGGCTTGAAAGAGCGATACTCTATTTT
1 TGGCTTGAAAGAGCGATACTCTATTTC
* *
24135546 TGGCTTGAAAGAGTGATACTCTGTTTC
1 TGGCTTGAAAGAGCGATACTCTATTTC
** * * * *
24135573 TAACTCGAATGAGCGGTACTCTATCTC
1 TGGCTTGAAAGAGCGATACTCTATTTC
* *
24135600 TGGCTTGAATGAGCAATACTCT
1 TGGCTTGAAAGAGCGATACTCT
24135622 GTACATGGCT
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (27 bp):
TGGCTTGAAAGAGCGATACTCTATTTC
Found at i:24135630 original size:27 final size:27
Alignment explanation
Indices: 24135600--24135665 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
24135590 ACTCTATCTC
24135600 TGGCTTGAATGAGCAATACTCTGTACA
1 TGGCTTGAATGAGCAATACTCTGTACA
* * *
24135627 TGGCTTAAATGAGCTATACTCTGTACT
1 TGGCTTGAATGAGCAATACTCTGTACA
*
24135654 TGGCTCGAATGA
1 TGGCTTGAATGA
24135666 ATAATATTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (27 bp):
TGGCTTGAATGAGCAATACTCTGTACA
Found at i:24137613 original size:7 final size:7
Alignment explanation
Indices: 24137601--24137651 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
24137591 TCGAGTCCCA
24137601 TTGATCG
1 TTGATCG
*
24137608 TTGATCA
1 TTGATCG
*
24137615 TTGACCG
1 TTGATCG
24137622 TTGA-C-
1 TTGATCG
*
24137627 TTGATCA
1 TTGATCG
*
24137634 TTGATTG
1 TTGATCG
24137641 TTGATCG
1 TTGATCG
24137648 TTGA
1 TTGA
24137652 CTTTTTTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 4 0.11
6 2 0.06
7 30 0.83
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (7 bp):
TTGATCG
Found at i:24137637 original size:26 final size:26
Alignment explanation
Indices: 24137601--24137654 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
24137591 TCGAGTCCCA
*
24137601 TTGATCGTTGATCATTGACCGTTGAC
1 TTGATCATTGATCATTGACCGTTGAC
** *
24137627 TTGATCATTGATTGTTGATCGTTGAC
1 TTGATCATTGATCATTGACCGTTGAC
24137653 TT
1 TT
24137655 TTTTGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (26 bp):
TTGATCATTGATCATTGACCGTTGAC
Found at i:24139839 original size:59 final size:59
Alignment explanation
Indices: 24139683--24140170 Score: 576
Period size: 58 Copynumber: 8.4 Consensus size: 59
24139673 CGGATACCCG
* * * * * *
24139683 GGGGCAAAATGGTAATTTTTGGTGAGATCAGGGTTAAAAATGGGATTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
* * *
24139742 GGGGT-AAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGGAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
* * * * * **
24139800 AGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATAGAATTTTAGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
* * * *
24139859 GGGGTAAAATGGTAA-TTTTGGCAAAATCGAGGTTAAAAATGGAATTTTAGGAAGTT-T
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
*** * *
24139916 GAGGGT-AAATGGTAATTTTTGGTAAAATTAAGGTT-AAAATGGGATTTTGGGAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
* *
24139974 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAAT-GAGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGA-ATTTTGGGAAGTTCA
* *
24140033 GGGGTAAAATGGTAATTTTTGGTAAAATCAGGATTAAAAATGGAATTTTGGGAAGTTC-
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
* * * * * *
24140091 GGGGGAAAATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGGATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
**
24140150 GGGGTAAAATTATAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
24140171 AGCAGTCCAG
Statistics
Matches: 375, Mismatches: 45, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
57 33 0.09
58 187 0.50
59 153 0.41
60 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
Found at i:24139856 original size:117 final size:118
Alignment explanation
Indices: 24139688--24140170 Score: 595
Period size: 117 Copynumber: 4.1 Consensus size: 118
24139678 ACCCGGGGGC
* * *
24139688 AAAATGGTAATTTTTGGTGAGATCAGGGTTAAAAATGGGATTTTGGGAAGTTTAGGGGT-AAATG
1 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATG
* * *
24139752 GTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGGAAGTTCAAGGGT
66 GTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
* ** * * *
24139805 AAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATAGAATTTTAGGAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATG
* **
24139870 GTAATTTTGGCA--AAATCGAGGTTAAAAATGGAATTTTAGG-AAGTTTGAGGGT
66 GTAATTTTTG-ATGAAATCGAGGTTAAAAATGGAATTTT-GGAAAGTTCAAGGGT
* * *
24139922 -AAATGGTAATTTTTGGTAAAATTAAGGTT-AAAATGGGATTTTGGGAAGTTTAGGGGTAAAATG
1 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATG
* * *
24139985 GTAATTTTTGGTAAAATCGAGGTTAAAAAT-GAGATTTTGGAAAGTTCAGGGGT
66 GTAATTTTTGATGAAATCGAGGTTAAAAATGGA-ATTTTGGAAAGTTCAAGGGT
* * *
24140038 AAAATGGTAATTTTTGGTAAAATCAGGATTAAAAATGGAATTTTGGGAAG-TTCGGGGGAAAATG
1 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATG
* * * * **
24140102 GTAATTTTTGGTGAATTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGT
66 GTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
**
24140155 AAAATTATAATTTTTG
1 AAAATGGTAATTTTTG
24140171 AGCAGTCCAG
Statistics
Matches: 319, Mismatches: 37, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
115 43 0.13
116 57 0.18
117 183 0.57
118 35 0.11
119 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.34
Consensus pattern (118 bp):
AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATG
GTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
Found at i:24140167 original size:29 final size:29
Alignment explanation
Indices: 24139727--24140168 Score: 117
Period size: 29 Copynumber: 15.2 Consensus size: 29
24139717 TAAAAATGGG
* ** *
24139727 ATTTTGGGAAGTTTAGGGGT-AAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAATTGTA
* * *
24139755 ATTTTTGATGAAA-TT-GGGGTTAAAAATGGA
1 A-TTTTG--GAAAGTTCGGGGGTAAAATTGTA
* ** *
24139785 ATTTTGGGAAGTTCAAGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAATTGTA
* *
24139814 ATTTTTGGTGAAA-TT-GGGGTTAAAAATAG-A
1 A-TTTT-G-GAAAGTTCGGGGGT-AAAATTGTA
* *
24139844 ATTTTAGG-AAGTTTGGGGGTAAAATGGTA
1 ATTTT-GGAAAGTTCGGGGGTAAAATTGTA
* * * * *
24139873 ATTTTGGCAAA-ATCGAGGTTAAAAATGGA
1 ATTTTGG-AAAGTTCGGGGGTAAAATTGTA
* * *
24139902 ATTTTAGG-AAGTTTGAGGGT-AAATGGTA
1 ATTTT-GGAAAGTTCGGGGGTAAAATTGTA
* ** * **
24139930 ATTTTTGGTAAAATT-AAGGTTAAAA-TGGG
1 A-TTTTGG-AAAGTTCGGGGGTAAAATTGTA
* ** *
24139959 ATTTTGGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAATTGTA
* * * *
24139988 ATTTTTGGTAAA-ATCGAGGTTAAAAATG-A
1 A-TTTTGG-AAAGTTCGGGGGTAAAATTGTA
* *
24140017 GATTTTGGAAAGTTCAGGGGTAAAATGGTA
1 -ATTTTGGAAAGTTCGGGGGTAAAATTGTA
* * ** * *
24140047 ATTTTTGGTAAA-ATCAGGATTAAAAATGGA
1 A-TTTTGG-AAAGTTCGGGGGTAAAATTGTA
* *
24140077 ATTTTGGGAAGTTCGGGGG-AAAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAATTGTA
* * * **
24140105 ATTTTTGGTGAA-TTCGGGGTTAAAAATGGG
1 A-TTTTGG-AAAGTTCGGGGGTAAAATTGTA
*
24140135 ATTTTGGAAAGTTCGGGGGTAAAATTATA
1 ATTTTGGAAAGTTCGGGGGTAAAATTGTA
24140164 ATTTT
1 ATTTT
24140169 TGAGCAGTCC
Statistics
Matches: 293, Mismatches: 86, Indels: 69
0.65 0.19 0.15
Matches are distributed among these distances:
27 9 0.03
28 52 0.18
29 139 0.47
30 73 0.25
31 17 0.06
32 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
ATTTTGGAAAGTTCGGGGGTAAAATTGTA
Found at i:24142010 original size:6 final size:6
Alignment explanation
Indices: 24141999--24142057 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
24141989 TTAAATTTGA
* *
24141999 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
24142047 ATAAAT TTAAA
1 TTAAAT TTAAA
24142058 ATCCATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.19
6 30 0.70
8 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:24142020 original size:17 final size:17
Alignment explanation
Indices: 24142000--24142057 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
24141990 TAAATTTGAT
24142000 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
24142017 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAG
*
24142031 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
24142048 TAAATTTAAA
1 TAAATTTAAA
24142058 ATCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 13 0.35
15 1 0.03
16 1 0.03
17 22 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:24142068 original size:11 final size:11
Alignment explanation
Indices: 24142006--24142059 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
24141996 TGATTAAATT
*
24142006 TAAATTTAAAG
1 TAAATTTAAAA
24142017 TAAATTT-AAA
1 TAAATTTAAAA
* *
24142027 T-AA-GTAAATT
1 TAAATTTAAA-A
24142037 TAAATTTAAAA
1 TAAATTTAAAA
24142048 TAAATTTAAAA
1 TAAATTTAAAA
24142059 T
1 T
24142060 CCATTTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
8 1 0.03
9 4 0.12
10 4 0.12
11 21 0.62
12 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:24142933 original size:201 final size:200
Alignment explanation
Indices: 24142466--24143062 Score: 896
Period size: 201 Copynumber: 3.0 Consensus size: 200
24142456 ATCTATTTTA
* * *
24142466 ATTCGCTTCTCTGGATCTCCTCAAGAAGATGAAT-TCGGTCCACTTCTCTGTGTCTCATCAGGAA
1 ATTCGCTTCTCTGGATCTCCTTAGGAAGACGAATCT-GGTCCACTTCTCTGTGTCTCATCAGGAA
* * * *
24142530 GCTAACCTTTTTATTGCTTCGTCCTGCTTCTCATTATTTCATCAGGAAGCTGGGTTCGAAGATTT
65 GCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTT
* * *
24142595 GCTCGCGTTGAGGGTTGAGTTGGTATTCTTCTCTGTATCTCATC-GGAAGATGACCGCCTCGCTT
130 GCTCGTGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGCTT
*
24142659 GTTTTG
195 GTTTCG
* * *
24142665 ATTCTCTTCTCTGGATCT-CTTCAGGAAGACGAATCTGGTCCACTTCTCCGCGTCTCATCAGGAA
1 ATTCGCTTCTCTGGATCTCCTT-AGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
* * * *
24142729 GCTAACTTTTTTATTGCTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTAGGTTCGAGGATTT
65 GCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTT
* * *
24142794 GCTCGTGTTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGCT
130 GCTCGTG-TTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGCT
24142859 TGTTTCG
194 TGTTTCG
* *
24142866 ATTCGCTTATCTGGATCTCCTTAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAAGAAG
1 ATTCGCTTCTCTGGATCTCCTTAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAG
*
24142931 CTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTG
66 CTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTG
* *
24142996 CTC-TCGTTGAGCGTTGAGTTCGTATTCTTCTCTGTATCTCATCAGGAAGATGACCACCTTGCTT
131 CTCGT-GTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGCTT
24143060 GTT
195 GTT
24143063 GAACTACTCT
Statistics
Matches: 356, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
198 2 0.01
199 116 0.33
200 91 0.26
201 144 0.40
202 3 0.01
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (200 bp):
ATTCGCTTCTCTGGATCTCCTTAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAG
CTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTG
CTCGTGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGCTTG
TTTCG
Found at i:24149478 original size:6 final size:6
Alignment explanation
Indices: 24149467--24149504 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
24149457 ACTTTTCGTA
24149467 TTAATT TTAATT TTAATT TTAATT AATTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAATT --TTAATT TTAATT
24149505 AATTAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 24 0.80
8 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTAATT
Found at i:24149498 original size:14 final size:14
Alignment explanation
Indices: 24149466--24149509 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
24149456 GACTTTTCGT
24149466 ATTAATTTTAATT-
1 ATTAATTTTAATTA
24149479 -TTAATTTTAATTA
1 ATTAATTTTAATTA
24149492 ATTAATTTTAATTA
1 ATTAATTTTAATTA
24149506 ATTA
1 ATTA
24149510 GTATTGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.41
14 17 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTTTAATTA
Found at i:24153589 original size:29 final size:28
Alignment explanation
Indices: 24153557--24153648 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
24153547 AAATCGGGGT
24153557 TAAAAATGAGATTTTGGAAAGTTTAAGGG
1 TAAAAATG-GATTTTGGAAAGTTTAAGGG
*
24153586 T-AAAATGGTAATTTTGGTGAAA--TTAAGGT
1 TAAAAATGG--ATTTT-G-GAAAGTTTAAGGG
** *
24153615 TAAAAATGGGATTTTAAAAAGTTTAGGGG
1 TAAAAAT-GGATTTTGGAAAGTTTAAGGG
24153644 TAAAA
1 TAAAA
24153649 TGGTAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 4 0.08
28 6 0.12
29 28 0.56
30 6 0.12
31 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (28 bp):
TAAAAATGGATTTTGGAAAGTTTAAGGG
Found at i:24153590 original size:59 final size:59
Alignment explanation
Indices: 24153485--24153954 Score: 569
Period size: 59 Copynumber: 8.0 Consensus size: 59
24153475 ATGCCCGGAG
* * * * * *
24153485 GGTGAGATCGAGG-TAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATAGTAAGTTTT
1 GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
24153543 GGTGAAATCGGGGTTAAAAAT-GAGATTTTGGAAAGTTTAAGGGTAAAATGGTAA-TTTT
1 GGTGAAATCGGGGTTAAAAATGGA-ATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
*** * ** *
24153601 GGTGAAATTAAGGTTAAAAATGGGATTTTAAAAAGTTTAGGGGTAAAATGGTAATTTTT
1 GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
* * *
24153660 TGTGAAATCGGGGTT-AAAATGGAATTTTGGGAAGTTT-AGAGGTGAAATGGTAATTTTT
1 GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAAG-GGTAAAATGGTAATTTTT
*
24153718 GGTGAAATCGGGGTTAAAAATGGAATTTTAGGAAA-TTTAGGGGTAAAATGGTAATTTTT
1 GGTGAAATCGGGGTTAAAAATGGAATTTT-GGAAAGTTTAAGGGTAAAATGGTAATTTTT
* ***
24153777 GATGAAATCGGGGTTAAAAATGGAATTTTAGG-AAGTTCGGGGGTAAAATGGTAATTTTT
1 GGTGAAATCGGGGTTAAAAATGGAATTTT-GGAAAGTTTAAGGGTAAAATGGTAATTTTT
* * * **
24153836 GATGAAATCGGGGTTATAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT
1 GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
* * * *
24153895 GATGAAATCGAGGTTATAAAT-GAGATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTT
1 GGTGAAATCGGGGTTAAAAATGGA-ATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
24153954 G
1 G
24153955 AATAGTCCAG
Statistics
Matches: 366, Mismatches: 35, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
57 1 0.00
58 116 0.32
59 244 0.67
60 5 0.01
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (59 bp):
GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
Done.