Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 42 of 182
Found at i:15474553 original size:17 final size:17
Alignment explanation
Indices: 15474533--15474565 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15474523 AAAATAGAAA
*
15474533 TATTATTTGAATAAAAC
1 TATTACTTGAATAAAAC
15474550 TATTACTTGAATAAAA
1 TATTACTTGAATAAAA
15474566 TTTTAAGCAT
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:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
TATTACTTGAATAAAAC
Found at i:15482249 original size:65 final size:65
Alignment explanation
Indices: 15482145--15482272 Score: 256
Period size: 65 Copynumber: 2.0 Consensus size: 65
15482135 TAGCTGTCCG
15482145 GCCTGTTTCTTTTAAACCTTAATTCCAACATATTACTTTAATTTAATAGTCAAATGAATATGTAT
1 GCCTGTTTCTTTTAAACCTTAATTCCAACATATTACTTTAATTTAATAGTCAAATGAATATGTAT
15482210 GCCTGTTTCTTTTAAACCTTAATTCCAACATATTACTTTAATTTAATAGTCAAATGAATATGT
1 GCCTGTTTCTTTTAAACCTTAATTCCAACATATTACTTTAATTTAATAGTCAAATGAATATGT
15482273 CCTAGCTTGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.43
Consensus pattern (65 bp):
GCCTGTTTCTTTTAAACCTTAATTCCAACATATTACTTTAATTTAATAGTCAAATGAATATGTAT
Found at i:15487194 original size:7 final size:6
Alignment explanation
Indices: 15487176--15487266 Score: 101
Period size: 7 Copynumber: 14.0 Consensus size: 6
15487166 TCTCTCAAAG
* *
15487176 GGGAAG GGGAAA GGAGAAA GGAGGAA GGGAAA GGGAAA GGGAAA GGGAAA
1 GGGAAA GGGAAA GG-GAAA GG-GAAA GGGAAA GGGAAA GGGAAA GGGAAA
15487226 GGGAAA GGGAAAA GGAGAAA GGAGAAA GGAGAAA GGAGAAA
1 GGGAAA GGG-AAA GG-GAAA GG-GAAA GG-GAAA GG-GAAA
15487267 ATTTTTGAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
6 37 0.47
7 41 0.52
8 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:15503606 original size:9 final size:9
Alignment explanation
Indices: 15503592--15503617 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
15503582 AATCAAAAGG
15503592 GAAGAAGAT
1 GAAGAAGAT
15503601 GAAGAAGAT
1 GAAGAAGAT
15503610 GAAGAAGA
1 GAAGAAGA
15503618 GAGGTGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (9 bp):
GAAGAAGAT
Found at i:15504411 original size:67 final size:67
Alignment explanation
Indices: 15504339--15504506 Score: 264
Period size: 67 Copynumber: 2.5 Consensus size: 67
15504329 TATTAGATTT
* * * * *
15504339 TGCAAATGAATGGTGCTTCCAATATAATTATCATGGTGATTCCAATACATCACTAAGATTTTAGA
1 TGCAAATGAATAGTGATTCCAATACAATTATCATAGTGATTCCAATACATCACTAAGATTTTAAA
15504404 AA
66 AA
* * *
15504406 TGCAAATGATTAGTGATTTCAATACAATTATCATAGTGATTCCAATACATTACTAAGATTTTAAA
1 TGCAAATGAATAGTGATTCCAATACAATTATCATAGTGATTCCAATACATCACTAAGATTTTAAA
15504471 AA
66 AA
15504473 TGCAAATGAATAGTGATTCCAATACAATTATCAT
1 TGCAAATGAATAGTGATTCCAATACAATTATCAT
15504507 TTTGCAAATG
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 91 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (67 bp):
TGCAAATGAATAGTGATTCCAATACAATTATCATAGTGATTCCAATACATCACTAAGATTTTAAA
AA
Found at i:15504971 original size:61 final size:61
Alignment explanation
Indices: 15504900--15505061 Score: 181
Period size: 61 Copynumber: 2.7 Consensus size: 61
15504890 TTTTAATAAG
* *
15504900 ATTATTATTAAATATAATTTAATAAAAATAATAATAAATAATTTAATTATATT-TTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAT-AATAATTTAATAACATTCTTAACATA
* * * *
15504961 ATTACTATTAAATACAATTTAAT-AAAATAAT-AT-ATAATTTAATAACATTCTTAATATT
1 ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTTAACATA
**
15505019 ATTATTATTAAAATATGAA-TTAATAAAAACCATAATATATAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAATA-ATAAT
15505062 ATTAGAAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
57 14 0.17
58 14 0.17
59 12 0.14
60 16 0.19
61 23 0.27
63 5 0.06
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (61 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTTAACATA
Found at i:15508159 original size:24 final size:26
Alignment explanation
Indices: 15508123--15508170 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
15508113 GAAGAAATGT
15508123 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
15508147 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
15508171 CCCATTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:15508309 original size:24 final size:23
Alignment explanation
Indices: 15508252--15508331 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 23
15508242 TTAGCACTGT
* *
15508252 GTGTGCTCTCTATTTAGCACATCTC
1 GTGTGCTCTTTA-TTAGCACTTC-C
15508277 GTGCT-CTCTATTATTAGCACTTCC
1 GTG-TGCTCT-TTATTAGCACTTCC
*
15508301 GTGTGCTCTCTGATTAGCACTT-C
1 GTGTGCTCT-TTATTAGCACTTCC
15508324 GTGTGCTC
1 GTGTGCTC
15508332 AGTACTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 10 0.21
24 19 0.40
25 16 0.33
26 3 0.06
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (23 bp):
GTGTGCTCTTTATTAGCACTTCC
Found at i:15508330 original size:23 final size:24
Alignment explanation
Indices: 15508233--15508331 Score: 82
Period size: 23 Copynumber: 4.2 Consensus size: 24
15508223 ACACTAGCGC
* * *
15508233 GCTCTTTGTTTAGCACTGT-GTGT
1 GCTCTCTGATTAGCACTCTCGTGT
15508256 GCTCTCT-ATTTAGCACATCTCGTGCT
1 GCTCTCTGA-TTAGCAC-TCTCGTG-T
* *
15508282 -CTCTATTATTAGCACT-TCCGTGT
1 GCTCTCTGATTAGCACTCT-CGTGT
15508305 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTCTCGTGT
15508328 GCTC
1 GCTC
15508332 AGTACTTTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
23 24 0.38
24 22 0.35
25 15 0.24
26 2 0.03
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.41
Consensus pattern (24 bp):
GCTCTCTGATTAGCACTCTCGTGT
Found at i:15517456 original size:13 final size:14
Alignment explanation
Indices: 15517440--15517470 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
15517430 AAATTTTAAA
15517440 TTTAAATTTATT-T
1 TTTAAATTTATTAT
15517453 TTTAAATTTATTAT
1 TTTAAATTTATTAT
15517467 TTTA
1 TTTA
15517471 TCAACCAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTAAATTTATTAT
Found at i:15517858 original size:21 final size:21
Alignment explanation
Indices: 15517797--15517859 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
15517787 GAGATAAGAT
*
15517797 ATATTTTTATTTTTTAGCTAAATA
1 ATATTTTTATTTTTT---TTAATA
* *
15517821 ATTATTATT-TTTATTTTAATA
1 A-TATTTTTATTTTTTTTAATA
15517842 ATATTTTTATTTTTTTTA
1 ATATTTTTATTTTTTTTA
15517860 TTTCTCAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.19
21 14 0.44
24 6 0.19
25 6 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
ATATTTTTATTTTTTTTAATA
Found at i:15521380 original size:2 final size:2
Alignment explanation
Indices: 15521335--15521367 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15521325 ATTCGAATAC
15521335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15521368 AAAGGTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15529472 original size:6 final size:6
Alignment explanation
Indices: 15529461--15529500 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
15529451 AGAATCCTTT
15529461 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAAAA TCAAAA TC
1 TCAAAA TCAAAA TCAAAA TCAAAA TC--AAAA TCAAAA TC
15529501 TTAAGTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 26 0.81
8 6 0.19
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
TCAAAA
Found at i:15563016 original size:23 final size:22
Alignment explanation
Indices: 15562990--15563041 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
15562980 AAAATTTTGA
*
15562990 TTTATTTTTAATTAATTAATTAG
1 TTTATTTTGAATTAATT-ATTAG
* *
15563013 TTTAATTTGAATTACTTATTAG
1 TTTATTTTGAATTAATTATTAG
*
15563035 ATTATTT
1 TTTATTT
15563042 AATCAGTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTATTTTGAATTAATTATTAG
Found at i:15574963 original size:33 final size:36
Alignment explanation
Indices: 15574921--15574986 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
15574911 TGTTTATGTG
* *
15574921 AAATTGAAGAGAAA-GAGAAGAG-AG-GCAAGGATC
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
15574954 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
15574987 GGTAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 2 0.07
36 6 0.21
ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09
Consensus pattern (36 bp):
AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
Found at i:15576047 original size:25 final size:23
Alignment explanation
Indices: 15576011--15576108 Score: 135
Period size: 23 Copynumber: 4.2 Consensus size: 23
15576001 ACACTAGCGC
15576011 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
15576034 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
15576059 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
15576082 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
15576105 GCTC
1 GCTC
15576109 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
22 1 0.01
23 44 0.66
24 1 0.01
25 21 0.31
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:15576087 original size:48 final size:46
Alignment explanation
Indices: 15576011--15576108 Score: 135
Period size: 48 Copynumber: 2.1 Consensus size: 46
15576001 ACACTAGCGC
*
15576011 GCTCTCTGATTAGCACTGTGTGTACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCCGATTAGCACTGTGTGTACTCTCTG--ATTAGCACTGTGTGT
* *
15576059 GCTCTCCGATTAGCACT-TCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCCGATTAGCACTGT-GTGTACTCTCTGATTAGCACTGTGTGT
15576105 GCTC
1 GCTC
15576109 AGTACTTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
46 18 0.39
47 1 0.02
48 27 0.59
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCCGATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGT
Found at i:15576145 original size:39 final size:39
Alignment explanation
Indices: 15576073--15576147 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
15576063 TCCGATTAGC
*
15576073 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* * *
15576112 ACTTTGTGTACTCTTTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
15576148 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:15583363 original size:89 final size:89
Alignment explanation
Indices: 15583194--15583387 Score: 291
Period size: 89 Copynumber: 2.2 Consensus size: 89
15583184 TGTTACAGTT
* * *
15583194 ACAACTCATATGAGCATTACAGGTTATATGAGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGG
1 ACAACTCGTGTGAGCATTACAGGTTATATGAGTGCTGGTCTTAGATGTCCTACCAATGGCTGAGG
*
15583259 TCCTGCATTGGTTGCGGATTCTTC
66 TCCTGCATTGATTGCGGATTCTTC
* * * *
15583283 ACAGCTCGTGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAGATGTCTTACCAATGGTTGAGG
1 ACAACTCGTGTGAGCATTACAGGTTATATGAGTGCTGGTCTTAGATGTCCTACCAATGGCTGAGG
*
15583348 TCC-GACATTTATTGCGGATTCTTC
66 TCCTG-CATTGATTGCGGATTCTTC
15583372 ACAACTCGTGTGAGCA
1 ACAACTCGTGTGAGCA
15583388 GCATCGTGTA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 1 0.01
89 93 0.99
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (89 bp):
ACAACTCGTGTGAGCATTACAGGTTATATGAGTGCTGGTCTTAGATGTCCTACCAATGGCTGAGG
TCCTGCATTGATTGCGGATTCTTC
Found at i:15586222 original size:28 final size:27
Alignment explanation
Indices: 15586187--15586257 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
15586177 CAATACTTGT
15586187 CACAAAGGTTTTCCTTT-TAGAGACTCGC
1 CACAAAGG-TTTCCTTTATAGAGA-TCGC
* * *
15586215 CACAAAGGCTTCATTTATAGAGATTGC
1 CACAAAGGTTTCCTTTATAGAGATCGC
*
15586242 CACGAAGGCTTTCCTT
1 CACAAAGG-TTTCCTT
15586258 GATTGGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (27 bp):
CACAAAGGTTTCCTTTATAGAGATCGC
Found at i:15608078 original size:2 final size:2
Alignment explanation
Indices: 15608073--15608116 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
15608063 AAAAGGAACG
15608073 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
15608115 GA
1 GA
15608117 AAGGTAGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:15608767 original size:21 final size:21
Alignment explanation
Indices: 15608729--15608770 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15608719 AATTTAAGCT
***
15608729 AAAATTAAATTTTTTTATTAA
1 AAAATTAAATTGAATTATTAA
15608750 AAAATTAAATTGAATTATTAA
1 AAAATTAAATTGAATTATTAA
15608771 TTTTAAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AAAATTAAATTGAATTATTAA
Found at i:15611183 original size:28 final size:29
Alignment explanation
Indices: 15611042--15611433 Score: 272
Period size: 29 Copynumber: 13.5 Consensus size: 29
15611032 GATCAAAACG
*
15611042 GAATTTTTGGACA-TTCGAGGGT-AAAATG
1 GAATTTTTGGA-AGTTCGAGGGTAAAAATA
* * * *
15611070 GTAATTTTTGTAAGTTTTG-GGATAAAAAATG
1 G-AATTTTTGGAAG-TTCGAGGGT-AAAAATA
* *
15611101 GAA-TTTTGGAAGTTTG-GGGGAAATAAT-
1 GAATTTTTGGAAGTTCGAGGGTAAA-AATA
***
15611128 GTAATTTTTGGAAGTTTCGAGACCAAAAATA
1 G-AATTTTTGGAAG-TTCGAGGGTAAAAATA
15611159 GAA-TTTTGGAAGTTCGAGGGTAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATA
*
15611187 TAATTTTTGGAAGTTTCGA-GGTAAAAATA
1 GAATTTTTGGAAG-TTCGAGGGTAAAAATA
** *
15611216 -AATTTTTAAAAGTTCAAGGGTAAAAA-A
1 GAATTTTTGGAAGTTCGAGGGTAAAAATA
** * *
15611243 GTAATTTTTGGAAGTTTTAGGG-CAAAATG
1 G-AATTTTTGGAAGTTCGAGGGTAAAAATA
* * *
15611272 GAATTTTGGGAAGTTTGGGGGTAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATA
* *
15611301 TAATTTTTGGAAGTTTCG-GAGTCAAAAATA
1 GAATTTTTGGAAG-TTCGAGGGT-AAAAATA
** *
15611331 GAATTTTTAAAAGTTCGGGGGTAAAAAT-
1 GAATTTTTGGAAGTTCGAGGGTAAAAATA
* * *
15611359 GTAAGTTTTGGAAGTTTTGAGGCTAAAAATA
1 G-AATTTTTGGAAG-TTCGAGGGTAAAAATA
* *
15611390 GAATTTTTGGAAGTTC-AGGGTTAAAACA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATA
*
15611418 TAATTTTTGGATAGTT
1 GAATTTTTGGA-AGTT
15611434 TAGGGACCTT
Statistics
Matches: 291, Mismatches: 48, Indels: 49
0.75 0.12 0.13
Matches are distributed among these distances:
27 9 0.03
28 87 0.30
29 118 0.41
30 64 0.22
31 13 0.04
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
GAATTTTTGGAAGTTCGAGGGTAAAAATA
Found at i:15611238 original size:57 final size:58
Alignment explanation
Indices: 15611042--15611434 Score: 367
Period size: 58 Copynumber: 6.8 Consensus size: 58
15611032 GATCAAAACG
* * * *
15611042 GAATTTTTGGACA-TTCGAGGGT-AAAATGGTAATTTTTGTAAGTTTTG-GGATAAAAAATG
1 GAATTTTTGGA-AGTTCGAGGGTAAAAAT-ATAATTTTTGGAAGTTTCGAGG-T-AAAAATA
* * * **
15611101 GAA-TTTTGGAAGTTTG-GGGGAAATAATGTAATTTTTGGAAGTTTCGAGACCAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAA-AATATAATTTTTGGAAGTTTCGAG-GTAAAAATA
15611159 GAA-TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAATA
** * * ** *
15611216 -AATTTTTAAAAGTTCAAGGGTAAAAA-AGTAATTTTTGGAAGTTT-TAGGGCAAAATG
1 GAATTTTTGGAAGTTCGAGGGTAAAAATA-TAATTTTTGGAAGTTTCGAGGTAAAAATA
* * *
15611272 GAATTTTGGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAGTTTCG-GAGTCAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCGAG-GT-AAAAATA
** * * * *
15611331 GAATTTTTAAAAGTTCGGGGGTAAAAATGTAAGTTTTGGAAGTTTTGAGGCTAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCGAGG-TAAAAATA
* *
15611390 GAATTTTTGGAAGTTC-AGGGTTAAAACATAATTTTTGGATAGTTT
1 GAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGA-AGTTT
15611435 AGGGACCTTT
Statistics
Matches: 275, Mismatches: 43, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
56 11 0.04
57 84 0.31
58 93 0.34
59 85 0.31
60 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
GAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAATA
Found at i:15612487 original size:3 final size:3
Alignment explanation
Indices: 15612466--15612545 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
15612456 TTCTTTTTTG
** **
15612466 TTA TTAA TTA TTA CCA TTA TTA CCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
15612512 TTA TTA TTA TTA TTA ACA TTTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
15612546 ACCAACATTT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
3 57 0.93
4 4 0.07
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:15616736 original size:7 final size:7
Alignment explanation
Indices: 15616726--15616771 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
15616716 GACCATATAA
15616726 AAACCCT
1 AAACCCT
15616733 AAACCCT
1 AAACCCT
*
15616740 AAATCCT
1 AAACCCT
*
15616747 AAATCCT
1 AAACCCT
15616754 AAACCCT
1 AAACCCT
15616761 AAACCCCT
1 AAA-CCCT
15616769 AAA
1 AAA
15616772 ATACCTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
7 29 0.81
8 7 0.19
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:15616749 original size:14 final size:14
Alignment explanation
Indices: 15616730--15616781 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
15616720 ATATAAAAAC
15616730 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
* *
15616744 CCTAAATCCTAAAC
1 CCTAAACCCTAAAT
15616758 CCTAAACCCCTAAAAT
1 CCTAAA-CCCT-AAAT
15616774 ACCTAAAC
1 -CCTAAAC
15616782 AAATAACCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 18 0.58
15 3 0.10
16 4 0.13
17 6 0.19
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (14 bp):
CCTAAACCCTAAAT
Found at i:15616754 original size:21 final size:24
Alignment explanation
Indices: 15616730--15616781 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 24
15616720 ATATAAAAAC
*
15616730 CCTAAACCCTAAA-TCCT-AAAT-
1 CCTAAACCCTAAACCCCTAAAATA
15616751 CCTAAACCCTAAACCCCTAAAATA
1 CCTAAACCCTAAACCCCTAAAATA
15616775 CCTAAAC
1 CCTAAAC
15616782 AAATAACCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.48
22 3 0.11
23 4 0.15
24 7 0.26
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (24 bp):
CCTAAACCCTAAACCCCTAAAATA
Found at i:15616814 original size:20 final size:20
Alignment explanation
Indices: 15616774--15616829 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
15616764 CCCCTAAAAT
* *
15616774 ACCTAAACAAATAACCCCTAA
1 ACCTAAA-AAACAAACCCTAA
15616795 ACCTAAAAAACAAACCCTAA
1 ACCTAAAAAACAAACCCTAA
*
15616815 ATCTAAAAAACAAAC
1 ACCTAAAAAACAAAC
15616830 TTAAAAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.59, C:0.29, G:0.00, T:0.12
Consensus pattern (20 bp):
ACCTAAAAAACAAACCCTAA
Found at i:15623071 original size:29 final size:29
Alignment explanation
Indices: 15623039--15623346 Score: 166
Period size: 29 Copynumber: 10.6 Consensus size: 29
15623029 AAAAATGGGG
15623039 TTTTGGAAAGTTTAGGGGTAAAATGGTAA
1 TTTTGGAAAGTTTAGGGGTAAAATGGTAA
15623068 TTTTGGTGAAA--TTA-GGGTCCAAAATGG-AA
1 TTTT-G-GAAAGTTTAGGGGT--AAAATGGTAA
* * *
15623097 TTTTGG-AAGATTCGAGGGCAAAATGGTAA
1 TTTTGGAAAGTTTAG-GGGTAAAATGGTAA
* *
15623126 TTTTGGTGAAA--TTAGGGTTAAAAATGG-AG
1 TTTT-G-GAAAGTTTAGGGGT-AAAATGGTAA
*
15623155 TTTTGGAAAGTTTAGGGGTAAAATAGTAA
1 TTTTGGAAAGTTTAGGGGTAAAATGGTAA
* *
15623184 TTTTGGGTGAAA--TT-GGGGTTAAAAATAG-AG
1 TTTT--G-GAAAGTTTAGGGG-T-AAAATGGTAA
*
15623214 TTTT-GAAAGATTCAGGGGTAAAATGGTAA
1 TTTTGGAAAG-TTTAGGGGTAAAATGGTAA
* * *
15623243 -TTTGG-AGGTTTCAGGGTTAAAGAT-GAAA
1 TTTTGGAAAGTTT-AGGGGTAAA-ATGGTAA
* **
15623271 TTTTAGAAAGTTT-GGGGTTAAAAAT-AAAA
1 TTTTGGAAAGTTTAGGGG-T-AAAATGGTAA
*
15623300 TTTTAGAAAGTTTAGGGGTAAAATGGTAA
1 TTTTGGAAAGTTTAGGGGTAAAATGGTAA
*
15623329 TTTTTGGATAGTTTAGGG
1 -TTTTGGAAAGTTTAGGG
15623347 ACCTATAAAC
Statistics
Matches: 218, Mismatches: 25, Indels: 71
0.69 0.08 0.23
Matches are distributed among these distances:
26 6 0.03
27 7 0.03
28 51 0.23
29 74 0.34
30 61 0.28
31 13 0.06
32 6 0.03
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGGTAAAATGGTAA
Found at i:15623094 original size:30 final size:29
Alignment explanation
Indices: 15623054--15623207 Score: 119
Period size: 30 Copynumber: 5.3 Consensus size: 29
15623044 GAAAGTTTAG
15623054 GGGT-AAAATGGTAATTTTGGTGAAATTA
1 GGGTCAAAATGGTAATTTTGGTGAAATTA
15623082 GGGTCCAAAATGG-AATTTT-G-GAAGATTCGA
1 GGGT-CAAAATGGTAATTTTGGTGAA-ATT--A
15623112 GGG-CAAAATGGTAATTTTGGTGAAATTA
1 GGGTCAAAATGGTAATTTTGGTGAAATTA
* *
15623140 GGGTTAAAAATGG-AGTTTT-G-GAAAGTTTA
1 GGG-TCAAAATGGTAATTTTGGTGAAA--TTA
* *
15623169 GGGGT-AAAATAGTAATTTTGGGTGAAATTG
1 -GGGTCAAAATGGTAATTTT-GGTGAAATTA
*
15623199 GGGTTAAAA
1 GGGTCAAAA
15623208 ATAGAGTTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 34
0.73 0.04 0.24
Matches are distributed among these distances:
27 7 0.07
28 27 0.26
29 30 0.29
30 31 0.30
31 4 0.04
32 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGTCAAAATGGTAATTTTGGTGAAATTA
Found at i:15623120 original size:58 final size:58
Alignment explanation
Indices: 15622941--15623245 Score: 293
Period size: 58 Copynumber: 5.2 Consensus size: 58
15622931 CTCGGGGGCA
* *
15622941 AAAAT-GTAATTTTAGG-AAAATTTAGGGTTAAAAATAGGA-TTTTGGAAGATTTG-GGAGT
1 AAAATGGTAATTTT-GGTGAAA-TTAGGGTTAAAAAT-GGAGTTTTGGAAGATTCGAGG-GT
* * * * * * *
15622999 AAAATGATAATTTTTAGTGAAA-TCGAAGTTAAAAATGGGGTTTTGGAAAGTTTAG-GGGT
1 AAAATGGTAA-TTTTGGTGAAATTAG-GGTTAAAAATGGAGTTTTGG-AAGATTCGAGGGT
** * *
15623058 AAAATGGTAATTTTGGTGAAATTAGGGTCCAAAATGGAATTTTGGAAGATTCGAGGGC
1 AAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATGGAGTTTTGGAAGATTCGAGGGT
* *
15623116 AAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATGGAGTTTTGGAAAGTTTAG-GGGT
1 AAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATGGAGTTTTGG-AAGATTCGAGGGT
* * * *
15623174 AAAATAGTAATTTTGGGTGAAATTGGGGTTAAAAATAGAGTTTTGAAAGATTC-AGGGGT
1 AAAATGGTAATTTT-GGTGAAATTAGGGTTAAAAATGGAGTTTTGGAAGATTCGA-GGGT
15623233 AAAATGGTAATTT
1 AAAATGGTAATTT
15623246 GGAGGTTTCA
Statistics
Matches: 203, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
57 6 0.03
58 100 0.49
59 82 0.40
60 15 0.07
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATGGAGTTTTGGAAGATTCGAGGGT
Found at i:15623120 original size:117 final size:117
Alignment explanation
Indices: 15622941--15623245 Score: 363
Period size: 117 Copynumber: 2.6 Consensus size: 117
15622931 CTCGGGGGCA
* *
15622941 AAAATGTAATTTTAGG-AAAATTTAGGGTTAAAAATAGG-ATTTTGGAAGATTTG-GGAGTAAAA
1 AAAATGTAATTTTAGGTGAAA-TTAGGGTTAAAAAT-GGAATTTTGGAAGATTCGAGG-GTAAAA
* *
15623003 TGATAATTTTTAGTGAAATCGA-AGTTAAAAATGGGGTTTTGGAAAGTTTAGGGGT
63 TGGTAATTTTTAGTGAAAT-GAGAGTTAAAAATGGAGTTTTGGAAAGTTTAGGGGT
** *
15623058 AAAATGGTAATTTT-GGTGAAATTAGGGTCCAAAATGGAATTTTGGAAGATTCGAGGGCAAAATG
1 AAAAT-GTAATTTTAGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGATTCGAGGGTAAAATG
* * *
15623122 GTAA-TTTTGGTGAAATTAGGGTTAAAAATGGAGTTTTGGAAAGTTTAGGGGT
65 GTAATTTTTAGTGAAATGAGAGTTAAAAATGGAGTTTTGGAAAGTTTAGGGGT
* * * * *
15623174 AAAATAGTAATTTTGGGTGAAATTGGGGTTAAAAATAGAGTTTTGAAAGATTC-AGGGGTAAAAT
1 AAAAT-GTAATTTTAGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGATTCGA-GGGTAAAAT
15623238 GGTAATTT
64 GGTAATTT
15623246 GGAGGTTTCA
Statistics
Matches: 162, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
115 1 0.01
116 58 0.36
117 88 0.54
118 15 0.09
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (117 bp):
AAAATGTAATTTTAGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGATTCGAGGGTAAAATGG
TAATTTTTAGTGAAATGAGAGTTAAAAATGGAGTTTTGGAAAGTTTAGGGGT
Found at i:15623259 original size:116 final size:116
Alignment explanation
Indices: 15623026--15623293 Score: 328
Period size: 116 Copynumber: 2.3 Consensus size: 116
15623016 TGAAATCGAA
* * *
15623026 GTTAAAAATGGGGTTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGTGAAATTAGGGTCCAAA
1 GTTAAAAATGGAGTTTTGGAAAGTTTAGGGGTAAAATAGTAATTTTGGTGAAATTAGGGTCAAAA
* * *
15623091 ATGGAATTTTGGAAGATTCGAGGGCAAAATGGTAATTTTGGTGAAATTAGG
66 ATAGAATTTTGAAAGATTCGAGGGCAAAATGGTAATTTTGGAGAAATTAGG
* *
15623142 GTTAAAAATGGAGTTTTGGAAAGTTTAGGGGTAAAATAGTAATTTTGGGTGAAATTGGGGTTAAA
1 GTTAAAAATGGAGTTTTGGAAAGTTTAGGGGTAAAATAGTAATTTT-GGTGAAATTAGGGTCAAA
* * **
15623207 AATAGAGTTTTGAAAGATTC-AGGGGTAAAATGGTAA-TTTGGAG-GTTTCAGG
65 AATAGAATTTTGAAAGATTCGA-GGGCAAAATGGTAATTTTGGAGAAATT-AGG
* * * *
15623258 GTTAAAGATGAAATTTTAGAAAGTTT-GGGGTTAAAA
1 GTTAAAAATGGAGTTTTGGAAAGTTTAGGGG-TAAAA
15623294 ATAAAATTTT
Statistics
Matches: 132, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
115 6 0.05
116 81 0.61
117 45 0.34
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.32
Consensus pattern (116 bp):
GTTAAAAATGGAGTTTTGGAAAGTTTAGGGGTAAAATAGTAATTTTGGTGAAATTAGGGTCAAAA
ATAGAATTTTGAAAGATTCGAGGGCAAAATGGTAATTTTGGAGAAATTAGG
Found at i:15625291 original size:6 final size:6
Alignment explanation
Indices: 15625282--15625347 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
15625272 TATAATAATG
* * * *
15625282 TTAAAT TTAAA- TTAAAT TCAAAT TTAAA- TTGAAT TCAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
15625327 TTAAAA TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
15625348 TTTCAAAATG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
5 16 0.36
6 29 0.64
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:15625298 original size:11 final size:11
Alignment explanation
Indices: 15625282--15625350 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
15625272 TATAATAATG
15625282 TTAAATTTAAA-
1 TTAAA-TTAAAT
15625293 TTAAATTCAAAT
1 TTAAATT-AAAT
*
15625305 TTAAATTGAAT
1 TTAAATTAAAT
* *
15625316 TCAAAATAAAT
1 TTAAATTAAAT
15625327 TTAAAATTAAA-
1 TT-AAATTAAAT
* *
15625338 ATAAATTTAAT
1 TTAAATTAAAT
15625349 TT
1 TT
15625351 CAAAATGGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
10 9 0.20
11 22 0.49
12 14 0.31
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:15625304 original size:17 final size:17
Alignment explanation
Indices: 15625284--15625320 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
15625274 TAATAATGTT
15625284 AAATTTAAATTAAATTC
1 AAATTTAAATTAAATTC
*
15625301 AAATTTAAATTGAATTC
1 AAATTTAAATTAAATTC
15625318 AAA
1 AAA
15625321 ATAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTAAATTC
Found at i:15625338 original size:17 final size:18
Alignment explanation
Indices: 15625313--15625356 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
15625303 ATTTAAATTG
15625313 AATTCAAAATAAATTTAA
1 AATTCAAAATAAATTTAA
15625331 AATT-AAAATAAATTT-A
1 AATTCAAAATAAATTTAA
*
15625347 ATTTCAAAAT
1 AATTCAAAAT
15625357 GGTTTGGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTCAAAATAAATTTAA
Found at i:15628974 original size:330 final size:329
Alignment explanation
Indices: 15628361--15629006 Score: 924
Period size: 330 Copynumber: 2.0 Consensus size: 329
15628351 TAAATAATGA
* * * * *
15628361 GATAAAAAAGTGGAGAAGAATGAACACAAATATTTTATGTGAAAAGCCCTCAAAGAGGGAAAAAC
1 GATAAAAAAATGGAGAAGAATGAACACAAATATTTTACGTGAAAAACCCTCAAAAAGGAAAAAAC
* * * * *
15628426 CAAGAGCAAAAGAGGTTTCAACTTTTCATTAAATGAGTAAATAAACGAGAGTATAATATGGAGAA
66 CAAGAGCAAAAGAGGCTTCAACTTTTCATTAAATGAGTAAACAAACGAGAGTACAATATGAAAAA
* * *
15628491 AATAAACTTAAATGTACTAAACGTACATTACTCAAAACCCTCAGTACAAAACTCAAAATCCCAAA
131 AATAAACCTAAATGTACTAAACGTACATTACCCAAAACCCTCAATACAAAACTCAAAATCCCAAA
* * *
15628556 GAGAAGATCGATAAACAATACCCTAAATTTCATAAGGCACTCACATAAGGGGTATAAAATACTCT
196 GAGAAGATCGATAAACAAAACCCTAAATTTCATAAGGCACTCACAAAAGAGGTATAAAATACTCT
* * * *
15628621 CCATAATTACCATGAAACTCTCACCAAAACTTATATGCGACTACATCTTGTCGCCCATATAAACA
261 CCATAATTACCACGAAACTCTCACAAAAACTCATATGAGACTACATCTTGTCGCCCATATAAACA
15628686 ACGT
326 ACGT
*
15628690 GATAATAAAAATGGAGAAGAATGAATACAAATATTTTACGTGAAAAACCCTCAAAAAGGAAAAAA
1 GATAA-AAAAATGGAGAAGAATGAACACAAATATTTTACGTGAAAAACCCTCAAAAAGGAAAAAA
* * *
15628755 CCACGGGCAAAAGAGGCTTCGACTTTTCACTT-AATGAGTAAACAAACGAGAGTACAATATGAAA
65 CCAAGAGCAAAAGAGGCTTCAACTTTTCA-TTAAATGAGTAAACAAACGAGAGTACAATATGAAA
*
15628819 AAAATTAACCTAAATGTA-TAAAACGTACATTACCCAAAA-CCTCGAATACAAAACTCAAAATCC
129 AAAATAAACCTAAATGTACT-AAACGTACATTACCCAAAACCCTC-AATACAAAACTCAAAATCC
* *
15628882 CAAAGAGCAA-ATCGGTAAACAAAACCCTAGATCTT-ATAAGGCACTCACAAAAGAGGTATAAAA
192 CAAAGAG-AAGATCGATAAACAAAACCCTAAAT-TTCATAAGGCACTCACAAAAGAGGTATAAAA
* * * *
15628945 TGCTCTCCATAATTATCACGAAGCTCTCACAAAAACTCATATGAGGCTACATCTTGTCGCCC
255 TACTCTCCATAATTACCACGAAACTCTCACAAAAACTCATATGAGACTACATCTTGTCGCCC
15629007 CTAAAGAAAA
Statistics
Matches: 280, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
329 10 0.04
330 264 0.94
331 6 0.02
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (329 bp):
GATAAAAAAATGGAGAAGAATGAACACAAATATTTTACGTGAAAAACCCTCAAAAAGGAAAAAAC
CAAGAGCAAAAGAGGCTTCAACTTTTCATTAAATGAGTAAACAAACGAGAGTACAATATGAAAAA
AATAAACCTAAATGTACTAAACGTACATTACCCAAAACCCTCAATACAAAACTCAAAATCCCAAA
GAGAAGATCGATAAACAAAACCCTAAATTTCATAAGGCACTCACAAAAGAGGTATAAAATACTCT
CCATAATTACCACGAAACTCTCACAAAAACTCATATGAGACTACATCTTGTCGCCCATATAAACA
ACGT
Found at i:15635914 original size:23 final size:22
Alignment explanation
Indices: 15635872--15635915 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
15635862 TACTATTAAT
*
15635872 TCAATATAAATTTTCATTCATC
1 TCAATATAAATTTACATTCATC
15635894 TCAATATTAAATCTTAC-TTCAT
1 TCAATA-TAAAT-TTACATTCAT
15635916 ATTCACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (22 bp):
TCAATATAAATTTACATTCATC
Found at i:15641023 original size:15 final size:15
Alignment explanation
Indices: 15641003--15641034 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
15640993 AACAAGTCAT
15641003 CATTAATTGTAGATA
1 CATTAATTGTAGATA
15641018 CATTAATTGTAGATA
1 CATTAATTGTAGATA
15641033 CA
1 CA
15641035 ATTAGTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (15 bp):
CATTAATTGTAGATA
Found at i:15649646 original size:12 final size:12
Alignment explanation
Indices: 15649629--15649653 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15649619 ACTGTAACAA
15649629 ACTAACTACTCT
1 ACTAACTACTCT
15649641 ACTAACTACTCT
1 ACTAACTACTCT
15649653 A
1 A
15649654 ACTGAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (12 bp):
ACTAACTACTCT
Found at i:15650447 original size:42 final size:41
Alignment explanation
Indices: 15650333--15650516 Score: 160
Period size: 42 Copynumber: 4.4 Consensus size: 41
15650323 TATAATGGCA
* *
15650333 CACGTAA-TGCATCATCGGATAAATCGAAG-AAATCATA-TTG
1 CACGTAAGTGCATCATCGGATAAA-CAAAGCAAAT-ATACTAG
* * ** * * *
15650373 ATACATAAGTGCATTGTC-GACTAAACTGAAGCAAATATATTGG
1 -CACGTAAGTGCATCATCGGA-TAAAC-AAAGCAAATATACTAG
15650416 CACGTAAGTGCATCATCGGATGAAACAAAGCAAATATACTAG
1 CACGTAAGTGCATCATCGGAT-AAACAAAGCAAATATACTAG
* * *
15650458 CACGTAAGTGCATCATCGAATGAACCAAAGCAAATAGACTAG
1 CACGTAAGTGCATCATCGGAT-AAACAAAGCAAATATACTAG
*
15650500 CATGTAAGTGCATCATC
1 CACGTAAGTGCATCATC
15650517 AGCTAAACCA
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
41 8 0.07
42 100 0.83
43 12 0.10
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (41 bp):
CACGTAAGTGCATCATCGGATAAACAAAGCAAATATACTAG
Found at i:15650466 original size:84 final size:84
Alignment explanation
Indices: 15650314--15650516 Score: 189
Period size: 84 Copynumber: 2.4 Consensus size: 84
15650304 TAAGATGAAT
* * * *
15650314 TGAAGCAATTATAATGGCACACGTAA-TGCATCATCGGATAAATCGAAGAAATCATATTGATACA
1 TGAAGCAAATATAATGG--CACGTAAGTGCATCATCGGATAAATCAAAGAAATCATATAGACACA
** *
15650378 TAAGTGCATTGTCGACTAAAC
64 TAAGTGCATCATCGAATAAAC
*
15650399 TGAAGCAAATATATTGGCACGTAAGTGCATCATCGGATGAAA-CAAAGCAAAT-ATACTAG-CAC
1 TGAAGCAAATATAATGGCACGTAAGTGCATCATCGGAT-AAATCAAAG-AAATCATA-TAGACAC
* *
15650461 GTAAGTGCATCATCGAATGAAC
63 ATAAGTGCATCATCGAATAAAC
** * * * *
15650483 CAAAGCAAATAGACTAGCATGTAAGTGCATCATC
1 TGAAGCAAATATAATGGCACGTAAGTGCATCATC
15650517 AGCTAAACCA
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
83 7 0.07
84 67 0.68
85 24 0.24
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (84 bp):
TGAAGCAAATATAATGGCACGTAAGTGCATCATCGGATAAATCAAAGAAATCATATAGACACATA
AGTGCATCATCGAATAAAC
Found at i:15650526 original size:42 final size:41
Alignment explanation
Indices: 15650378--15650529 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 41
15650368 TATTGATACA
** ** * *
15650378 TAAGTGCATTGTCGACTAAACTGAAGCAAATATATTGGCACG
1 TAAGTGCATCATCGA-TAAACCAAAGCAAATATACTAGCACG
15650420 TAAGTGCATCATCGGATGAAA-CAAAGCAAATATACTAGCACG
1 TAAGTGCATCATC-GAT-AAACCAAAGCAAATATACTAGCACG
* * *
15650462 TAAGTGCATCATCGAATGAACCAAAGCAAATAGACTAGCATG
1 TAAGTGCATCATCG-ATAAACCAAAGCAAATATACTAGCACG
*
15650504 TAAGTGCATCATCAGCTAAACCAAAG
1 TAAGTGCATCATC-GATAAACCAAAG
15650530 TATAAACTCA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
41 3 0.03
42 85 0.90
43 6 0.06
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (41 bp):
TAAGTGCATCATCGATAAACCAAAGCAAATATACTAGCACG
Found at i:15650738 original size:88 final size:89
Alignment explanation
Indices: 15650575--15650777 Score: 275
Period size: 88 Copynumber: 2.3 Consensus size: 89
15650565 TTCCAATTTC
* * * * * *
15650575 CAATTTCATTACATATTTCAATTCACATTCCATCGTTCTCAGTTCATCGTTAATTCACCATTCCG
1 CAATTTCA-TACATATTTCAATACACATTCAATCGTACTCAATTCATCATTAATTCACCATTCCA
* *
15650640 ATTCATCATATAACATGTTTTAACT
65 ATACACCATATAACATGTTTTAACT
*
15650665 CAATTTCATA-ATATTTCAATACACATTCAATTC-TACTCAATTCATCATTAATTCACCATTTCA
1 CAATTTCATACATATTTCAATACACATTCAA-TCGTACTCAATTCATCATTAATTCACCATTCCA
15650728 ATACACCATATAACATGTTTTAACT
65 ATACACCATATAACATGTTTTAACT
* *
15650753 CAATTTCATACATATTCCAACACAC
1 CAATTTCATACATATTTCAATACAC
15650778 CATATAACAT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
88 76 0.76
89 16 0.16
90 8 0.08
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (89 bp):
CAATTTCATACATATTTCAATACACATTCAATCGTACTCAATTCATCATTAATTCACCATTCCAA
TACACCATATAACATGTTTTAACT
Found at i:15655274 original size:32 final size:32
Alignment explanation
Indices: 15655219--15655301 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 32
15655209 ATAAGCTTAG
* * *
15655219 TTAAAGTTGTTTATTTTATTAATTTTATTTTGA
1 TTAAATTTG-TTATTTTACTAATTTCATTTTGA
*
15655252 TTAAATTTGTTATTTTCCTAATTTCATTTTGA
1 TTAAATTTGTTATTTTACTAATTTCATTTTGA
15655284 TTGAAATTAT-TTATTTTA
1 TT-AAATT-TGTTATTTTA
15655302 AGTAAATAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
32 22 0.51
33 20 0.47
34 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (32 bp):
TTAAATTTGTTATTTTACTAATTTCATTTTGA
Found at i:15658620 original size:9 final size:9
Alignment explanation
Indices: 15658594--15658631 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
15658584 TGAATTTCAC
15658594 AATTCGAAT
1 AATTCGAAT
15658603 AACTT-GAAT
1 AA-TTCGAAT
*
15658612 AGTTCGAAT
1 AATTCGAAT
15658621 AATTCGAAT
1 AATTCGAAT
15658630 AA
1 AA
15658632 AATATTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:15658711 original size:11 final size:11
Alignment explanation
Indices: 15658695--15658728 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
15658685 TGGTCTCTCA
15658695 TACAAAAAAAT
1 TACAAAAAAAT
15658706 TACAAAAAAAT
1 TACAAAAAAAT
15658717 TA-AAAAAAAT
1 TACAAAAAAAT
15658727 TA
1 TA
15658729 AGATTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (11 bp):
TACAAAAAAAT
Found at i:15659921 original size:24 final size:24
Alignment explanation
Indices: 15659893--15659949 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
15659883 TAGAGTAATA
*
15659893 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
15659917 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
15659941 AGAGTTTAA
1 AGAGTTTAA
15659950 TTGAAAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:15659950 original size:24 final size:24
Alignment explanation
Indices: 15659905--15659955 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
15659895 AGTTTGACTC
15659905 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
15659929 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
15659953 AAA
1 AAA
15659956 GATTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:15663779 original size:29 final size:30
Alignment explanation
Indices: 15663736--15663794 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
15663726 GAATTGGATC
15663736 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
*
15663766 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
15663795 TTAAATCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTGCACA
Found at i:15665089 original size:56 final size:56
Alignment explanation
Indices: 15665029--15665135 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
15665019 AATAAATTCA
* *
15665029 AAATAAATAATAAAAATCCTAATTTTAATATATGTTTTTAAAA-TATTTTTTGTTAC
1 AAATAAATAATAAAAATCCTAATTTTAAAATAT-ATTTTAAAATTATTTTTTGTTAC
** **
15665085 AAATAAATAATACTAATTTTAATTTTAAAATATATTTTAAAATTATTTTTT
1 AAATAAATAATAAAAATCCTAATTTTAAAATATATTTTAAAATTATTTTTT
15665136 AGAACAACCC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
55 8 0.18
56 36 0.82
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (56 bp):
AAATAAATAATAAAAATCCTAATTTTAAAATATATTTTAAAATTATTTTTTGTTAC
Found at i:15666772 original size:30 final size:29
Alignment explanation
Indices: 15666731--15667069 Score: 305
Period size: 29 Copynumber: 11.5 Consensus size: 29
15666721 ACTTTCTTTA
* *
15666731 AAAATTACATTTTTGACCCTTAACTTTTCC
1 AAAATTACA-TTTTAACCCTAAACTTTTCC
* * * * * *
15666761 AAAGTTTCATTTTCACCTTGAACTTTTCA
1 AAAATTACATTTTAACCCTAAACTTTTCC
*
15666790 AAAATCACATTTTAAACCCTAAACTTTTCC
1 AAAATTACATTTT-AACCCTAAACTTTTCC
* *
15666820 AAAATTACATTTTGACCCCTAAACTTTTCT
1 AAAATTACATTTT-AACCCTAAACTTTTCC
*
15666850 AAAATTGCATTTTAACCCTTAAAC-TTTCC
1 AAAATTACATTTTAACCC-TAAACTTTTCC
*
15666879 AAAATTACATTTTAACCCCTAAACTTCTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* *
15666909 AAAA-T-CATTTTTAACCCTTAAACTCTTCT
1 AAAATTACA-TTTTAACCC-TAAACTTTTCC
15666938 AAAATTACATTTTAACCCTAAAC-TTTCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
* * * *
15666966 TAAGATCACATTTTGACCCTAAACTTCTCC
1 -AAAATTACATTTTAACCCTAAACTTTTCC
*
15666996 AAAATCACATTTTGAACCC-AAAC-TTTCTC
1 AAAATTACATTTT-AACCCTAAACTTTTC-C
* * *
15667025 AAAATTATATTTTTACCCCCAAAC-TTTCTC
1 AAAATTACA-TTTTAACCCTAAACTTTTC-C
*
15667055 AAAATTATATTTTAA
1 AAAATTACATTTTAA
15667070 TCTCGTATTC
Statistics
Matches: 257, Mismatches: 38, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
28 11 0.04
29 130 0.51
30 114 0.44
31 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:15666800 original size:59 final size:60
Alignment explanation
Indices: 15666730--15667069 Score: 288
Period size: 59 Copynumber: 5.8 Consensus size: 60
15666720 TACTTTCTTT
* * * * * * *
15666730 AAAAATTACATTTTTGACCCTTAACTTTTCCAAAGTTTCATTTTCA-CCTTGAACTTTTC
1 AAAAATCACATTTTTAACCCTTAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTC
* * *
15666789 AAAAATCACATTTTAAACCCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTC
1 AAAAATCACATTTTTAACCCTTAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTC
* ** *
15666849 TAAAATTGCA-TTTTAACCCTTAAAC-TTTCCAAAATTACATTTTAACCCCTAAACTTCTC
1 AAAAATCACATTTTTAACCCTT-AACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTC
* * * *
15666908 CAAAAT--CATTTTTAACCCTTAAACTCTTCTAAAATTACATTTTAA-CCCTAAACTTTCC
1 AAAAATCACATTTTTAACCCTT-AACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTC
* * * * * *
15666966 TAAGATCACA-TTTTGACCCTAAACTTCTCCAAAATCACATTTTGAA-CCC-AAACTTTCTC
1 AAAAATCACATTTTTAACCCTTAACTTTTCCAAAATTACATTTT-AACCCCTAAACTTT-TC
* * * ** *
15667025 -AAAATTATATTTTTACCCCCAAAC-TTTCTCAAAATTATATTTTAA
1 AAAAATCACATTTTTAACCCTTAACTTTTC-CAAAATTACATTTTAA
15667070 TCTCGTATTC
Statistics
Matches: 232, Mismatches: 39, Indels: 21
0.79 0.13 0.07
Matches are distributed among these distances:
57 2 0.01
58 66 0.28
59 141 0.61
60 23 0.10
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (60 bp):
AAAAATCACATTTTTAACCCTTAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTC
Found at i:15679052 original size:78 final size:77
Alignment explanation
Indices: 15678933--15679938 Score: 1237
Period size: 78 Copynumber: 12.9 Consensus size: 77
15678923 ATCACAGTTG
*
15678933 GCCAATCTCTTACTC-CGATCATGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAG
1 GCCAATCTCTTACCCGCGA-CA-GGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAG
*
15678997 GCAGATCACAGTCA
64 GCAGATCACCGTCA
* * * * * *
15679011 GTCAATCACTTACCC-CGATCATGGGGCAGATTGCAACCATCCAATCTTTTATCCCAATCATGGG
1 GCCAATCTCTTACCCGCGA-CA-GGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAG
*
15679075 GCAAATCACCGTCA
64 GCAGATCACCGTCA
* ** ** * * * *
15679089 GCCAATCTTTTACCC-TTATCATAAGGCAGATTGCAACTATTCGATATTTTAACCCGATCATGAG
1 GCCAATCTCTTACCCGCGA-CA-GGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAG
*
15679153 GCAGATCACCATCA
64 GCAGATCACCGTCA
* *
15679167 GCCAATCCCTTACCTCGCGATAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
1 GCCAATCTCTTACC-CGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
15679232 CAGATCACCGTCA
65 CAGATCACCGTCA
* * * *
15679245 GCCAATCTCTTACCCCGTGATAGGGGCAGATCGTAACCATCCGATCTTTTACCCCGATCATGAGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
* *
15679310 TAAATCACCGTCA
65 CAGATCACCGTCA
* ** * * ** *
15679323 GCTAATCTCTTACCCCGCGACAAAGGCAAATTGCAATCATTTGATCTTTTACCCCGATCATAAGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
15679388 CAGATCACCGTCA
65 CAGATCACCGTCA
* * *
15679401 GCCAATCTCTTACCCCGCGACAAGGGCAGATTGTAACCATCCGATCTTTTACCCCGATCATGAGA
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
15679466 CAGATCACCGTCA
65 CAGATCACCGTCA
* * * * *
15679479 GCCAATCTCTTACCCCGCGATAGGGACAGATTGCAACCATCTGATCTTTTAACCCGATCATGGGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
*
15679544 CAGATTACCGTCA
65 CAGATCACCGTCA
* *
15679557 GCCAATCTCTTACCCCGCGACAGGGGCATATTGTAACCATCCGATCTTTTACCCCGATCATGAGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
*
15679622 CAAATCACCGTCA
65 CAGATCACCGTCA
* * * * * * *
15679635 GCCAATTTCTTACCCCACGACAAGGGTAGATTGCAACCATCTGATCTTTTACCTCGATCATGGGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
*
15679700 CAGATCACCATCA
65 CAGATCACCGTCA
* *
15679713 GCCAATCTCTTACCCCGCGACAGGGGTAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
*
15679778 CAGATAACCGTCA
65 CAGATCACCGTCA
* * *
15679791 GTCAATCTCTTACCCCGTGACAGGGGCAGATTGCAACCATCCGATATTTTACCCCGATCAT-AGG
1 GCCAATCTCTTA-CCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
* *
15679855 ATAAATCACCGTCA
65 -CAGATCACCGTCA
* * *
15679869 GCCAATCTCTTACCCTGCGACAAGGGCAGATTGCAACCATCCGATCTTTCACCCCGATCATGGGG
1 GCCAATCTCTTACCC-GCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGG
15679934 CAGAT
65 CAGAT
15679939 TGATGACATC
Statistics
Matches: 804, Mismatches: 118, Indels: 12
0.86 0.13 0.01
Matches are distributed among these distances:
77 5 0.01
78 792 0.99
79 6 0.01
80 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (77 bp):
GCCAATCTCTTACCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGAGGC
AGATCACCGTCA
Found at i:15679958 original size:42 final size:41
Alignment explanation
Indices: 15679906--15680173 Score: 233
Period size: 42 Copynumber: 6.4 Consensus size: 41
15679896 AGATTGCAAC
* * *
15679906 CATCCGATCTTTCACCCCGATCATGGGGCAGATTGATGACAT
1 CATCCAATCTTT-ACCCCAATCATGGGGCAGATTGAAGACAT
* * **
15679948 CATCCAATCTTTTACCCTAATTAAAGGGCAGATTGAAGACA-
1 CATCCAATC-TTTACCCCAATCATGGGGCAGATTGAAGACAT
* *
15679989 CA-CCAATCTATTACCCCAATGATAAGGG-AGATTGAAGACAT
1 CATCCAATCT-TTACCCCAATCAT-GGGGCAGATTGAAGACAT
* *
15680030 CATCCAATCTTTTACCCTAATCA-GAGGGCATATTGAAGACA-
1 CATCCAATC-TTTACCCCAATCATG-GGGCAGATTGAAGACAT
* *
15680071 CA-CCAATCTCTTATCCCGATCATGGGGCAGATTGAAGACAT
1 CATCCAATCT-TTACCCCAATCATGGGGCAGATTGAAGACAT
* * *
15680112 CATCCAATCTTCTACCTCTAAACCAAGAGGGGCAGATTGAAGACAT
1 CATCCAATCTT-TACC-C-CAATC-A-TGGGGCAGATTGAAGACAT
15680158 CATCCAATCTTCTACC
1 CATCCAATCTT-TACC
15680174 TCTAAATCAA
Statistics
Matches: 186, Mismatches: 23, Indels: 30
0.78 0.10 0.13
Matches are distributed among these distances:
39 2 0.01
40 58 0.31
41 17 0.09
42 67 0.36
43 5 0.03
44 2 0.01
45 1 0.01
46 34 0.18
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (41 bp):
CATCCAATCTTTACCCCAATCATGGGGCAGATTGAAGACAT
Found at i:15680003 original size:40 final size:42
Alignment explanation
Indices: 15679931--15680207 Score: 271
Period size: 46 Copynumber: 6.5 Consensus size: 42
15679921 CCCGATCATG
* *
15679931 GGGCAGATTGATGACATCATCCAATCTTTTACCCTAATTAAA
1 GGGCAGATTGAAGACATCATCCAATCTTTTACCCTAATCAAA
* * *
15679973 GGGCAGATTGAAGACA-CA-CCAATCTATTACCCCAATGATAA
1 GGGCAGATTGAAGACATCATCCAATCTTTTACCCTAATCA-AA
*
15680014 GGG-AGATTGAAGACATCATCCAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAGACATCATCCAATCTTTTACCCTAATCAAA
* * * **
15680055 GGGCATATTGAAGACA-CA-CCAATCTCTTATCCC-GATCATG
1 GGGCAGATTGAAGACATCATCCAATCTTTTA-CCCTAATCAAA
* *
15680095 GGGCAGATTGAAGACATCATCCAATCTTCTACCTCTAAACCAAGA
1 GGGCAGATTGAAGACATCATCCAATCTTTTACC-CT-AATCAA-A
*
15680140 GGGGCAGATTGAAGACATCATCCAATCTTCTACCTCTAAATCAAAA
1 -GGGCAGATTGAAGACATCATCCAATCTTTTACC-CT-AATC-AAA
*
15680186 GGGGCAAATTGAAG-CTATCATC
1 -GGGCAGATTGAAGAC-ATCATC
15680208 TCATAGAAGC
Statistics
Matches: 199, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
40 58 0.29
41 22 0.11
42 53 0.27
44 3 0.02
45 1 0.01
46 60 0.30
47 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (42 bp):
GGGCAGATTGAAGACATCATCCAATCTTTTACCCTAATCAAA
Found at i:15680038 original size:82 final size:82
Alignment explanation
Indices: 15679890--15680167 Score: 312
Period size: 82 Copynumber: 3.3 Consensus size: 82
15679880 ACCCTGCGAC
* * * * *
15679890 AAGGGCAGATTGCA-AC-CATCCGATCT-TTCACCCCGATCATGGGGCAGATTGATGACATCATC
1 AAGGGCAGATTGAAGACACA-CCAATCTATT-ACCCCAATCATAGGGCAGATTGAAGACATCATC
*
15679952 CAATCTTTTACCCTAATTA
64 CAATCTTTTACCCTAATCA
*
15679971 AAGGGCAGATTGAAGACACACCAATCTATTACCCCAATGATAAGGG-AGATTGAAGACATCATCC
1 AAGGGCAGATTGAAGACACACCAATCTATTACCCCAATCAT-AGGGCAGATTGAAGACATCATCC
15680035 AATCTTTTACCCTAATCA
65 AATCTTTTACCCTAATCA
* * * * * *
15680053 GAGGGCATATTGAAGACACACCAATCTCTTATCCCGATCATGGGGCAGATTGAAGACATCATCCA
1 AAGGGCAGATTGAAGACACACCAATCTATTACCCCAATCATAGGGCAGATTGAAGACATCATCCA
* *
15680118 ATCTTCTACCTCTAAACCA
66 ATCTTTTACC-CT-AATCA
15680137 AGAGGGGCAGATTGAAGACATCATCCAATCT
1 A-A-GGGCAGATTGAAGACA-CA-CCAATCT
15680168 TCTACCTCTA
Statistics
Matches: 168, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
81 16 0.10
82 114 0.68
83 9 0.05
84 4 0.02
85 1 0.01
86 15 0.09
87 2 0.01
88 7 0.04
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (82 bp):
AAGGGCAGATTGAAGACACACCAATCTATTACCCCAATCATAGGGCAGATTGAAGACATCATCCA
ATCTTTTACCCTAATCA
Found at i:15682189 original size:59 final size:58
Alignment explanation
Indices: 15682102--15682438 Score: 272
Period size: 59 Copynumber: 5.7 Consensus size: 58
15682092 AAATTTTCCA
* * *
15682102 AAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCT
1 AAAATTACATTTTAACCC-CAAATTTTTCCAAAATTACATTTTGACCC-TAAACTTTTCT
* * * *
15682162 AAAATTACATTTTGACCTCC-AATTTTTCTAAATTTGCATTTTGACCCCTAAACTTTTCT
1 AAAATTACATTTTAACC-CCAAATTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTCT
* * ** *
15682221 AAATTTTCATTTTAACCAATAAATTTTTCCAAAATTACATTTTAACCCCTAAACTTCTT-T
1 AAAATTACATTTTAACC-CCAAATTTTTCCAAAATTACATTTTGA-CCCTAAACTT-TTCT
* * * ** *
15682281 AAAATCACATTTTAACCCCAAACTCTTT-AAAAATTACATTTTGATCCC-AAACTTCCCC
1 AAAATTACATTTTAACCCCAAA-TTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTCT
* * * * * *
15682339 AAAATCACA-TTTGACCCCAAACTTCTCCAAAATCACATTTTGAACCC-AAACTTTCCT
1 AAAATTACATTTTAACCCCAAATTTTTCCAAAATTACATTTTG-ACCCTAAACTTTTCT
** * * *
15682396 AAAATTATGTTTTTACCCCAAACTTTTTCTAAAATTATATTTT
1 AAAATTACATTTTAACCCCAAA-TTTTTCCAAAATTACATTTT
15682439 AACCTCGTAT
Statistics
Matches: 221, Mismatches: 46, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
56 2 0.01
57 41 0.19
58 27 0.12
59 80 0.36
60 68 0.31
61 3 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (58 bp):
AAAATTACATTTTAACCCCAAATTTTTCCAAAATTACATTTTGACCCTAAACTTTTCT
Found at i:15682214 original size:89 final size:89
Alignment explanation
Indices: 15682044--15682441 Score: 286
Period size: 89 Copynumber: 4.5 Consensus size: 89
15682034 TATTTCTTTA
* *
15682044 AAAATTACATTTTTAATCCTT-AACTTTTCT-AAATTTCATTTTAACTCCAAATTTTCCAAAAAT
1 AAAATTACA-TTTTAACCCTTAAACTTTTCTAAAATTACATTTTAACTCCAAATTTTCCAAAAAT
*
15682107 CACATTTTAACCCTTAAACTTTTCC
65 CACATTTTAACCCCTAAACTTTTCC
* * * * *
15682132 AAAATTACATTTTGACCCTTAAACTTTTCTAAAATTACATTTTGACCTCC-AATTTTTCTAAATT
1 AAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTT-AACTCCAAATTTTCCAAAAAT
** * *
15682196 TGCATTTTGACCCCTAAACTTTTCT
65 CACATTTTAACCCCTAAACTTTTCC
* * ** * * * *
15682221 AAATTTTCATTTTAACCAATAAATTTTTCCAAAATTACATTTTAACCCCTAAACTTCTT--TAAA
1 AAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTAACTCC-AAA-TT-TTCCAAAA
*
15682284 ATCACATTTTAACCCC-AAACTCTTT-A
63 ATCACATTTTAACCCCTAAACT-TTTCC
* ** * * * * *
15682310 AAAATTACATTTTGATCCC--AAACTTCCCCAAAATCACA-TTTGACCCCAAACTTCTCC-AAAA
1 AAAATTACATTTT-AACCCTTAAACTTTTCTAAAATTACATTTTAACTCCAAA-TTTTCCAAAAA
15682371 TCACATTTTGAA-CCC-AAAC-TTTCC
64 TCACATTTT-AACCCCTAAACTTTTCC
** * * *
15682395 TAAAATTATGTTTTTACCC-CAAACTTTTTCTAAAATTATATTTTAAC
1 -AAAATTACATTTTAACCCTTAAAC-TTTTCTAAAATTACATTTTAAC
15682442 CTCGTATTCT
Statistics
Matches: 246, Mismatches: 47, Indels: 34
0.75 0.14 0.10
Matches are distributed among these distances:
84 3 0.01
85 4 0.02
86 41 0.17
87 29 0.12
88 42 0.17
89 94 0.38
90 29 0.12
91 2 0.01
92 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (89 bp):
AAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTAACTCCAAATTTTCCAAAAATC
ACATTTTAACCCCTAAACTTTTCC
Found at i:15682321 original size:119 final size:118
Alignment explanation
Indices: 15682109--15682334 Score: 287
Period size: 119 Copynumber: 1.9 Consensus size: 118
15682099 CCAAAAATCA
** * * *
15682109 CATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCTAAAATTACATTT
1 CATTTTAACCAATAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTT
* * * * *
15682174 TGACCTCCAATTTTTCTAAATTTGCATTTTGACCCCTAAACTTTTCTAAATTTT
66 TAACCTCCAATCTTTCAAAAATTACATTTTGACCCC-AAACTTTTCTAAATTTT
*
15682228 CATTTTAACCAATAAATTTTTCCAAAATTACATTTTAACCCCTAAACTTCTT-TAAAATCACATT
1 CATTTTAACCAATAAACTTTTCCAAAATTACATTTTAACCCCTAAACTT-TTCTAAAATCACATT
*
15682292 TTAACC-CCAAACTCTTT-AAAAATTACATTTTGATCCCAAACTT
65 TTAACCTCC-AA-TCTTTCAAAAATTACATTTTGACCCCAAACTT
15682335 CCCCAAAATC
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 8 0.09
119 78 0.85
120 6 0.07
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (118 bp):
CATTTTAACCAATAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTT
TAACCTCCAATCTTTCAAAAATTACATTTTGACCCCAAACTTTTCTAAATTTT
Found at i:15682400 original size:86 final size:88
Alignment explanation
Indices: 15682249--15682420 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 88
15682239 ATAAATTTTT
* **
15682249 CCAAAATTACATTTTAACCCCTAAACTTCTTTAAAATCACATTTTAACCCCAAACTCTTTAAAAA
1 CCAAAATCACATTTTAACCCCTAAACTTCTCCAAAATCACATTTTAACCCCAAACTCTTTAAAAA
*
15682314 TTACATTTTGATCCCAAACTTCC
66 TTACATTTTGACCCCAAACTTCC
*
15682337 CCAAAATCACA-TTTGACCCC-AAACTTCTCCAAAATCACATTTTGAA-CCCAAACT-TTCCT-A
1 CCAAAATCACATTTTAACCCCTAAACTTCTCCAAAATCACATTTT-AACCCCAAACTCTT--TAA
** *
15682397 AAATTATGTTTTTACCCCAAACTT
63 AAATTACATTTTGACCCCAAACTT
15682421 TTTCTAAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
85 2 0.03
86 50 0.68
87 11 0.15
88 10 0.14
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (88 bp):
CCAAAATCACATTTTAACCCCTAAACTTCTCCAAAATCACATTTTAACCCCAAACTCTTTAAAAA
TTACATTTTGACCCCAAACTTCC
Found at i:15682421 original size:29 final size:29
Alignment explanation
Indices: 15682065--15682438 Score: 158
Period size: 29 Copynumber: 12.8 Consensus size: 29
15682055 TTTAATCCTT
* * *
15682065 AACTTTTCT-AAATT-TCATTTTAACTCCA
1 AACTTTCCTAAAATTAT-ATTTTGACCCCA
* * * * * *
15682093 AATTTTCCAAAAATCACATTTTAACCCTTA
1 AACTTTCCTAAAATTATATTTTGACCC-CA
* *
15682123 AACTTTTCC-AAAATTACATTTTGACCCTTA
1 AAC-TTTCCTAAAATTATATTTTGACCC-CA
* *
15682153 AACTTTTCTAAAATTACATTTTGACCTCC-
1 AACTTTCCTAAAATTATATTTTGACC-CCA
* * * **
15682182 AATTTTTCTAAATTTGCATTTTGACCCCTA
1 AACTTTCCTAAAATTATATTTTGACCCC-A
* * * **
15682212 AACTTTTCT-AAATTTTCATTTTAACCAATA
1 AACTTTCCTAAAATTAT-ATTTTGACC-CCA
* * *
15682242 AATTTTTCC-AAAATTACATTTTAACCCCTA
1 AA-CTTTCCTAAAATTATATTTTGACCCC-A
* * * *
15682272 AAC-TTCTTTAAAATCACATTTTAACCCCA
1 AACTTTC-CTAAAATTATATTTTGACCCCA
* *
15682301 AACTCTT--TAAAAATTACATTTTGATCCCA
1 AACT-TTCCT-AAAATTATATTTTGACCCCA
* * * *
15682330 AACTTCCCCAAAATCACA-TTTGACCCCA
1 AACTTTCCTAAAATTATATTTTGACCCCA
* * *
15682358 AACTTCTCC-AAAATCACATTTTGAACCCA
1 AACTT-TCCTAAAATTATATTTTGACCCCA
* *
15682387 AACTTTCCTAAAATTATGTTTTTACCCCA
1 AACTTTCCTAAAATTATATTTTGACCCCA
*
15682416 AACTTTTTCTAAAATTATATTTT
1 AAC-TTTCCTAAAATTATATTTT
15682439 AACCTCGTAT
Statistics
Matches: 275, Mismatches: 47, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
28 39 0.14
29 111 0.40
30 108 0.39
31 17 0.06
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (29 bp):
AACTTTCCTAAAATTATATTTTGACCCCA
Found at i:15682439 original size:29 final size:29
Alignment explanation
Indices: 15682065--15682438 Score: 283
Period size: 30 Copynumber: 12.8 Consensus size: 29
15682055 TTTAATCCTT
* * *
15682065 AACTTTTCT-AAATTTCATTTTAACTCCA
1 AACTTTTCTAAAATTACATTTTGACCCCA
* * * *
15682093 AA-TTTTCCAAAAATCACATTTTAACCCTTA
1 AACTTTT-CTAAAATTACATTTTGACCC-CA
* *
15682123 AACTTTTCCAAAATTACATTTTGACCCTTA
1 AACTTTTCTAAAATTACATTTTGACCC-CA
15682153 AACTTTTCTAAAATTACATTTTGACCTCC-
1 AACTTTTCTAAAATTACATTTTGACC-CCA
* * *
15682182 AATTTTTCTAAATTTGCATTTTGACCCCTA
1 AACTTTTCTAAAATTACATTTTGACCCC-A
* * * **
15682212 AACTTTTCTAAATTTTCATTTTAACCAATA
1 AACTTTTCTAAAATTACATTTTGACC-CCA
* * *
15682242 AATTTTTCCAAAATTACATTTTAACCCCTA
1 AACTTTTCTAAAATTACATTTTGACCCC-A
* *
15682272 AACTTCTT-TAAAATCACATTTTAACCCCA
1 AACTT-TTCTAAAATTACATTTTGACCCCA
* *
15682301 AACTCTTT-AAAAATTACATTTTGATCCCA
1 AACT-TTTCTAAAATTACATTTTGACCCCA
** * *
15682330 AACTTCCCCAAAATCACA-TTTGACCCCA
1 AACTTTTCTAAAATTACATTTTGACCCCA
* * * *
15682358 AACTTCTCCAAAATCACATTTTGAACCCA
1 AACTTTTCTAAAATTACATTTTGACCCCA
* ** *
15682387 AACTTTCCTAAAATTATGTTTTTACCCCA
1 AACTTTTCTAAAATTACATTTTGACCCCA
*
15682416 AACTTTTTCTAAAATTATATTTT
1 AAC-TTTTCTAAAATTACATTTT
15682439 AACCTCGTAT
Statistics
Matches: 284, Mismatches: 48, Indels: 26
0.79 0.13 0.07
Matches are distributed among these distances:
27 4 0.01
28 32 0.11
29 106 0.37
30 135 0.48
31 7 0.02
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (29 bp):
AACTTTTCTAAAATTACATTTTGACCCCA
Found at i:15684252 original size:18 final size:19
Alignment explanation
Indices: 15684229--15684267 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
15684219 ACGAATTGAG
* *
15684229 TTATTCGAGTTAA-TCGAA
1 TTATTCAAGTCAATTCGAA
15684247 TTATTCAAGTCAATTCGAA
1 TTATTCAAGTCAATTCGAA
15684266 TT
1 TT
15684268 TTTTTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (19 bp):
TTATTCAAGTCAATTCGAA
Found at i:15684379 original size:22 final size:23
Alignment explanation
Indices: 15684347--15684393 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
15684337 AACTATAATA
15684347 TTTTACATTTTTACCTC-AAACAT
1 TTTTACATTTTTACC-CAAAACAT
*
15684370 TTTTAC-TTTTTTCCCAAAACAT
1 TTTTACATTTTTACCCAAAACAT
15684392 TT
1 TT
15684394 ACTCCTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 15 0.68
23 6 0.27
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTACATTTTTACCCAAAACAT
Found at i:15684674 original size:19 final size:18
Alignment explanation
Indices: 15684650--15684687 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15684640 TTTTGAATAT
15684650 TTTCCCTCCAAAATTTTAC
1 TTTCCCT-CAAAATTTTAC
*
15684669 TTTCCCTTAAAATTTTAC
1 TTTCCCTCAAAATTTTAC
15684687 T
1 T
15684688 CCTAAAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCCCTCAAAATTTTAC
Found at i:15686691 original size:26 final size:27
Alignment explanation
Indices: 15686657--15686716 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
15686647 GTTAAAACTC
15686657 TTTTAAAA-GAAAACTC-AAGAGAAGT
1 TTTTAAAAGGAAAACTCAAAGAGAAGT
*
15686682 TTTTGAAAAGGAAAACTCAAAGAGAAAT
1 TTTT-AAAAGGAAAACTCAAAGAGAAGT
15686710 TTATTAA
1 TT-TTAA
15686717 CTCAAAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 8 0.27
28 12 0.40
29 2 0.07
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.27
Consensus pattern (27 bp):
TTTTAAAAGGAAAACTCAAAGAGAAGT
Found at i:15693842 original size:21 final size:21
Alignment explanation
Indices: 15693812--15693858 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
15693802 AACCTATTGT
* *
15693812 TTTTGCTGCTATTTTTCCATG
1 TTTTGATGCTATTTTCCCATG
* *
15693833 TTTTGATGCTGTTTTCCCATT
1 TTTTGATGCTATTTTCCCATG
15693854 TTTTG
1 TTTTG
15693859 CTATTGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.17, G:0.15, T:0.60
Consensus pattern (21 bp):
TTTTGATGCTATTTTCCCATG
Found at i:15697079 original size:21 final size:21
Alignment explanation
Indices: 15697040--15697079 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15697030 TTTATTTAAA
*
15697040 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
15697061 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
15697080 TGCTGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:15697129 original size:23 final size:21
Alignment explanation
Indices: 15697087--15697127 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15697077 AATTGCTGAT
*
15697087 AAAAGTTCTATATATCTATAG
1 AAAAGTTCGATATATCTATAG
*
15697108 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
15697128 TAATTAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:15699097 original size:26 final size:25
Alignment explanation
Indices: 15699068--15699116 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
15699058 TTTTAAGCAA
*
15699068 TTTAA-TTATTTTTCTTTCATTTTCTT
1 TTTAACTTATATTT-TTTC-TTTTCTT
15699094 TTTAACTTATATTTTTTCTTTTC
1 TTTAACTTATATTTTTTCTTTTC
15699117 CTTGTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 9 0.43
27 7 0.33
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTAACTTATATTTTTTCTTTTCTT
Found at i:15699757 original size:50 final size:50
Alignment explanation
Indices: 15699682--15699785 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
15699672 ATAATATACA
15699682 AATAATATACTTTTAATTATTTGAAACAATTGAACCCAATGAGTGGCTCC
1 AATAATATACTTTTAATTATTTGAAACAATTGAACCCAATGAGTGGCTCC
15699732 AATAATATACTTTTAATTATTTGAAACAATTGAACCCAATGAGTGGCTCC
1 AATAATATACTTTTAATTATTTGAAACAATTGAACCCAATGAGTGGCTCC
15699782 AATA
1 AATA
15699786 GAAAAGAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (50 bp):
AATAATATACTTTTAATTATTTGAAACAATTGAACCCAATGAGTGGCTCC
Found at i:15700116 original size:16 final size:17
Alignment explanation
Indices: 15700089--15700124 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
15700079 TTAATTTTTT
*
15700089 ATATATATATTTTAAAA
1 ATATATATATTTAAAAA
15700106 ATATA-ATATTTAAAAA
1 ATATATATATTTAAAAA
15700122 ATA
1 ATA
15700125 CTAAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATATATTTAAAAA
Found at i:15700310 original size:22 final size:22
Alignment explanation
Indices: 15700285--15700326 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15700275 TATACAAACA
15700285 ATAACAATAAAATAATAGTAGC
1 ATAACAATAAAATAATAGTAGC
* * *
15700307 ATAATAGTAAAATAGTAGTA
1 ATAACAATAAAATAATAGTA
15700327 AAATAGTGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (22 bp):
ATAACAATAAAATAATAGTAGC
Found at i:15700332 original size:11 final size:11
Alignment explanation
Indices: 15700292--15700345 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
15700282 ACAATAACAA
15700292 TAAAATAATAG
1 TAAAATAATAG
**
15700303 TAGCATAATAG
1 TAAAATAATAG
*
15700314 TAAAATAGTAG
1 TAAAATAATAG
*
15700325 TAAAATAGTGAG
1 TAAAATAAT-AG
15700337 TAAACATAA
1 TAAA-ATAA
15700346 AAAAAAATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 26 0.74
12 6 0.17
13 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.26
Consensus pattern (11 bp):
TAAAATAATAG
Found at i:15711878 original size:18 final size:20
Alignment explanation
Indices: 15711841--15711887 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
15711831 TGGAATGATA
15711841 AGAAGAGGAAGAGAGGGAAGG
1 AGAAGAGGAAGAGA-GGAAGG
15711862 AGAAGAGG-AGAGA-GAAGG
1 AGAAGAGGAAGAGAGGAAGG
*
15711880 CGAAGAGG
1 AGAAGAGG
15711888 GTGGGAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 12 0.48
20 5 0.20
21 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (20 bp):
AGAAGAGGAAGAGAGGAAGG
Found at i:15712440 original size:32 final size:32
Alignment explanation
Indices: 15712399--15712466 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
15712389 TAAAATTTAG
*
15712399 TTTTTATATTCATATTTTTAAAAATATAATTT
1 TTTTTATATTCATATTTTTAAAAATATAATCT
*
15712431 TTTTTATATTTATATTTTTAAAAATATAATCT
1 TTTTTATATTCATATTTTTAAAAATATAATCT
15712463 TTTT
1 TTTT
15712467 AGAATCCGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTTTATATTCATATTTTTAAAAATATAATCT
Found at i:15716866 original size:16 final size:15
Alignment explanation
Indices: 15716828--15716879 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
15716818 TTTAAGCCCA
15716828 AACCTAAACCCAA-T-
1 AACC-AAACCCAAGTG
15716842 AACCCAAACCCAAAGTG
1 AA-CCAAACCC-AAGTG
*
15716859 AACCAAACCCAATTG
1 AACCAAACCCAAGTG
15716874 AACCAA
1 AACCAA
15716880 GTCTAAACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 8 0.24
15 14 0.42
16 9 0.27
17 2 0.06
ACGTcount: A:0.50, C:0.35, G:0.06, T:0.10
Consensus pattern (15 bp):
AACCAAACCCAAGTG
Found at i:15716978 original size:7 final size:7
Alignment explanation
Indices: 15716968--15717031 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
15716958 CCGTTGACCA
15716968 TTGACTG
1 TTGACTG
15716975 TTGACT-
1 TTGACTG
*
15716981 TTGACCG
1 TTGACTG
*
15716988 TTGACCG
1 TTGACTG
*
15716995 TTGA-TT
1 TTGACTG
*
15717001 TTGACCG
1 TTGACTG
15717008 TTGACTG
1 TTGACTG
*
15717015 TTAACT-
1 TTGACTG
15717021 TTGACT-
1 TTGACTG
15717027 TTGAC
1 TTGAC
15717032 CCGTTGACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
6 19 0.40
7 28 0.60
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (7 bp):
TTGACTG
Found at i:15717005 original size:40 final size:41
Alignment explanation
Indices: 15716961--15717043 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 41
15716951 TGATCGACCG
*
15716961 TTGACCATTGACTGTTGACTTTGACCGTTGA-CCGTTGA-TT
1 TTGACCATTGACTGTTAACTTTGA-CGTTGACCCGTTGACTT
* *
15717001 TTGACCGTTGACTGTTAACTTTGACTTTGACCCGTTGACTT
1 TTGACCATTGACTGTTAACTTTGACGTTGACCCGTTGACTT
15717042 TT
1 TT
15717044 TTCCAAGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 5 0.13
40 29 0.76
41 4 0.11
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (41 bp):
TTGACCATTGACTGTTAACTTTGACGTTGACCCGTTGACTT
Found at i:15717011 original size:27 final size:27
Alignment explanation
Indices: 15716956--15717039 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
15716946 GCCGTTGATC
* *
15716956 GACCGTTGACCATTGACTGTTGA-CTTT
1 GACCGTTGACCATTGA-TTTTGACCGTT
*
15716983 GACCGTTGACCGTTGATTTTGACCGTT
1 GACCGTTGACCATTGATTTTGACCGTT
* * * *
15717010 GACTGTT-AACTTTGACTTTGACCCGTT
1 GACCGTTGACCATTGATTTTGA-CCGTT
15717037 GAC
1 GAC
15717040 TTTTTTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
26 16 0.33
27 32 0.67
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
GACCGTTGACCATTGATTTTGACCGTT
Found at i:15717041 original size:20 final size:20
Alignment explanation
Indices: 15716961--15717042 Score: 94
Period size: 20 Copynumber: 4.1 Consensus size: 20
15716951 TGATCGACCG
* *
15716961 TTGACCATTGACTGTTGACT
1 TTGACCGTTGACCGTTGACT
*
15716981 TTGACCGTTGACCGTTGATT
1 TTGACCGTTGACCGTTGACT
* *
15717001 TTGACCGTTGACTGTTAACT
1 TTGACCGTTGACCGTTGACT
*
15717021 TTGA-CTTTGACCCGTTGACT
1 TTGACCGTTGA-CCGTTGACT
15717041 TT
1 TT
15717043 TTTCCAAGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 5 0.10
20 47 0.90
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:15717189 original size:12 final size:12
Alignment explanation
Indices: 15717167--15717196 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
15717157 ACTTTAAGTT
15717167 ATTTGGAGTTTTA
1 ATTT-GAGTTTTA
15717180 ATTTGAGTTTTA
1 ATTTGAGTTTTA
15717192 ATTTG
1 ATTTG
15717197 GGATTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (12 bp):
ATTTGAGTTTTA
Found at i:15722588 original size:41 final size:41
Alignment explanation
Indices: 15722523--15722619 Score: 122
Period size: 41 Copynumber: 2.4 Consensus size: 41
15722513 CTTATTCGTA
* * **
15722523 TAGAATTCTTGTCAATGTGGAGATTGTTAGAATTGAATGAC
1 TAGAATTCTTGTTAAGGTAAAGATTGTTAGAATTGAATGAC
**
15722564 TAGAATTCTTGTTAAGGTAAAGATTGTTAGAATTGGGTGAC
1 TAGAATTCTTGTTAAGGTAAAGATTGTTAGAATTGAATGAC
* *
15722605 TAAAATTTTTGTTAA
1 TAGAATTCTTGTTAA
15722620 AATAAAATTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (41 bp):
TAGAATTCTTGTTAAGGTAAAGATTGTTAGAATTGAATGAC
Found at i:15730949 original size:29 final size:28
Alignment explanation
Indices: 15730912--15730966 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
15730902 TATGTGAGAG
* *
15730912 AAAATTACATTATCTTTCTAAATAATCT
1 AAAATTACAATATCTTTCAAAATAATCT
*
15730940 AAAACTTACAATATTTTTCAAAATAAT
1 AAAA-TTACAATATCTTTCAAAATAAT
15730967 TTTTAAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATTACAATATCTTTCAAAATAATCT
Found at i:15731093 original size:31 final size:31
Alignment explanation
Indices: 15731058--15731122 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
15731048 ATTTGATCAT
*
15731058 TGAATTATTCGAAA-GTTTTCATTTAAGTCAC
1 TGAATTATTC-AAATGTTTTCATTTAAGTAAC
*
15731089 TGAATTATTCAAATGTTTTTATTTAAGTAAC
1 TGAATTATTCAAATGTTTTCATTTAAGTAAC
15731120 TGA
1 TGA
15731123 GTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
TGAATTATTCAAATGTTTTCATTTAAGTAAC
Found at i:15731361 original size:15 final size:15
Alignment explanation
Indices: 15731341--15731371 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15731331 CTATATAGAA
15731341 TCGATTTTAATAATT
1 TCGATTTTAATAATT
15731356 TCGATTTTAATAATT
1 TCGATTTTAATAATT
15731371 T
1 T
15731372 GATGACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (15 bp):
TCGATTTTAATAATT
Found at i:15734904 original size:43 final size:43
Alignment explanation
Indices: 15734801--15734949 Score: 144
Period size: 43 Copynumber: 3.5 Consensus size: 43
15734791 TCCAGGAAAT
* * * *
15734801 CACCTTCTAATACATAAAATACGAGAATATCTTTCCCACATAC
1 CACCTTCTAATACATGAAATACGAGAATTTCTTTTCCAAATAC
** * *
15734844 GGCCTTCTAATAAATGAAATACGAGAATTTCTTTTCCAAACAC
1 CACCTTCTAATACATGAAATACGAGAATTTCTTTTCCAAATAC
*
15734887 CACCTT-TAAATACATGAAATATTC-A-AATTTCTTTCTCC-AATAT
1 CACCTTCT-AATACATGAAATA--CGAGAATTTCTTT-TCCAAATAC
*
15734930 CACCTTTTAATACATGAAAT
1 CACCTTCTAATACATGAAAT
15734950 GTGAGAGTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 81 0.92
44 5 0.06
45 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (43 bp):
CACCTTCTAATACATGAAATACGAGAATTTCTTTTCCAAATAC
Found at i:15736897 original size:2 final size:2
Alignment explanation
Indices: 15736890--15736914 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15736880 AACCAAAATA
15736890 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15736915 ATTGTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15740988 original size:31 final size:31
Alignment explanation
Indices: 15740953--15741015 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
15740943 TAAATAATCC
* * *
15740953 AGTGACTTAAGTAAAAACTTTCGAATAGTTT
1 AGTGACTTAAATAAAAACTTTAGAATAATTT
*
15740984 AGTGACTTAAATGAAAACTTTAGAATAATTT
1 AGTGACTTAAATAAAAACTTTAGAATAATTT
15741015 A
1 A
15741016 ATGATCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTAGAATAATTT
Found at i:15743482 original size:31 final size:31
Alignment explanation
Indices: 15743447--15743507 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
15743437 TTAACAATCA
15743447 AGTAACTTAAAT-AAAAATTTTCAAATAGTTC
1 AGTAACTTAAATGAAAAATTTT-AAATAGTTC
* *
15743478 AGTAACTTAAATGAAAACTTTTGAATAGTT
1 AGTAACTTAAATGAAAAATTTTAAATAGTT
15743508 AAAAATCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (31 bp):
AGTAACTTAAATGAAAAATTTTAAATAGTTC
Found at i:15748727 original size:20 final size:20
Alignment explanation
Indices: 15748699--15748737 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15748689 TGGTTGGGGG
*
15748699 AATGAAATAGGGCTGTAATT
1 AATGAAATAGAGCTGTAATT
*
15748719 AATGGAATAGAGCTGTAAT
1 AATGAAATAGAGCTGTAAT
15748738 CAGTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (20 bp):
AATGAAATAGAGCTGTAATT
Found at i:15752485 original size:10 final size:10
Alignment explanation
Indices: 15752470--15752494 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15752460 TAGTACTATT
15752470 TAAGTTACTG
1 TAAGTTACTG
15752480 TAAGTTACTG
1 TAAGTTACTG
15752490 TAAGT
1 TAAGT
15752495 CACGTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (10 bp):
TAAGTTACTG
Found at i:15755815 original size:27 final size:27
Alignment explanation
Indices: 15755750--15755820 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
15755740 CTTCATGTTA
* *
15755750 ATTTTTATGAATTCT---TTTTTATAT
1 ATTTTTATGAATTTTAAATTTTTAAAT
* *
15755774 ATTTTTTTGAATTTTGAATTTTTAAAT
1 ATTTTTATGAATTTTAAATTTTTAAAT
15755801 ATTTTTAT-AATTTTTAAATT
1 ATTTTTATGAA-TTTTAAATT
15755821 ATTCATTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
24 13 0.34
26 2 0.05
27 23 0.61
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (27 bp):
ATTTTTATGAATTTTAAATTTTTAAAT
Found at i:15759859 original size:2 final size:2
Alignment explanation
Indices: 15759852--15759885 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15759842 TTGGCAACAA
15759852 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
15759886 GTATGTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15759967 original size:13 final size:13
Alignment explanation
Indices: 15759949--15759977 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15759939 GTTTCAGCAA
15759949 TGAGCACAAATAC
1 TGAGCACAAATAC
15759962 TGAGCACAAATAC
1 TGAGCACAAATAC
15759975 TGA
1 TGA
15759978 ATACAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (13 bp):
TGAGCACAAATAC
Found at i:15760228 original size:12 final size:13
Alignment explanation
Indices: 15760200--15760230 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
15760190 TATAAGTTGG
15760200 TTTAAAATTTGTA
1 TTTAAAATTTGTA
15760213 TTTAAAATTT-TA
1 TTTAAAATTTGTA
15760225 TTTAAA
1 TTTAAA
15760231 TTCGTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TTTAAAATTTGTA
Found at i:15761031 original size:61 final size:63
Alignment explanation
Indices: 15760916--15761033 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 63
15760906 AGGTATAATA
* * * *
15760916 ACAAATTTAACCCTTAACATGATTTCACATTCTATTAATTTGGTCCTAACTCTAAAAAATTCT
1 ACAAATTTAACCCTTAACATGATTGCACATTCTATCAATTTAGTCCAAACTCTAAAAAATTCT
* * * * *
15760979 ACAAATTTAA-CCTTCA-ATGCTTGCACATTTTGTCAATTTAGTCCAAATTCTAAAA
1 ACAAATTTAACCCTTAACATGATTGCACATTCTATCAATTTAGTCCAAACTCTAAAA
15761034 CTCAACAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
61 31 0.67
62 5 0.11
63 10 0.22
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.37
Consensus pattern (63 bp):
ACAAATTTAACCCTTAACATGATTGCACATTCTATCAATTTAGTCCAAACTCTAAAAAATTCT
Found at i:15766643 original size:22 final size:20
Alignment explanation
Indices: 15766618--15766672 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
15766608 TCCAAAAAAT
15766618 TATTATTTTAAATTTTTTTATA
1 TATT-TTTTAAATTTTTTTA-A
* *
15766640 TATTCTTTAGATTTTTTTAA
1 TATTTTTTAAATTTTTTTAA
15766660 TA-TTTTTAAATTT
1 TATTTTTTAAATTT
15766673 ATATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 13 0.45
22 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTTTAAATTTTTTTAA
Found at i:15773196 original size:23 final size:23
Alignment explanation
Indices: 15773170--15773215 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
15773160 TTACAAACTC
15773170 AAATTATCCTCAAGAGTAAGGGT
1 AAATTATCCTCAAGAGTAAGGGT
*
15773193 AAATTATCCTCAATAGTAAGGGT
1 AAATTATCCTCAAGAGTAAGGGT
15773216 GAACGTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (23 bp):
AAATTATCCTCAAGAGTAAGGGT
Found at i:15773349 original size:26 final size:24
Alignment explanation
Indices: 15773320--15773368 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
15773310 GAGACAAGTA
*
15773320 AAATGAAATTTGATTCGAGTTAAATC
1 AAATGAAA-TTG-TTCAAGTTAAATC
15773346 AAATGAAATTGTTCAAGTTAAAT
1 AAATGAAATTGTTCAAGTTAAAT
15773369 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 3 0.14
26 8 0.36
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (24 bp):
AAATGAAATTGTTCAAGTTAAATC
Found at i:15773618 original size:17 final size:18
Alignment explanation
Indices: 15773593--15773626 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15773583 ATATTTTTAA
*
15773593 AAATTTTATAAA-ATTTG
1 AAATCTTATAAATATTTG
15773610 AAATCTTATAAATATTT
1 AAATCTTATAAATATTT
15773627 TGAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATCTTATAAATATTTG
Found at i:15774041 original size:15 final size:15
Alignment explanation
Indices: 15774021--15774160 Score: 77
Period size: 15 Copynumber: 9.1 Consensus size: 15
15774011 AAAATATTTG
15774021 AAATATTTTAATATA
1 AAATATTTTAATATA
* *
15774036 AAATATTCT-ATTTCA
1 AAATATTTTAATAT-A
*
15774051 AAATATAATTTAAAATA
1 AAATAT--TTTAATATA
15774068 AAATATTTTAATATA
1 AAATATTTTAATATA
** * * *
15774083 ATTTAATATAAAATA
1 AAATATTTTAATATA
15774098 AAA-ATATTTAATATA
1 AAATAT-TTTAATATA
* *
15774113 AAAGATTCTAATATA
1 AAATATTTTAATATA
** * * *
15774128 ATTTAATATAAATAAAA
1 AAAT-ATTTTAAT-ATA
15774145 AAATATTTTAATATA
1 AAATATTTTAATATA
15774160 A
1 A
15774161 TTTAATATAA
Statistics
Matches: 88, Mismatches: 29, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
14 4 0.05
15 56 0.64
16 13 0.15
17 13 0.15
18 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:15774087 original size:10 final size:10
Alignment explanation
Indices: 15774074--15774170 Score: 52
Period size: 10 Copynumber: 9.0 Consensus size: 10
15774064 AATAAAATAT
15774074 TTTAATATAA
1 TTTAATATAA
15774084 TTTAATATAA
1 TTTAATATAA
** *
15774094 AATAA-AAATA
1 TTTAATATA-A
15774104 TTTAATATAAAAGA
1 TTTAATAT---A-A
15774118 TTCTAATATAA
1 TT-TAATATAA
15774129 TTTAATATAAA
1 TTTAATAT-AA
** * *
15774140 TAAAAAAATAT
1 T-TTAATATAA
15774151 TTTAATATAA
1 TTTAATATAA
15774161 TTTAATATAA
1 TTTAATATAA
15774171 AAATAATTAT
Statistics
Matches: 64, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
9 2 0.03
10 38 0.59
11 9 0.14
12 5 0.08
14 4 0.06
15 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (10 bp):
TTTAATATAA
Found at i:15774097 original size:30 final size:29
Alignment explanation
Indices: 15774001--15774106 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 29
15773991 CGACTCAAAA
* * *
15774001 AATATAAAAAAAAATATTTGAAATATTTT
1 AATATAAAATAAAATATTTTAAATAATTT
*** * *
15774030 AATATAAAATATTCTA-TTTCAA-AATAT
1 AATATAAAATAAAATATTTTAAATAATTT
*
15774057 AATTTAAAATAAAATATTTTAATATAATTT
1 AATATAAAATAAAATATTTTAA-ATAATTT
15774087 AATATAAAATAAAAATATTT
1 AATATAAAAT-AAAATATTT
15774107 AATATAAAAG
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
27 15 0.26
28 8 0.14
29 13 0.22
30 13 0.22
31 9 0.16
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (29 bp):
AATATAAAATAAAATATTTTAAATAATTT
Found at i:15774108 original size:30 final size:28
Alignment explanation
Indices: 15774001--15774113 Score: 102
Period size: 30 Copynumber: 3.9 Consensus size: 28
15773991 CGACTCAAAA
* *
15774001 AATATAAAAAAAAATATTTGAAATATTTT
1 AATATAAAATAAAATATTT-AAATAATTT
*** * *
15774030 AATATAAAATATTCTATTTCAA-AATAT
1 AATATAAAATAAAATATTTAAATAATTT
*
15774057 AATTTAAAATAAAATATTTTAATATAATTT
1 AATATAAAATAAAATA-TTTAA-ATAATTT
15774087 AATATAAAATAAAAATATTTAATATAA
1 AATATAAAAT-AAAATATTTAA-ATAA
15774114 AAGATTCTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
27 15 0.23
28 6 0.09
29 16 0.24
30 23 0.35
31 6 0.09
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (28 bp):
AATATAAAATAAAATATTTAAATAATTT
Found at i:15774110 original size:77 final size:78
Alignment explanation
Indices: 15774021--15774172 Score: 211
Period size: 77 Copynumber: 2.0 Consensus size: 78
15774011 AAAATATTTG
* * * *
15774021 AAATATTTTAATATAAAATATTCTATTTCAAAATATAAT-TTAA-AATAAAATATTTTAATATAA
1 AAATATTTTAATATAAAAGATTCTA-AT-AAAATATAATATAAATAAAAAAATATTTTAATATAA
15774084 TTTAATATAAAATAA
64 TTTAATATAAAATAA
* *
15774099 AAATA-TTTAATATAAAAGATTCTAATATAATTTAATATAAATAAAAAAATATTTTAATATAATT
1 AAATATTTTAATATAAAAGATTCTAATAAAATATAATATAAATAAAAAAATATTTTAATATAATT
15774163 TAATATAAAA
66 TAATATAAAA
15774173 ATAATTATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
75 8 0.12
76 4 0.06
77 49 0.74
78 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (78 bp):
AAATATTTTAATATAAAAGATTCTAATAAAATATAATATAAATAAAAAAATATTTTAATATAATT
TAATATAAAATAA
Found at i:15774125 original size:45 final size:46
Alignment explanation
Indices: 15774058--15774160 Score: 154
Period size: 45 Copynumber: 2.2 Consensus size: 46
15774048 TCAAAATATA
* * * *
15774058 ATTTAAAATAAAATATTTTAATATAATTTAATATAAA-ATAAAAAT
1 ATTTAATATAAAAGATTCTAATATAATTTAATATAAATAAAAAAAT
15774103 ATTTAATATAAAAGATTCTAATATAATTTAATATAAATAAAAAAAT
1 ATTTAATATAAAAGATTCTAATATAATTTAATATAAATAAAAAAAT
15774149 ATTTTAATATAA
1 A-TTTAATATAA
15774161 TTTAATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 34 0.65
46 8 0.15
47 10 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (46 bp):
ATTTAATATAAAAGATTCTAATATAATTTAATATAAATAAAAAAAT
Found at i:15774290 original size:59 final size:61
Alignment explanation
Indices: 15774172--15774293 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 61
15774162 TTAATATAAA
* *
15774172 AATAATTATATTAAGAATGTTATAAATTATATATTATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAGAATGTTATAAATTATATATTATCATTTTTATAAAATTATATTTAAT
*
15774233 AATAATTATATTAA-AAT-TTATTAAATTATTTATTATCA-TTTTATAAAATTATATTTAAT
1 AATAATTATATTAAGAATGTTA-TAAATTATATATTATCATTTTTATAAAATTATATTTAAT
15774292 AA
1 AA
15774294 CAATAACAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
59 25 0.44
60 18 0.32
61 14 0.25
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (61 bp):
AATAATTATATTAAGAATGTTATAAATTATATATTATCATTTTTATAAAATTATATTTAAT
Found at i:15774312 original size:60 final size:60
Alignment explanation
Indices: 15774194--15774305 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 60
15774184 AAGAATGTTA
* * * * * *
15774194 TAAATTATATATTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATTTAT
1 TAAATTATATATTATCATTTTTATAAAATTATATTTAATAACAATAACAATAAAATTTAT
*
15774254 TAAATTATTTATTATCA-TTTTATAAAATTATATTTAATAACAATAACAATAA
1 TAAATTATATATTATCATTTTTATAAAATTATATTTAATAACAATAACAATAA
15774306 TTATTTACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 30 0.67
60 15 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (60 bp):
TAAATTATATATTATCATTTTTATAAAATTATATTTAATAACAATAACAATAAAATTTAT
Found at i:15774497 original size:16 final size:16
Alignment explanation
Indices: 15774478--15774514 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
15774468 CGTTACAGCT
*
15774478 CTATTCCATTACATTC
1 CTATTCCATTACAATC
*
15774494 CTATTCTATTACAATC
1 CTATTCCATTACAATC
15774510 CTATT
1 CTATT
15774515 TAATTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (16 bp):
CTATTCCATTACAATC
Found at i:15775779 original size:25 final size:25
Alignment explanation
Indices: 15775751--15775802 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
15775741 GTAAAATGTC
*
15775751 TTACAATTTTTTTCTATAAGATATT
1 TTACAAATTTTTTCTATAAGATATT
15775776 TTACAAATTTTTTCTATAAGATATT
1 TTACAAATTTTTTCTATAAGATATT
15775801 TT
1 TT
15775803 TTCTCTACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.56
Consensus pattern (25 bp):
TTACAAATTTTTTCTATAAGATATT
Found at i:15780413 original size:25 final size:25
Alignment explanation
Indices: 15780385--15780433 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
15780375 GTCTAGAGCA
15780385 AACTTGGACAATGTGTCCATGTTCG
1 AACTTGGACAATGTGTCCATGTTCG
15780410 AACTTGGACAATGTGTCCATGTTC
1 AACTTGGACAATGTGTCCATGTTC
15780434 AGATGAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (25 bp):
AACTTGGACAATGTGTCCATGTTCG
Found at i:15788464 original size:31 final size:31
Alignment explanation
Indices: 15788429--15788507 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 31
15788419 AATAATTTTC
* *
15788429 ACATATTAATACCTTGTAATTATCCACATTT
1 ACATATTCATACCTTGTAATCATCCACATTT
* * * *
15788460 ACATA-TCATACCCTGTGATCCTTCACATTT
1 ACATATTCATACCTTGTAATCATCCACATTT
*
15788490 TCATATTCATACCTTGTA
1 ACATATTCATACCTTGTA
15788508 CCATTTCATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 23 0.61
31 15 0.39
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (31 bp):
ACATATTCATACCTTGTAATCATCCACATTT
Found at i:15794300 original size:30 final size:30
Alignment explanation
Indices: 15794264--15794336 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
15794254 CAACATTTAA
*
15794264 TTAATTTTTTATAAATAATTTTAATAATTT
1 TTAATTTTTTAAAAATAATTTTAATAATTT
* * *
15794294 TTAA-TTTTTAAAAATAGTTTTTATATTTT
1 TTAATTTTTTAAAAATAATTTTAATAATTT
15794323 TTAAATTTTTTAAA
1 TT-AATTTTTTAAA
15794337 TTTTTTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 23 0.62
30 6 0.16
31 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TTAATTTTTTAAAAATAATTTTAATAATTT
Found at i:15794356 original size:10 final size:9
Alignment explanation
Indices: 15794311--15794348 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
15794301 TTAAAAATAG
*
15794311 TTTTTATAT
1 TTTTTAAAT
15794320 TTTTTAAAT
1 TTTTTAAAT
15794329 TTTTTAAAT
1 TTTTTAAAT
15794338 TTTTTAAAT
1 TTTTTAAAT
15794347 TT
1 TT
15794349 AATTAAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:15802689 original size:78 final size:78
Alignment explanation
Indices: 15802555--15802706 Score: 232
Period size: 78 Copynumber: 1.9 Consensus size: 78
15802545 ACCAATTTTG
* * * * *
15802555 TGCAAGCCAAAGAAATTAAGGACTCAACCCTGGTACAGCCCAAAGAGTCGGGCCTGGAGGAGCAA
1 TGCAAGCCAAAGAAAATAAAGACTCAACCCTGGCACAGCCCAAAGAGTCAGACCTGGAGGAGCAA
15802620 CCTCAACAAGCGT
66 CCTCAACAAGCGT
* * *
15802633 TGCAAGCCAAAGAAAATAAAGACTCAACCCTGGCACAGTCCAAAGCGTCAGACCTGGAGGGGCAA
1 TGCAAGCCAAAGAAAATAAAGACTCAACCCTGGCACAGCCCAAAGAGTCAGACCTGGAGGAGCAA
15802698 CCTCAACAA
66 CCTCAACAA
15802707 TCGGAACACC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.37, C:0.28, G:0.24, T:0.12
Consensus pattern (78 bp):
TGCAAGCCAAAGAAAATAAAGACTCAACCCTGGCACAGCCCAAAGAGTCAGACCTGGAGGAGCAA
CCTCAACAAGCGT
Found at i:15803579 original size:29 final size:29
Alignment explanation
Indices: 15803524--15803580 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
15803514 TTTAATACAT
* *
15803524 TTGAGATTTTTTATATTTTTATTATTTAA
1 TTGAGATTTTTTATATTTATATAATTTAA
*
15803553 TTGAGTTTATTTTATATTTATA-AATTTA
1 TTGAGATT-TTTTATATTTATATAATTTA
15803581 TATTTTACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (29 bp):
TTGAGATTTTTTATATTTATATAATTTAA
Done.