Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 130 of 161
Found at i:40733167 original size:18 final size:18
Alignment explanation
Indices: 40733146--40733188 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40733136 CAATTTTTGG
40733146 ATTTAATAATTTTA-CATA
1 ATTTAATAATTTTATC-TA
*
40733164 ATTTGATAATTTTATCTA
1 ATTTAATAATTTTATCTA
40733182 ATTTAAT
1 ATTTAAT
40733189 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTAATAATTTTATCTA
Found at i:40733185 original size:122 final size:121
Alignment explanation
Indices: 40733047--40733288 Score: 326
Period size: 122 Copynumber: 2.0 Consensus size: 121
40733037 TTTGGACTTA
*** *
40733047 ATAATTTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAGTTTTACATAAGTTTAAATAATTT
1 ATAATTTTACCTAATTTAATTAAAAAAATTTTGGCTTAATAATTTTACATAAGTTTAAATAATTT
* * *
40733112 GATAA-AAAACCCTAACCATTAACACAATTTTTGG-ATTTAATAATTTTACATAATTTG
66 GATAATAAAA--CTAACCATTAACA-AAATTTTGGAACTTAATAATCTTACATAATTTG
* * *
40733169 ATAATTTTATCTAATTTAATTAAAAAAATTTTGGCTTAATAATTTTACATAATTTTACATAATTT
1 ATAATTTTACCTAATTTAATTAAAAAAATTTTGGCTTAATAATTTTACATAAGTTTAAATAATTT
***
40733234 GATAATTTTACTAACCATTAACAAAATTTTGGAACTTAATAATCTTACATAATTT
66 GATAATAAAACTAACCATTAACAAAATTTTGGAACTTAATAATCTTACATAATTT
40733289 TACATAATGT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
120 8 0.08
121 33 0.31
122 63 0.60
123 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (121 bp):
ATAATTTTACCTAATTTAATTAAAAAAATTTTGGCTTAATAATTTTACATAAGTTTAAATAATTT
GATAATAAAACTAACCATTAACAAAATTTTGGAACTTAATAATCTTACATAATTTG
Found at i:40733222 original size:10 final size:10
Alignment explanation
Indices: 40733207--40733233 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40733197 TTTTGGCTTA
40733207 ATAATTTTAC
1 ATAATTTTAC
40733217 ATAATTTTAC
1 ATAATTTTAC
40733227 ATAATTT
1 ATAATTT
40733234 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:40733295 original size:65 final size:65
Alignment explanation
Indices: 40733151--40733296 Score: 215
Period size: 65 Copynumber: 2.2 Consensus size: 65
40733141 TTTGGATTTA
* *
40733151 ATAATTTTACATAATTTGATAATTTTATCTAATTTAATTAAAAAAATTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTATCTAA-TCAATTAAAAAAATTTTGGCTTAATAATCTTA
40733216 C
65 C
* *
40733217 ATAATTTTACATAATTTGATAATTTTA-CTAA-CCATTAACAAAATTTTGGAACTTAATAATCTT
1 ATAATTTTACATAATTTGATAATTTTATCTAATCAATTAAAAAAATTTTGG--CTTAATAATCTT
40733280 AC
64 AC
40733282 ATAATTTTACATAAT
1 ATAATTTTACATAAT
40733297 GTTAGATTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
63 15 0.20
65 32 0.43
66 27 0.36
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (65 bp):
ATAATTTTACATAATTTGATAATTTTATCTAATCAATTAAAAAAATTTTGGCTTAATAATCTTAC
Found at i:40735193 original size:28 final size:29
Alignment explanation
Indices: 40735161--40735222 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
40735151 CAATTTCTTG
*
40735161 AAAAAT-AACCCATTCCAATAAATAATCA
1 AAAAATCAACCCATTCCAATAAATAATAA
* *
40735189 AAAAATCAACCCATTTCAATAAATATTAA
1 AAAAATCAACCCATTCCAATAAATAATAA
40735218 AAAAA
1 AAAAA
40735223 AAACTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.23
Consensus pattern (29 bp):
AAAAATCAACCCATTCCAATAAATAATAA
Found at i:40739682 original size:4 final size:4
Alignment explanation
Indices: 40739673--40739700 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40739663 CAAATCTTTG
40739673 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
40739701 CCTATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:40740142 original size:16 final size:16
Alignment explanation
Indices: 40740117--40740167 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
40740107 GGTTGGGGAG
40740117 AATAGAATAGAACTGT
1 AATAGAATAGAACTGT
* *
40740133 AATGGAATAGAGCTGT
1 AATAGAATAGAACTGT
*
40740149 AATAGAATAGAATTGT
1 AATAGAATAGAACTGT
40740165 AAT
1 AAT
40740168 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (16 bp):
AATAGAATAGAACTGT
Found at i:40740493 original size:24 final size:23
Alignment explanation
Indices: 40740466--40740515 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
40740456 TATTATTAAA
*
40740466 ATATGAAT-TAATAAAAATCATAAT
1 ATAT-AATATAATAAAAATAAT-AT
*
40740490 ATATAATATTATAAAAATAATAT
1 ATATAATATAATAAAAATAATAT
40740513 ATA
1 ATA
40740516 ACTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAAAAATAATAT
Found at i:40743996 original size:108 final size:107
Alignment explanation
Indices: 40743815--40744021 Score: 238
Period size: 108 Copynumber: 1.9 Consensus size: 107
40743805 CGGAACCAAA
* *
40743815 CTTTCAAAAATACTTACTGGATTGAACCAAAACTTTTGAAAATGAAACAGGATAAAACCAAAGTT
1 CTTTCAAAAATACTTACTGGA-TGAACCAAAACTTTTGAAAATGAAACAAGATAAAACCAAACTT
* *
40743880 GCATAAATACTTACTAGGTGGAACCAAAACTTTTGAAGATGAG
65 GCAAAAATACTTACTAGGTGAAACCAAAACTTTTGAAGATGAG
* * * * * *
40743923 CTTTCAAAAATACTTATTAGG-TGAAACCAGAACTTTTGAAAATG-AACATAGTTGAAATCAGAC
1 CTTTCAAAAATACTTACT-GGATG-AACCAAAACTTTTGAAAATGAAACA-AGATAAAACCAAAC
* * * *
40743986 TTTCAAAAATACTTATTGGGTGAAACTAAAACTTTT
63 TTGCAAAAATACTTACTAGGTGAAACCAAAACTTTT
40744022 AAGTTACTAC
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
107 6 0.07
108 74 0.90
109 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (107 bp):
CTTTCAAAAATACTTACTGGATGAACCAAAACTTTTGAAAATGAAACAAGATAAAACCAAACTTG
CAAAAATACTTACTAGGTGAAACCAAAACTTTTGAAGATGAG
Found at i:40745666 original size:64 final size:64
Alignment explanation
Indices: 40745585--40745710 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
40745575 CCACCAATAG
* ** **
40745585 ATTACTGATGTGACACATTAATTTATTGAATTTTTGACATGTGCCATTTTATACTTTTGACTCT
1 ATTACTGATGTGACACATTAATCTATTGAATAATTGACACATGCCATTTTATACTTTTGACTCT
* * *
40745649 ATTATTGATGTGGCACATTAATCTATTGAATAATTGATACATGCCATTTTATACTTTTGACT
1 ATTACTGATGTGACACATTAATCTATTGAATAATTGACACATGCCATTTTATACTTTTGACT
40745711 AAAGTTATCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (64 bp):
ATTACTGATGTGACACATTAATCTATTGAATAATTGACACATGCCATTTTATACTTTTGACTCT
Found at i:40750394 original size:13 final size:14
Alignment explanation
Indices: 40750368--40750398 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
40750358 TAAAAAAATT
40750368 TTATTATGTTATTA
1 TTATTATGTTATTA
40750382 TTATTAT-TTATTA
1 TTATTATGTTATTA
40750395 TTAT
1 TTAT
40750399 AAAAGGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TTATTATGTTATTA
Found at i:40750796 original size:63 final size:63
Alignment explanation
Indices: 40750697--40750822 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
40750687 CTCCACAGTC
*
40750697 GAAGATCTTTCAAAAAAAAAATCCGGTAATTATTTTTTTGCTATTATTGTAATTATTATTAAT
1 GAAGATCTTTCAAAAAAAAAATCAGGTAATTATTTTTTTGCTATTATTGTAATTATTATTAAT
40750760 GAAGATCTTTCAAAAAAAAAATCAGGTAATTATTTTTTTGCTATTATTGTAATTATTATTAAT
1 GAAGATCTTTCAAAAAAAAAATCAGGTAATTATTTTTTTGCTATTATTGTAATTATTATTAAT
40750823 AGATTAGAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (63 bp):
GAAGATCTTTCAAAAAAAAAATCAGGTAATTATTTTTTTGCTATTATTGTAATTATTATTAAT
Found at i:40752781 original size:21 final size:21
Alignment explanation
Indices: 40752755--40752795 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40752745 CGAATACACC
40752755 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
40752776 AACAGAAGCTCGTGAGAGCT
1 AACAGAAGCTCATAAGAGCT
40752796 AATCCACCCA
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:0.39, C:0.20, G:0.27, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:40759580 original size:11 final size:11
Alignment explanation
Indices: 40759565--40759759 Score: 117
Period size: 11 Copynumber: 18.4 Consensus size: 11
40759555 AAAAATTAAA
40759565 AAAAAGTATTTT
1 AAAAA-TATTTT
40759577 AAAAATATTTT
1 AAAAATATTTT
**
40759588 --AAA-ATTAA
1 AAAAATATTTT
* *
40759596 AAAAAAAATTT
1 AAAAATATTTT
40759607 AAAAAGTATTTT
1 AAAAA-TATTTT
40759619 AAAAATATTTT
1 AAAAATATTTT
**
40759630 --AAA-ATTAA
1 AAAAATATTTT
* *
40759638 AAAAAAAATTT
1 AAAAATATTTT
40759649 AAAAAGTATTTT
1 AAAAA-TATTTT
40759661 AAAAATATTTT
1 AAAAATATTTT
**
40759672 --AAA-ATTAA
1 AAAAATATTTT
* *
40759680 AAAAAAAATTT
1 AAAAATATTTT
40759691 AAAAAGTATTTT
1 AAAAA-TATTTT
40759703 AAAAATATTTT
1 AAAAATATTTT
**
40759714 --AAA-ATTAA
1 AAAAATATTTT
* *
40759722 AAAAAAAATTT
1 AAAAATATTTT
40759733 AAAAAGTATTTT
1 AAAAA-TATTTT
40759745 AAAAATATTTT
1 AAAAATATTTT
40759756 AAAA
1 AAAA
40759760 TTAAAAAAAT
Statistics
Matches: 139, Mismatches: 28, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
8 12 0.09
9 12 0.09
10 12 0.09
11 62 0.45
12 41 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40759614 original size:42 final size:42
Alignment explanation
Indices: 40759565--40759768 Score: 408
Period size: 42 Copynumber: 4.9 Consensus size: 42
40759555 AAAAATTAAA
40759565 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
40759607 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
40759649 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
40759691 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
40759733 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA
40759769 TAAAAATATA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 162 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (42 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAATTT
Found at i:40763145 original size:10 final size:11
Alignment explanation
Indices: 40763130--40763175 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
40763120 AACTAAATCC
40763130 TTTCTCTC-AA
1 TTTCTCTCAAA
*
40763140 TTTCTCTCTAA
1 TTTCTCTCAAA
40763151 TATTCTCTCAAA
1 T-TTCTCTCAAA
*
40763163 TTCCTCTCAAA
1 TTTCTCTCAAA
40763174 TT
1 TT
40763176 CCTATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
12 10 0.31
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:40763156 original size:12 final size:10
Alignment explanation
Indices: 40763130--40763172 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
40763120 AACTAAATCC
40763130 TTTCTCTCAA
1 TTTCTCTCAA
40763140 TTTCTCTCTAA
1 TTTCTCTC-AA
40763151 TATTCTCTCAAA
1 T-TTCTCTC-AA
*
40763163 TTCCTCTCAA
1 TTTCTCTCAA
40763173 ATTCCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 10 0.34
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:40765494 original size:49 final size:49
Alignment explanation
Indices: 40765441--40766431 Score: 1894
Period size: 49 Copynumber: 20.2 Consensus size: 49
40765431 AATATATTTG
* *
40765441 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
* *
40765490 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAAT-AAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
* *
40765538 TGCAAAATAGTTTATTTTGAATATTTTGATACTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
*
40765587 TACAAAATATTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
*
40765636 TACAAAATAGTTTATTTTGAATATTTTGATACTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
*
40765685 TACAAAATATTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40765734 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40765783 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40765832 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40765881 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40765930 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40765979 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766028 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766077 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766126 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766175 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766224 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766273 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766322 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766371 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
1 TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
40766420 TACAAAATAGTT
1 TACAAAATAGTT
40766432 AATATTCTTA
Statistics
Matches: 929, Mismatches: 12, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
48 44 0.05
49 885 0.95
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (49 bp):
TACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAA
Found at i:40769908 original size:125 final size:124
Alignment explanation
Indices: 40769627--40769913 Score: 450
Period size: 125 Copynumber: 2.3 Consensus size: 124
40769617 TCCAAACATG
* *
40769627 CTACTGTAGTAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
40769692 TTGAAGCGTTTTTATACTATTTTCTCAGAAACGTCAACTCAATATTATTTTTTCAGGAC
66 TTCAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAATATTATTTTTTCAGGAC
*
40769751 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
40769816 TTCAAGTGTTTTTTATACTATTTGCTTAGAAACGTCAACTCGAA-ATTATTTTTTCAGGAC
66 TTCAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTC-AATATTATTTTTTCAGGAC
* * * *
40769876 CTACTGTAGCAAAAGCACGTTCACATGTGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
40769914 CTTAATAAAT
Statistics
Matches: 149, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
124 68 0.46
125 79 0.53
126 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTCAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAATATTATTTTTTCAGGAC
Found at i:40773516 original size:35 final size:35
Alignment explanation
Indices: 40773470--40773597 Score: 202
Period size: 35 Copynumber: 3.6 Consensus size: 35
40773460 ACTTTCTGTT
*
40773470 TTGGTGTGTTTCAAATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
*
40773505 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
*
40773540 TTGGTGTGTTTCAGATAGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
* *
40773575 TTTGGTGTGTTTCGGTTGGATTA
1 -TTGGTGTGTTTCAGATGGATTA
40773598 TCGATGTACT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 66 0.78
36 19 0.22
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
Found at i:40775697 original size:62 final size:59
Alignment explanation
Indices: 40775593--40775710 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 59
40775583 ATCACTTTAA
* *
40775593 TATTAAATGAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATGAATAGAATATTTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
40775652 TATTAAAAT-AATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAAA
1 TATT-AAATGAATAGAATATTTA--T-CAAGATAAATATTAAATTAAATTTAATATTAAA
40775711 ATAATCATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
59 16 0.30
60 4 0.08
61 1 0.02
62 32 0.60
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (59 bp):
TATTAAATGAATAGAATATTTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:40775733 original size:25 final size:26
Alignment explanation
Indices: 40775700--40775760 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
40775690 TAAATTAAAT
40775700 TTAATATTAA-AATAATCATT-TTAATA
1 TTAATATTAATAA-AAT-ATTATTAATA
40775726 TTAA-ATTAATAAAATATTATTAATA
1 TTAATATTAATAAAATATTATTAATA
40775751 -TAAGTATTAA
1 TTAA-TATTAA
40775761 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 6 0.19
25 14 0.45
26 11 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TTAATATTAATAAAATATTATTAATA
Found at i:40780818 original size:23 final size:23
Alignment explanation
Indices: 40780775--40780819 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40780765 TTTTATGAAC
**
40780775 TTTTTATATTTTATATTTTATTT
1 TTTTTATATTTTATAAATTATTT
40780798 TTTTTATAATTTT-TAAATTATT
1 TTTTTAT-ATTTTATAAATTATT
40780820 ATTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTATATTTTATAAATTATTT
Found at i:40785220 original size:38 final size:38
Alignment explanation
Indices: 40785169--40785248 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
40785159 ACATTGAATC
*
40785169 ATTTATTTCTTTTATCATCCTACATATAACTATTTATA
1 ATTTATTTCTTTTATCATCCTACATATAACTATTTAAA
*
40785207 ATTTATTTCTTTTATCATCCTACATATAATTATTTAAA
1 ATTTATTTCTTTTATCATCCTACATATAACTATTTAAA
40785245 ATTT
1 ATTT
40785249 TTTGTAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.54
Consensus pattern (38 bp):
ATTTATTTCTTTTATCATCCTACATATAACTATTTAAA
Found at i:40791398 original size:45 final size:45
Alignment explanation
Indices: 40791334--40791451 Score: 204
Period size: 45 Copynumber: 2.7 Consensus size: 45
40791324 GAAAAGCAAT
* *
40791334 AAGGAAGCAACGTGTGGAAGCAACCACATCTATGTCCAGACAAAA
1 AAGGAAGCAACGTGTGGAAGCAACCACATCTACGTCCAAACAAAA
40791379 AAGGAAGCAACGTGTGGAAGCAACCACATCTACGTCCAAACAAAA
1 AAGGAAGCAACGTGTGGAAGCAACCACATCTACGTCCAAACAAAA
40791424 AAGGAAGCAAC--GTGGAAGCAACCACATC
1 AAGGAAGCAACGTGTGGAAGCAACCACATC
40791452 AGGACAAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
43 17 0.24
45 54 0.76
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (45 bp):
AAGGAAGCAACGTGTGGAAGCAACCACATCTACGTCCAAACAAAA
Found at i:40792409 original size:45 final size:45
Alignment explanation
Indices: 40792348--40792459 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
40792338 AAGAAAAGAC
* * *
40792348 AAAGGAAGCAATGTGTGGAAGCAATCACATCTATATCCAGACAAA
1 AAAGGAAGCAACGTGTGGAAGCAATCAAATCTATATCCAAACAAA
*
40792393 AAAGGAAGCAACGTGTGGAAGCAATCAAATCTATGTCCAAACAAA
1 AAAGGAAGCAACGTGTGGAAGCAATCAAATCTATATCCAAACAAA
40792438 AAAGGAAGCAAC--GTGGAAGCAA
1 AAAGGAAGCAACGTGTGGAAGCAA
40792460 CTACATCAGG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 10 0.16
45 53 0.84
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (45 bp):
AAAGGAAGCAACGTGTGGAAGCAATCAAATCTATATCCAAACAAA
Found at i:40797467 original size:2 final size:2
Alignment explanation
Indices: 40797460--40797485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40797450 AAGAGCTTTT
40797460 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40797486 AATCAAGTGA
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):
TA
Found at i:40803757 original size:30 final size:30
Alignment explanation
Indices: 40803721--40803799 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 30
40803711 GGCTAGCTTG
40803721 ATTAAATTAGGGTTTAGGGTTTTTAATTTA
1 ATTAAATTAGGGTTTAGGGTTTTTAATTTA
40803751 ATTAAATTAAGTAGGGTTTAGGGTTTTTAATTTA
1 ATTAAA-T---TAGGGTTTAGGGTTTTTAATTTA
40803785 ATTAAATTAGGGTTT
1 ATTAAATTAGGGTTT
40803800 TTAATTAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
30 14 0.31
31 1 0.02
33 1 0.02
34 29 0.64
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (30 bp):
ATTAAATTAGGGTTTAGGGTTTTTAATTTA
Found at i:40803770 original size:34 final size:34
Alignment explanation
Indices: 40803728--40803793 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
40803718 TTGATTAAAT
40803728 TAGGGTTTAGGGTTTTTAATTTAATTAAATTAAG
1 TAGGGTTTAGGGTTTTTAATTTAATTAAATTAAG
40803762 TAGGGTTTAGGGTTTTTAATTTAATTAAATTA
1 TAGGGTTTAGGGTTTTTAATTTAATTAAATTA
40803794 GGGTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (34 bp):
TAGGGTTTAGGGTTTTTAATTTAATTAAATTAAG
Found at i:40803814 original size:17 final size:18
Alignment explanation
Indices: 40803781--40803815 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40803771 GGGTTTTTAA
*
40803781 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
40803799 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
40803816 AGGGATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:40803817 original size:23 final size:23
Alignment explanation
Indices: 40803755--40803827 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
40803745 AATTTAATTA
40803755 AATTAAGTAGGGTTTAGGGTTTTT
1 AATTAAGTAGGG-TTAGGGTTTTT
* **
40803779 AATTTAATTA-AATTAGGGTTTTT
1 AA-TTAAGTAGGGTTAGGGTTTTT
*
40803802 AATTAAGTAGGGTTAGGGATTTT
1 AATTAAGTAGGGTTAGGGTTTTT
40803825 AAT
1 AAT
40803828 CAAATAATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.15
23 26 0.65
24 2 0.05
25 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (23 bp):
AATTAAGTAGGGTTAGGGTTTTT
Found at i:40807061 original size:14 final size:14
Alignment explanation
Indices: 40807010--40807062 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
40807000 TCCTTAAACC
40807010 CTGAACCTTGAACT
1 CTGAACCTTGAACT
*
40807024 C-GAACCCTGAAC-
1 CTGAACCTTGAACT
* *
40807036 CTTAAACATTGAACT
1 C-TGAACCTTGAACT
40807051 CTGAACCTTGAA
1 CTGAACCTTGAA
40807063 GTTTAGGGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 1 0.03
13 10 0.33
14 18 0.60
15 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (14 bp):
CTGAACCTTGAACT
Found at i:40807928 original size:37 final size:37
Alignment explanation
Indices: 40807866--40807949 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
40807856 ACTGAAATTT
**
40807866 ATATCGAAACGGAATTTAGACTTATTATTTTAGTTTA
1 ATATCGAAACGGAAACTAGACTTATTATTTTAGTTTA
* *
40807903 ATATTGAAACGGAAACTAGATTTATTATTTTAGTTTA
1 ATATCGAAACGGAAACTAGACTTATTATTTTAGTTTA
*
40807940 GTATCGAAAC
1 ATATCGAAAC
40807950 ATGATGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (37 bp):
ATATCGAAACGGAAACTAGACTTATTATTTTAGTTTA
Found at i:40809114 original size:17 final size:17
Alignment explanation
Indices: 40809047--40809114 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 17
40809037 TTAGTTTCAA
*
40809047 TTTTAATTATTTATTAT
1 TTTTAATTATTTAATAT
* * **
40809064 ATTT-ATAATAAAATAT
1 TTTTAATTATTTAATAT
* *
40809080 TTTTGA-TATATTATTAT
1 TTTTAATTAT-TTAATAT
40809097 TTTTAATTATTTAATAT
1 TTTTAATTATTTAATAT
40809114 T
1 T
40809115 AATAAAAATA
Statistics
Matches: 36, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
16 13 0.36
17 20 0.56
18 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (17 bp):
TTTTAATTATTTAATAT
Found at i:40820178 original size:41 final size:41
Alignment explanation
Indices: 40820115--40820217 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
40820105 AAGCTTATGC
*
40820115 CTAGCAGGCTTAATGCCAGTGAAATATTTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATACGT
* *
40820156 CTAGTAGGCTTAATGCCGGTGAAATATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATACGT
*
40820197 CTAGCAGGCTTAATGTCGGTG
1 CTAGCAGGCTTAATGCCGGTG
40820218 TACTAGATCA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATACGT
Found at i:40823300 original size:19 final size:18
Alignment explanation
Indices: 40823262--40823300 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
40823252 GAATGTTTCC
* *
40823262 CATTTCTTTTTTTCTTTT
1 CATTTCTTTATTTCTATT
40823280 CATTTCGTTTATTTCTATT
1 CATTTC-TTTATTTCTATT
40823299 CA
1 CA
40823301 ACACGCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.67
Consensus pattern (18 bp):
CATTTCTTTATTTCTATT
Found at i:40823544 original size:11 final size:11
Alignment explanation
Indices: 40823524--40823602 Score: 53
Period size: 11 Copynumber: 7.4 Consensus size: 11
40823514 TAAAAGTTTA
40823524 AAAAAGTATTTT
1 AAAAA-TATTTT
40823536 AAAAATATTTT
1 AAAAATATTTT
40823547 --AAA-A--TT
1 AAAAATATTTT
40823553 AAAAA-ATTTT
1 AAAAATATTTT
40823563 AAAAAAAGTATTTT
1 --AAAAA-TATTTT
* *
40823577 AAAAAAAATTT
1 AAAAATATTTT
*
40823588 AAAAAAATTTT
1 AAAAATATTTT
40823599 AAAA
1 AAAA
40823603 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.04
8 5 0.09
9 3 0.05
10 2 0.04
11 24 0.43
12 15 0.27
14 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40823573 original size:41 final size:42
Alignment explanation
Indices: 40823497--40823591 Score: 122
Period size: 41 Copynumber: 2.2 Consensus size: 42
40823487 ACCAAAAATT
40823497 TATTTTAAAAATTAAAATAAAAGTTTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAATAAAAGTTTAAAAAAGTATTTTAAAAA
*
40823541 TATTTTAAAATT-AA-AAAATTTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAATAAAAGTTT-AAAAAAGTATTTTAAAAA
* *
40823582 AAATTTAAAA
1 TATTTTAAAA
40823592 AAATTTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
40 7 0.15
41 28 0.60
43 6 0.13
44 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (42 bp):
TATTTTAAAATTAAATAAAAGTTTAAAAAAGTATTTTAAAAA
Found at i:40823580 original size:12 final size:11
Alignment explanation
Indices: 40823553--40823602 Score: 64
Period size: 11 Copynumber: 4.3 Consensus size: 11
40823543 TTTTAAAATT
40823553 AAAAAATTTTAA
1 AAAAAATTTT-A
40823565 AAAAAGTATTTTA
1 AAAAA--ATTTTA
*
40823578 AAAAAAATTTA
1 AAAAAATTTTA
40823589 AAAAAATTTTA
1 AAAAAATTTTA
40823600 AAA
1 AAA
40823603 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 18 0.53
12 5 0.15
13 6 0.18
14 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AAAAAATTTTA
Found at i:40823582 original size:26 final size:24
Alignment explanation
Indices: 40823553--40823631 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 24
40823543 TTTTAAAATT
*
40823553 AAAAAATTTTAAAAAAAGTATTTTA
1 AAAAAAATTTAAAAAAA-TATTTTA
*
40823578 AAAAAAATTTAAAAAAAT-TTTAAA
1 AAAAAAATTTAAAAAAATATTT-TA
*
40823602 ATTAAAAAAATTAAAAAAATTATTTTA
1 A--AAAAAATTTAAAAAAA-TATTTTA
40823629 AAA
1 AAA
40823632 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 3 0.07
24 3 0.07
25 18 0.40
26 15 0.33
27 3 0.07
28 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (24 bp):
AAAAAAATTTAAAAAAATATTTTA
Found at i:40823593 original size:9 final size:9
Alignment explanation
Indices: 40823578--40823623 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
40823568 AAGTATTTTA
40823578 AAAAAAATTT
1 AAAAAAA-TT
40823588 AAAAAAATT
1 AAAAAAATT
**
40823597 -TTAAAATT
1 AAAAAAATT
40823605 AAAAAAATT
1 AAAAAAATT
40823614 AAAAAAATT
1 AAAAAAATT
40823623 A
1 A
40823624 TTTTAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
8 6 0.19
9 18 0.58
10 7 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAAAATT
Found at i:40823601 original size:52 final size:51
Alignment explanation
Indices: 40823503--40823631 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
40823493 AATTTATTTT
* * *
40823503 AAAAATTAAAATAAA--AGTTTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAA-AAAGTATTTTAAAAAA--AATTTAAAAAAATTTTAAAATTAA
*
40823555 AAAATTTTAAAAAAAGTATTTTAAAAAAAATTTAAAAAAATTTTAAAATTAA
1 AAAA-ATTAAAAAAAGTATTTTAAAAAAAATTTAAAAAAATTTTAAAATTAA
*
40823607 AAAAATTAAAAAAATTATTTTAAAA
1 AAAAATTAAAAAAAGTATTTTAAAA
40823632 GTATTTTAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
51 19 0.28
52 33 0.49
53 6 0.09
54 10 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (51 bp):
AAAAATTAAAAAAAGTATTTTAAAAAAAATTTAAAAAAATTTTAAAATTAA
Found at i:40823661 original size:40 final size:40
Alignment explanation
Indices: 40823585--40823659 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
40823575 TTAAAAAAAA
*
40823585 TTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAATTAT
1 TTTAAAAAAATTTTAAAATTAAAAAAATAAAAAAAATTAT
**
40823625 TTTAAAAGTATTTTAAAATT-AAAAAATAAAAAAAA
1 TTTAAAAAAATTTTAAAATTAAAAAAATAAAAAAAA
40823660 ATAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 14 0.44
40 18 0.56
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (40 bp):
TTTAAAAAAATTTTAAAATTAAAAAAATAAAAAAAATTAT
Found at i:40824428 original size:25 final size:25
Alignment explanation
Indices: 40824374--40824428 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
40824364 AAACATTAAA
*
40824374 TTTAATTTAACATTAAGATAATCAC
1 TTTAATTTAACATTAAGAAAATCAC
*
40824399 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAACATTAAGAAAATCAC
40824423 TATTAA
1 T-TTAA
40824429 GATATGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (25 bp):
TTTAATTTAACATTAAGAAAATCAC
Found at i:40834671 original size:24 final size:24
Alignment explanation
Indices: 40834635--40834705 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
40834625 TTTTTAAGCA
*
40834635 GGGTATTCCGTAAGTGCCTTTGTG
1 GGGTATTCTGTAAGTGCCTTTGTG
*
40834659 GGGTATTCTGTAAGTGCCTTTTTG
1 GGGTATTCTGTAAGTGCCTTTGTG
* *
40834683 GCGTATTCTGTAAGTACCTTTGT
1 GGGTATTCTGTAAGTGCCTTTGT
40834706 TACGTATTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.14, C:0.15, G:0.28, T:0.42
Consensus pattern (24 bp):
GGGTATTCTGTAAGTGCCTTTGTG
Found at i:40834711 original size:24 final size:24
Alignment explanation
Indices: 40834637--40834722 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
40834627 TTTAAGCAGG
* * *
40834637 GTATTCCGTAAGTGCCTTTGTGGG
1 GTATTCTGTAAGTGCCTTTGTTGC
40834661 GTATTCTGTAAGTGCCTTT-TTGGC
1 GTATTCTGTAAGTGCCTTTGTT-GC
* *
40834685 GTATTCTGTAAGTACCTTTGTTAC
1 GTATTCTGTAAGTGCCTTTGTTGC
*
40834709 GTATTCTATAAGTG
1 GTATTCTGTAAGTG
40834723 TTTTGTAGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.43
Consensus pattern (24 bp):
GTATTCTGTAAGTGCCTTTGTTGC
Found at i:40841332 original size:20 final size:20
Alignment explanation
Indices: 40841289--40841330 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
40841279 TTAAAAAAGT
40841289 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAGTAATG
40841309 AAATGCAAAT-GAAAGTAA-G
1 AAATGC-AATGGAAAGTAATG
40841328 AAA
1 AAA
40841331 ATTTGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGCAATGGAAAGTAATG
Found at i:40841796 original size:15 final size:16
Alignment explanation
Indices: 40841778--40841807 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40841768 TTGTGCCATG
40841778 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
40841793 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
40841808 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:40853975 original size:18 final size:18
Alignment explanation
Indices: 40853952--40853994 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40853942 TCTTCCCCCC
*
40853952 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
40853970 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
40853988 TGCTTTC
1 TTCTTTC
40853995 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:40863534 original size:22 final size:20
Alignment explanation
Indices: 40863492--40863541 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
40863482 AAACTTTAAC
* *
40863492 TTATTTTTAGGAGGTTTTATT
1 TTATTTTTAGCAGGTTCTA-T
*
40863513 TTATTTTTATCAGAGTTCTAT
1 TTATTTTTAGCAG-GTTCTAT
40863534 TTATTTTT
1 TTATTTTT
40863542 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.64
Consensus pattern (20 bp):
TTATTTTTAGCAGGTTCTAT
Found at i:40864720 original size:31 final size:31
Alignment explanation
Indices: 40864635--40864721 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
40864625 TTGACACAAG
* * * *
40864635 AATTTTAA-TTTGATGTAACTATAAATATGA
1 AATTTTAATTTTGATTTAATTGTATATATGA
* * *
40864665 AATTTTTATTGTGGTTT-ATATGTATATATGA
1 AATTTTAATTTTGATTTAAT-TGTATATATGA
40864696 AATTTTAATTTTGATTTAATTGTATA
1 AATTTTAATTTTGATTTAATTGTATA
40864722 CCTTTCAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
30 8 0.18
31 34 0.77
32 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (31 bp):
AATTTTAATTTTGATTTAATTGTATATATGA
Found at i:40864763 original size:19 final size:19
Alignment explanation
Indices: 40864739--40864775 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40864729 AAAATAAATA
40864739 TATAAATATATT-TTTATAT
1 TATAAATA-ATTATTTATAT
40864758 TATAAATAATTATTTATA
1 TATAAATAATTATTTATA
40864776 GTGCAGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAAATAATTATTTATAT
Found at i:40869554 original size:22 final size:23
Alignment explanation
Indices: 40869511--40869563 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
40869501 TTAAATCGAG
* *
40869511 ATTAAAAT-TTTAAAATTCAAAA
1 ATTAAAATAATTAAAATTAAAAA
*
40869533 ATTACAATAATTAAAA-TAAAAA
1 ATTAAAATAATTAAAATTAAAAA
*
40869555 CTTAAAATA
1 ATTAAAATA
40869564 TAAAAAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
ATTAAAATAATTAAAATTAAAAA
Found at i:40882887 original size:16 final size:16
Alignment explanation
Indices: 40882866--40882897 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40882856 GTGCCATAGC
40882866 ATCTTTCAACTATGGT
1 ATCTTTCAACTATGGT
40882882 ATCTTTCAACTATGGT
1 ATCTTTCAACTATGGT
40882898 CTTACACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (16 bp):
ATCTTTCAACTATGGT
Found at i:40883108 original size:45 final size:45
Alignment explanation
Indices: 40882970--40883188 Score: 168
Period size: 45 Copynumber: 4.9 Consensus size: 45
40882960 AGACTACTAG
* * * *
40882970 GATGCCATAGTGTCTTTCAGCTATGGTCTTAGTCATGTTTACCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTATCAT
* * ** * * *
40883015 AATGTCATAGCATCTTTCAACCATGGTCTTATTCATTTATATCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTATCAT
* * **
40883060 GATGCCATAGTGTCTTTCAACTATGGTTTTACTAATTTTTATGGT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTATCAT
* *** * ** * *
40883105 GATGTCATAACATCTTTTAGTTACGGTCTTACTCATCTTTATCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTATCAT
** * * * *
40883150 GATGCCATAGAATCTTTTAGCTACGTTCTTACTCATTTT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTT
40883189 ATGCGTATAG
Statistics
Matches: 134, Mismatches: 40, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTATCAT
Found at i:40883133 original size:90 final size:90
Alignment explanation
Indices: 40882970--40883159 Score: 220
Period size: 90 Copynumber: 2.1 Consensus size: 90
40882960 AGACTACTAG
* * * *
40882970 GATGCCATAGTGTCTTTCAGCTATGGTCTTAGTCATGTTTACCATAATGTCATAGCATCTTTCAA
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTAATGTTTACCATAATGTCATAACATCTTTCAA
* *
40883035 CCATGGTCTTATTCAT-TTATATCAT
66 CCACGGTCTTACTCATCTT-TATCAT
* * *** * * *
40883060 GATGCCATAGTGTCTTTCAACTATGGTTTTACTAATTTTTATGGTGATGTCATAACATCTTTTAG
1 GATGCCATAGTGTCTTTCAACTATGGTCTTACTAATGTTTACCATAATGTCATAACATCTTTCAA
**
40883125 TTACGGTCTTACTCATCTTTATCAT
66 CCACGGTCTTACTCATCTTTATCAT
40883150 GATGCCATAG
1 GATGCCATAG
40883160 AATCTTTTAG
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
90 81 0.98
91 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (90 bp):
GATGCCATAGTGTCTTTCAACTATGGTCTTACTAATGTTTACCATAATGTCATAACATCTTTCAA
CCACGGTCTTACTCATCTTTATCAT
Found at i:40884426 original size:34 final size:34
Alignment explanation
Indices: 40884383--40884450 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
40884373 CACTTGACGA
*
40884383 ATGTGAATTCTTATTTATTTGAGGGTATATAACC
1 ATGTGAATTCTTATTTATTGGAGGGTATATAACC
*
40884417 ATGTGAATTCTTATTTATTGGCGGGTATATAACC
1 ATGTGAATTCTTATTTATTGGAGGGTATATAACC
40884451 CTTTCATCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (34 bp):
ATGTGAATTCTTATTTATTGGAGGGTATATAACC
Found at i:40885015 original size:44 final size:44
Alignment explanation
Indices: 40884952--40885039 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
40884942 CAACTCCCCA
*
40884952 CGCTCTTCTTTGGTCATAAATAAACCAAAATGTCAAGAGGATTT
1 CGCTCTTCCTTGGTCATAAATAAACCAAAATGTCAAGAGGATTT
40884996 CGCTCTTCCTTGGTCATAAATAAACCAAAATGTCAAGAGGATTT
1 CGCTCTTCCTTGGTCATAAATAAACCAAAATGTCAAGAGGATTT
40885040 TTACAACTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (44 bp):
CGCTCTTCCTTGGTCATAAATAAACCAAAATGTCAAGAGGATTT
Found at i:40885567 original size:45 final size:45
Alignment explanation
Indices: 40885483--40885687 Score: 220
Period size: 45 Copynumber: 4.6 Consensus size: 45
40885473 TATCCTCTTG
* * * * **
40885483 TTTCAGCTATGGTTTTAGTC-T-TGTTACCATGATGTCATAGTATC
1 TTTCAGCTATGGTCTTACTCATCT-TTATCATGATGCCATAACATC
* * *
40885527 TTTCAGCCATGGTCTTACTCAT-TTATATCATGATGCCATAGCGTC
1 TTTCAGCTATGGTCTTACTCATCTT-TATCATGATGCCATAACATC
* ** *
40885572 TTTCAGCTATGGTTTTACTCATCTTTATGGTGATGCCATAAAATC
1 TTTCAGCTATGGTCTTACTCATCTTTATCATGATGCCATAACATC
** *
40885617 TTTCAATTATGGTCTTTCTCATCTTTATCATGATGCCATAACATC
1 TTTCAGCTATGGTCTTACTCATCTTTATCATGATGCCATAACATC
40885662 TTTCAGCTATGGTCTTACTCAT-TTTA
1 TTTCAGCTATGGTCTTACTCATCTTTA
40885688 GGCGTATAGC
Statistics
Matches: 134, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
44 22 0.16
45 110 0.82
46 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (45 bp):
TTTCAGCTATGGTCTTACTCATCTTTATCATGATGCCATAACATC
Found at i:40888259 original size:35 final size:36
Alignment explanation
Indices: 40888220--40888287 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
40888210 TTATAATCAC
* *
40888220 TGTCACAAGGTATGGA-AACATACCCACATATTTAT
1 TGTCACAAGGCATGAATAACATACCCACATATTTAT
*
40888255 TGTCACATGGCATGAATAACATACCCACATATT
1 TGTCACAAGGCATGAATAACATACCCACATATT
40888288 CTCTTTCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (36 bp):
TGTCACAAGGCATGAATAACATACCCACATATTTAT
Found at i:40890856 original size:15 final size:13
Alignment explanation
Indices: 40890826--40890858 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40890816 ACTTTTAGAC
40890826 TATATAAAATAAA
1 TATATAAAATAAA
*
40890839 TATATAAAATATA
1 TATATAAAATAAA
40890852 TATATAA
1 TATATAA
40890859 TTTTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATATAAAATAAA
Found at i:40894366 original size:118 final size:125
Alignment explanation
Indices: 40894123--40894370 Score: 312
Period size: 129 Copynumber: 2.0 Consensus size: 125
40894113 AGGCTTCATC
** * ** *
40894123 TGTTGCATGACTTTAGTGTTGGGGGAAATGAGGTGAGAATGAATTCCCAATACACTGAAGCCATT
1 TGTTGCATGACTCAAGTGTTGGGAGAAATGAGAAGAGAATGAATTCCCAAAACACTGAAGCCATT
*
40894188 CACAGAACAGGCACTTAGACTGTTGTTTTCTATTTTAATTTAACTGTTTATATTTGACTTGAATT
66 CACAGAACAGGCA--TAGACTCTTGTTTTCTA--TT-ATTTAACTGTTTATATTTGACTTGAATT
40894253 TGTTGCATGACTCAAGTGTTGGGAG-AATGAGAAGAGAATGAATTCCCAAAACACTGAAGCCATT
1 TGTTGCATGACTCAAGTGTTGGGAGAAATGAGAAGAGAATGAATTCCCAAAACACTGAAGCCATT
** *
40894317 CAGTGAACA-G-A-AGACTCTTGTTTT-TA-T-TTTAACTGTTTATATTTTACTTGAATT
66 CACAGAACAGGCATAGACTCTTGTTTTCTATTATTTAACTGTTTATATTTGACTTGAATT
40894371 GAGGACTCCT
Statistics
Matches: 108, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
118 26 0.24
120 1 0.01
123 2 0.02
124 12 0.11
127 1 0.01
128 1 0.01
129 43 0.40
130 22 0.20
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (125 bp):
TGTTGCATGACTCAAGTGTTGGGAGAAATGAGAAGAGAATGAATTCCCAAAACACTGAAGCCATT
CACAGAACAGGCATAGACTCTTGTTTTCTATTATTTAACTGTTTATATTTGACTTGAATT
Found at i:40895896 original size:45 final size:44
Alignment explanation
Indices: 40895847--40895955 Score: 166
Period size: 45 Copynumber: 2.5 Consensus size: 44
40895837 GTCAATATGT
*
40895847 TCTTCTCAGTTTTGCAAACATCTATGTGTTTT-CTTGTTCTTATTA
1 TCTTCTCAGTTTTGCAAACATCTACGTGTTTTCCTT-TTCTTA-TA
* *
40895892 TCTTCTCAGTTCTGCAAGCATCTACGTGTTTTCCTTTTCTTATA
1 TCTTCTCAGTTTTGCAAACATCTACGTGTTTTCCTTTTCTTATA
40895936 TCTTCTCAGTTTTGCAAACA
1 TCTTCTCAGTTTTGCAAACA
40895956 CATTATCTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
44 20 0.34
45 35 0.60
46 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (44 bp):
TCTTCTCAGTTTTGCAAACATCTACGTGTTTTCCTTTTCTTATA
Found at i:40898854 original size:61 final size:61
Alignment explanation
Indices: 40898746--40898863 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 61
40898736 TTAATTACCG
* ** *
40898746 TTTGATTTTATATCTTTATTTTGACAAAAGAAATTGATTTAAATAACCAAGTATTTTCTTC
1 TTTGATTTTATATCTTTATTTGGACAAAAGAAACAGATGTAAATAACCAAGTATTTTCTTC
* * *
40898807 TTTGATTTTATATCTTTGTTATGGA-AAAAGAAACAGATGTAAGTAACCGAGTATTTT
1 TTTGATTTTATATCTTTATT-TGGACAAAAGAAACAGATGTAAATAACCAAGTATTTT
40898864 AACAGATTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 46 0.94
62 3 0.06
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (61 bp):
TTTGATTTTATATCTTTATTTGGACAAAAGAAACAGATGTAAATAACCAAGTATTTTCTTC
Found at i:40904261 original size:26 final size:26
Alignment explanation
Indices: 40904221--40904273 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40904211 CCTGTCGGAT
* * *
40904221 TACTGCTGTTGGCCTGCTGGGCCTGC
1 TACTACTGTTAGCCTACTGGGCCTGC
*
40904247 TACTACTGTTAGCCTACTGGGCTTGC
1 TACTACTGTTAGCCTACTGGGCCTGC
40904273 T
1 T
40904274 GGATTGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.28, T:0.34
Consensus pattern (26 bp):
TACTACTGTTAGCCTACTGGGCCTGC
Found at i:40904424 original size:6 final size:6
Alignment explanation
Indices: 40904415--40904469 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
40904405 TGTTTTTATT
*
40904415 TTTTTC TTTTTC TTTTT- TCTTTC TTTTTTC TTCTTT- TTCTTTC TTTTTCC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TT-TTTC TT-TTTC TTTTT-C
40904465 TTTTT
1 TTTTT
40904470 GCTCCTTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
5 4 0.10
6 22 0.52
7 16 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:40904433 original size:7 final size:7
Alignment explanation
Indices: 40904401--40904469 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
40904391 CGACCTATCC
*
40904401 TTTTTGT
1 TTTTTCT
40904408 TTTTAT-T
1 TTTT-TCT
40904415 TTTTTC-
1 TTTTTCT
40904421 TTTTTCT
1 TTTTTCT
40904428 TTTTTC-
1 TTTTTCT
40904434 --TTTCT
1 TTTTTCT
40904439 TTTTTCT
1 TTTTTCT
*
40904446 TCTTT-T
1 TTTTTCT
*
40904452 TCTTTCT
1 TTTTTCT
*
40904459 TTTTCCT
1 TTTTTCT
40904466 TTTT
1 TTTT
40904470 GCTCCTTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
4 4 0.08
6 13 0.25
7 34 0.65
8 1 0.02
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:40904448 original size:10 final size:11
Alignment explanation
Indices: 40904423--40904467 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
40904413 TTTTTTTCTT
40904423 TTTCTTTTTTC
1 TTTCTTTTTTC
40904434 TTTCTTTTTTC
1 TTTCTTTTTTC
40904445 -TTC-TTTTTC
1 TTTCTTTTTTC
*
40904454 TTTCTTTTTCC
1 TTTCTTTTTTC
40904465 TTT
1 TTT
40904468 TTGCTCCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 6 0.19
10 6 0.19
11 19 0.61
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:40904453 original size:20 final size:18
Alignment explanation
Indices: 40904413--40904469 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 18
40904403 TTTGTTTTTA
40904413 TTTT-TTTC-TTTTTCTT
1 TTTTCTTTCTTTTTTCTT
40904429 TTTTCTTTCTTTTTTCTTCT
1 TTTTCTTTCTTTTTTC-T-T
*
40904449 TTTTCTTTCTTTTTCCTT
1 TTTTCTTTCTTTTTTCTT
40904467 TTT
1 TTT
40904470 GCTCCTTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 10 0.28
19 2 0.06
20 16 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTCTTTTTTCTT
Found at i:40904481 original size:27 final size:27
Alignment explanation
Indices: 40904424--40904481 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
40904414 TTTTTTCTTT
* * * *
40904424 TTCTTTTTTCTTTCTTTTTTCTTCTTT
1 TTCTTTTTTCTTCCTTTTTGCTCCTTC
40904451 TTCTTTCTTT-TTCCTTTTTGCTCCTTC
1 TTCTTT-TTTCTTCCTTTTTGCTCCTTC
40904478 TTCT
1 TTCT
40904482 CAAGCCCTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (27 bp):
TTCTTTTTTCTTCCTTTTTGCTCCTTC
Found at i:40904625 original size:20 final size:21
Alignment explanation
Indices: 40904586--40904625 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40904576 TTTTCTTTTT
*
40904586 TCTTTTCTTCTCTTCTTTCTC
1 TCTTTTCTTCTCTCCTTTCTC
*
40904607 TCTTTT-TTTTCTCCTTTCT
1 TCTTTTCTTCTCTCCTTTCT
40904626 TCCTCCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTTTTCTTCTCTCCTTTCTC
Found at i:40904636 original size:24 final size:24
Alignment explanation
Indices: 40904582--40904637 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
40904572 CATATTTTCT
* *
40904582 TTTTTCTTTTCTTCTCTTCTTTCTC
1 TTTTT-TTTTCTCCTCTTCTTCCTC
40904607 TCTTTTTTTTCTCCT-TTCTTCCTC
1 T-TTTTTTTTCTCCTCTTCTTCCTC
*
40904631 CTTTTTT
1 TTTTTTT
40904638 CCTTCTCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.22
24 8 0.30
25 9 0.33
26 4 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTTTTTCTCCTCTTCTTCCTC
Found at i:40905193 original size:29 final size:30
Alignment explanation
Indices: 40905148--40905246 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 30
40905138 TAAAACTTTT
* * **
40905148 GGGGTTAAAGTGCAATTTTAGGAAG-TTAA
1 GGGGTTAAAATGTAATTTTAAAAAGTTTAA
40905177 GGGGTTAAAATGTAATTTTAAAAAAGTTTAA
1 GGGGTTAAAATGTAATTTT-AAAAAGTTTAA
*
40905208 -GGGTTAAAATATAATTTTAAAAAAG-TT-A
1 GGGGTTAAAATGTAATTTT-AAAAAGTTTAA
*
40905236 GGGGTCAAAAT
1 GGGGTTAAAAT
40905247 TTAAAATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.02
29 28 0.46
30 28 0.46
31 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.32
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTAAAAAGTTTAA
Found at i:40905231 original size:31 final size:31
Alignment explanation
Indices: 40905173--40905246 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
40905163 TTTTAGGAAG
*
40905173 TTAAGGGGTTAAAATGTAATTTTAAAAAAGT
1 TTAAGGGGTTAAAATATAATTTTAAAAAAGT
40905204 TTAA-GGGTTAAAATATAATTTTAAAAAAG-
1 TTAAGGGGTTAAAATATAATTTTAAAAAAGT
*
40905233 TT-AGGGGTCAAAAT
1 TTAAGGGGTTAAAAT
40905247 TTAAAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.03
29 11 0.28
30 24 0.60
31 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.19, T:0.34
Consensus pattern (31 bp):
TTAAGGGGTTAAAATATAATTTTAAAAAAGT
Found at i:40905825 original size:150 final size:150
Alignment explanation
Indices: 40905562--40906699 Score: 1225
Period size: 150 Copynumber: 7.4 Consensus size: 150
40905552 ACACCTCGGC
*
40905562 GTGCAACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
*
40905627 GGACCTCAGTGTGCGACCCGAGGCTCAAAC-CACCTCTCAGATTATGAGTTGATTTTTGAAAAAC
66 GGACCTCAGTGTGCGACCCGAGGCTC-AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAAC
40905691 AGAAATTAAAAGGACCTCAGT
130 AGAAATTAAAAGGACCTCAGT
40905712 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
* *
40905777 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAATTTTTTAAAAACA
66 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
* *
40905842 GAAATTAAAAGTACCTCAGC
131 GAAATTAAAAGGACCTCAGT
*** * ** *** *** * * **** *
40905862 GTGCGACCCGAGGCTCAAAGGA-C-CTCAG-TGTGCGACCCGA-GGCT-CAAACCACCTCTCAGA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGAT-TATGAGTTGATTTTTGAAAAACAGAAATTA-A
* * ** * * * ** * * *** * *** * ***
40905922 TTATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGACCTCAGTGTGCGA-CCCGAGGCTCAACT
64 -AAGGACCTCA-GTGTG-CGACCCGAGGCTCAACTCACCTC--T-CG-GATTATGA-G-T----T
* * ** * *** **
40905986 CACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGACCTCAGT
116 GA--TTTTTGA--A-AAACAGA-AATT-AAAA-------------GGACCTCAGT
40906041 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
40906106 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
66 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
40906171 GAAATTAAAAGGACCTCAGT
131 GAAATTAAAAGGACCTCAGT
40906191 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
40906256 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
66 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
40906321 GAAATTAAAAGGACCTCAGT
131 GAAATTAAAAGGACCTCAGT
40906341 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
40906406 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
66 GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
40906471 GAAATTAAAAGGACCTCAGT
131 GAAATTAAAAGGACCTCAGT
40906491 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATT-AAA
* ** * * * * *
40906556 A-TACCTCAGCCTGCAACCCAATGCTCAACTCACCTCTCCGATTATAAGTTGATTTTTGAAAAAC
65 AGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAAC
*
40906620 AGAAATTGAAAA-TACCTCAGCT
130 AGAAATT-AAAAGGACCTCAG-T
* * * *
40906642 -TGTGACCCGAGGCTCAACTCACCTATCAGATTATGAGTTGATTTTTGAAAAATAGAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAA
40906700 AAAAATGGTT
Statistics
Matches: 819, Mismatches: 124, Indels: 90
0.79 0.12 0.09
Matches are distributed among these distances:
146 7 0.01
147 3 0.00
148 14 0.02
149 7 0.01
150 665 0.81
151 9 0.01
152 1 0.00
153 3 0.00
154 3 0.00
155 1 0.00
159 2 0.00
161 3 0.00
163 5 0.01
164 5 0.01
165 5 0.01
166 5 0.01
168 4 0.00
170 2 0.00
174 1 0.00
175 3 0.00
176 3 0.00
177 1 0.00
179 39 0.05
180 4 0.00
181 14 0.02
182 3 0.00
183 7 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (150 bp):
GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
GGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACA
GAAATTAAAAGGACCTCAGT
Found at i:40905887 original size:75 final size:75
Alignment explanation
Indices: 40905562--40905879 Score: 566
Period size: 75 Copynumber: 4.2 Consensus size: 75
40905552 ACACCTCGGC
*
40905562 GTGCAACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
40905627 GGACCTCAGT
66 GGACCTCAGT
*
40905637 GTGCGACCCGAGGCTCAAAC-CACCTCTCAGATTATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 GTGCGACCCGAGGCTC-AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAA
40905701 AGGACCTCAGT
65 AGGACCTCAGT
40905712 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
40905777 GGACCTCAGT
66 GGACCTCAGT
* *
40905787 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAATTTTTTAAAAACAGAAATTAAAA
1 GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
* *
40905852 GTACCTCAGC
66 GGACCTCAGT
40905862 GTGCGACCCGAGGCTCAA
1 GTGCGACCCGAGGCTCAA
40905880 AGGACCTCAG
Statistics
Matches: 234, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
74 3 0.01
75 228 0.97
76 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (75 bp):
GTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTAAAA
GGACCTCAGT
Found at i:40905894 original size:29 final size:29
Alignment explanation
Indices: 40905849--40905909 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
40905839 ACAGAAATTA
*
40905849 AAAGTACCTCAGCGTGCGACCCGAGGCTC
1 AAAGGACCTCAGCGTGCGACCCGAGGCTC
*
40905878 AAAGGACCTCAGTGTGCGACCCGAGGCTC
1 AAAGGACCTCAGCGTGCGACCCGAGGCTC
40905907 AAA
1 AAA
40905910 CCACCTCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (29 bp):
AAAGGACCTCAGCGTGCGACCCGAGGCTC
Found at i:40905915 original size:29 final size:29
Alignment explanation
Indices: 40905854--40905916 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
40905844 AATTAAAAGT
**
40905854 ACCTCAGCGTGCGACCCGAGGCTCAAAGG
1 ACCTCAGCGTGCGACCCGAGGCTCAAACC
*
40905883 ACCTCAGTGTGCGACCCGAGGCTCAAACC
1 ACCTCAGCGTGCGACCCGAGGCTCAAACC
40905912 ACCTC
1 ACCTC
40905917 TCAGATTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.38, G:0.25, T:0.13
Consensus pattern (29 bp):
ACCTCAGCGTGCGACCCGAGGCTCAAACC
Found at i:40905915 original size:104 final size:104
Alignment explanation
Indices: 40905774--40905983 Score: 359
Period size: 104 Copynumber: 2.0 Consensus size: 104
40905764 ACAGAAATTA
* *
40905774 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAATTTTTTAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCAGATTATGAGTTAATTTTTGAAAA
*
40905839 ACAGAAATTAAAAGTACCTCAGCGTGCGACCCGAGGCTC
66 ACAGAAATTAAAAGGACCTCAGCGTGCGACCCGAGGCTC
*
40905878 AAAGGACCTCAGTGTGCGACCCGAGGCTCAAAC-CACCTCTCAGATTATGAGTTGATTTTTGAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTC-AACTCACCTCTCAGATTATGAGTTAATTTTTGAAA
*
40905942 AACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTC
65 AACAGAAATTAAAAGGACCTCAGCGTGCGACCCGAGGCTC
40905982 AA
1 AA
40905984 CTCACCTCTC
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 97 0.97
105 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (104 bp):
AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCAGATTATGAGTTAATTTTTGAAAA
ACAGAAATTAAAAGGACCTCAGCGTGCGACCCGAGGCTC
Found at i:40905999 original size:179 final size:179
Alignment explanation
Indices: 40905699--40906058 Score: 659
Period size: 179 Copynumber: 2.0 Consensus size: 179
40905689 ACAGAAATTA
*
40905699 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCAGATTATGAGTTGATTTTTGAAAA
40905764 ACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAA
66 ACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAA
* *
40905829 TTTTTTAAAAACAGAAATTAAAAGTACCTCAGCGTGCGACCCGAGGCTC
131 TTTTTGAAAAACAGAAATTAAAAGGACCTCAGCGTGCGACCCGAGGCTC
40905878 AAAGGACCTCAGTGTGCGACCCGAGGCTCAAAC-CACCTCTCAGATTATGAGTTGATTTTTGAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTC-AACTCACCTCTCAGATTATGAGTTGATTTTTGAAA
*
40905942 AACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTG
65 AACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTA
*
40906007 ATTTTTGAAAAACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTC
130 ATTTTTGAAAAACAGAAATTAAAAGGACCTCAGCGTGCGACCCGAGGCTC
40906057 AA
1 AA
40906059 CTCACCTCTC
Statistics
Matches: 175, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
179 172 0.98
180 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (179 bp):
AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCAGATTATGAGTTGATTTTTGAAAA
ACAGAAATTAAAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAA
TTTTTGAAAAACAGAAATTAAAAGGACCTCAGCGTGCGACCCGAGGCTC
Found at i:40906001 original size:75 final size:75
Alignment explanation
Indices: 40905878--40906699 Score: 1454
Period size: 75 Copynumber: 11.0 Consensus size: 75
40905868 CCCGAGGCTC
*
40905878 AAAGGACCTCAGTGTGCGACCCGAGGCTCAAAC-CACCTCTCAGATTATGAGTTGATTTTTGAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTC-AACTCACCTCTCGGATTATGAGTTGATTTTTGAAA
40905942 AACAGAAATTA
65 AACAGAAATTA
40905953 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906018 ACAGAAATTA
66 ACAGAAATTA
40906028 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906093 ACAGAAATTA
66 ACAGAAATTA
40906103 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906168 ACAGAAATTA
66 ACAGAAATTA
40906178 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906243 ACAGAAATTA
66 ACAGAAATTA
40906253 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906318 ACAGAAATTA
66 ACAGAAATTA
40906328 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906393 ACAGAAATTA
66 ACAGAAATTA
40906403 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906468 ACAGAAATTA
66 ACAGAAATTA
40906478 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906543 ACAGAAATTGA
66 ACAGAAATT-A
* ** * * * * *
40906554 AAA-TACCTCAGCCTGCAACCCAATGCTCAACTCACCTCTCCGATTATAAGTTGATTTTTGAAAA
1 AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
40906618 ACAGAAATTGA
66 ACAGAAATT-A
* * * *
40906629 AAA-TACCTCAGCT-TGTGACCCGAGGCTCAACTCACCTATCAGATTATGAGTTGATTTTTGAAA
1 AAAGGACCTCAG-TGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAA
*
40906692 AATAGAAA
65 AACAGAAA
40906700 AAAAATGGTT
Statistics
Matches: 726, Mismatches: 18, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
74 3 0.00
75 719 0.99
76 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (75 bp):
AAAGGACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAA
ACAGAAATTA
Found at i:40915793 original size:13 final size:13
Alignment explanation
Indices: 40915775--40915819 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
40915765 GCTTCTTCCC
40915775 TTTTTTTTCTCTT
1 TTTTTTTTCTCTT
40915788 TTTTTTTTCT-TT
1 TTTTTTTTCTCTT
40915800 CTTTATTTTTCCTCTT
1 -TTT-TTTTT-CTCTT
40915816 TTTT
1 TTTT
40915820 CTCCTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.07
13 13 0.46
14 6 0.21
15 5 0.18
16 2 0.07
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:40915827 original size:26 final size:26
Alignment explanation
Indices: 40915774--40915828 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
40915764 GGCTTCTTCC
* * *
40915774 CTTTTTTTTCTCTTTTTTTTTTCTTT
1 CTTTTTTTTCTCTCTTTTTTCTCCTT
40915800 CTTTATTTTTC-CTCTTTTTTCTCCTT
1 CTTT-TTTTTCTCTCTTTTTTCTCCTT
40915826 CTT
1 CTT
40915829 CTCAAGCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (26 bp):
CTTTTTTTTCTCTCTTTTTTCTCCTT
Found at i:40916597 original size:30 final size:30
Alignment explanation
Indices: 40916490--40916599 Score: 152
Period size: 30 Copynumber: 3.7 Consensus size: 30
40916480 AAAATTTCTA
* * *
40916490 GGGTAAAAATGTAACTTTA-AGAAAGTTAAG
1 GGGTCAAAATGTAATTTTAGA-AAAGTTTAG
40916520 GGGTCAAAATGTAATTTTAGAAAA-TTTGAG
1 GGGTCAAAATGTAATTTTAGAAAAGTTT-AG
*
40916550 GGGTCAAAATATAATTTTAGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAG
40916580 GGGTCAAAATGTAATTTTAG
1 GGGTCAAAATGTAATTTTAG
40916600 GAAATTAGAG
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
29 2 0.03
30 66 0.92
31 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAGAAAAGTTTAG
Found at i:40918416 original size:28 final size:27
Alignment explanation
Indices: 40918355--40918418 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
40918345 CATAAAAGAT
*
40918355 TATGA-AAA-TTTAAAAACTTTAAAAA
1 TATGATAAATTTTAAAAAATTTAAAAA
**
40918380 TAAAAATAAATTTTAAAACAATTTAAAAA
1 T-ATGATAAATTTTAAAA-AATTTAAAAA
40918409 TATGATAAAT
1 TATGATAAAT
40918419 ATAAAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 2 0.07
27 3 0.10
28 14 0.47
29 10 0.33
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (27 bp):
TATGATAAATTTTAAAAAATTTAAAAA
Found at i:40923309 original size:13 final size:13
Alignment explanation
Indices: 40923291--40923318 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40923281 CATGTTAAAG
40923291 CTCATTTCACACA
1 CTCATTTCACACA
40923304 CTCATTTCACACA
1 CTCATTTCACACA
40923317 CT
1 CT
40923319 TTTGAACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (13 bp):
CTCATTTCACACA
Found at i:40931488 original size:12 final size:13
Alignment explanation
Indices: 40931463--40931491 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40931453 ATAGTTTATA
40931463 TATACTTACATTT
1 TATACTTACATTT
40931476 TATACTT-CATTT
1 TATACTTACATTT
40931488 TATA
1 TATA
40931492 TATACCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (13 bp):
TATACTTACATTT
Found at i:40931561 original size:13 final size:12
Alignment explanation
Indices: 40931525--40931573 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
40931515 TTTCACACAC
40931525 ATATATATATTT
1 ATATATATATTT
*
40931537 -TCATAGTTTATTT
1 AT-ATA-TATATTT
40931550 ATATATTATATTT
1 ATATA-TATATTT
40931563 ATATATATATT
1 ATATATATATT
40931574 GTTCTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.03
12 9 0.29
13 20 0.65
14 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
ATATATATATTT
Found at i:40931569 original size:17 final size:19
Alignment explanation
Indices: 40931526--40931573 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
40931516 TTCACACACA
*
40931526 TATATATATTTTCATAGTT
1 TATATATATATTCATAGTT
*
40931545 TATTTATATATT-ATA-TT
1 TATATATATATTCATAGTT
40931562 TATATATATATT
1 TATATATATATT
40931574 GTTCTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATATATATTCATAGTT
Found at i:40934710 original size:17 final size:17
Alignment explanation
Indices: 40934688--40934731 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
40934678 TAATCACTTT
40934688 AATATTAAATT-AATATA
1 AATATTAAATTAAAT-TA
* *
40934705 AATATTAGATTAAATTT
1 AATATTAAATTAAATTA
40934722 AATATTAAAT
1 AATATTAAAT
40934732 CTTTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTAAATTAAATTA
Found at i:40934728 original size:12 final size:12
Alignment explanation
Indices: 40934685--40934731 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
40934675 ACTTAATCAC
40934685 TTTAATATTAAA
1 TTTAATATTAAA
40934697 -TTAATA-TAAA
1 TTTAATATTAAA
*
40934707 TATT-AGATTAAA
1 T-TTAATATTAAA
40934719 TTTAATATTAAA
1 TTTAATATTAAA
40934731 T
1 T
40934732 CTTTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
11 10 0.34
12 15 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:40934820 original size:20 final size:19
Alignment explanation
Indices: 40934773--40934822 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
40934763 GTAGATAAAC
40934773 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
40934790 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
40934810 ATTAAATTAATAA
1 ATTAAATTAATAA
40934823 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 3 0.11
20 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:40940209 original size:13 final size:13
Alignment explanation
Indices: 40940191--40940215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40940181 TGTATTTGAT
40940191 TTGATTATGTAAA
1 TTGATTATGTAAA
40940204 TTGATTATGTAA
1 TTGATTATGTAA
40940216 TCTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:40943861 original size:50 final size:50
Alignment explanation
Indices: 40943744--40943929 Score: 196
Period size: 50 Copynumber: 3.7 Consensus size: 50
40943734 GATAATAACA
* * * ** * *
40943744 TGCCAAAGCCATGTCCCAGACATGTTCTTACATGGGATATTTCATGTAC--
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
40943793 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGG
** * *
40943843 TGCCCTTGCCATGTCCTAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
40943893 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
40943930 TCTCATTCCC
Statistics
Matches: 113, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
48 1 0.01
49 38 0.34
50 74 0.65
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40944304 original size:30 final size:30
Alignment explanation
Indices: 40944270--40944327 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
40944260 CCTCGACTCT
40944270 AACTTTTGA-AAAATTACAATTTTGCCCCTA
1 AACTTTT-ACAAAATTACAATTTTGCCCCTA
* *
40944300 AACTTTTACATAATTACACTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
40944328 AAAGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:40952388 original size:18 final size:18
Alignment explanation
Indices: 40952365--40952413 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
40952355 TTTTTGTCAA
40952365 AAAATAATTAAATATTAT
1 AAAATAATTAAATATTAT
40952383 AAAATAATTAAATATTAT
1 AAAATAATTAAATATTAT
*
40952401 AAAATAAATAAAT
1 AAAATAATTAAAT
40952414 TATGTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATAATTAAATATTAT
Found at i:40964531 original size:16 final size:16
Alignment explanation
Indices: 40964510--40964545 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40964500 AAGCGAAAAA
* *
40964510 GAAAGAAAGGAAAGGG
1 GAAAGAAAAGAAAAGG
40964526 GAAAGAAAAGAAAAGG
1 GAAAGAAAAGAAAAGG
40964542 GAAA
1 GAAA
40964546 AACTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAAGG
Found at i:40965622 original size:23 final size:23
Alignment explanation
Indices: 40965595--40965661 Score: 109
Period size: 23 Copynumber: 2.9 Consensus size: 23
40965585 TTTGCCGATT
40965595 AGACACTTTATGTGTCGTA-CATC
1 AGACACTTTATGTGTCGTATC-TC
40965618 AGACACTTTATGTGTCGTATCTC
1 AGACACTTTATGTGTCGTATCTC
*
40965641 AGACACTTTATGTGTTGTATC
1 AGACACTTTATGTGTCGTATC
40965662 AGGCACCTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
23 41 0.98
24 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (23 bp):
AGACACTTTATGTGTCGTATCTC
Found at i:40972167 original size:140 final size:141
Alignment explanation
Indices: 40971867--40972168 Score: 311
Period size: 140 Copynumber: 2.1 Consensus size: 141
40971857 GATGTAATTA
** * * * *
40971867 CATCTAACCATCTAAGGAAAAAACTAAAATGTTAAAAAACATTAATTAAAAATTTAAAAAGGATG
1 CATCTAACCATCTAACCAAAGAACTAAAATGATAAAAAACATTAATTAAAAATTTAAAAAGCATA
* * * * * *
40971932 AAGTAACATGAAATAAAAAAATACAAATATAAGTAGGAGAGAAATCAAACTTGAGACTCAAGGAT
66 AAGCAACATAAAATAAAAAAATACAAATATAAGTAGGAAAGAAATCAAACATGAAACTCAAAGAT
* ** *
40971997 ATAATTACAAT
131 AAAAACACAAG
* * * * * *
40972008 TATCTAACTATCTAACCAAAGAACTAATATGATAACAAA-ATTAATTAAAATTTTAAAAAGCTTA
1 CATCTAACCATCTAACCAAAGAACTAAAATGATAAAAAACATTAATTAAAAATTTAAAAAGCATA
* * * *
40972072 AAGCAACATAAAATAAAAAAATATAAATATGAGTAGGAAA-AGAATCGAACATGAAATTCAAAGA
66 AAGCAACATAAAATAAAAAAATACAAATATAAGTAGGAAAGA-AATCAAACATGAAACTCAAAGA
*
40972136 TAAAAACACTAG
130 TAAAAACACAAG
* * *
40972148 CATTTAACCATTTAGCCAAAG
1 CATCTAACCATCTAACCAAAG
40972169 CTGAAAGCAC
Statistics
Matches: 128, Mismatches: 32, Indels: 3
0.79 0.20 0.02
Matches are distributed among these distances:
139 1 0.01
140 96 0.75
141 31 0.24
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (141 bp):
CATCTAACCATCTAACCAAAGAACTAAAATGATAAAAAACATTAATTAAAAATTTAAAAAGCATA
AAGCAACATAAAATAAAAAAATACAAATATAAGTAGGAAAGAAATCAAACATGAAACTCAAAGAT
AAAAACACAAG
Found at i:40972631 original size:20 final size:22
Alignment explanation
Indices: 40972589--40972633 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40972579 GAAAATAGTA
*
40972589 TTTTTTTAATATAATTAAGTGT
1 TTTTTTTAATATAAGTAAGTGT
*
40972611 TTTTTTTATTA-AAGTAA-TGT
1 TTTTTTTAATATAAGTAAGTGT
40972631 TTT
1 TTT
40972634 AGTTCATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (22 bp):
TTTTTTTAATATAAGTAAGTGT
Found at i:40980836 original size:29 final size:30
Alignment explanation
Indices: 40980777--40980834 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40980767 TTCGAGCCTT
* *
40980777 GGGGTAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
40980807 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
40980835 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:40981064 original size:13 final size:13
Alignment explanation
Indices: 40981046--40981077 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40981036 TTTCCAGCAA
40981046 TTATGAATTTATT
1 TTATGAATTTATT
40981059 TTATGAATTTATT
1 TTATGAATTTATT
*
40981072 TGATGA
1 TTATGA
40981078 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:40981285 original size:50 final size:50
Alignment explanation
Indices: 40981172--40981413 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
40981162 ATTTGGGTAA
* * *
40981172 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
40981228 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
40981278 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
40981328 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
40981378 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
40981414 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:40981361 original size:100 final size:103
Alignment explanation
Indices: 40981172--40981421 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
40981162 ATTTGGGTAA
40981172 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
40981237 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
40981278 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
40981340 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
40981378 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
40981422 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:40990055 original size:29 final size:30
Alignment explanation
Indices: 40990002--40990061 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40989992 TCCAAGCCTT
*
40990002 GGGGCAAAAATGTAATTATGTAAAAATTTA
1 GGGGCAAAAATGTAATTATGTAAAAAGTTA
* *
40990032 GGGGCAAAATTGTAATTTTG-AAAAAGTTA
1 GGGGCAAAAATGTAATTATGTAAAAAGTTA
40990061 G
1 G
40990062 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAAGTTA
Found at i:40990289 original size:13 final size:13
Alignment explanation
Indices: 40990271--40990302 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40990261 TTTCCAGCAA
40990271 TTATGAATTTATT
1 TTATGAATTTATT
40990284 TTATGAATTTATT
1 TTATGAATTTATT
*
40990297 TGATGA
1 TTATGA
40990303 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:40990510 original size:50 final size:50
Alignment explanation
Indices: 40990397--40990638 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
40990387 ATTTGGGTAA
* * **
40990397 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAGA-C--G
*
40990453 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
40990503 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
40990553 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
40990603 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
40990639 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.18
52 1 0.01
53 3 0.02
55 1 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:40990586 original size:100 final size:103
Alignment explanation
Indices: 40990397--40990646 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
40990387 ATTTGGGTAA
40990397 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC--T-AGATCATGAGAGGTCCC
* *
40990462 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * * *
40990503 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTAGATCATGAGAGGTCCCCTA
40990565 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
40990603 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
40990647 GTTATTATAG
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 39 0.30
105 1 0.01
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:40993728 original size:22 final size:22
Alignment explanation
Indices: 40993703--40993749 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
40993693 AAAATTATAA
40993703 TAAGGTCG-TATTAAAATTTTGT
1 TAAGG-CGTTATTAAAATTTTGT
40993725 TAA-GCGTTATTAAAATTTTGT
1 TAAGGCGTTATTAAAATTTTGT
40993746 TAAG
1 TAAG
40993750 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (22 bp):
TAAGGCGTTATTAAAATTTTGT
Found at i:41002701 original size:51 final size:51
Alignment explanation
Indices: 41002625--41002745 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
41002615 CAAAGACACC
* * *
41002625 AATCTCGTTTCCTTGGCGTTGCAGTGGTAA-AGATTGAAGTTGAGGGCAGCG
1 AATCTCATTTCCTTGGCGTTGCAGTGG-AATAAATTGAAGCTGAGGGCAGCG
41002676 AATCTCATTTCCTTGGCGTTGCAGTGGAATAAATTGAAGCTGAGGGCAGCG
1 AATCTCATTTCCTTGGCGTTGCAGTGGAATAAATTGAAGCTGAGGGCAGCG
* *
41002727 AATCTTATTTCCCTGGCGT
1 AATCTCATTTCCTTGGCGT
41002746 CATAGCATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.03
51 62 0.97
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (51 bp):
AATCTCATTTCCTTGGCGTTGCAGTGGAATAAATTGAAGCTGAGGGCAGCG
Found at i:41004271 original size:24 final size:24
Alignment explanation
Indices: 41004242--41004356 Score: 94
Period size: 23 Copynumber: 4.9 Consensus size: 24
41004232 GTATTGTATA
*
41004242 TTATTATTTTAGATTTATCATGTT
1 TTATTATTTTAAATTTATCATGTT
* * * *
41004266 TTATTATTTTTAATTTCTCA-ATA
1 TTATTATTTTAAATTTATCATGTT
*
41004289 TTATTATTTTAAATTCAT--TGTT
1 TTATTATTTTAAATTTATCATGTT
**
41004311 AACATTATTTTAAATTTATCATG-T
1 -TTATTATTTTAAATTTATCATGTT
* *
41004335 ATATCTATTTCAAATTTATCAT
1 TTAT-TATTTTAAATTTATCAT
41004357 TAATATTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
22 1 0.01
23 34 0.48
24 34 0.48
25 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAATTTATCATGTT
Found at i:41004362 original size:24 final size:22
Alignment explanation
Indices: 41004314--41004374 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
41004304 CATTGTTAAC
41004314 ATTATTTTAAATTTATCATGTAT
1 ATTA-TTTAAATTTATCATGTAT
41004337 ATCTATTTCAAATTTATCAT-TAAT
1 AT-TATTT-AAATTTATCATGT-AT
41004361 ATT-TTTAAATTTAT
1 ATTATTTAAATTTAT
41004375 TATTTTGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 8 0.23
22 3 0.09
23 7 0.20
24 17 0.49
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATTTAAATTTATCATGTAT
Found at i:41004387 original size:59 final size:59
Alignment explanation
Indices: 41004314--41004431 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 59
41004304 CATTGTTAAC
* * *
41004314 ATTATTTTAAATTTATCATGTAT-ATCTATT-TCA-AATTTATCATTAATATTTTTAAATTT
1 ATTATTTTAAATTTATCACGTATGAT-TATTCT-ATAA-TTATCATCAAAATTTTTAAATTT
**
41004373 ATTATTTTGGATTTATCACGTATGATTATTCTATAATTATCATCAAAATTTTTAAATTT
1 ATTATTTTAAATTTATCACGTATGATTATTCTATAATTATCATCAAAATTTTTAAATTT
41004432 TATATGTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 46 0.90
60 5 0.10
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (59 bp):
ATTATTTTAAATTTATCACGTATGATTATTCTATAATTATCATCAAAATTTTTAAATTT
Found at i:41004481 original size:24 final size:23
Alignment explanation
Indices: 41004423--41004481 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 23
41004413 CATCAAAATT
41004423 TTTAAATT-TTATATGTATTATTA
1 TTTAAATTATTATA-GTATTATTA
41004446 TTTCAAATTTATTATA-TATTATTTA
1 TTT-AAA-TTATTATAGTATTA-TTA
41004471 TTGTAAATTAT
1 TT-TAAATTAT
41004482 CTAATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 12 0.39
25 10 0.32
26 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTAAATTATTATAGTATTATTA
Found at i:41015158 original size:24 final size:24
Alignment explanation
Indices: 41015068--41015160 Score: 60
Period size: 25 Copynumber: 3.8 Consensus size: 24
41015058 GCTAAATAAT
* * *
41015068 GGGAAGATTATGTGAGCCATGTAAC
1 GGGAAGCTTATGCGAGCCAT-AAAC
* * * **
41015093 GGGAAACTTATCCGGGCTGTATAAC
1 GGGAAGCTTATGCGAGCCATA-AAC
* * **
41015118 AGGAAGCTCATAAGAGCCATAAAC
1 GGGAAGCTTATGCGAGCCATAAAC
41015142 GGGAAGCTTATGCGAGCCA
1 GGGAAGCTTATGCGAGCCA
41015161 ATAACGAGTA
Statistics
Matches: 47, Mismatches: 20, Indels: 3
0.67 0.29 0.04
Matches are distributed among these distances:
24 18 0.38
25 29 0.62
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.19
Consensus pattern (24 bp):
GGGAAGCTTATGCGAGCCATAAAC
Found at i:41015166 original size:24 final size:24
Alignment explanation
Indices: 41015062--41015166 Score: 59
Period size: 25 Copynumber: 4.3 Consensus size: 24
41015052 TCTCAAGCTA
* * *
41015062 AATAATGGGAAGATTATGTGAGCC
1 AATAACGGGAAGCTTATGCGAGCC
* * * * *
41015086 ATGTAACGGGAAACTTATCCGGGCTG
1 A-ATAACGGGAAGCTTATGCGAGC-C
* * * **
41015112 TATAACAGGAAGCTCATAAGAGCC
1 AATAACGGGAAGCTTATGCGAGCC
41015136 -ATAAACGGGAAGCTTATGCGAGCC
1 AAT-AACGGGAAGCTTATGCGAGCC
41015160 AATAACG
1 AATAACG
41015167 AGTAGCTCCA
Statistics
Matches: 56, Mismatches: 21, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
23 2 0.04
24 22 0.39
25 32 0.57
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (24 bp):
AATAACGGGAAGCTTATGCGAGCC
Found at i:41015254 original size:23 final size:23
Alignment explanation
Indices: 41015192--41015257 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
41015182 CCATTAACGG
* *
41015192 GAAGCTTCAGATAGCCATATATCGA
1 GAAGCTTAAGAGAGCC--ATATCGA
*
41015217 GAAG-TTCAAGCGAGCCATATCGA
1 GAAGCTT-AAGAGAGCCATATCGA
*
41015240 GAAGCTTTAGAGAGCCAT
1 GAAGCTTAAGAGAGCCAT
41015258 TAATTAGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 20 0.59
24 4 0.12
25 10 0.29
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (23 bp):
GAAGCTTAAGAGAGCCATATCGA
Found at i:41015281 original size:26 final size:26
Alignment explanation
Indices: 41015250--41015309 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
41015240 GAAGCTTTAG
*
41015250 AGAGCCATTAATTAG-GAAGCTCACAA
1 AGAGCCATTAA-TAGACAAGCTCACAA
* * *
41015276 AGAGCCTTTAATCGACAAGCTCACGA
1 AGAGCCATTAATAGACAAGCTCACAA
41015302 AGAGCCAT
1 AGAGCCAT
41015310 ATAACAGGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATAGACAAGCTCACAA
Found at i:41015629 original size:22 final size:22
Alignment explanation
Indices: 41015603--41015654 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
41015593 TAATAATACA
41015603 AACACATACATACAATTCAATT
1 AACACATACATACAATTCAATT
*
41015625 AACACATAGATACAATTCAATT
1 AACACATACATACAATTCAATT
41015647 AACACATA
1 AACACATA
41015655 TAAATTCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.25
Consensus pattern (22 bp):
AACACATACATACAATTCAATT
Found at i:41015818 original size:5 final size:5
Alignment explanation
Indices: 41015789--41015827 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
41015779 TAAATTTAGC
* *
41015789 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
41015828 CATCTTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Done.