Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 131 of 168
Found at i:38217933 original size:19 final size:19
Alignment explanation
Indices: 38217891--38217956 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
38217881 AAAATTACAA
*
38217891 AAAAATTTAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
38217910 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
*
38217929 AAAAACATCAAAATTTATATTTT
1 AAAAA-TTCAAAA--TA-ATTTT
38217952 AAAAA
1 AAAAA
38217957 AATTATAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.11
19 16 0.43
20 6 0.16
22 1 0.03
23 6 0.16
24 4 0.11
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:38217975 original size:19 final size:19
Alignment explanation
Indices: 38217948--38217984 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38217938 AAAATTTATA
38217948 TTTTAAAAAAATTATAAAC
1 TTTTAAAAAAATTATAAAC
* *
38217967 TTTTTAAAAAATTCTAAA
1 TTTTAAAAAAATTATAAA
38217985 AAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAAAAAAATTATAAAC
Found at i:38218007 original size:38 final size:40
Alignment explanation
Indices: 38217954--38218028 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
38217944 TATATTTTAA
*
38217954 AAAAATTATAAACTTTTTAAAAA-ATTCTAAAA-AATATAT
1 AAAAATTAGAAAC-TTTTAAAAATATTCTAAAATAATATAT
38217993 AAAAATT-GAAACTTTTAAAAATATTCTAAAATAATA
1 AAAAATTAGAAACTTTTAAAAATATTCTAAAATAATA
38218029 ATTTTGGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
37 9 0.27
38 13 0.39
39 11 0.33
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (40 bp):
AAAAATTAGAAACTTTTAAAAATATTCTAAAATAATATAT
Found at i:38228831 original size:114 final size:112
Alignment explanation
Indices: 38228632--38228998 Score: 545
Period size: 114 Copynumber: 3.2 Consensus size: 112
38228622 GAAATAAGAA
** * * *
38228632 TTAGCGGCGTTTTCCAGAAAGCGCCGTAAAAAACCTAAGCCCAACGACGCCGTTTACCGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * *
38228697 CGGGGATTTTGTGGCGTTTTTAAAAAAGCGCCGCTAATTCTCAGGGCT
66 CGGGG-TTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
38228745 TTAGCGGCGATTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCG-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
38228810 TCGTGGGTTTAGCGGTGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCT
65 TCG-GGGTTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
38228859 TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGTTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAG-CTT
*
38228924 TCGGGTGTTTAGTGGCGTTTTTAAGAAAGCGCCTCTAATGCTCAGGGCT
65 TCGGG-GTTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
38228973 TTAGCGGCGTTTTTGAGAAAGCGCCG
1 TTAGCGGCGTTTTTGAGAAAGCGCCG
38228999 CTAATGCTCA
Statistics
Matches: 229, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
113 58 0.25
114 168 0.73
115 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (112 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGTTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:38228992 original size:41 final size:41
Alignment explanation
Indices: 38228931--38229040 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
38228921 TTTTCGGGTG
* * *
38228931 TTTAGTGGCGTTTTTAAGAAAGCGCCTCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
*
38228972 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* *
38229013 TTTAGCGGCGTTTTTGGGGAAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
38229041 AAAAAAACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:38229019 original size:155 final size:155
Alignment explanation
Indices: 38228817--38229154 Score: 493
Period size: 155 Copynumber: 2.2 Consensus size: 155
38228807 CTTTCGTGGG
* * *
38228817 TTTAGCGGTGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
* * * * *
38228882 CCG-AAAAAAACCTAAGCCCAACGACGCCGTTT-TTTGAGTTTTTCGGGTG-TTTAGTGGCGTTT
66 CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTT-AG-CTTTCGGG-GAATTAGCGGCGTTT
* *
38228944 TTAAGAAAGCGCCTCTAATGCTCAGGGC
128 TTAAGAAAGCGCCGCTAATGCTCAGGGA
* * *
38228972 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGGAAGCG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
*
38229037 CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCGGGGAATTAGCGGCGTTTTTC
66 CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCGGGGAATTAGCGGCGTTTTTA
38229102 AGAAAGCGCCGCTAATGCTCAGGGA
131 AGAAAGCGCCGCTAATGCTCAGGGA
*
38229127 TTTAGCGGCGTTTTTGGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
38229155 AAGAAAAACT
Statistics
Matches: 165, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
154 1 0.01
155 132 0.80
156 30 0.18
157 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (155 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCGGGGAATTAGCGGCGTTTTTA
AGAAAGCGCCGCTAATGCTCAGGGA
Found at i:38229091 original size:114 final size:113
Alignment explanation
Indices: 38228973--38229244 Score: 397
Period size: 114 Copynumber: 2.4 Consensus size: 113
38228963 GCTCAGGGCT
* * *
38228973 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGGAAGCGC
1 TTAGCGGCGTTTTT-AGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGC
*
38229038 CGCAA-AAAAACCTAAGCCCAAC-GACACCGTTTCCT-TAGCTTTCGGGGAA
65 CGCAAGAAAAA-CTAAGCCAAACAG-CACCGTTTCCTGT-GCTTTCGGGGAA
38229087 TTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGC
1 TTAGCGGCGTTTTT-AGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGC
* * *
38229152 CGCAAGAAAAACTAAGCCAAACAGCGCCGTTTTCTGTGCTTTCGGGGAT
65 CGCAAGAAAAACTAAGCCAAACAGCACCGTTTCCTGTGCTTTCGGGGAA
*
38229201 TTAGCGGCGTTTTTATGAAAGCGCCGCTAATGCTTAGGGATTTA
1 TTAGCGGCGTTTTTA-GAAAGCGCCGCTAATGCTCAGGGATTTA
38229245 AAATAATTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
113 1 0.01
114 137 0.94
115 7 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (113 bp):
TTAGCGGCGTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGCC
GCAAGAAAAACTAAGCCAAACAGCACCGTTTCCTGTGCTTTCGGGGAA
Found at i:38229197 original size:269 final size:269
Alignment explanation
Indices: 38228699--38229244 Score: 760
Period size: 269 Copynumber: 2.0 Consensus size: 269
38228689 CGAGCTTTCG
* * *
38228699 GGGATTTTGTGGCGTTTTTAAAAAAGCGCCGCTAATTCTCAGGGCTTTAGCGGCGATTTTGAGAA
1 GGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAA
* * * * *
38228764 AGCGCCGCAAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTTTCGTGGGTTTAGCGGTGTT
66 AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTGAGCTTTCGTGGGATTAGCGGCGTT
* *
38228829 TTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACC
131 TTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACC
* * * * *
38228894 TAAGCCCAACGACGCCGTTTTTTGAGTTTTTCGGGTG-TTTAGTGGCGTTTTTAAGAAAGCGCCT
196 TAAGCCAAACGACGCCGTTTTCTGAGTCTTTCGGG-GATTTAGCGGCGTTTTTAAGAAAGCGCCG
38228958 CTAATGCTCA
260 CTAATGCTCA
* * * * * * *
38228968 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGGA
1 GGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAA
*
38229033 AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCG-GGGAATTAGCGGCGT
66 AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTGAGCTTTCGTGGG-ATTAGCGGCGT
* *
38229097 TTTTCAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAGAAAA
130 TTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCG-AA-AAAA
* *
38229162 A-CTAAGCCAAAC-AGCGCCGTTTTCTGTG-CTTTCGGGGATTTAGCGGCGTTTTTATGAAAGCG
193 ACCTAAGCCAAACGA-CGCCGTTTTCTGAGTCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCG
*
38229224 CCGCTAATGCTTA
257 CCGCTAATGCTCA
38229237 GGGATTTA
1 GGGATTTA
38229245 AAATAATTTA
Statistics
Matches: 243, Mismatches: 29, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
268 4 0.02
269 210 0.86
270 24 0.10
271 5 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (269 bp):
GGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAA
AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTGAGCTTTCGTGGGATTAGCGGCGTT
TTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACC
TAAGCCAAACGACGCCGTTTTCTGAGTCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
TAATGCTCA
Found at i:38229547 original size:15 final size:15
Alignment explanation
Indices: 38229456--38229566 Score: 77
Period size: 15 Copynumber: 7.5 Consensus size: 15
38229446 GCCGGGGTAT
*
38229456 GGATTTA-GGGTTTG
1 GGATTTAGGGGTTAG
* *
38229470 GGATTTAAGGTTTAG
1 GGATTTAGGGGTTAG
* *
38229485 GG-GTTAGGTGTTA-
1 GGATTTAGGGGTTAG
* *
38229498 TGCTTTA-GGGTTAG
1 GGATTTAGGGGTTAG
* *
38229512 AAGGATATAAGGGTTAGG
1 --GGATTTAGGGGTTA-G
38229530 GGATTTAGGGGTTAG
1 GGATTTAGGGGTTAG
38229545 GGATTTAGGGGTTAG
1 GGATTTAGGGGTTAG
*
38229560 GGTTTTA
1 GGATTTA
38229567 ACGGTTAGGT
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
13 6 0.08
14 17 0.23
15 29 0.39
16 16 0.21
17 6 0.08
18 1 0.01
ACGTcount: A:0.22, C:0.01, G:0.41, T:0.37
Consensus pattern (15 bp):
GGATTTAGGGGTTAG
Found at i:38229572 original size:15 final size:15
Alignment explanation
Indices: 38229523--38229575 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
38229513 AGGATATAAG
**
38229523 GGTTAGGGGATTTAGG
1 GGTTA-GGGATTTAAC
**
38229539 GGTTAGGGATTTAGG
1 GGTTAGGGATTTAAC
*
38229554 GGTTAGGGTTTTAAC
1 GGTTAGGGATTTAAC
38229569 GGTTAGG
1 GGTTAGG
38229576 TTAGAGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 29 0.85
16 5 0.15
ACGTcount: A:0.19, C:0.02, G:0.45, T:0.34
Consensus pattern (15 bp):
GGTTAGGGATTTAAC
Found at i:38229870 original size:17 final size:17
Alignment explanation
Indices: 38229848--38229949 Score: 82
Period size: 17 Copynumber: 5.6 Consensus size: 17
38229838 GGGGTTATGC
38229848 TTTAGGGGTTAAGGGGA
1 TTTAGGGGTTAAGGGGA
*
38229865 TTTAGGGGTT-AGGGTTA
1 TTTAGGGGTTAAGGG-GA
*
38229882 TGTTTCAGGGGTTAGGGGGA
1 --TTT-AGGGGTTAAGGGGA
*
38229902 TTTAGGGGTT-AGGGCTA
1 TTTAGGGGTTAAGGG-GA
*
38229919 TGTTTCAGGGGTTAGGGGGA
1 --TTT-AGGGGTTAAGGGGA
38229939 TTTAGGGGTTA
1 TTTAGGGGTTA
38229950 TTAAATTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
16 7 0.10
17 27 0.40
18 6 0.09
19 6 0.09
20 16 0.24
21 6 0.09
ACGTcount: A:0.18, C:0.03, G:0.45, T:0.34
Consensus pattern (17 bp):
TTTAGGGGTTAAGGGGA
Found at i:38229882 original size:37 final size:37
Alignment explanation
Indices: 38229839--38229949 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
38229829 TGTGGTTTAG
*
38229839 GGGTTATGCTTT-AGGGGTTAAGGGGATTTAGGGGTTA
1 GGGTTATG-TTTCAGGGGTTAGGGGGATTTAGGGGTTA
38229876 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
1 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
*
38229913 GGGCTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
1 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
38229950 TTAAATTTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
36 3 0.04
37 68 0.96
ACGTcount: A:0.17, C:0.04, G:0.45, T:0.34
Consensus pattern (37 bp):
GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
Found at i:38229893 original size:20 final size:20
Alignment explanation
Indices: 38229868--38229935 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
38229858 AAGGGGATTT
*
38229868 AGGGGTTAGGGTTATGTTTC
1 AGGGGTTAGGGCTATGTTTC
**
38229888 AGGGGTTAGGGGGA--TTT-
1 AGGGGTTAGGGCTATGTTTC
38229905 AGGGGTTAGGGCTATGTTTC
1 AGGGGTTAGGGCTATGTTTC
38229925 AGGGGTTAGGG
1 AGGGGTTAGGG
38229936 GGATTTAGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 12 0.29
18 3 0.07
19 3 0.07
20 23 0.56
ACGTcount: A:0.16, C:0.04, G:0.47, T:0.32
Consensus pattern (20 bp):
AGGGGTTAGGGCTATGTTTC
Found at i:38231435 original size:26 final size:27
Alignment explanation
Indices: 38231399--38231449 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
38231389 CTTATATTTT
38231399 AGCTAGAAATCGACGATG-CCAGAAGA
1 AGCTAGAAATCGACGATGACCAGAAGA
38231425 AGCTAGAAATCGACGATGACCAGAA
1 AGCTAGAAATCGACGATGACCAGAA
38231450 ACTGTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (27 bp):
AGCTAGAAATCGACGATGACCAGAAGA
Found at i:38232294 original size:43 final size:43
Alignment explanation
Indices: 38232246--38232401 Score: 204
Period size: 43 Copynumber: 3.6 Consensus size: 43
38232236 TCTCTAAATA
* * * *
38232246 CGCCGCTAAAGGTCTTGCTCTTTAGTGGCGTTTTCAGGTAAAG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* * *
38232289 AGCCGCTAAAAGTCTTGTTCTTTAGCGGCGTTTTTATGAAAAG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* * *
38232332 CGCCGTTAAAGTTCTTGTTCTTTAGCGGCGTTTTTGGGAAAAG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* *
38232375 CGCCGCTAAAGGTCATGATCTTTAGCG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCG
38232402 ACGCTTATTT
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 96 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (43 bp):
CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
Found at i:38234198 original size:7 final size:7
Alignment explanation
Indices: 38234186--38234212 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38234176 CTTAGCTGAT
38234186 AGTTGAA
1 AGTTGAA
38234193 AGTTGAA
1 AGTTGAA
38234200 AGTTGAA
1 AGTTGAA
38234207 AGTTGA
1 AGTTGA
38234213 TATTTGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
AGTTGAA
Found at i:38234786 original size:15 final size:15
Alignment explanation
Indices: 38234766--38234795 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38234756 GGTGGCTCTC
38234766 TCTTTTCTAAAGATG
1 TCTTTTCTAAAGATG
38234781 TCTTTTCTAAAGATG
1 TCTTTTCTAAAGATG
38234796 GGATATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TCTTTTCTAAAGATG
Found at i:38240335 original size:51 final size:52
Alignment explanation
Indices: 38240202--38240337 Score: 129
Period size: 51 Copynumber: 2.7 Consensus size: 52
38240192 CTATGAAAAT
* * *
38240202 TTGATAGAATATATAAATATT--ATAGATTAAATTTGTTAAATAAGGATTAAA
1 TTGATAAAATATGTAAATATTACATAG-TTAAATTTGTTAAATAAGGACTAAA
* * *
38240253 TTGATAAAATTTGTAAATATTACA-GGATAAATTTGTTAAATCAA-GACTAAA
1 TTGATAAAATATGTAAATATTACATAGTTAAATTTGTTAAAT-AAGGACTAAA
** * *
38240304 TTGATTGAATATGTTAATTTTA-ATAGTTAAATTT
1 TTGATAAAATATGTAAATATTACATAGTTAAATTT
38240338 ATTATTATGC
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
50 1 0.01
51 63 0.93
52 3 0.04
53 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (52 bp):
TTGATAAAATATGTAAATATTACATAGTTAAATTTGTTAAATAAGGACTAAA
Found at i:38252703 original size:2 final size:2
Alignment explanation
Indices: 38252696--38252731 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38252686 AAATACATGG
38252696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38252732 TGGAGGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38254107 original size:57 final size:57
Alignment explanation
Indices: 38254022--38254129 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
38254012 AATATATAGC
*
38254022 TAAATTAACTATGGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCTGCTAAT
1 TAAATTAACTATAGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCTGCTAAT
**
38254079 TAAATTAACTATAGTAATGGCAATCACATGCATTTTTTCATGCATGGCCCT
1 TAAATTAACTATAGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCT
38254130 AAAGAGGAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (57 bp):
TAAATTAACTATAGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCTGCTAAT
Found at i:38268535 original size:2 final size:2
Alignment explanation
Indices: 38268528--38268557 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38268518 TGAAGTGATA
38268528 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
38268558 TGCAAGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38274541 original size:25 final size:25
Alignment explanation
Indices: 38274507--38274557 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
38274497 TCAAAGCATA
38274507 CAAGGATTCTTTTAATGCTAGTCAC
1 CAAGGATTCTTTTAATGCTAGTCAC
38274532 CAAGGATTCTTTTAATGCTAGTCAC
1 CAAGGATTCTTTTAATGCTAGTCAC
38274557 C
1 C
38274558 TGCAGAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (25 bp):
CAAGGATTCTTTTAATGCTAGTCAC
Found at i:38275833 original size:17 final size:16
Alignment explanation
Indices: 38275801--38275844 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
38275791 ATAAAAAATT
38275801 AAATTTTAAATATATA
1 AAATTTTAAATATATA
*
38275817 AAATTTATAAATTTATA
1 AAATTT-TAAATATATA
38275834 ACATATTTTAA
1 A-A-ATTTTAA
38275845 CCTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 10 0.42
18 4 0.17
19 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTTAAATATATA
Found at i:38282682 original size:2 final size:2
Alignment explanation
Indices: 38282675--38282702 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38282665 TATTTCTAAC
38282675 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
38282703 TCTGTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38292636 original size:2 final size:2
Alignment explanation
Indices: 38292623--38292652 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38292613 TAGCTATGAG
*
38292623 AT AT AC 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
38292653 TCTTTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38302475 original size:2 final size:2
Alignment explanation
Indices: 38302468--38302493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38302458 TCCTCCTGAA
38302468 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
38302494 TCACAGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38303241 original size:2 final size:2
Alignment explanation
Indices: 38303234--38303261 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38303224 TACAGTACTC
38303234 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
38303262 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:38303266 original size:2 final size:2
Alignment explanation
Indices: 38303261--38303288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38303251 TCTCTCTCTC
38303261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38303289 CTTCTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38307158 original size:84 final size:83
Alignment explanation
Indices: 38307046--38307298 Score: 398
Period size: 84 Copynumber: 3.0 Consensus size: 83
38307036 CGCAAAAAAT
* * *
38307046 AAAAAACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTAGCGTTTTTGGTCTAGCGCCTCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGT-GCGTTTTTTGTCTAGCGCCACT
38307111 AATGGTCTGTGTTTTTAGC
65 AATGGTCTGTGTTTTTAGC
* *
38307130 AAAATACAACGGCGTCGTTTAGTGGCCTTCGATGGCCTTAGTGACGTTTTTTGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTG-CGTTTTTTGTCTAGCGCCACT
38307195 AATGGTCTGTGTTTTTAGC
65 AATGGTCTGTGTTTTTAGC
* *
38307214 AAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGGGTTTTTTGTCTAGCGCCAC
1 AAAAT-ACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGT-GCGTTTTTTGTCTAGCGCCAC
*
38307279 TAATGATCTGTGTTTTTAGC
64 TAATGGTCTGTGTTTTTAGC
38307299 GGCGTTTTAA
Statistics
Matches: 157, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
83 1 0.01
84 83 0.53
85 72 0.46
86 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (83 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGCGTTTTTTGTCTAGCGCCACTA
ATGGTCTGTGTTTTTAGC
Found at i:38307473 original size:84 final size:84
Alignment explanation
Indices: 38307328--38307495 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 84
38307318 CGCAAAAAAT
38307328 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
38307393 AATGGTCTATGTTTTTAGC
66 AATGGTCTATGTTTTTAGC
* * * * * *
38307412 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTTGCGCCGCT
1 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
*
38307477 AATGGTCTGTGTTTTTAGC
66 AATGGTCTATGTTTTTAGC
38307496 GGCATTTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (84 bp):
AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
AATGGTCTATGTTTTTAGC
Found at i:38307513 original size:198 final size:196
Alignment explanation
Indices: 38307130--38307598 Score: 713
Period size: 198 Copynumber: 2.4 Consensus size: 196
38307120 TGTTTTTAGC
*
38307130 AAAATACAACGGCGTCGTTTAGTGGCCTTCGATGGCCTTAGTGACGTTTTTTGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCG-TGGCC-TAGTGACGTTTTTGGTCTAGCGCCGCT
*
38307195 AATGGTCTGTGTTTTTAGCAAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGG
64 AATGGTCTGTGTTTTTAGCAAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGC
*
38307260 GTTTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCGTTTTAAAAAAAACGCCGCAAAA
129 GTTTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCATTTTAAAAAAAACGCCGCAAAA
38307325 AAT
194 AAT
*
38307328 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTC-GTGGCC-TAGTGACGTTTTTGGTCTAGCGCCGCT
* * *
38307393 AATGGTCTATGTTTTTAGCAAAAT-ACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGC
64 AATGGTCTGTGTTTTTAGCAAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGC
* * * *
38307457 GTTTTTTGTCTTGCGCCGCTAATGGTCTGTGTTTTTAGCGGCATTTTCAGAAAAAACGCCGCAAA
129 GTTTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCATTTT-AAAAAAAACGCCGCAAA
38307522 AAAT
193 AAAT
* *
38307526 AAAATACAACGGCATCGTTTAGTGG-C--C-T----TAGTGGCGTTTTTGGTCTAGCGCCGCTAA
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGTGGCCTAGTGACGTTTTTGGTCTAGCGCCGCTAA
38307583 TGGTCTGTGTTTTTAG
66 TGGTCTGTGTTTTTAG
38307599 TGGCGTTTTT
Statistics
Matches: 253, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
188 43 0.17
193 1 0.00
195 1 0.00
197 81 0.32
198 126 0.50
199 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (196 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGTGGCCTAGTGACGTTTTTGGTCTAGCGCCGCTAA
TGGTCTGTGTTTTTAGCAAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
TTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCATTTTAAAAAAAACGCCGCAAAAAA
T
Found at i:38307691 original size:113 final size:113
Alignment explanation
Indices: 38307412--38307888 Score: 481
Period size: 113 Copynumber: 4.3 Consensus size: 113
38307402 TGTTTTTAGC
* * * * * *
38307412 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTTGCGCCGCT
1 AAAATACAACGACGTCGTTTAGTGGCCTACGATGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* * * * *
38307477 AATGGTCTGTGTTTTTAGCGGCATTTTCAGAAAAAACGCCGCAAAAAAT
66 AATGGTCTGTGTTTTTAGTGGCGTTTTTAG-GAAAACGCCGTAAAAAAT
* *
38307526 AAAATACAACGGCATCG--T--T----TA-G-TGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGACGTCGTTTAGTGGCCTACGATGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
38307581 AATGGTCTGTGTTTTTAGTGGCGTTTTTAGGAAGAACGCCGTAAAAAAT
66 AATGGTCTGTGTTTTTAGTGGCGTTTTTAGGAA-AACGCCGTAAAAAAT
* * * *
38307630 AAAATATAGCGACGTCGTTTAGTGG-CTACGATGGCGTTAGTGGCTTTTTTGGTCT-GACGCCGC
1 AAAATACAACGACGTCGTTTAGTGGCCTACGATGGCCTTAGTGGCGTTTTTGGTCTAG-CGCCGC
* * * *
38307693 TAATGGTCTGTGTTTTTAGTGGCGTTTTCAGGATAAACACAGCAAAAAAT
65 TAATGGTCTGTGTTTTTAGTGGCGTTTTTAGGA-AAACGCCGTAAAAAAT
* * * * * *
38307743 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCCTAGTGGCGTTTTTGGTATAGCGCCGCT
1 AAAATACAACGACGTCGTTTAGTGGCCTACGATGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* * *
38307808 AATGGTCT-TTTTTTTAGCGGTGTTTTCT-GGAAAAACGCCGTAAAAAAT
66 AATGGTCTGTGTTTTTAGTGGCGTTTT-TAGG-AAAACGCCGTAAAAAAT
*
38307856 AAAAT------ACGTCGTTTAGTGGCCTTCGATGGCCTT
1 AAAATACAACGACGTCGTTTAGTGGCCTACGATGGCCTT
38307889 TTACCTTAAT
Statistics
Matches: 307, Mismatches: 40, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
103 2 0.01
104 85 0.28
105 1 0.00
106 2 0.01
107 25 0.08
108 1 0.00
110 1 0.00
111 2 0.01
112 3 0.01
113 128 0.42
114 56 0.18
115 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (113 bp):
AAAATACAACGACGTCGTTTAGTGGCCTACGATGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
AATGGTCTGTGTTTTTAGTGGCGTTTTTAGGAAAACGCCGTAAAAAAT
Found at i:38309083 original size:340 final size:332
Alignment explanation
Indices: 38308470--38309142 Score: 1109
Period size: 340 Copynumber: 2.0 Consensus size: 332
38308460 TTAATTAAGG
* *
38308470 GTTGGCCGGGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTTAGTGGTTAAGACTTAGGGATTTT
1 GTTGGCCGGGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTCAGTGGTTAAGACTTAGGGATTTA
*
38308535 GTGTTTAGGGTTTCAAGGGTCGGGTTACAGTTTTGGTTTAGATTAATTTTTTTATTTATATTTTA
66 GTGTTTAGGGTTTCAAGGGTCGGGTTACAATTTTGGTTTAGATTAATTTTTTTATTTATATTTTA
** *
38308600 AATATGTTCTTATGTAATTGTAAATTATGTATAATTTAGGGTTTAATTAATTATGCCTTGAGAGA
131 AATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAA-TAATTATGCCTTGAGAGA
* *
38308665 GAGAGATATAATAGATAGAGTACTTAAATATTTTTATCCCTTCAATGGTTAATTTAGGCGGGTTT
195 GAGAGATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTTAATTTAGGCGGGTTT
38308730 AATATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTAATGTTTAGGG
260 AATATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTAATGTTTAGGG
38308795 AATACTAT
325 AATACTAT
*
38308803 GTTGGCCGGGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTCAGTTGTTAAGACTTAGG
1 GTTGGCCGGGATTTAAGGTTT-----AGGGG-TTAGGGGTTAGATGTCAGTGGTTAAGACTTAGG
*
38308868 GATTTAAG-GTTTAGGGTTTCAAGGGTCTGGTTACAATTTTGGGTTTAGATTAATTTTTTTATTT
60 GATTT-AGTGTTTAGGGTTTCAAGGGTCGGGTTACAATTTT-GGTTTAGATTAATTTTTTTATTT
38308932 ATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTT-A-AATTATGCCT
123 ATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAATAATTATGCCT
*
38308995 TGAGAGAGAGATATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTTAATTTAGG
188 TGAGAGAGAGAGATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTTAATTTAGG
38309060 CGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTA
253 CGGGTTTAAT---ATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTA
*
38309125 ATGTTTAGGGAGTACTAT
315 ATGTTTAGGGAATACTAT
38309143 ATATATATGG
Statistics
Matches: 317, Mismatches: 12, Indels: 15
0.92 0.03 0.04
Matches are distributed among these distances:
333 21 0.07
337 82 0.26
338 5 0.02
339 67 0.21
340 142 0.45
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.42
Consensus pattern (332 bp):
GTTGGCCGGGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTCAGTGGTTAAGACTTAGGGATTTA
GTGTTTAGGGTTTCAAGGGTCGGGTTACAATTTTGGTTTAGATTAATTTTTTTATTTATATTTTA
AATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAATAATTATGCCTTGAGAGAG
AGAGATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTTAATTTAGGCGGGTTTA
ATATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTAATGTTTAGGGA
ATACTAT
Found at i:38309360 original size:28 final size:28
Alignment explanation
Indices: 38309329--38309383 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
38309319 AAATGAAATA
* *
38309329 AAAACGCTAAAATTTATAAATTTTAGTT
1 AAAACACTAAAAATTATAAATTTTAGTT
*
38309357 AAAACACTAAAAATTATAATTTTTAGT
1 AAAACACTAAAAATTATAAATTTTAGT
38309384 ACAATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAACACTAAAAATTATAAATTTTAGTT
Found at i:38310047 original size:28 final size:28
Alignment explanation
Indices: 38310015--38310071 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
38310005 AATAAAAAAA
*
38310015 TAAAAAT-GAAATAAAAACACTAAAATT
1 TAAAAATATAAATAAAAACACTAAAATT
* * *
38310042 TAAAAATATTAGTGAAAACACTAAAATT
1 TAAAAATATAAATAAAAACACTAAAATT
38310070 TA
1 TA
38310072 TAATTATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26
Consensus pattern (28 bp):
TAAAAATATAAATAAAAACACTAAAATT
Found at i:38310079 original size:28 final size:28
Alignment explanation
Indices: 38310028--38310082 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
38310018 AAATGAAATA
38310028 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
* *
38310056 AAAACACTAAAATTTATAATTATTAGT
1 AAAACACTAAAATTTAAAAATATTAGT
38310083 ACTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAACACTAAAATTTAAAAATATTAGTG
Found at i:38310768 original size:14 final size:14
Alignment explanation
Indices: 38310749--38310778 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38310739 ATAAAAGGTT
38310749 TTTAGTTAATCATC
1 TTTAGTTAATCATC
38310763 TTTAGTTAATCATC
1 TTTAGTTAATCATC
38310777 TT
1 TT
38310779 GTTGTTCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:38311527 original size:55 final size:55
Alignment explanation
Indices: 38311466--38311581 Score: 214
Period size: 55 Copynumber: 2.1 Consensus size: 55
38311456 TTAATATAAG
38311466 ATATTTTTAATATATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
1 ATATTTTTAATATATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
* *
38311521 ATATTTTTAATATATGCAATCTATATTTTTAATATATGGTATGGATATGTAACAT
1 ATATTTTTAATATATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
38311576 ATATTT
1 ATATTT
38311582 CAAATTTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (55 bp):
ATATTTTTAATATATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
Found at i:38311715 original size:32 final size:32
Alignment explanation
Indices: 38311653--38311715 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
38311643 AAACTGATAT
* *
38311653 ACTTACATAACTTATATAGAACTTATATAACA
1 ACTTACATAACTTACATAGAACATATATAACA
* *
38311685 ACTTGCATAACTTACATAATAACATA-ATAAC
1 ACTTACATAACTTACAT-AGAACATATATAAC
38311716 GTACATACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (32 bp):
ACTTACATAACTTACATAGAACATATATAACA
Found at i:38311819 original size:22 final size:22
Alignment explanation
Indices: 38311791--38311849 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
38311781 AACTTACGTA
38311791 ATACATAACTTACATTAATATT
1 ATACATAACTTACATTAATATT
38311813 ATACATAACTTACATTAATATT
1 ATACATAACTTACATTAATATT
38311835 ATACATAACTTACAT
1 ATACATAACTTACAT
38311850 AACTTAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (22 bp):
ATACATAACTTACATTAATATT
Found at i:38311850 original size:9 final size:9
Alignment explanation
Indices: 38311744--38312107 Score: 140
Period size: 9 Copynumber: 42.0 Consensus size: 9
38311734 ACGTAAATTG
*
38311744 CATAACTCA
1 CATAACTTA
38311753 CATAA--TA
1 CATAACTTA
*
38311760 CACAACTTA
1 CATAACTTA
*
38311769 CATAACTAA
1 CATAACTTA
*
38311778 AATAACTTA
1 CATAACTTA
*
38311787 CGTAA--TA
1 CATAACTTA
38311794 CATAACTTA
1 CATAACTTA
*
38311803 CATTAATATTATA
1 CA-T-A-ACT-TA
38311816 CATAACTTA
1 CATAACTTA
*
38311825 CATTAATATTATA
1 CA-T-A-ACT-TA
38311838 CATAACTTA
1 CATAACTTA
38311847 CATAACTTA
1 CATAACTTA
38311856 -ATTAA-TTA
1 CA-TAACTTA
*
38311864 -AT-ACTAAA
1 CATAACT-TA
*
38311872 CATAACTTGT
1 CATAACTT-A
* *
38311882 CA-GACTTG
1 CATAACTTA
38311890 CATAACTTA
1 CATAACTTA
38311899 CATAA--TA
1 CATAACTTA
*
38311906 CACAACTTA
1 CATAACTTA
38311915 CATAACTTA
1 CATAACTTA
38311924 -ATTAA-TTA
1 CA-TAACTTA
*
38311932 -AT-ACTAAA
1 CATAACT-TA
*
38311940 CATAACTTGT
1 CATAACTT-A
*
38311950 CA-GACTTA
1 CATAACTTA
38311958 CATAACTTA
1 CATAACTTA
38311967 CATAA--TA
1 CATAACTTA
*
38311974 CACAACTTA
1 CATAACTTA
38311983 CATAACTTA
1 CATAACTTA
38311992 CATAA--TA
1 CATAACTTA
*
38311999 CACAACTTA
1 CATAACTTA
*
38312008 TATAACTTA
1 CATAACTTA
* *
38312017 AAAAACTTA
1 CATAACTTA
38312026 CATAA--TA
1 CATAACTTA
*
38312033 CACAACTTTTA
1 CATAAC--TTA
* *
38312044 TATAACTTT
1 CATAACTTA
38312053 CATAACTTA
1 CATAACTTA
*
38312062 C-TTA--TA
1 CATAACTTA
38312068 -ATAACTTA
1 CATAACTTA
*
38312076 CACAACTTA
1 CATAACTTA
*
38312085 C-TTA--TA
1 CATAACTTA
38312091 -ATAACTTA
1 CATAACTTA
38312099 CATAACTTA
1 CATAACTTA
38312108 TTAATATTTA
Statistics
Matches: 262, Mismatches: 49, Indels: 88
0.66 0.12 0.22
Matches are distributed among these distances:
6 10 0.04
7 39 0.15
8 23 0.09
9 150 0.57
10 16 0.06
11 10 0.04
12 6 0.02
13 8 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:38311875 original size:34 final size:34
Alignment explanation
Indices: 38311826--38311947 Score: 117
Period size: 34 Copynumber: 3.6 Consensus size: 34
38311816 CATAACTTAC
* *
38311826 ATTAATATTATACATAACTTACATAACTTAATTA
1 ATTAATACTAAACATAACTTACATAACTTAATTA
* * *
38311860 ATTAATACTAAACATAACTTGTCA-GACTTGCA-TA
1 ATTAATACTAAACATAACTT-ACATAACTT-AATTA
* *
38311894 ACTTACATA--ATACACAACTTACATAACTTAATTA
1 A-TTA-ATACTAAACATAACTTACATAACTTAATTA
38311928 ATTAATACTAAACATAACTT
1 ATTAATACTAAACATAACTT
38311948 GTCAGACTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
32 3 0.04
33 6 0.09
34 50 0.74
35 6 0.09
36 3 0.04
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.35
Consensus pattern (34 bp):
ATTAATACTAAACATAACTTACATAACTTAATTA
Found at i:38311914 original size:68 final size:68
Alignment explanation
Indices: 38311835--38311991 Score: 296
Period size: 68 Copynumber: 2.3 Consensus size: 68
38311825 CATTAATATT
* *
38311835 ATACATAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTGCATAACTTAC
1 ATACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACATAACTTAC
38311900 ATA
66 ATA
38311903 ATACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACATAACTTAC
1 ATACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACATAACTTAC
38311968 ATA
66 ATA
38311971 ATACACAACTTACATAACTTA
1 ATACACAACTTACATAACTTA
38311992 CATAATACAC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 87 1.00
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (68 bp):
ATACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACATAACTTAC
ATA
Found at i:38311983 original size:25 final size:25
Alignment explanation
Indices: 38311953--38312016 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
38311943 AACTTGTCAG
38311953 ACTTACATAACTTACATAATACACA
1 ACTTACATAACTTACATAATACACA
38311978 ACTTACATAACTTACATAATACACA
1 ACTTACATAACTTACATAATACACA
*
38312003 ACTTATATAACTTA
1 ACTTACATAACTTA
38312017 AAAAACTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACACA
Found at i:38312025 original size:68 final size:68
Alignment explanation
Indices: 38311835--38312030 Score: 218
Period size: 68 Copynumber: 2.9 Consensus size: 68
38311825 CATTAATATT
* * *** * *
38311835 ATACATAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTGCATAACTTAC
1 ATACACAACTTACATAACTTAATTAATTAAAACTAAACATAACTTAAAAAACTTACATAACTTAC
38311900 ATA
66 ATA
* *** *
38311903 ATACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACATAACTTAC
1 ATACACAACTTACATAACTTAATTAATTAAAACTAAACATAACTTAAAAAACTTACATAACTTAC
38311968 ATA
66 ATA
* *
38311971 ATACACAACTTACATAACTTACA-TAA-TACACAACT-TATATAACTTAAAAAACTTACATAA
1 ATACACAACTTACATAACTTA-ATTAATTA-A-AACTAAACATAACTTAAAAAACTTACATAA
38312031 TACACAACTT
Statistics
Matches: 116, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
67 2 0.02
68 110 0.95
69 4 0.03
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.32
Consensus pattern (68 bp):
ATACACAACTTACATAACTTAATTAATTAAAACTAAACATAACTTAAAAAACTTACATAACTTAC
ATA
Found at i:38312082 original size:23 final size:23
Alignment explanation
Indices: 38312031--38312107 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
38312021 ACTTACATAA
38312031 TACACAACTT--TTAT-ATAACT
1 TACACAACTTACTTATAATAACT
* *
38312051 TTCATAACTTACTTATAATAACT
1 TACACAACTTACTTATAATAACT
38312074 TACACAACTTACTTATAATAACT
1 TACACAACTTACTTATAATAACT
*
38312097 TACATAACTTA
1 TACACAACTTA
38312108 TTAATATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.16
22 4 0.08
23 37 0.76
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (23 bp):
TACACAACTTACTTATAATAACT
Found at i:38318020 original size:21 final size:21
Alignment explanation
Indices: 38317994--38318064 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
38317984 CTACAACTTA
*
38317994 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
38318015 AAGCAGCGGCTGCAGCGAAGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
38318036 AAGCAGAGGTTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
38318057 AAGCAGAG
1 AAGCAGAG
38318065 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:38318449 original size:40 final size:42
Alignment explanation
Indices: 38318400--38318493 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
38318390 GCTAAAGAAC
*
38318400 AGAAA-AAACGCCGCTAAAGA-C-TGTTATTTAGCGGCGCTT
1 AGAAAGAAACGCCGCTAAAGACCATGTTATTTAGAGGCGCTT
* *
38318439 AGAAAGAAACGCCGCTAAAGACCATGTTCTTTAGAGGGGCTT
1 AGAAAGAAACGCCGCTAAAGACCATGTTATTTAGAGGCGCTT
*
38318481 AGAATGTAAACGC
1 AGAAAG-AAACGC
38318494 TGCAAACGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 5 0.11
40 15 0.32
41 1 0.02
42 20 0.43
43 6 0.13
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (42 bp):
AGAAAGAAACGCCGCTAAAGACCATGTTATTTAGAGGCGCTT
Found at i:38323689 original size:2 final size:2
Alignment explanation
Indices: 38323682--38323737 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
38323672 NNNNNNNNNN
38323682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38323724 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
38323738 CCTACTTGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38325904 original size:24 final size:22
Alignment explanation
Indices: 38325859--38325905 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
38325849 AATGGAAAAT
* *
38325859 AAGAATAAAAAAAGAAAGTTAA
1 AAGAATAAAAAAAAAAAATTAA
38325881 AAGAATATAAAAAATAAAAATTAA
1 AAGAATA-AAAAAA-AAAAATTAA
38325905 A
1 A
38325906 TTACTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAGAATAAAAAAAAAAAATTAA
Found at i:38328922 original size:6 final size:6
Alignment explanation
Indices: 38328913--38328947 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
38328903 TTTCCACTTC
38328913 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCT
38328948 AACATGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCCTT
Found at i:38335177 original size:16 final size:15
Alignment explanation
Indices: 38335143--38335178 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
38335133 TATTACAATT
38335143 TATAAATTTTTTATA
1 TATAAATTTTTTATA
38335158 -ATAAATTTTTTATA
1 TATAAATTTTTTATA
38335172 GTATAAA
1 -TATAAA
38335179 ATATGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.74
16 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TATAAATTTTTTATA
Found at i:38335391 original size:17 final size:18
Alignment explanation
Indices: 38335369--38335406 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
38335359 TTTATATATG
*
38335369 ATATTA-ATTATTGTAAA
1 ATATTATATTATTATAAA
*
38335386 ATATTATTTTATTATAAA
1 ATATTATATTATTATAAA
38335404 ATA
1 ATA
38335407 AATTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTATATTATTATAAA
Found at i:38340086 original size:17 final size:18
Alignment explanation
Indices: 38340050--38340087 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
38340040 TTGGGCCGTG
38340050 CACTAGTCTCTTCATAAA
1 CACTAGTCTCTTCATAAA
* *
38340068 CACTAGT-TTTTCTTAAA
1 CACTAGTCTCTTCATAAA
38340085 CAC
1 CAC
38340088 AAGCACTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (18 bp):
CACTAGTCTCTTCATAAA
Found at i:38340358 original size:40 final size:40
Alignment explanation
Indices: 38340304--38340382 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
38340294 TTTTCGTGAT
* * *
38340304 TTTTAGTTTTTATACTTTTTGAGTTTTAAAATTTTAATCA
1 TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATCA
38340344 TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATC
1 TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATC
38340383 TCAATCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.59
Consensus pattern (40 bp):
TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATCA
Found at i:38341790 original size:92 final size:93
Alignment explanation
Indices: 38341660--38341844 Score: 336
Period size: 92 Copynumber: 2.0 Consensus size: 93
38341650 AGCAATCCTT
38341660 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
38341725 TGTTGATTCATCTTTTTTATATTATTTC
66 TGTTGATTCATCTTTTTTATATTATTTC
* *
38341753 TTCTTCGCCTTTTTTTAC-TTTGTTAGGATTGAGCTCTGATTAGAGATTTTTTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
*
38341817 TGTTGATTCATCTTTTTTCTATTATTTC
66 TGTTGATTCATCTTTTTTATATTATTTC
38341845 CTGGCAGCTC
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 72 0.81
93 17 0.19
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (93 bp):
TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
TGTTGATTCATCTTTTTTATATTATTTC
Found at i:38346012 original size:5 final size:5
Alignment explanation
Indices: 38346002--38346026 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38345992 TCTTGATGGC
38346002 ATGCT ATGCT ATGCT ATGCT ATGCT
1 ATGCT ATGCT ATGCT ATGCT ATGCT
38346027 TCCATGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
ATGCT
Found at i:38346969 original size:21 final size:21
Alignment explanation
Indices: 38346944--38347000 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
38346934 GACATTACCT
38346944 AAAAAGAATTTACAAAAAAAA
1 AAAAAGAATTTACAAAAAAAA
* *
38346965 AAAAAGACTTTA-AAATAAAA
1 AAAAAGAATTTACAAAAAAAA
* *
38346985 TAAAATAATATTACAA
1 AAAAAGAAT-TTACAA
38347001 TGTAGACTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 13 0.45
21 14 0.48
22 2 0.07
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAGAATTTACAAAAAAAA
Found at i:38353464 original size:6 final size:6
Alignment explanation
Indices: 38353453--38353497 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
38353443 GGAAAATTTT
* * *
38353453 CCTTTC CCTTTC CCTTTC CCTTCC CCTTCC CCTTCC CCTTCC CCT
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCT
38353498 ATCCTTGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CCTTCC
Found at i:38356087 original size:32 final size:33
Alignment explanation
Indices: 38356051--38356137 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
38356041 AACTTTTCCG
* * *
38356051 GAAAATATTTT-CAGGAAATCTATCAAACAGCA
1 GAAAATATTTTACAGCAAATCAATCAAACACCA
*
38356083 GAAAATATTTTACA-CAGATTCAATCAAACACCA
1 GAAAATATTTTACAGCA-AATCAATCAAACACCA
* *
38356116 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTACAGCAAATCA
38356138 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 12 0.27
33 32 0.71
34 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCAATCAAACACCA
Found at i:38356135 original size:14 final size:15
Alignment explanation
Indices: 38356113--38356189 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38356103 CAATCAAACA
38356113 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
38356127 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
38356142 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
38356162 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
38356176 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
38356190 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:38356154 original size:20 final size:20
Alignment explanation
Indices: 38356129--38356168 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38356119 AATATTTTCC
*
38356129 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
38356149 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
38356169 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:38356174 original size:34 final size:35
Alignment explanation
Indices: 38356117--38356183 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38356107 CAAACACCAG
*
38356117 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38356152 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38356184 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38356190 original size:14 final size:14
Alignment explanation
Indices: 38356152--38356191 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38356142 ACAGAAAAGT
*
38356152 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
38356166 AAATCATTTTACGG
1 AAAACATTTTACAG
38356180 AAAACATTTTAC
1 AAAACATTTTAC
38356192 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:38358530 original size:29 final size:30
Alignment explanation
Indices: 38358471--38358528 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38358461 TCCGAGCCTT
*
38358471 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* * *
38358501 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
38358529 AGAGTTAAGG
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:38359129 original size:30 final size:30
Alignment explanation
Indices: 38359094--38359151 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38359084 CCTTGACTCT
*
38359094 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* * *
38359124 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTACCCC
38359152 AAGGCTCGGA
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:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:38366149 original size:17 final size:17
Alignment explanation
Indices: 38366127--38366159 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38366117 ATATTTTTTA
38366127 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
38366144 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
38366160 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:38366297 original size:127 final size:127
Alignment explanation
Indices: 38366155--38366387 Score: 423
Period size: 127 Copynumber: 1.8 Consensus size: 127
38366145 TTTTAATCAA
*
38366155 ATATATATTAAATATATATTTTTTTGGTGTTGTAAAATTTAATATGGG-CTGGGCCGAGCTGGGC
1 ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCT-GGCCGAGCTGGGC
*
38366219 TTGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGTGGGGCTCGGGCTTGGACAAAT
65 TCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGTGGGGCTCGGGCTTGGACAAAT
38366282 ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCTGGCCGAGCTGGGCT
1 ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCTGGCCGAGCTGGGCT
*
38366347 CGGGTTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGT
66 CGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGT
38366388 CGAGATCGAG
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
127 100 0.98
128 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.36
Consensus pattern (127 bp):
ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCTGGCCGAGCTGGGCT
CGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGTGGGGCTCGGGCTTGGACAAAT
Found at i:38368877 original size:2 final size:2
Alignment explanation
Indices: 38368872--38368902 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38368862 TAATATTTTT
38368872 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38368903 TTTTTTACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38375864 original size:24 final size:23
Alignment explanation
Indices: 38375822--38375877 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
38375812 TGATTTCCTT
*
38375822 CAACGGTCAAATTTCAAATCCGAC
1 CAACGGTAAAATTTCAAAT-CGAC
* *
38375846 CAACGGTAAAATTAT-AAATGGCC
1 CAACGGTAAAATT-TCAAATCGAC
38375869 CAACGGTAA
1 CAACGGTAA
38375878 CTTTTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.39
24 16 0.57
25 1 0.04
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (23 bp):
CAACGGTAAAATTTCAAATCGAC
Found at i:38379949 original size:2 final size:2
Alignment explanation
Indices: 38379942--38379970 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38379932 ATTTATCATG
38379942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38379971 GCATATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38380196 original size:2 final size:2
Alignment explanation
Indices: 38380142--38380185 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
38380132 TCTTATACTT
38380142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38380184 TA
1 TA
38380186 CACTTATATA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38381939 original size:97 final size:97
Alignment explanation
Indices: 38381773--38381967 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 97
38381763 CTTCATAAGT
38381773 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
1 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
* *
38381838 ATAGGTTGTAATGTAGCTTGGCTAGGGGTAGG
66 ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
* *
38381870 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCATCATAGAAATTTGAATCAATAGGTATTTTAA
1 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
38381935 ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
66 ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
38381967 T
1 T
38381968 AAAAGATAGA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (97 bp):
TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
Found at i:38403817 original size:6 final size:6
Alignment explanation
Indices: 38403808--38403832 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38403798 AAAAATAAAA
38403808 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
38403833 TGAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:38404302 original size:28 final size:28
Alignment explanation
Indices: 38404249--38404302 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
38404239 AAATTAAAAA
* * *
38404249 AAAAATTACTAGATTAGGCTATTTTTTC
1 AAAAATTACGAGACTAGGCTAATTTTTC
38404277 AAAAATTACGAGACTAGG-TCAATTTT
1 AAAAATTACGAGACTAGGCT-AATTTT
38404303 AGGAAAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.05
28 21 0.95
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
AAAAATTACGAGACTAGGCTAATTTTTC
Found at i:38404366 original size:20 final size:19
Alignment explanation
Indices: 38404341--38404378 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
38404331 TTCGTGTCCA
38404341 TTTTTTAAAAGTTAGGGTTT
1 TTTTTTAAAAG-TAGGGTTT
*
38404361 TTTTTTTAAAGTAGGGTT
1 TTTTTTAAAAGTAGGGTT
38404379 AGGAAAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (19 bp):
TTTTTTAAAAGTAGGGTTT
Found at i:38406596 original size:9 final size:9
Alignment explanation
Indices: 38406542--38406600 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
38406532 TTTGGTTAAA
*
38406542 AATTACCTG
1 AATTACCCG
38406551 AATTACCCG
1 AATTACCCG
*
38406560 AATTAACCG
1 AATTACCCG
38406569 AATTA-CCG
1 AATTACCCG
*
38406577 AAAAATACCCG
1 --AATTACCCG
38406588 AATTACCCG
1 AATTACCCG
38406597 AATT
1 AATT
38406601 TTTTTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:38406707 original size:40 final size:40
Alignment explanation
Indices: 38406662--38406751 Score: 171
Period size: 40 Copynumber: 2.2 Consensus size: 40
38406652 GACTTTAGTA
38406662 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
*
38406702 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGGTTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
38406742 AATTGGGTTG
1 AATTGGGTTG
38406752 GGTAATTGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.14, C:0.02, G:0.30, T:0.53
Consensus pattern (40 bp):
AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
Found at i:38406748 original size:13 final size:13
Alignment explanation
Indices: 38406730--38406759 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38406720 TTTTAGTTTT
38406730 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
38406743 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
38406756 ATTG
1 ATTG
38406760 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:38407885 original size:2 final size:2
Alignment explanation
Indices: 38407875--38407907 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
38407865 TACTACATTG
38407875 AT AT CAT 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
38407908 TCTATGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38408831 original size:14 final size:15
Alignment explanation
Indices: 38408812--38408840 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38408802 AAAAGAAAAA
38408812 AATTTAATAT-TTTT
1 AATTTAATATATTTT
38408826 AATTTAATATATTTT
1 AATTTAATATATTTT
38408841 TTCATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTAATATATTTT
Found at i:38409192 original size:16 final size:17
Alignment explanation
Indices: 38409161--38409205 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
38409151 CCGATATAAT
* * *
38409161 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
38409178 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
38409194 AAATATTTTTAA
1 AAATATTTTTAA
38409206 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:38409203 original size:11 final size:11
Alignment explanation
Indices: 38409189--38409256 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
38409179 AATTTTTTAA
38409189 TTTTAAAATAT
1 TTTTAAAATAT
38409200 TTTTAAAATACT
1 TTTTAAAATA-T
** *
38409212 TTTTTTATTAT
1 TTTTAAAATAT
*
38409223 TTTT----TAA
1 TTTTAAAATAT
38409230 TTTTAAAATAT
1 TTTTAAAATAT
38409241 TTTTAAAATACT
1 TTTTAAAATA-T
38409253 TTTT
1 TTTT
38409257 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
7 6 0.13
11 27 0.59
12 13 0.28
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:38409225 original size:41 final size:40
Alignment explanation
Indices: 38409172--38409265 Score: 163
Period size: 41 Copynumber: 2.4 Consensus size: 40
38409162 AATATATTTA
38409172 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATACT
*
38409212 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTA-AATTTTTTAATTTTAAAATATTTTTAAAATACT
38409253 TTTTTT-AATTTTT
1 TTTTTTAAATTTTT
38409266 AAAATAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 6 0.12
40 7 0.14
41 38 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:38409234 original size:30 final size:31
Alignment explanation
Indices: 38409198--38409271 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
38409188 ATTTTAAAAT
** *
38409198 ATTTTTAAAATACTTTTTTTATTA-TTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTTA
38409229 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATAC-TTTTTTA
38409260 ATTTTTAAAATA
1 ATTTTTAAAATA
38409272 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 8 0.22
30 10 0.27
31 9 0.24
32 10 0.27
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:38409277 original size:21 final size:21
Alignment explanation
Indices: 38409239--38409278 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38409229 ATTTTAAAAT
**
38409239 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
38409260 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
38409279 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:38409285 original size:22 final size:20
Alignment explanation
Indices: 38409238--38409292 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
38409228 AATTTTAAAA
* *
38409238 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
38409258 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
38409281 TATTTATTAAAA
1 TATTT-TTAAAA
38409293 AAGGGCCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:38409359 original size:13 final size:13
Alignment explanation
Indices: 38409341--38409365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38409331 GGCCTGAGCA
38409341 AAATTTTAGGCCC
1 AAATTTTAGGCCC
38409354 AAATTTTAGGCC
1 AAATTTTAGGCC
38409366 AGGCCAAAAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
AAATTTTAGGCCC
Found at i:38409673 original size:30 final size:31
Alignment explanation
Indices: 38409639--38409698 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
38409629 AAACCTTTTA
*
38409639 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
38409669 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
38409699 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:38415156 original size:13 final size:13
Alignment explanation
Indices: 38415138--38415177 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
38415128 AGTTCTTTAT
38415138 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
38415151 TACTTTTTAGAAG
1 TACTTTTGAAAAG
*
38415164 TATTTTTGAAAAG
1 TACTTTTGAAAAG
38415177 T
1 T
38415178 TTGATTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:38416765 original size:19 final size:21
Alignment explanation
Indices: 38416719--38416768 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
38416709 GGGCTTGAAT
*
38416719 AATATTATTTTATA-AATTATA
1 AATA-TATTTTAAATAATTATA
*
38416740 AATATATTTTAAATAATTAAA
1 AATATATTTTAAATAATTATA
38416761 AATATATT
1 AATATATT
38416769 AAATTAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATATTTTAAATAATTATA
Found at i:38416770 original size:19 final size:21
Alignment explanation
Indices: 38416733--38416772 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
38416723 TTATTTTATA
*
38416733 AATTATAAATATATTTTAAAT
1 AATTATAAATATATATTAAAT
38416754 AATTA-AAA-ATATATTAAAT
1 AATTATAAATATATATTAAAT
38416773 TAAATCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATAAATATATATTAAAT
Found at i:38424946 original size:17 final size:18
Alignment explanation
Indices: 38424924--38424961 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
38424914 AATTTATATG
*
38424924 TATATG-AAGAATATTAT
1 TATATGAAAAAATATTAT
38424941 TATATGTAAAAAATATTAT
1 TATATG-AAAAAATATTAT
38424960 TA
1 TA
38424962 CGTAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
TATATGAAAAAATATTAT
Found at i:38426974 original size:133 final size:133
Alignment explanation
Indices: 38426717--38426977 Score: 316
Period size: 133 Copynumber: 2.0 Consensus size: 133
38426707 ATCACACTAA
* *
38426717 TGGTCTTTTATGCATCTAGACATCCACAATATGCAAAATGCATGTATTACAACACTTCCTTTTGG
1 TGGTCTTTTATGCATCTAGACATCCACAACATGCAAAATGCATGTATTACAACACTTCCCTTTGG
* * * * * * *
38426782 ATGACTATTTACTATGAATGTATTTCATTAAAACTTTGTGATAAAAAACCCGATGAGATAAAAGC
66 ATGACTATTTACTATAAATGTACTTCACTAAAACCTTGTCATAAAAAACCCAATAAGATAAAAGC
38426847 TAT
131 TAT
* * *
38426850 TGGTCTTTTATGTATCTAGCCATCTACAACATGCAAAATGCATGTATTACAACACTTTCCCTTT-
1 TGGTCTTTTATGCATCTAGACATCCACAACATGCAAAATGCATGTATTACAACAC-TTCCCTTTG
**
38426914 GATGACTATTCT-CTATAAACATGT-CTT-ACTAAAACCTTGTCA-AGAAAAATTCAATAAGATA
65 GATGACTATT-TACTAT-AA-ATGTACTTCACTAAAACCTTGTCATA-AAAAACCCAATAAGATA
38426975 AAA
126 AAA
38426978 ACTTAGTAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
132 1 0.01
133 93 0.85
134 11 0.10
135 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (133 bp):
TGGTCTTTTATGCATCTAGACATCCACAACATGCAAAATGCATGTATTACAACACTTCCCTTTGG
ATGACTATTTACTATAAATGTACTTCACTAAAACCTTGTCATAAAAAACCCAATAAGATAAAAGC
TAT
Found at i:38427096 original size:26 final size:24
Alignment explanation
Indices: 38427046--38427096 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
38427036 ACAGAAAATG
*
38427046 ATAAAATATTTTTTATTAGATCAA
1 ATAAAATATTTTTTATTAGACCAA
*
38427070 ATAAAATTATTTTTTGATTGGACCAA
1 ATAAAA-TATTTTTT-ATTAGACCAA
38427096 A
1 A
38427097 GATTACACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 8 0.35
26 9 0.39
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (24 bp):
ATAAAATATTTTTTATTAGACCAA
Found at i:38427787 original size:14 final size:15
Alignment explanation
Indices: 38427765--38427841 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38427755 CAATCAAACA
38427765 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
38427779 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
38427794 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
38427814 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
38427828 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
38427842 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:38427806 original size:20 final size:20
Alignment explanation
Indices: 38427781--38427820 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38427771 AATATTTTCC
*
38427781 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
38427801 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
38427821 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:38427826 original size:34 final size:35
Alignment explanation
Indices: 38427769--38427835 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38427759 CAAACACCAG
*
38427769 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38427804 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38427836 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38440980 original size:18 final size:18
Alignment explanation
Indices: 38440959--38440994 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
38440949 GAGAATTTAT
38440959 TCTACAGTGAGAAGGTGA
1 TCTACAGTGAGAAGGTGA
38440977 TCTACAGTGAGAAGGTGA
1 TCTACAGTGAGAAGGTGA
38440995 GAATGCCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (18 bp):
TCTACAGTGAGAAGGTGA
Found at i:38443905 original size:16 final size:17
Alignment explanation
Indices: 38443872--38443906 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38443862 TGAATTTCTT
38443872 TTCAATTTATACCCTAA
1 TTCAATTTATACCCTAA
*
38443889 TTCAATTTA-ATCCTAA
1 TTCAATTTATACCCTAA
38443905 TT
1 TT
38443907 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (17 bp):
TTCAATTTATACCCTAA
Found at i:38444634 original size:19 final size:19
Alignment explanation
Indices: 38444597--38444635 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
38444587 ATAGAAAACC
* *
38444597 ATAATAATAATTAATAATT
1 ATAATAATAATAAAAAATT
*
38444616 ATAATTATAATAAAAAATT
1 ATAATAATAATAAAAAATT
38444635 A
1 A
38444636 ATAACAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATAATAATAAAAAATT
Found at i:38452714 original size:19 final size:17
Alignment explanation
Indices: 38452674--38452707 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38452664 TAAAAACTTG
*
38452674 TAAAAGTTATAATAATA
1 TAAAAGTTATAAGAATA
38452691 TAAAAGTTATATAGAAT
1 TAAAAGTTATA-AGAAT
38452708 TTTAAAAATC
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:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
TAAAAGTTATAAGAATA
Found at i:38457709 original size:25 final size:25
Alignment explanation
Indices: 38457672--38457722 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
38457662 ATAATTGTAG
38457672 TTTTTTTAACCAATGATT-TAAATATTA
1 TTTTTTT-ACCAA-G-TTCTAAATATTA
38457699 TTTTTTT-CCAAGTTCTAAATATTA
1 TTTTTTTACCAAGTTCTAAATATTA
38457723 AATAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.09
24 10 0.43
25 4 0.17
27 7 0.30
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTTTTACCAAGTTCTAAATATTA
Found at i:38457873 original size:15 final size:15
Alignment explanation
Indices: 38457844--38457877 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38457834 ATGATTTTAA
38457844 TTAATTATTTAATTT
1 TTAATTATTTAATTT
38457859 TTAA-TATTTATATTT
1 TTAATTATTTA-ATTT
38457874 TTAA
1 TTAA
38457878 GAAGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATTATTTAATTT
Found at i:38469905 original size:80 final size:80
Alignment explanation
Indices: 38469772--38469934 Score: 256
Period size: 80 Copynumber: 2.0 Consensus size: 80
38469762 ATAAAATATG
* * * *
38469772 TTGGTGTGATCAGGGTGAGATGCTTGAACATATTCTTTTATATTGTCCGAATGTTAAGCCACTTT
1 TTGGTATGATCAGGCTGAGATGCTTGAACATATTCTTTTATATTGTCAGAATGTTAAGCCACTTC
38469837 GG-GCTTCTATACATA
66 GGCG-TTCTATACATA
* *
38469852 TTGGTATGATCAGGCTGAGATGCTTGACCATATTCTTTTATATTGTCAGAATGTTGAGCCACTTC
1 TTGGTATGATCAGGCTGAGATGCTTGAACATATTCTTTTATATTGTCAGAATGTTAAGCCACTTC
38469917 GGCGTTCTATACATA
66 GGCGTTCTATACATA
38469932 TTG
1 TTG
38469935 ATGCTCTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
80 75 0.99
81 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (80 bp):
TTGGTATGATCAGGCTGAGATGCTTGAACATATTCTTTTATATTGTCAGAATGTTAAGCCACTTC
GGCGTTCTATACATA
Found at i:38470155 original size:29 final size:30
Alignment explanation
Indices: 38470098--38470154 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
38470088 ATAAATACAT
38470098 AAATATAAATAAATATTTATATATAAAATA
1 AAATATAAATAAATATTTATATATAAAATA
*
38470128 AAATA-AAATAAATAATTTATATTTAAA
1 AAATATAAATAAAT-ATTTATATATAAA
38470155 TTATCAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
AAATATAAATAAATATTTATATATAAAATA
Found at i:38490147 original size:6 final size:6
Alignment explanation
Indices: 38490136--38490165 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
38490126 TGAGTAACAT
38490136 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
1 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
38490166 GAAAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
AGGCAA
Found at i:38497651 original size:101 final size:101
Alignment explanation
Indices: 38497471--38497679 Score: 265
Period size: 101 Copynumber: 2.1 Consensus size: 101
38497461 GGATAAGAGT
* * * * * *
38497471 ATGGTTGAACCATGACAATGTTTATATGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAA
1 ATGGTTGAACCATGACAATATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTAATGAAAAA
* ** *
38497536 ACCACAACTAGGTTATGGCACTTTGAATGTAAGATC
66 ACCACAACTAGGTTATGACACTACGAATGTAAGACC
* * * *
38497572 ATGGTTGAACCATGACAGTATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTGATGATAAG
1 ATGGTTGAACCATGACAATATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTAATGAAAAA
* *
38497637 ACCATAACTGGGTTATGACACTACGAATGTAAGACC
66 ACCACAACTAGGTTATGACACTACGAATGTAAGACC
*
38497673 ATCGTTG
1 ATGGTTG
38497680 GGCCATGGCA
Statistics
Matches: 91, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 91 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (101 bp):
ATGGTTGAACCATGACAATATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTAATGAAAAA
ACCACAACTAGGTTATGACACTACGAATGTAAGACC
Found at i:38505527 original size:49 final size:48
Alignment explanation
Indices: 38505395--38505547 Score: 161
Period size: 49 Copynumber: 3.1 Consensus size: 48
38505385 GCACGAACTA
* * ***
38505395 TTTTCTTTCTCAGTATTTTCTTTGTTTGAAAACCCCAAATTCATTTCTCC
1 TTTTCTTTCTCAGTCTTTTCTTTG-TTGAAAACCCCAAAATCCCGTC-CC
*
38505445 -TTTCTTTC-CTAGAC-TTTCTTTGCTTG-AAACCCCAAAATCCCGTCCC
1 TTTTCTTTCTC-AGTCTTTTCTTTG-TTGAAAACCCCAAAATCCCGTCCC
*
38505491 TTTTCTTTCTCAGTCTTTTCGTTGTTGGAAAACCCCAAAATCCCGTCCC
1 TTTTCTTTCTCAGTCTTTTCTTTGTT-GAAAACCCCAAAATCCCGTCCC
38505540 TTGTTCTT
1 TT-TTCTT
38505548 CTATTTTAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
46 2 0.02
47 27 0.31
48 21 0.24
49 32 0.37
50 5 0.06
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (48 bp):
TTTTCTTTCTCAGTCTTTTCTTTGTTGAAAACCCCAAAATCCCGTCCC
Found at i:38507533 original size:43 final size:43
Alignment explanation
Indices: 38507470--38507619 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 43
38507460 ATCACTTGAT
* ** * * *
38507470 TTTGTGGGGAAAGCATCGCTAAATGTTATGTTCTTTAGCGGCT
1 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
*
38507513 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTATTTAGCGGCG
1 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
* * * * * * * * *
38507556 TTTGTAAGAAAAGTGTCACCAGAGGTCATGCTCTTTAGCGGCG
1 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
38507599 TTTGT-GGGAAAAGCGCCGCTA
1 TTTGTAGGG-AAAGCGCCGCTA
38507620 TAGAACCGCT
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 1 0.01
43 82 0.99
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
Found at i:38509721 original size:19 final size:18
Alignment explanation
Indices: 38509677--38509721 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
38509667 ATTACTCCTG
38509677 CTTAGCTTTTCCTTATCA
1 CTTAGCTTTTCCTTATCA
38509695 CTTGAGCTTCTTCCTTATCA
1 CTT-AGCTT-TTCCTTATCA
*
38509715 GTTAGCT
1 CTTAGCT
38509722 AAACATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.47
Consensus pattern (18 bp):
CTTAGCTTTTCCTTATCA
Found at i:38511780 original size:21 final size:21
Alignment explanation
Indices: 38511717--38511865 Score: 97
Period size: 21 Copynumber: 7.1 Consensus size: 21
38511707 TAGAAGGCTG
* *
38511717 AACAGAAGCTCATTAGAGTTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
38511738 AACAAAACCT-ATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* *
38511758 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
38511779 AACGGAAACCCATAA-AGGTTA
1 AACAGAAGCTCATAAGA-GCTA
*
38511800 AACAGAAGTTCA-ATAGAGCTA
1 AACAGAAGCTCATA-AGAGCTA
* * *
38511821 AACAGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
*
38511842 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
38511863 AAC
1 AAC
38511866 GGAAAGTAAA
Statistics
Matches: 94, Mismatches: 29, Indels: 10
0.71 0.22 0.08
Matches are distributed among these distances:
20 17 0.18
21 75 0.80
22 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:38511805 original size:42 final size:42
Alignment explanation
Indices: 38511717--38511870 Score: 152
Period size: 42 Copynumber: 3.7 Consensus size: 42
38511707 TAGAAGGCTG
* * * * * * *
38511717 AACAGAAGCTCATTAGAGTTAAAC-AAAACCTATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAACGGAAACCCATAAAGGTTA
*
38511758 AACAGAAGCTCGTAAGAGCTGAACGGAAACCCATAAAGGTTA
1 AACAGAAGCTCGTAAGAGCTAAACGGAAACCCATAAAGGTTA
* * * * *
38511800 AACAGAAGTTC-AATAGAGCTAAACAGAAACTCAT-ATGAGTTA
1 AACAGAAGCTCGTA-AGAGCTAAACGGAAACCCATAAAG-GTTA
38511842 AACAGAAGCTCGTAAGAGCTAAACGGAAA
1 AACAGAAGCTCGTAAGAGCTAAACGGAAA
38511871 GTAAACACAA
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 23 0.25
42 68 0.74
43 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAACGGAAACCCATAAAGGTTA
Found at i:38511860 original size:84 final size:83
Alignment explanation
Indices: 38511717--38511870 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 83
38511707 TAGAAGGCTG
* * * * *
38511717 AACAGAAGCTCATTAGAGTTAAACAAAACCTATAAGGGTTGAACAGAAGCTCGTAAGAGCTGAAC
1 AACAGAAGCTCAATAGAGCTAAACAAAACCTATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
38511782 GGAAACCCATAAAGGTTA
66 GGAAACCCATAAAGGTTA
* *
38511800 AACAGAAGTTCAATAGAGCTAAACAGAAA-CTCATATGAGTTAAACAGAAGCTCGTAAGAGCTAA
1 AACAGAAGCTCAATAGAGCTAAACA-AAACCT-ATAAGAGTTAAACAGAAGCTCGTAAGAGCTAA
38511864 ACGGAAA
64 ACGGAAA
38511871 GTAAACACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
83 24 0.39
84 38 0.61
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (83 bp):
AACAGAAGCTCAATAGAGCTAAACAAAACCTATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
GGAAACCCATAAAGGTTA
Found at i:38513512 original size:46 final size:46
Alignment explanation
Indices: 38513416--38513675 Score: 217
Period size: 46 Copynumber: 5.8 Consensus size: 46
38513406 TACGTATGAT
*
38513416 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
38513459 CACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*** * ** *
38513505 CACTTATCACTTTGTCACCGCTT-ATCACTTG-TTCTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCA---CTTGATCA---GATAAGTG-T-AGCTAAGGCTAC
*
38513557 CACTTATCACTTTTTCACTTGATCAGATAA--GT-G-T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
38513593 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
38513639 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
38513676 ACTTATCACT
Statistics
Matches: 178, Mismatches: 16, Indels: 43
0.75 0.07 0.18
Matches are distributed among these distances:
36 30 0.17
38 2 0.01
39 1 0.01
40 1 0.01
41 2 0.01
42 2 0.01
43 11 0.06
44 5 0.03
45 20 0.11
46 60 0.34
47 1 0.01
48 4 0.02
49 6 0.03
50 7 0.04
51 2 0.01
52 24 0.13
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:38513583 original size:36 final size:36
Alignment explanation
Indices: 38513525--38513701 Score: 205
Period size: 36 Copynumber: 4.7 Consensus size: 36
38513515 TTTGTCACCG
*
38513525 CTTATCACTTGTT--CTTGATCAGATAAGTATAGCA
1 CTTATCACTTTTTCACTTGATCAGATAAGTATAGCA
*
38513559 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCA
1 CTTATCACTTTTTCACTTGATCAGATAAGTATAGCA
38513595 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTGCCA
1 CTTATCACTTTTTCACTTGATCAGATAA--GTA--T--A---G-CA
* * *
38513641 CTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
1 CTTATCACTTTTTCACTTGATCAGATAAGTATAGCA
38513677 CTTATCACTTTTTCACTTGATCAGA
1 CTTATCACTTTTTCACTTGATCAGA
38513702 AGTACTCAAA
Statistics
Matches: 123, Mismatches: 8, Indels: 22
0.80 0.05 0.14
Matches are distributed among these distances:
34 12 0.10
36 73 0.59
37 1 0.01
38 2 0.02
40 2 0.02
42 2 0.02
44 2 0.02
45 1 0.01
46 28 0.23
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
CTTATCACTTTTTCACTTGATCAGATAAGTATAGCA
Found at i:38517788 original size:9 final size:8
Alignment explanation
Indices: 38517767--38517798 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
38517757 ATAATTTTAG
38517767 TTTAAAAT
1 TTTAAAAT
38517775 TTTAAAATT
1 TTTAAAA-T
38517784 TTTAAAAT
1 TTTAAAAT
38517792 TTTAAAA
1 TTTAAAA
38517799 AGTTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:38524999 original size:15 final size:16
Alignment explanation
Indices: 38524974--38525003 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38524964 AAAATATAAT
38524974 TTTATTATTTTTATAG
1 TTTATTATTTTTATAG
38524990 TTTA-TATTTTTATA
1 TTTATTATTTTTATA
38525004 ATTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTATTATTTTTATAG
Found at i:38525048 original size:53 final size:55
Alignment explanation
Indices: 38524944--38525048 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 55
38524934 CGAAATTAAA
* * *
38524944 TTATAATTTTTACAATAATAAAAATATAATTTTATTATTTTTATAGTTTATATTT
1 TTATAATTTTTACAAAAATAAAAATATAATTTTATTATTTTTAGAGGTTATATTT
* * *
38524999 TTATAATTTTTA-AAAAAT-TAAAT-TAATTTTTTATATTTTTAGGGGTTATA
1 TTATAATTTTTACAAAAATAAAAATATAATTTTAT-TATTTTTAGAGGTTATA
38525049 ATGTAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
52 8 0.19
53 18 0.42
54 5 0.12
55 12 0.28
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (55 bp):
TTATAATTTTTACAAAAATAAAAATATAATTTTATTATTTTTAGAGGTTATATTT
Found at i:38525086 original size:17 final size:19
Alignment explanation
Indices: 38525064--38525107 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
38525054 ATTTTACTTT
*
38525064 AAAATTTTAAAATA-TT-A
1 AAAATTTTAAAAAATTTAA
38525081 AAAATTTTAAAAAATTTAA
1 AAAATTTTAAAAAATTTAA
38525100 AAAATTTT
1 AAAATTTT
38525108 TCCATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTTAAAAAATTTAA
Done.