Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 314 of 444
Found at i:90539112 original size:2 final size:2
Alignment explanation
Indices: 90539105--90539133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
90539095 ATAAACAAAA
90539105 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
90539134 AGATTACTTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:90543469 original size:15 final size:16
Alignment explanation
Indices: 90543449--90543478 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
90543439 TCTCAATACA
90543449 AATATA-TTCATAATC
1 AATATATTTCATAATC
90543464 AATATATTTCATAAT
1 AATATATTTCATAAT
90543479 ATACAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATTTCATAATC
Found at i:90543912 original size:30 final size:30
Alignment explanation
Indices: 90543873--90543932 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
90543863 ATTTAACTTC
*
90543873 TTTTCCAATTT-GACCCTTTAATTTCAAAAT
1 TTTTACAATTTAGACCCTTTAA-TTCAAAAT
* *
90543903 TTTTACAATTTAGTCCCTTTTATTCAAAAT
1 TTTTACAATTTAGACCCTTTAATTCAAAAT
90543933 CAACAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTACAATTTAGACCCTTTAATTCAAAAT
Found at i:90544210 original size:21 final size:22
Alignment explanation
Indices: 90544176--90544225 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
90544166 AGCCGTGCAC
*
90544176 TTCTTCTCCTTTTTCCTTTTC-T
1 TTCTT-TCATTTTTCCTTTTCTT
*
90544198 TTCTTTCATTTTTTCTTTTCTT
1 TTCTTTCATTTTTCCTTTTCTT
90544220 TTCTTT
1 TTCTTT
90544226 GTTTAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTCATTTTTCCTTTTCTT
Found at i:90544271 original size:3 final size:3
Alignment explanation
Indices: 90544265--90544305 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
90544255 TTTTTTTTCT
90544265 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
90544306 GTCGAAACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:90546094 original size:15 final size:15
Alignment explanation
Indices: 90546073--90546127 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
90546063 TTTTTTTTTG
90546073 TTTTTTTTGCTGAAAA
1 TTTTTTTTGCTG-AAA
90546089 TTTTTTTT--TGAAA
1 TTTTTTTTGCTGAAA
*
90546102 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGAAA
90546117 TTTTTTTTGCT
1 TTTTTTTTGCT
90546128 CTTTTTTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
13 11 0.31
14 2 0.06
15 15 0.42
16 8 0.22
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.65
Consensus pattern (15 bp):
TTTTTTTTGCTGAAA
Found at i:90546123 original size:14 final size:14
Alignment explanation
Indices: 90546074--90546123 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
90546064 TTTTTTTTGT
90546074 TTTTTTTGCTGAAAA
1 TTTTTTTGCTG-AAA
*
90546089 TTTTTTT-TTGAAA
1 TTTTTTTGCTGAAA
*
90546102 TTTTTTTTGCTGGAA
1 -TTTTTTTGCTGAAA
90546117 TTTTTTT
1 TTTTTTT
90546124 TGCTCTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 3 0.10
14 16 0.53
15 11 0.37
ACGTcount: A:0.18, C:0.04, G:0.12, T:0.66
Consensus pattern (14 bp):
TTTTTTTGCTGAAA
Found at i:90546386 original size:29 final size:29
Alignment explanation
Indices: 90546336--90546422 Score: 72
Period size: 30 Copynumber: 3.0 Consensus size: 29
90546326 AAACTTCTGG
*
90546336 GGTTAAATGTAACTTTTAGAAAATTTA-A
1 GGTTAAATGTAACTTTAAGAAAATTTAGA
*
90546364 GGTTAAAATGTAA-TTTAAGGAAAGTTTAGA
1 GGTT-AAATGTAACTTTAA-GAAAATTTAGA
* * *
90546394 GGTCTAAGTG-AAATTTAAAGAAAGTTTAG
1 GGT-TAAATGTAACTTT-AAGAAAATTTAG
90546423 GGGTCAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
28 8 0.16
29 18 0.36
30 21 0.42
31 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (29 bp):
GGTTAAATGTAACTTTAAGAAAATTTAGA
Found at i:90546439 original size:30 final size:30
Alignment explanation
Indices: 90546353--90546439 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
90546343 TGTAACTTTT
* * *
90546353 AGAAAATTTA-AGGTTAAAATGTAATTTAA
1 AGAAAGTTTAGAGGTCAAAATGAAATTTAA
* * *
90546382 GGAAAGTTTAGAGGTCTAAGTGAAATTTAA
1 AGAAAGTTTAGAGGTCAAAATGAAATTTAA
* *
90546412 AGAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAGTTTAGAGGTCAAAATGAAATTT
90546440 TTTTATTAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 8 0.17
30 38 0.83
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
AGAAAGTTTAGAGGTCAAAATGAAATTTAA
Found at i:90546929 original size:14 final size:14
Alignment explanation
Indices: 90546906--90546940 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
90546896 TGAGTTGATT
90546906 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
90546919 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
90546933 TTTGAAAA
1 TTTGAAAA
90546941 TACATCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:90546938 original size:88 final size:88
Alignment explanation
Indices: 90546835--90546996 Score: 220
Period size: 88 Copynumber: 1.8 Consensus size: 88
90546825 ATTTAAAAAA
* *
90546835 AAAAACAGAAATTGAAAATAGC-TC-AGCACGTAAGCCAAGGCTCAACTCACTTCTCGCAATATG
1 AAAAACAGAAATTGAAAATA-CATCGA-CACGTAACCCAAGGCTCAACTCACATCTCGCAATATG
90546898 AGTTGATTTTTGAAAACAGAATTTG
64 AGTTGATTTTTGAAAACAGAATTTG
** * * * *
90546923 AAAAACAGATTTTGAAAATACATCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGAAATTGAAAATACATCGACACGTAACCCAAGGCTCAACTCACATCTCGCAATATGAG
90546988 TTGATTTTT
66 TTGATTTTT
90546997 TTGAAAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 1 0.02
88 62 0.97
89 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACATCGACACGTAACCCAAGGCTCAACTCACATCTCGCAATATGAG
TTGATTTTTGAAAACAGAATTTG
Found at i:90547210 original size:243 final size:236
Alignment explanation
Indices: 90546793--90547325 Score: 588
Period size: 243 Copynumber: 2.2 Consensus size: 236
90546783 AGAAATTAAA
***** * *
90546793 AAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTAAAAAAAAAAACAGAAATTGAAAATAGCT
1 AAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTT-TTTTGAAAGACAAAAATTGAAAATAGCT
* * * *
90546858 CAGCACGTAAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTG
64 CAGCACGT-AG-C-AGGCTCAACTCACCTATCGCAATATGAGTCGATTTTTGAAAACAGAAATTG
** **
90546923 AAAAACAGATTTTGAAAATACATCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAG
126 AAAAACAGAAATTGAAAATACATCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATACGAG
* * *
90546988 TTGATTTTTTTGAAAAATATAAATTGAAAAAAATACCTCAGTGTGTGATCTG
191 TTGATTTTTTTG-AAAATAGAAATTG---AAAATACCTCAGCGTGT--CCTG
*
90547040 AAGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATAGCTCA
1 AAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATAGCTCA
**
90547105 GCACGT-G-A-GC-CAACTCACCTATCGCAATATGAGTCGATTTTTTTTTGAAAGGTAGAAATTG
66 GCACGTAGCAGGCTCAACTCACCTATCGCAATATGAGTCGA----TTTTTGAAA-ACAGAAATTG
* * * * * * *
90547166 AAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAG
126 AAAAACAGAAATTGAAAATACATCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATACGAG
* *
90547231 TTGATTTTTTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTG
191 TTGATTTTTTTGAAAATAGAAATTGAAAATACCTCAGCGTGTCCTG
* *
90547277 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTGAAAGACA
1 AAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACA
90547326 TACCTCAGCA
Statistics
Matches: 246, Mismatches: 33, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
237 32 0.13
238 24 0.10
239 32 0.13
240 1 0.00
242 20 0.08
243 74 0.30
245 29 0.12
246 4 0.02
247 30 0.12
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (236 bp):
AAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATAGCTCA
GCACGTAGCAGGCTCAACTCACCTATCGCAATATGAGTCGATTTTTGAAAACAGAAATTGAAAAA
CAGAAATTGAAAATACATCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATACGAGTTGAT
TTTTTTGAAAATAGAAATTGAAAATACCTCAGCGTGTCCTG
Found at i:90547234 original size:163 final size:165
Alignment explanation
Indices: 90547017--90547322 Score: 411
Period size: 163 Copynumber: 1.9 Consensus size: 165
90547007 TAAATTGAAA
* * * *
90547017 AAAATACCTCAGTGTGTGATCTGAAGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
* *
90547082 AGACAAAAATTGAAAATAGCTCAGC-ACGTGA-GC-CAACTCACCTATCGCAATATGAGTCGATT
66 A-ACAAAAATTGAAAATACCTCAGCGACCTGAGGCTCAACTCACCTATCGCAATATGAGTCGATT
90547144 TTTTTTTGAAAGGTAGAAATTGAAAAACGGAAATTG
130 TTTTTTTGAAAGGTAGAAATTGAAAAACGGAAATTG
* * * *
90547180 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
* * * * * * *
90547245 AATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAT
66 AACAAAAATTGAAAATACCTCAGC--GACCTGAGGCTCAACTCACCTATCGCAATATGAGTCGAT
90547310 TTTTTTTTGAAAG
129 TTTTTTTTGAAAG
90547323 ACATACCTCA
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
162 19 0.16
163 58 0.48
165 4 0.03
166 2 0.02
167 38 0.31
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (165 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAA
AACAAAAATTGAAAATACCTCAGCGACCTGAGGCTCAACTCACCTATCGCAATATGAGTCGATTT
TTTTTTGAAAGGTAGAAATTGAAAAACGGAAATTG
Found at i:90547367 original size:66 final size:67
Alignment explanation
Indices: 90547199--90547388 Score: 193
Period size: 66 Copynumber: 2.7 Consensus size: 67
90547189 CGGCGTGTGA
* * * * * *
90547199 CCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAATAGAAATTGAAATTACC
1 CCTGAGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTTT----TTTGAAA--GACA-TACC
*
90547264 TCAGCGTGT
59 TCAGCATGT
* *
90547273 CCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTTTTTTGAAAGACATACCTCAGCAT
1 CCTGAGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAGACATACCTCAGCAT
90547337 GT
66 GT
* ** *
90547339 CTTGAGGCTCAACCCATTTCTCGTAATATGAGTTGATTTTTTTTTTGAAA
1 CCTGAGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAA
90547389 AATAGAAATT
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
66 42 0.41
67 16 0.16
69 5 0.05
73 6 0.06
74 33 0.32
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (67 bp):
CCTGAGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAGACATACCTCAGCAT
GT
Found at i:90547507 original size:72 final size:72
Alignment explanation
Indices: 90547325--90547535 Score: 287
Period size: 72 Copynumber: 2.8 Consensus size: 72
90547315 TTTGAAAGAC
* * * *
90547325 ATACCTCAGCATGTCTTGAGGCTCAACCCATTTCTCGTAATATGAGTTGATTTTTTTTTTGAAAA
1 ATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-----ATTTTG-AAA
*
90547390 ATAGAAATTGAAA
60 ACAGAAATTGAAA
* *
90547403 ATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAACAGAA
1 ATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
90547468 ATTGAAA
66 ATTGAAA
* *
90547475 TTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAC
1 ATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAC
90547536 GGAAGTAACA
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
72 72 0.58
73 5 0.04
78 47 0.38
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (72 bp):
ATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
ATTGAAA
Found at i:90555140 original size:26 final size:23
Alignment explanation
Indices: 90555096--90555196 Score: 80
Period size: 23 Copynumber: 4.3 Consensus size: 23
90555086 ATATTTGGTA
*
90555096 ATAATAATAATAATAATATGTAC
1 ATAAAAATAATAATAATATGTAC
*
90555119 ATAAAAATACATATATATATATGTAT
1 ATAAAAATA-ATA-ATA-ATATGTAC
** *
90555145 ATGTATATAATAA-AAGTATGTA-
1 ATAAAAATAATAATAA-TATGTAC
* *
90555167 ATAATAATAATAATAATATCTAC
1 ATAAAAATAATAATAATATGTAC
90555190 AATAAAA
1 -ATAAAA
90555197 GAAAATATTA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
22 15 0.25
23 17 0.28
24 9 0.15
25 6 0.10
26 13 0.22
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (23 bp):
ATAAAAATAATAATAATATGTAC
Found at i:90556111 original size:15 final size:15
Alignment explanation
Indices: 90556093--90556133 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
90556083 TTTTTTTGGT
90556093 TTTTTTTTGCTGAAA
1 TTTTTTTTGCTGAAA
*
90556108 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGAAA
90556123 TTTTTTTTGCT
1 TTTTTTTTGCT
90556134 CTTTTATCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.15, T:0.66
Consensus pattern (15 bp):
TTTTTTTTGCTGAAA
Found at i:90556446 original size:30 final size:30
Alignment explanation
Indices: 90556347--90556446 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 30
90556337 TTCTAGGGCT
** * *
90556347 AAATGTAATTTTTAGAAAATTTA-GGGTTA
1 AAATGTAATTTAAAGAAAGTTTAGGGGTCA
* * *
90556376 AAATGTAATTTAAGGAAAGTTTAGAGGTCT
1 AAATGTAATTTAAAGAAAGTTTAGGGGTCA
* *
90556406 AAGTGAAATTTAAAGAAAGTTTAGGGGTCA
1 AAATGTAATTTAAAGAAAGTTTAGGGGTCA
90556436 AAATGTAATTT
1 AAATGTAATTT
90556447 TTTTATTAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
29 19 0.34
30 37 0.66
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (30 bp):
AAATGTAATTTAAAGAAAGTTTAGGGGTCA
Found at i:90557607 original size:30 final size:30
Alignment explanation
Indices: 90557571--90557627 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
90557561 CCAATGTTAG
90557571 GGCCTAATTAGGGGTCGTTTGAGGGACGCA
1 GGCCTAATTAGGGGTCGTTTGAGGGACGCA
90557601 GGCCTAATTAGGGGTCGTTTGAGGGAC
1 GGCCTAATTAGGGGTCGTTTGAGGGAC
90557628 ACAAAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.16, G:0.40, T:0.25
Consensus pattern (30 bp):
GGCCTAATTAGGGGTCGTTTGAGGGACGCA
Found at i:90558042 original size:5 final size:5
Alignment explanation
Indices: 90558032--90558082 Score: 84
Period size: 5 Copynumber: 10.2 Consensus size: 5
90558022 ATAGGGGTAG
* *
90558032 GATAT GATAT GATAT AATCT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
90558082 G
1 G
90558083 TGATAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (5 bp):
GATAT
Found at i:90559063 original size:26 final size:26
Alignment explanation
Indices: 90559034--90559117 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
90559024 TGATACAAAT
90559034 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
90559060 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
90559086 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
90559112 TGATAA
1 TGATAA
90559118 GAATTTCATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:90561170 original size:136 final size:136
Alignment explanation
Indices: 90560890--90561174 Score: 527
Period size: 135 Copynumber: 2.1 Consensus size: 136
90560880 GAGTAGTCTC
90560890 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
90560955 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATTGAAAAGGGCTCTGGCCCAGTACCA
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATTGAAAAGGGCTCTGGCCCAGTACCA
90561020 CTGTTA
131 CTGTTA
*
90561026 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
90561090 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAAT-TGAAAAGGGCTCTGGCCCAGTACC
90561155 ACTGTTA
130 ACTGTTA
**
90561162 CCTGAATGGGCTT
1 CCCAAATGGGCTT
90561175 AGGCCCAATG
Statistics
Matches: 145, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
135 83 0.57
136 62 0.43
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:90564975 original size:26 final size:26
Alignment explanation
Indices: 90564946--90565029 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
90564936 TGATACAAAT
90564946 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
90564972 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
90564998 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
90565024 TGATAA
1 TGATAA
90565030 GAATTTCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:90566993 original size:135 final size:137
Alignment explanation
Indices: 90566809--90567092 Score: 520
Period size: 135 Copynumber: 2.1 Consensus size: 137
90566799 GAGTAGTCTC
*
90566809 CCCAAATGGGCTTGCATATGTTTACTGATGTTGTATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
90566874 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAAT-TGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
90566938 ACTGTTA
131 ACTGTTA
*
90566945 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
90567009 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
90567074 ACTGTTA
131 ACTGTTA
*
90567081 -CCTAATGGGCTT
1 CCCAAATGGGCTT
90567093 AGGCCCAATG
Statistics
Matches: 144, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
135 93 0.65
136 51 0.35
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:90570092 original size:37 final size:37
Alignment explanation
Indices: 90570019--90570192 Score: 170
Period size: 37 Copynumber: 4.7 Consensus size: 37
90570009 ACCTTCAAAT
* * * **
90570019 ATTCCCTGCAAAGTAAAGA-TGAAGATAAACCGGAGTG
1 ATTCCCTGCAAAGAAAAGACAG-AGATGAACAAGAGTG
*
90570056 ATTCCCTGCAAAGCAAAGACAGAGATGAACAAGAGTG
1 ATTCCCTGCAAAGAAAAGACAGAGATGAACAAGAGTG
** * * *
90570093 ATTCCCTATAAAGAAAAGATAGAGATGAATAAGAGAG
1 ATTCCCTGCAAAGAAAAGACAGAGATGAACAAGAGTG
* * * *
90570130 ATTCTCTACAAAGAAAAGACGGAGATGAACATGAGTG
1 ATTCCCTGCAAAGAAAAGACAGAGATGAACAAGAGTG
** *
90570167 ATTCTTTGCAAAGAAAAAACAGAGAT
1 ATTCCCTGCAAAGAAAAGACAGAGAT
90570193 AAATAGTAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
37 113 0.99
38 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.18
Consensus pattern (37 bp):
ATTCCCTGCAAAGAAAAGACAGAGATGAACAAGAGTG
Found at i:90570238 original size:37 final size:37
Alignment explanation
Indices: 90570169--90570253 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
90570159 CATGAGTGAT
* *
90570169 TCTTTGCAAAGAAAAAACAGAGATAAATAGTAAAAAA
1 TCTTTGCAAAGAAAAAACAAAGATAAACAGTAAAAAA
* * * * *
90570206 TCTTTGCAAATAAAAAATAAAGATGAACAGTAACAAT
1 TCTTTGCAAAGAAAAAACAAAGATAAACAGTAAAAAA
90570243 TCTTTGACAAA
1 TCTTTG-CAAA
90570254 ATTCTCTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.24
Consensus pattern (37 bp):
TCTTTGCAAAGAAAAAACAAAGATAAACAGTAAAAAA
Found at i:90583097 original size:21 final size:21
Alignment explanation
Indices: 90583073--90583133 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
90583063 TGAGTTTCAT
90583073 TTCAACCCTTATGGGTTTCTG
1 TTCAACCCTTATGGGTTTCTG
* * * *
90583094 TTCAGCTC-TATTGAGCTTCTG
1 TTCAACCCTTA-TGGGTTTCTG
*
90583115 TTTAACCCTTATGGGTTTC
1 TTCAACCCTTATGGGTTTC
90583134 CGTTTAGGTA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTCAACCCTTATGGGTTTCTG
Found at i:90583182 original size:42 final size:42
Alignment explanation
Indices: 90583073--90583183 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
90583063 TGAGTTTCAT
* * *
90583073 TTCAACCCTTATGGGTTTCTGTTCAGCTCTATTGAGCTTCTG
1 TTCAACCCTTATGGGTTTCTGTTTAGCTCTATTGAACTTCCG
* * * *
90583115 TTTAACCCTTATGGGTTTCCGTTTAGGTAT-TATGAACTTCCG
1 TTCAACCCTTATGGGTTTCTGTTTAGCTCTAT-TGAACTTCCG
*
90583157 TTCAACCCTTATGGGTTTCTTTTTAGC
1 TTCAACCCTTATGGGTTTCTGTTTAGC
90583184 ACTTATGTGC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCAACCCTTATGGGTTTCTGTTTAGCTCTATTGAACTTCCG
Found at i:90585194 original size:40 final size:40
Alignment explanation
Indices: 90585145--90585242 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
90585135 TTACAGTACC
* * *
90585145 ACTTTGTGTGTAGGGCTGGATGGGTCGATTTTATCCCTAT
1 ACTTGGTGTGTAGGGCTGGATGGGACGATTTTATACCTAT
* *
90585185 ACTTGGTGTGTATGGCTGGGTGGGACGATTTTATACCTAT
1 ACTTGGTGTGTAGGGCTGGATGGGACGATTTTATACCTAT
* *
90585225 A--TGGTGTGTTGGGTTGGA
1 ACTTGGTGTGTAGGGCTGGA
90585243 CGGAGATGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 13 0.27
40 36 0.73
ACGTcount: A:0.15, C:0.11, G:0.35, T:0.39
Consensus pattern (40 bp):
ACTTGGTGTGTAGGGCTGGATGGGACGATTTTATACCTAT
Found at i:90591373 original size:19 final size:19
Alignment explanation
Indices: 90591349--90591388 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
90591339 AGAAACAAAT
* * *
90591349 AGAAAAAGACAAAGATAAA
1 AGAAAAAAAAAAAGAAAAA
90591368 AGAAAAAAAAAAAGAAAAA
1 AGAAAAAAAAAAAGAAAAA
90591387 AG
1 AG
90591389 TTTGTAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AGAAAAAAAAAAAGAAAAA
Found at i:90592556 original size:14 final size:14
Alignment explanation
Indices: 90592534--90592567 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
90592524 TTGTCGTACC
90592534 ATATATTTTTATAT
1 ATATATTTTTATAT
* *
90592548 ATATCTTTTTATGT
1 ATATATTTTTATAT
90592562 ATATAT
1 ATATAT
90592568 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (14 bp):
ATATATTTTTATAT
Found at i:90596904 original size:18 final size:20
Alignment explanation
Indices: 90596869--90596905 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
90596859 AAGGTTGATT
*
90596869 TCGATCTTTTCTTTTTTATC
1 TCGATCTTTTCTTATTTATC
90596889 TCGAT-TTTT-TTATTTAT
1 TCGATCTTTTCTTATTTAT
90596906 TTTTGTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.68
Consensus pattern (20 bp):
TCGATCTTTTCTTATTTATC
Found at i:90596934 original size:15 final size:15
Alignment explanation
Indices: 90596901--90596947 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
90596891 GATTTTTTTA
* *
90596901 TTTATTTTTGTTTCG
1 TTTATTTTTATTTCT
90596916 TTTA-TTTTATCTTCT
1 TTTATTTTTAT-TTCT
90596931 TTTATTTTTATTTCT
1 TTTATTTTTATTTCT
90596946 TT
1 TT
90596948 AACTTACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 5 0.18
15 17 0.61
16 6 0.21
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (15 bp):
TTTATTTTTATTTCT
Found at i:90597758 original size:2 final size:2
Alignment explanation
Indices: 90597753--90597786 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
90597743 ATTTACCTAA
* *
90597753 AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90597787 CTTCCTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:90597780 original size:24 final size:24
Alignment explanation
Indices: 90597734--90597786 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
90597724 GCTATTTTTT
* * *
90597734 TATATATCTATTTACCTAAATATA
1 TATATATATATATACATAAATATA
*
90597758 TATATATATATATACATACATATA
1 TATATATATATATACATAAATATA
90597782 TATAT
1 TATAT
90597787 CTTCCTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATATATATATACATAAATATA
Found at i:90598085 original size:14 final size:14
Alignment explanation
Indices: 90598063--90598096 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
90598053 TTGTCGTACC
90598063 ATATATTTTTATAT
1 ATATATTTTTATAT
* *
90598077 ATATCTTTTTATGT
1 ATATATTTTTATAT
90598091 ATATAT
1 ATATAT
90598097 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (14 bp):
ATATATTTTTATAT
Found at i:90600548 original size:40 final size:40
Alignment explanation
Indices: 90600477--90600553 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
90600467 ACAGTACCAT
*
90600477 TTGGTGTGTAGGGTTGGATGGATCAAATTTATCCCCATAC
1 TTGGTGTGTAGGGCTGGATGGATCAAATTTATCCCCATAC
* * * *
90600517 TTGGTGTGTAGGGCTGGGTGGGTCGATTTTATCCCCA
1 TTGGTGTGTAGGGCTGGATGGATCAAATTTATCCCCA
90600554 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (40 bp):
TTGGTGTGTAGGGCTGGATGGATCAAATTTATCCCCATAC
Found at i:90602307 original size:36 final size:36
Alignment explanation
Indices: 90602260--90602328 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
90602250 TGTTCTTCAT
*
90602260 CTACTACTACTACCGTTGACTACTCATTTGCCTCTA
1 CTACTACTACTACCATTGACTACTCATTTGCCTCTA
*
90602296 CTACTACTACTACCATTGACTACTTATTTGCCT
1 CTACTACTACTACCATTGACTACTCATTTGCCT
90602329 TAGTCCTCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.32, G:0.07, T:0.38
Consensus pattern (36 bp):
CTACTACTACTACCATTGACTACTCATTTGCCTCTA
Found at i:90610747 original size:19 final size:19
Alignment explanation
Indices: 90610715--90610797 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
90610705 GTGTACCATG
*
90610715 ATGCATTTTATGTG-TCAGT
1 ATGCACTTTATGTGCT-AGT
*
90610734 ATGCACTTTGTGTGCTAGT
1 ATGCACTTTATGTGCTAGT
* * * *
90610753 ATGTACTTTGTGTACTAGG
1 ATGCACTTTATGTGCTAGT
* *
90610772 ATGCTCTTTATGTGCCAGT
1 ATGCACTTTATGTGCTAGT
90610791 ATGCACT
1 ATGCACT
90610798 ATATCTACCA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
19 50 0.98
20 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (19 bp):
ATGCACTTTATGTGCTAGT
Found at i:90616261 original size:16 final size:17
Alignment explanation
Indices: 90616242--90616277 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
90616232 TTACATTAAA
90616242 AAATAAAACATTTT-TT
1 AAATAAAACATTTTCTT
*
90616258 AAATAAAAGATTTTCTT
1 AAATAAAACATTTTCTT
90616275 AAA
1 AAA
90616278 GAATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATAAAACATTTTCTT
Found at i:90618095 original size:33 final size:30
Alignment explanation
Indices: 90618013--90618098 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 30
90618003 AATAGTTTAT
*
90618013 ATTTTTATAATTTT-TAAAAAATTAAAATAA
1 ATTTTTATTATTTTAT-AAAAATTAAAATAA
90618043 ATTTTTATTATTTTATAAAAATTAAAATACA
1 ATTTTTATTATTTTATAAAAATTAAAATA-A
90618074 A-TTTTATTATTATTAATTAAAAATT
1 ATTTTTATTATT-TT-A-TAAAAATT
90618099 TTATAAATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 36 0.72
31 5 0.10
32 1 0.02
33 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTTTATTATTTTATAAAAATTAAAATAA
Found at i:90618116 original size:22 final size:22
Alignment explanation
Indices: 90618052--90618116 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
90618042 AATTTTTATT
*
90618052 ATTTTATAAAAATTA-AAAT-ACA
1 ATTTTAT--AAATTATAAATAAAA
* *
90618074 ATTTTAT-TATTATTAATTAAAA
1 ATTTTATAAATTA-TAAATAAAA
90618096 ATTTTATAAATTATAAATAAA
1 ATTTTATAAATTATAAATAAA
90618117 CAAAATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.12
21 3 0.09
22 23 0.68
23 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTATAAATTATAAATAAAA
Found at i:90618563 original size:3 final size:3
Alignment explanation
Indices: 90618555--90618610 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
90618545 TTACCCTTCA
90618555 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
90618603 ATT ATT AT
1 ATT ATT AT
90618611 GTAGTCTAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:90619503 original size:21 final size:23
Alignment explanation
Indices: 90619479--90619536 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
90619469 ACATTTTATA
90619479 ATAAAAAAAT-CATAC-AAAATT
1 ATAAAAAAATGCATACAAAAATT
90619500 AT--AAAAATGCATACAAAAATT
1 ATAAAAAAATGCATACAAAAATT
* *
90619521 ATAAATAAATGTATAC
1 ATAAAAAAATGCATAC
90619537 TCATTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 10 0.32
23 10 0.32
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (23 bp):
ATAAAAAAATGCATACAAAAATT
Found at i:90620644 original size:40 final size:39
Alignment explanation
Indices: 90620596--90620672 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
90620586 ATATATTTTC
* *
90620596 ATATATATACATATATGAAAAA-AAGCATTTTTAAATAT
1 ATATATATATACATATGAAAAAGAAGCATTTTTAAATAT
*
90620634 ATATATATATACATATGAAAAAGAAGTATTTTTAAATAT
1 ATATATATATACATATGAAAAAGAAGCATTTTTAAATAT
90620673 GGATAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 20 0.57
39 15 0.43
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (39 bp):
ATATATATATACATATGAAAAAGAAGCATTTTTAAATAT
Found at i:90622668 original size:33 final size:33
Alignment explanation
Indices: 90622626--90622695 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
90622616 TATTAATGAG
*
90622626 TAATGTTAAGTTTAAATAATGATGATAATACAT
1 TAATGTTAAGTTTAAATAATGATGATAACACAT
** *
90622659 TAATGTTAAGTTTATGTAATGATGATGACACAT
1 TAATGTTAAGTTTAAATAATGATGATAACACAT
90622692 TAAT
1 TAAT
90622696 ATGATGACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.40
Consensus pattern (33 bp):
TAATGTTAAGTTTAAATAATGATGATAACACAT
Found at i:90622798 original size:2 final size:2
Alignment explanation
Indices: 90622791--90622816 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90622781 GTGTAGTTTA
90622791 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
90622817 TGACCAGCAA
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:90624621 original size:217 final size:218
Alignment explanation
Indices: 90624204--90625733 Score: 1432
Period size: 217 Copynumber: 6.9 Consensus size: 218
90624194 AAAGTTACGT
* * * * * * * *
90624204 CTGTTCACTACCAAA-CTGATAATAAGTATGTGCAAAAGTCAATGATTGTCGTATCACTTCAATA
1 CTGTTCACTAACAAATC-GACAATAAATATGAGGAAAAGTTAATGATTGTCATATCGCTTCAATA
* * ** * * * ** *
90624268 TTCAATCACATGGAAACATGTATCACATTCATTAATGTAAAAGTCACAAATCCCTGAAAATCAAA
65 CTCAATCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCCAAAAAATCAGA
** *
90624333 ACGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTA-CAAGTTGACTTTCATTGTT
130 ACGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAA-TTGACTTTCAAGGTC
90624397 GTCACTCATGTTCCCAACGTTATGA
194 GTCACTCATGTTCCCAACGTTATGA
* * * *
90624422 CAG-TCACTAGCAAATCGACAATAAATATGAGGAAAAGTTAATGATTGTTATATCGATTCAATAC
1 CTGTTCACTAACAAATCGACAATAAATATGAGGAAAAGTTAATGATTGTCATATCGCTTCAATAC
* * * *
90624486 TCAATCACATGAAAATGTGCATTACATTTATTAATGCAAAAGTTGCAAATCCCAAAAAATCAGAG
66 TCAATCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCCAAAAAATCAGAA
* * * *
90624551 CGCTTGTTACCACGCATGTTCCTAACATACGCTAATTATAAGTACCAATTGACTTTCAAGGTCAT
131 CGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAATTGACTTTCAAGGTCGT
*
90624616 CACTCATGTTCCCAACGTTTTGA
196 CACTCATGTTCCCAACGTTATGA
* * **
90624639 TTGTTCACTAACAAATCGATAATAAATACAAGGAAAAGTTAATGATTGTCATATCGCTTCAATAA
1 CTGTTCACTAACAAATCGACAATAAATATGAGGAAAAGTTAATGATTGTCATATCG---C--T--
* * * *
90624704 TCAAACATATCGCTTCAATAATCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTT
59 TC--A-ATA---C-TC---AATC-A-CA-T-GAAAATGTGTATCACATTTATTAATGCAAAAGTC
* * * ** * * * * * * *
90624769 GCAAAACCCACAAAA-CCGAACCGCTTATTACCATGCGTGTTCCCAACGTATGCTAATCATAAAT
110 GCAAATCCCAAAAAATCAGAA-CGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGT
* * * *
90624833 ACCAACTGGCCTTTCAAGGTCATCA-TCATGTTCCCAACGTTATGG
174 ACCAA-TTGACTTTCAAGGTCGTCACTCATGTTCCCAACGTTATGA
* * * * *
90624878 CTGCTCACTAACAGA-CTGACAATAAGTATGTA-CAAAATTTAATGATTGTCGA-ATCGCTTCAA
1 CTGTTCACTAACAAATC-GACAATAAATATG-AGGAAAAGTTAATGATTGTC-ATATCGCTTCAA
* * * * ** * * **
90624940 TATTCAATCACATGGAAACGTGTATCACATTCATTAATGTTAAAGTCACAACTCCCTGAAAATCA
63 TACTCAATCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCCAAAAAATCA
* ** * * *
90625005 GAATGCTTATTACCATGCATGTTCCTAACATATGTTAATTATAAGTACCAGTTAACTTTCAAGGT
128 GAACGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAATTGACTTTCAAGGT
** *
90625070 CACCACTTATGTTCCCAACGTTATGA
193 CGTCACTCATGTTCCCAACGTTATGA
* * *
90625096 CTGTT-ACTAGCAAATCGACAATAAATACGAGGAAAAGTTAATGATTGTCATGTCGCTTCAATAC
1 CTGTTCACTAACAAATCGACAATAAATATGAGGAAAAGTTAATGATTGTCATATCGCTTCAATAC
* ***
90625160 TCAGTCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCTTGAAAATCAGAA
66 TCAATCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCCAAAAAATCAGAA
** *
90625225 CGCTTATTACCATGCATGTTCCTAACATACGTTAATTATAAGTACCAAATGACTTTCAAGGTCGT
131 CGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAATTGACTTTCAAGGTCGT
*
90625290 CACTCATGTTCCCAACGTTCTGA
196 CACTCATGTTCCCAACGTTATGA
* * * * *
90625313 CTGTTCACTAACAAATCAATAATAAATATGAGGAAAAGTTAATGATTGTCACATTGCTTTAATAC
1 CTGTTCACTAACAAATCGACAATAAATATGAGGAAAAGTTAATGATTGTCATATCGCTTCAATAC
* * * * * * * *
90625378 TCAGTCACATGGAAACGTGTATCAGATTTATTAATGCAAAAGTTGCAAAACCTAAAAAAT-TGCA
66 TCAATCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCCAAAAAATCAG-A
* * * * * * *
90625442 ACGCTTATTACTACACATGTTCCCAACATATGCTAATCATAAGCACCATTTGACCTTTCAAGGTC
130 ACGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAATTGA-CTTTCAAGGTC
* * *
90625507 GTCACTCATGTTCCTAATGTTATGG
194 GTCACTCATGTTCCCAACGTTATGA
* * ** * *
90625532 CTGCTCATTAACAACCCGACAATAAATATGTGGTAAAA-TTAATAATTGTCATATCGCTTCAATA
1 CTGTTCACTAACAAATCGACAATAAATATGAGG-AAAAGTTAATGATTGTCATATCGCTTCAATA
* ** * *
90625596 CTCAATCACATGGAAACATGTATCAC-TTTCATTAATGCAAAAGTCACAAAAACCC-AAAAATCA
65 CTCAATCACATGAAAATGTGTATCACATTT-ATTAATGCAAAAGTCGC-AAATCCCAAAAAATCA
* * * * * * * *
90625659 AAATGCTTATGACTACACATGTTCCTAACATACGTTGATCATAA-TACCATTTGACCTTTTAAGG
128 GAACGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAATTGA-CTTTCAAGG
*
90625723 TTGTCACTCAT
192 TCGTCACTCAT
90625734 ATCTCTAAAA
Statistics
Matches: 1089, Mismatches: 182, Indels: 82
0.80 0.13 0.06
Matches are distributed among these distances:
216 2 0.00
217 378 0.35
218 335 0.31
219 165 0.15
220 12 0.01
221 1 0.00
222 4 0.00
223 1 0.00
225 4 0.00
227 1 0.00
228 3 0.00
229 3 0.00
230 1 0.00
231 1 0.00
232 4 0.00
234 1 0.00
235 4 0.00
236 2 0.00
237 2 0.00
238 4 0.00
239 142 0.13
240 19 0.02
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (218 bp):
CTGTTCACTAACAAATCGACAATAAATATGAGGAAAAGTTAATGATTGTCATATCGCTTCAATAC
TCAATCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAATCCCAAAAAATCAGAA
CGCTTATTACCACACATGTTCCTAACATACGTTAATTATAAGTACCAATTGACTTTCAAGGTCGT
CACTCATGTTCCCAACGTTATGA
Found at i:90624712 original size:21 final size:21
Alignment explanation
Indices: 90624688--90624728 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
90624678 TAATGATTGT
90624688 CATATCGCTTCAATAATCAAA
1 CATATCGCTTCAATAATCAAA
90624709 CATATCGCTTCAATAATCAA
1 CATATCGCTTCAATAATCAA
90624729 TCACATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (21 bp):
CATATCGCTTCAATAATCAAA
Found at i:90624922 original size:239 final size:239
Alignment explanation
Indices: 90624471--90625559 Score: 630
Period size: 218 Copynumber: 4.8 Consensus size: 239
90624461 AATGATTGTT
* * * *
90624471 ATATCGATTCAATACTCAATCACATGAAAATGTGCATTACATTTATTAATGCAAAAGTTGCAAAT
1 ATATCGATTCAATAATCAATCACATGAAAACGTGCATCACATTTATTAATGCAAAAGTTGCAAAA
* * * * * * *
90624536 CCCAAAAAATCAGAGCGCTTGTTACCACGCATGTTCCTAACATACGCTAATTATAAGTACCAATT
66 CCCAAAAAACCAGACCGCTTATTACCACGCATGTTCCCAACATACGCTAATCATAAATACCAATG
* * * *
90624601 GACTTTCAAGGTCATCACTCATGTTCCCAACGTTTTGATTGTTCACTAACAAATCGATAATAAAT
131 GACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAAAT
*
90624666 ACAAGGAAAAGTTAATGATTGTC-ATATCGCTTCAATAATCAAAC
196 ACAAGCAAAAGTTAATGATTGTCGA-ATCGCTTCAATAATCAAAC
* * *
90624710 ATATCGCTTCAATAATCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTTGCAAAA
1 ATATCGATTCAATAATCAATCACATGAAAACGTGCATCACATTTATTAATGCAAAAGTTGCAAAA
* * * * *
90624775 CCCACAAAACC-GAACCGCTTATTACCATGCGTGTTCCCAACGTATGCTAATCATAAATACCAAC
66 CCCAAAAAACCAG-ACCGCTTATTACCACGCATGTTCCCAACATACGCTAATCATAAATACCAA-
* * *
90624839 TGGCCTTTCAAGGTCATCA-TCATGTTCCCAACGTTATGGCTGCTCACTAACAGA-CTGACAATA
129 TGGACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATC-GACAATA
* ** *
90624902 AGTATGTA-CAAAATTTAATGATTGTCGAATCG---C--T--T----C
193 AATA-CAAGCAAAAGTTAATGATTGTCGAATCGCTTCAATAATCAAAC
* * * ** ** **
90624938 --A---A-T--AT--TCAATCACATGGAAACGTGTATCACATTCATTAATGTTAAAGTCACAACT
1 ATATCGATTCAATAATCAATCACATGAAAACGTGCATCACATTTATTAATGCAAAAGTTGCAAAA
** * ** * * * * * * * *
90624993 CCCTGAAAATCAGAATGCTTATTACCATGCATGTTCCTAACATATGTTAATTATAAGTACCAGTT
66 CCCAAAAAACCAGACCGCTTATTACCACGCATGTTCCCAACATACGCTAATCATAAATACCAATG
* * * * *
90625058 AACTTTCAAGGTCACCACTTATGTTCCCAACGTTATGACTG-TTACTAGCAAATCGACAATAAAT
131 GACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAAAT
* *
90625122 ACGAGGAAAAGTTAATGATTGTC--AT-G---------------
196 ACAAGCAAAAGTTAATGATTGTCGAATCGCTTCAATAATCAAAC
* * * * * * *
90625148 ---TCGCTTCAATACTCAGTCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAAT
1 ATATCGATTCAATAATCAATCACATGAAAACGTGCATCACATTTATTAATGCAAAAGTTGCAAAA
*** * * * * * * *
90625210 CCTTGAAAATCAGAACGCTTATTACCATGCATGTTCCTAACATACGTTAATTATAAGTACCAAAT
66 CCCAAAAAACCAGACCGCTTATTACCACGCATGTTCCCAACATACGCTAATCATAAATACC-AAT
* * * * *
90625275 -GACTTTCAAGGTCGTCACTCATGTTCCCAACGTTCTGACTGTTCACTAACAAATCAATAATAAA
130 GGACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAAA
** * *
90625339 TATGAGGAAAAGTTAATGATTGTC--A------C-AT--T---GC
195 TACAAGCAAAAGTTAATGATTGTCGAATCGCTTCAATAATCAAAC
* * * * *
90625370 ---T---TT-AATACTCAGTCACATGGAAACGTGTATCAGATTTATTAATGCAAAAGTTGCAAAA
1 ATATCGATTCAATAATCAATCACATGAAAACGTGCATCACATTTATTAATGCAAAAGTTGCAAAA
* * * * * ** *
90625428 CCTAAAAAATTGCA-A-CGCTTATTACTACACATGTTCCCAACATATGCTAATCATAAGCACCAT
66 CCCAAAAAA--CCAGACCGCTTATTACCACGCATGTTCCCAACATACGCTAATCATAAATACCAA
* * * * * * **
90625491 TTGACCTTTCAAGGTCGTCACTCATGTTCCTAATGTTATGGCTGCTCATTAACAACCCGACAATA
129 TGGA-CTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATA
90625556 AATA
193 AATA
90625560 TGTGGTAAAA
Statistics
Matches: 706, Mismatches: 115, Indels: 78
0.79 0.13 0.09
Matches are distributed among these distances:
213 1 0.00
214 1 0.00
215 4 0.01
216 1 0.00
217 187 0.26
218 255 0.36
219 58 0.08
220 4 0.01
222 2 0.00
226 1 0.00
228 1 0.00
232 1 0.00
234 1 0.00
236 1 0.00
238 2 0.00
239 167 0.24
240 19 0.03
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (239 bp):
ATATCGATTCAATAATCAATCACATGAAAACGTGCATCACATTTATTAATGCAAAAGTTGCAAAA
CCCAAAAAACCAGACCGCTTATTACCACGCATGTTCCCAACATACGCTAATCATAAATACCAATG
GACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAAAT
ACAAGCAAAAGTTAATGATTGTCGAATCGCTTCAATAATCAAAC
Found at i:90625090 original size:218 final size:218
Alignment explanation
Indices: 90624709--90625707 Score: 1061
Period size: 218 Copynumber: 4.6 Consensus size: 218
90624699 AATAATCAAA
* *
90624709 CATATCGCTTCAATAATCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTTGCAAA
1 CATATCGCTTCAATACTCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTCGCAAA
* * * * * *
90624774 ACCC-ACAAAA-CCGAACCGCTTATTACCATGCGTGTTCCCAACGTATGCTAATCATAAATACCA
66 ACCCTA-AAAATCAGAA-CGCTTATTACCATGCATGTTCCTAACATATGTTAATCATAAGTACCA
*** * *
90624837 ACTGGCCTTTCAAGGTCATCA-TCATGTTCCCAACGTTATGGCTGCTCACTAACAGA-CTGACAA
129 A-TTAACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATC-GACAA
* * *
90624900 TAAGTATGTA-CAAAATTTAATGATTGT
192 TAAATATG-AGGAAAAGTTAATGATTGT
* * ** *
90624927 CGA-ATCGCTTCAATATTCAATCACATGGAAACGTGTATCACATTCATTAATGTTAAAGTCACAA
1 C-ATATCGCTTCAATACTCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTCGCAA
** * * * *
90624991 CTCCCTGAAAATCAGAATGCTTATTACCATGCATGTTCCTAACATATGTTAATTATAAGTACCAG
65 AACCCTAAAAATCAGAACGCTTATTACCATGCATGTTCCTAACATATGTTAATCATAAGTACCAA
* * * *
90625056 TTAACTTTCAAGGTCACCACTTATGTTCCCAACGTTATGACTG-TTACTAGCAAATCGACAATAA
130 TTAACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAA
*
90625120 ATACGAGGAAAAGTTAATGATTGT
195 ATATGAGGAAAAGTTAATGATTGT
* * * *
90625144 CATGTCGCTTCAATACTCAGTCACATGAAAATGTGTATCACATTTATTAATGCAAAAGTCGCAAA
1 CATATCGCTTCAATACTCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTCGCAAA
* * * * * *
90625209 TCCTTGAAAATCAGAACGCTTATTACCATGCATGTTCCTAACATACGTTAATTATAAGTACCAAA
66 ACCCTAAAAATCAGAACGCTTATTACCATGCATGTTCCTAACATATGTTAATCATAAGTACCAAT
* * * * * *
90625274 TGACTTTCAAGGTCGTCACTCATGTTCCCAACGTTCTGACTGTTCACTAACAAATCAATAATAAA
131 TAACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAAA
90625339 TATGAGGAAAAGTTAATGATTGT
196 TATGAGGAAAAGTTAATGATTGT
* * * * * *
90625362 CACATTGCTTTAATACTCAGTCACATGGAAACGTGTATCAGATTTATTAATGCAAAAGTTGCAAA
1 CATATCGCTTCAATACTCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTCGCAAA
* * ** * * *
90625427 A-CCTAAAAAAT-TGCAACGCTTATTACTACACATGTTCCCAACATATGCTAATCATAAGCACCA
66 ACCCT-AAAAATCAG-AACGCTTATTACCATGCATGTTCCTAACATATGTTAATCATAAGTACCA
* * * * * * * **
90625490 TTTGACCTTTCAAGGTCGTCACTCATGTTCCTAATGTTATGGCTGCTCATTAACAACCCGACAAT
129 ATT-AACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAAT
* *
90625555 AAATATGTGGTAAAA-TTAATAATTGT
193 AAATATGAGG-AAAAGTTAATGATTGT
* *
90625581 CATATCGCTTCAATACTCAATCACATGGAAACATGTATCAC-TTTCATTAATGCAAAAGTCACAA
1 CATATCGCTTCAATACTCAATCACATGGAAACGTGTATCACATTT-ATTAATGCAAAAGTCGC-A
* * * * ** * *
90625645 AAACCC-AAAAATCAAAATGCTTATGACTACACATGTTCCTAACATACGTTGATCATAA-TACCA
64 AAACCCTAAAAATCAGAACGCTTATTACCATGCATGTTCCTAACATATGTTAATCATAAGTACCA
90625708 TTTGACCTTT
Statistics
Matches: 656, Mismatches: 109, Indels: 32
0.82 0.14 0.04
Matches are distributed among these distances:
216 2 0.00
217 202 0.31
218 276 0.42
219 166 0.25
220 8 0.01
221 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (218 bp):
CATATCGCTTCAATACTCAATCACATGGAAACGTGTATCACATTTATTAATGCAAAAGTCGCAAA
ACCCTAAAAATCAGAACGCTTATTACCATGCATGTTCCTAACATATGTTAATCATAAGTACCAAT
TAACTTTCAAGGTCATCACTCATGTTCCCAACGTTATGACTGCTCACTAACAAATCGACAATAAA
TATGAGGAAAAGTTAATGATTGT
Found at i:90629692 original size:3 final size:3
Alignment explanation
Indices: 90629686--90629714 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
90629676 TTCTTTAAGC
90629686 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
90629715 TAAAGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:90630403 original size:30 final size:29
Alignment explanation
Indices: 90630362--90630445 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 29
90630352 AATAGAGGAT
* *
90630362 TTAATTAATTTTTAATTATTTTATAAGGTG
1 TTAATTGATTTTTAATTATTTTA-AAAGTG
90630392 TTAATTGATTTTTTAAAATTATTTTAAAAGTG
1 TTAATTGA-TTTTT--AATTATTTTAAAAGTG
90630424 TCTAATTGATTTTTAATTATTT
1 T-TAATTGATTTTTAATTATTT
90630446 AATCATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
30 15 0.31
31 5 0.10
32 11 0.23
33 17 0.35
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.57
Consensus pattern (29 bp):
TTAATTGATTTTTAATTATTTTAAAAGTG
Found at i:90630635 original size:20 final size:21
Alignment explanation
Indices: 90630603--90630650 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
90630593 TTATAGAATT
*
90630603 TAAAAGAATATATAAAAACTAA
1 TAAAA-AAAATATAAAAACTAA
* *
90630625 -AAAAAAAATATTAAAAGTAA
1 TAAAAAAAATATAAAAACTAA
90630645 TAAAAA
1 TAAAAA
90630651 GTTATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (21 bp):
TAAAAAAAATATAAAAACTAA
Found at i:90635156 original size:28 final size:28
Alignment explanation
Indices: 90635124--90635183 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
90635114 AACCACATCA
90635124 TTTTGCCTCAATCCTAAAGATAATCTAC
1 TTTTGCCTCAATCCTAAAGATAATCTAC
90635152 TTTTGCCTCAATCCTAAAGATAATCTAC
1 TTTTGCCTCAATCCTAAAGATAATCTAC
90635180 TTTT
1 TTTT
90635184 AGAGCCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (28 bp):
TTTTGCCTCAATCCTAAAGATAATCTAC
Found at i:90637217 original size:3 final size:3
Alignment explanation
Indices: 90637211--90637261 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
90637201 ATAAGAGTAT
90637211 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
90637259 ATA
1 ATA
90637262 TCTAGAATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:90637481 original size:29 final size:27
Alignment explanation
Indices: 90637434--90637488 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
90637424 ATATATAACT
*
90637434 TAATAATATTAAAAATAAATA-ATAGG
1 TAATAATAGTAAAAATAAATATATAGG
90637460 TAATAATAGTAAAAAGGGTAAATATATAG
1 TAATAATAGTAAAAA---TAAATATATAG
90637489 TAAACACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (27 bp):
TAATAATAGTAAAAATAAATATATAGG
Found at i:90637638 original size:26 final size:27
Alignment explanation
Indices: 90637582--90637644 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
90637572 TAGCAATAAT
*
90637582 AATACTAATATAATAAATGTACTAGTG
1 AATAATAATATAATAAATGTACTAGTG
*
90637609 -ATAATAATATAAT-AATGGTAGTA-TG
1 AATAATAATATAATAAAT-GTACTAGTG
90637634 AATAAT-ATATA
1 AATAATAATATA
90637645 CAAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (27 bp):
AATAATAATATAATAAATGTACTAGTG
Found at i:90637702 original size:22 final size:23
Alignment explanation
Indices: 90637677--90637723 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
90637667 ACGATATATG
* *
90637677 AATATATACAT-ATATGTATTAA
1 AATATATACATGATATATATAAA
90637699 AATATATACATGATATATATAAA
1 AATATATACATGATATATATAAA
90637722 AA
1 AA
90637724 ATACAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
AATATATACATGATATATATAAA
Found at i:90637946 original size:26 final size:27
Alignment explanation
Indices: 90637917--90637974 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
90637907 TAGTATATAT
*
90637917 ATACATATAATATA-ATTATTAAGAAA
1 ATACATATAATATATAGTATTAAGAAA
*
90637943 ATACATATAATATATAGTATTAAGAAT
1 ATACATATAATATATAGTATTAAGAAA
90637970 ATACA
1 ATACA
90637975 CAATACGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (27 bp):
ATACATATAATATATAGTATTAAGAAA
Found at i:90637973 original size:27 final size:26
Alignment explanation
Indices: 90637915--90637974 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
90637905 CATAGTATAT
*
90637915 ATATACATATAATATAATTATTAAGA
1 ATATACATATAATATAAGTATTAAGA
*
90637941 AAATACATATAATATATAGTATTAAGA
1 ATATACATATAATATA-AGTATTAAGA
90637968 ATATACA
1 ATATACA
90637975 CAATACGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (26 bp):
ATATACATATAATATAAGTATTAAGA
Found at i:90638239 original size:16 final size:16
Alignment explanation
Indices: 90638206--90638251 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
90638196 AATCATAGGC
90638206 ATAATA-AT-AAATATA
1 ATAATATATGAAA-ATA
90638221 ATAATATATGAAAATA
1 ATAATATATGAAAATA
*
90638237 ATACTATATGTAAAA
1 ATAATATATG-AAAA
90638252 AAATGTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (16 bp):
ATAATATATGAAAATA
Found at i:90640387 original size:86 final size:84
Alignment explanation
Indices: 90640293--90641183 Score: 439
Period size: 90 Copynumber: 10.4 Consensus size: 84
90640283 GCATGAGCCA
* * ** *
90640293 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAACT-TAATTTGATTAGATTTTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATTAAACAGAATTTG
*
90640356 AAAATACCTCATCATGTGACCCG
66 AAAATACCTCAGC--GT--CCCG
* * *
90640379 AGGCTCAACTCACTTTTCGCAATATGAGTTGA--TTTTTGAAAAGTATAAATTAAACAGAATTTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATTAAACAGAATTTG
*
90640442 AAAATACCTCAGCGTCCTG
66 AAAATACCTCAGCGTCCCG
* *
90640461 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG---AC----AA--ACAGA-AATTT-
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATTAAACAGAATTTG
* *
90640513 AAAATACCTTAGCGCGTCCTG
66 AAAATACCTCA--GCGTCCCG
* * * *
90640534 AGGCTCAACTCACCTCTTGCAATATGAGTTGA----TTT----A--A-AAA-CAGACAGAAATTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATTAAACAGAATTTG
* * *
90640587 AAAATAGCTCAGCACGTGAGCCA
66 AAAATACCTCAG--CGT--CCCG
* * *
90640610 AGACTCAACTCACCTCTCGCAATACGAGTTGGTCTTTTTTG-AAACT-T-AATTCGAAA-AGTAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTTGAAAACTATAAATT--AAACAG-A-
*
90640671 CTTTTGAAAATACCTC-GTCATGTAACCCG
61 -ATTTGAAAATACCTCAG-C--GT--CCCG
* *
90640700 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAGTATAAATTGAAATA-AATAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATT-AAACAGAAT--
* * *
90640762 AAACTAAAAATACCTCAGCATGCCCTG
63 ---TTGAAAATACCTCAGCGT-CCC-G
* *
90640789 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAGC-ATAACTTGAAAAACGGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-CTATAAATT---AAACAGAA
* *
90640852 ATTGAAAATACCTCAGCGTGTCCTG
62 TTTGAAAATACCTCAGC--GTCCCG
* * *
90640877 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCTTTTTGAAAAGC-AGAATTTGAAAAGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA---TT-TTTTTGAAAA-CTATAAATT--AAA-C
* * **
90640941 AGAAATTGAAAATACCTCAGTGTGCGTTG
58 AGAATTTGAAAATACCTCAGCGT-C-CCG
* * *
90640970 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTTGAAAAGC-AGAGATTGAAA-AGCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAA-CTATAAATT-AAACAG--
** * * *
90641033 AAAATGAAAATTCCTCAGCTTGCCTTG
60 AATTTGAAAATACCTCAGCGT-CC-CG
* * * *
90641060 AGGCTGAACTCACCTCTCACAATATGAGTTGA--TTTTTGAAAAATATAAATTGAAAAGCAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATT--AAA-CAGAAT
*
90641123 TTGAAAATACCTCAGCGTATCCTG
63 TTGAAAATACCTCAGCG--TCCCG
** *
90641147 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
90641184 GAAAAATAAA
Statistics
Matches: 649, Mismatches: 87, Indels: 135
0.75 0.10 0.15
Matches are distributed among these distances:
70 1 0.00
71 15 0.02
72 9 0.01
73 46 0.07
74 12 0.02
75 2 0.00
76 29 0.04
79 1 0.00
81 3 0.00
82 39 0.06
84 9 0.01
85 6 0.01
86 71 0.11
87 58 0.09
88 63 0.10
89 48 0.07
90 121 0.19
91 31 0.05
92 14 0.02
93 71 0.11
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (84 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACTATAAATTAAACAGAATTTG
AAAATACCTCAGCGTCCCG
Found at i:90640547 original size:73 final size:74
Alignment explanation
Indices: 90640430--90640640 Score: 243
Period size: 73 Copynumber: 2.9 Consensus size: 74
90640420 AGTATAAATT
90640430 AAACAG-AATTTGAAAATACCTCA--GCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACAGAAATTT-AAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
***
90640492 ATTT-TTGAC
65 ATTTAAAAAC
* *
90640501 AAACAGAAATTTAAAATACCTTAGCGCGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA
1 AAACAGAAATTTAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
90640566 TTTAAAAAC
66 TTTAAAAAC
* * * * * * *
90640575 AGACAGAAATTGAAAATAGCTCAGCACGTGAGCC-AAGACTCAACTCACCTCTCGCAATACGAGT
1 AAACAGAAATTTAAAATACCTCAGCGCGT---CCTGAGGCTCAACTCACCTCTCGCAATATGAGT
90640639 TG
63 TG
90640641 GTCTTTTTTG
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
71 16 0.13
72 5 0.04
73 42 0.35
74 26 0.22
76 28 0.24
77 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (74 bp):
AAACAGAAATTTAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTAAAAAC
Found at i:90640911 original size:177 final size:174
Alignment explanation
Indices: 90640699--90641188 Score: 590
Period size: 177 Copynumber: 2.8 Consensus size: 174
90640689 CATGTAACCC
* *
90640699 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTATAAATTGAAATAAATAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTATAAATTG-AA-AAGTAGAA
* * *
90640764 ACTAAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
64 ATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
* * *
90640829 AAAGCATA-ACTTGAAAAACGGAAATTGAAAATACCTCAGCGTGTCC-T
129 AAAGCAGAGA-TTGAAAAAC-AAAAATGAAAATACCTCAGCGTG-CCTT
* * *
90640876 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCTTTTTGAAAAGCAGAATTTGAAAAGT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA------TTTTTGAAAAGTATAAATTGAAAAGT
* ** *
90640941 AGAAATTGAAAATACCTCAGTGTGCGTTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
60 AGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---T
* * *
90641006 TTTTTGAAAAGCAGAGATTGAAAAGCAAAAATGAAAATTCCTCAGCTTGCCTT
122 TTTTTGAAAAGCAGAGATTGAAAAACAAAAATGAAAATACCTCAGCGTGCCTT
* * * *
90641059 GAGGCTGAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAGCAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTATAAATTGAAAAGTAGAAAT
** ** *
90641124 TGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAA
66 TGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA
90641188 A
131 A
90641189 ATAAAAACAT
Statistics
Matches: 268, Mismatches: 34, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
173 9 0.03
177 107 0.40
181 56 0.21
182 4 0.01
183 68 0.25
184 23 0.09
185 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (174 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTATAAATTGAAAAGTAGAAAT
TGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA
AGCAGAGATTGAAAAACAAAAATGAAAATACCTCAGCGTGCCTT
Found at i:90640936 original size:14 final size:14
Alignment explanation
Indices: 90640917--90640952 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
90640907 GATTTTTCTT
90640917 TTTGAAAAGCAGAA
1 TTTGAAAAGCAGAA
*
90640931 TTTGAAAAGTAGAA
1 TTTGAAAAGCAGAA
*
90640945 ATTGAAAA
1 TTTGAAAA
90640953 TACCTCAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (14 bp):
TTTGAAAAGCAGAA
Found at i:90640972 original size:93 final size:87
Alignment explanation
Indices: 90640578--90641188 Score: 556
Period size: 90 Copynumber: 6.8 Consensus size: 87
90640568 TAAAAACAGA
* * * *
90640578 CAGAAATTGAAAATAGCTCAGCACGTGAGCC-AAGACTCAACTCACCTCTCGCAATACGAGTTGG
1 CAGAAATTGAAAATACCTCAG--CGT--GCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT-G
* *
90640642 TCTTTTTTG-AAA-C-TTAATTCGAAAAG
61 -ATTTTTTGAAAAGCATAAATT-GAAAAG
* *** * *
90640668 TAGCTTTTGAAAATACCTC-GTCATGTAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 CAGAAATTGAAAATACCTCAG-C--GT-GCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* *
90640732 -TTTTTGAAAAGTATAAATTGAAATAAA
62 TTTTTTGAAAAGCATAAATTG-AA-AAG
* * * * *
90640759 TAAAAACTAAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* *
90640824 TTTGAAAAGCATAACTTGAAAAA
65 TTTGAAAAGCATAAATTGAAAAG
*
90640847 CGGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---
* *
90640912 TTCTTTTTGAAAAGCAGAATTTGAAAAG
62 -T-TTTTTGAAAAGCATAAATTGAAAAG
* * * *
90640940 TAGAAATTGAAAATACCTCAGTGTGCGTTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGTGC-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---
* *
90641005 TTTTTTGAAAAGCAGAGATTGAAAAG
62 TTTTTTGAAAAGCATAAATTGAAAAG
* * * * *
90641031 CA-AAAATGAAAATTCCTCAGCTTGCCTTGAGGCTGAACTCACCTCTCACAATATGAGTTGA-TT
1 CAGAAATTGAAAATACCTCAGCGTGCC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
**
90641094 TTTGAAAAATATAAATTGAAAAG
65 TTTGAAAAGCATAAATTGAAAAG
* ** *
90641117 CAGAAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-AT
1 CAGAAATTGAAAATACCTCAGCGT-GCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
90641181 TTTGAAAA
65 TTTGAAAA
90641189 ATAAAAACAT
Statistics
Matches: 437, Mismatches: 64, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
86 23 0.05
87 63 0.14
88 64 0.15
89 44 0.10
90 119 0.27
91 40 0.09
92 7 0.02
93 77 0.18
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (87 bp):
CAGAAATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTGAAAAGCATAAATTGAAAAG
Found at i:90649594 original size:4 final size:4
Alignment explanation
Indices: 90649548--90649575 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
90649538 TGGGATATGC
90649548 AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG
90649576 CATAAATGTC
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:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:90653306 original size:3 final size:3
Alignment explanation
Indices: 90653294--90653383 Score: 171
Period size: 3 Copynumber: 30.0 Consensus size: 3
90653284 ATAAGAGTAT
*
90653294 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
90653342 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
90653384 TCTACAATAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:90653581 original size:17 final size:18
Alignment explanation
Indices: 90653515--90653584 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
90653505 AATGATAATG
* *
90653515 ATAATAATAAAAGAATAT
1 ATAAAAATAAAATAATAT
*
90653533 ATAAAAATAATATATATAT
1 ATAAAAATAAAATA-ATAT
* * *
90653552 ATATAACT-TAATAATAT
1 ATAAAAATAAAATAATAT
90653569 -TAAAAATAAAATAATA
1 ATAAAAATAAAATAATA
90653585 GGTAATAATA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 14 0.35
19 10 0.25
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
ATAAAAATAAAATAATAT
Found at i:90653765 original size:26 final size:27
Alignment explanation
Indices: 90653709--90653771 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
90653699 TAGCAATAAT
*
90653709 AATACTAATATAATAAATGTACTAGTG
1 AATAATAATATAATAAATGTACTAGTG
*
90653736 -ATAATAATATAAT-AATGGTAGTA-TG
1 AATAATAATATAATAAAT-GTACTAGTG
90653761 AATAAT-ATATA
1 AATAATAATATA
90653772 CAAAAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (27 bp):
AATAATAATATAATAAATGTACTAGTG
Found at i:90653831 original size:22 final size:23
Alignment explanation
Indices: 90653803--90653851 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
90653793 ACGATATATG
* *
90653803 AATATATACAT-ATATGTATTAA
1 AATATATACATGATATATATAAA
90653825 AATATATACATGATATATATAAA
1 AATATATACATGATATATATAAA
90653848 AATA
1 AATA
90653852 CAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATATATACATGATATATATAAA
Found at i:90654097 original size:27 final size:26
Alignment explanation
Indices: 90654039--90654100 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
90654029 CATAGTATAT
* *
90654039 ATATACATATAATATAATTATTAAGA
1 ATATACATACAATATAAGTATTAAGA
*
90654065 AAATACATACAATATATAGTATTAAGA
1 ATATACATACAATATA-AGTATTAAGA
90654092 ATATACATA
1 ATATACATA
90654101 ATACGTAGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (26 bp):
ATATACATACAATATAAGTATTAAGA
Found at i:90654364 original size:16 final size:16
Alignment explanation
Indices: 90654331--90654376 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
90654321 AATCATAGGC
90654331 ATAATA-AT-AAATATA
1 ATAATATATGAAA-ATA
90654346 ATAATATATGAAAATA
1 ATAATATATGAAAATA
*
90654362 ATACTATATGTAAAA
1 ATAATATATG-AAAA
90654377 AATGTTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (16 bp):
ATAATATATGAAAATA
Found at i:90654442 original size:24 final size:24
Alignment explanation
Indices: 90654415--90654463 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
90654405 TATAGATAAA
*
90654415 AATA-GATATAATAATAATATATGT
1 AATATGATATAAAAAT-ATATATGT
*
90654439 AATATGGTATAAAAATATATATGT
1 AATATGATATAAAAATATATATGT
90654463 A
1 A
90654464 TGTAATAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (24 bp):
AATATGATATAAAAATATATATGT
Found at i:90655445 original size:18 final size:18
Alignment explanation
Indices: 90655420--90655460 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
90655410 TTTTTTGTAT
*
90655420 TATAT-TTTT-ATATATT
1 TATATGTTTTGATATATA
*
90655436 TATATGTTTTGGTATATA
1 TATATGTTTTGATATATA
90655454 TATATGT
1 TATATGT
90655461 GAAAAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 5 0.24
17 4 0.19
18 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (18 bp):
TATATGTTTTGATATATA
Found at i:90655501 original size:23 final size:23
Alignment explanation
Indices: 90655464--90655507 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
90655454 TATATGTGAA
** *
90655464 AAAATGAAACCAAAACAGAATTT
1 AAAATGAAAAAAAAAAAGAATTT
90655487 AAAATGAAAAAAAAAAAGAAT
1 AAAATGAAAAAAAAAAAGAAT
90655508 AATCACCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (23 bp):
AAAATGAAAAAAAAAAAGAATTT
Found at i:90656032 original size:16 final size:15
Alignment explanation
Indices: 90656011--90656040 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
90656001 GAGTTGGAAA
90656011 TATATATATGTATAAT
1 TATATATA-GTATAAT
90656027 TATATATAGTATAA
1 TATATATAGTATAA
90656041 ATATGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
TATATATAGTATAAT
Found at i:90658534 original size:14 final size:14
Alignment explanation
Indices: 90658515--90658543 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90658505 CTTCTTTTTC
90658515 TGTTTAAGGGCCAA
1 TGTTTAAGGGCCAA
90658529 TGTTTAAGGGCCAA
1 TGTTTAAGGGCCAA
90658543 T
1 T
90658544 CTCATATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (14 bp):
TGTTTAAGGGCCAA
Found at i:90667904 original size:23 final size:23
Alignment explanation
Indices: 90667873--90667919 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
90667863 GATATCATAA
90667873 GTTGAATTTATAATTTGATAAGG
1 GTTGAATTTATAATTTGATAAGG
*
90667896 GTTGTATTTATAATTTGATAAGG
1 GTTGAATTTATAATTTGATAAGG
90667919 G
1 G
90667920 GCCAAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (23 bp):
GTTGAATTTATAATTTGATAAGG
Found at i:90671586 original size:40 final size:38
Alignment explanation
Indices: 90671541--90671635 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 38
90671531 CGGTACCTCT
* *
90671541 TGGTGTGTAGGGTTGGATGGGTTGATTTTATCCCCATAC-
1 TGGTGTGTAGGGTTGGATGGGTCGATCTTAT-CCCA-ACA
* * *
90671580 TAGGTGTGTAAGGCTGGGTGGGTCGATCTTATCCCAACA
1 T-GGTGTGTAGGGTTGGATGGGTCGATCTTATCCCAACA
*
90671619 TGGTGTGTTGGGTTGGA
1 TGGTGTGTAGGGTTGGA
90671636 CAGAGATGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
38 14 0.31
39 6 0.13
40 25 0.56
ACGTcount: A:0.16, C:0.13, G:0.37, T:0.35
Consensus pattern (38 bp):
TGGTGTGTAGGGTTGGATGGGTCGATCTTATCCCAACA
Found at i:90673443 original size:30 final size:29
Alignment explanation
Indices: 90673407--90673464 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
90673397 AACGAAAGTT
90673407 TTGGCACTAAGTGTGCGATTTAAACTAGCC
1 TTGGCACTAAGTGTGCGATTT-AACTAGCC
90673437 TTGGCACTAAGTGTGCGATTTAACTAGC
1 TTGGCACTAAGTGTGCGATTTAACTAGC
90673465 TCCAACTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (29 bp):
TTGGCACTAAGTGTGCGATTTAACTAGCC
Found at i:90677702 original size:2 final size:2
Alignment explanation
Indices: 90677695--90677721 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
90677685 TAAACTAGCT
90677695 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 T
90677722 TTGGTGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90683018 original size:40 final size:40
Alignment explanation
Indices: 90682971--90683116 Score: 213
Period size: 40 Copynumber: 3.6 Consensus size: 40
90682961 TTGATGACAA
**
90682971 TTCGGCTATGTATGGCACTTAGTGTA-CGATTCAAGATAGC
1 TTCGGCTATGTATGGCACTTAGTG-AGCGATTTGAGATAGC
* *
90683011 TTTGGCTATGTGTGGCACTTAGTGAGCGATTTGAGATAGC
1 TTCGGCTATGTATGGCACTTAGTGAGCGATTTGAGATAGC
90683051 TTCGGCTATGTATGGCACTTAGTGAGCGATTTGAGATAGC
1 TTCGGCTATGTATGGCACTTAGTGAGCGATTTGAGATAGC
*
90683091 TTCGGGCTATGAATTGGCACTTAGTG
1 TTC-GGCTATGTA-TGGCACTTAGTG
90683117 TGTGAGAATT
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 75 0.78
41 8 0.08
42 12 0.12
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (40 bp):
TTCGGCTATGTATGGCACTTAGTGAGCGATTTGAGATAGC
Found at i:90691726 original size:9 final size:9
Alignment explanation
Indices: 90691714--90691775 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
90691704 TAAAAATATT
90691714 TTTTTAAAA
1 TTTTTAAAA
* *
90691723 TTTTTATAC
1 TTTTTAAAA
*
90691732 TTTTTAAAG
1 TTTTTAAAA
*
90691741 TTTTTAATAT
1 TTTTTAA-AA
*
90691751 TTTTTATATA
1 TTTTTA-AAA
90691761 TTTTTAAAA
1 TTTTTAAAA
90691770 TTTTTA
1 TTTTTA
90691776 TGTTTAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 29 0.67
10 13 0.30
11 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:90691883 original size:12 final size:13
Alignment explanation
Indices: 90691856--90691883 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
90691846 AGATGTTAAC
90691856 TTTTTCGATAATT
1 TTTTTCGATAATT
90691869 TTTTTCGATAATT
1 TTTTTCGATAATT
90691882 TT
1 TT
90691884 CAGAGTAATT
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:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTTCGATAATT
Found at i:90710549 original size:19 final size:19
Alignment explanation
Indices: 90710525--90710562 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
90710515 ATCCAAAAGA
90710525 ATGAATCGAATATCCCAAT
1 ATGAATCGAATATCCCAAT
90710544 ATGAATCGAATATCCCAAT
1 ATGAATCGAATATCCCAAT
90710563 CCACACCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (19 bp):
ATGAATCGAATATCCCAAT
Found at i:90718822 original size:75 final size:77
Alignment explanation
Indices: 90718650--90718828 Score: 201
Period size: 79 Copynumber: 2.4 Consensus size: 77
90718640 TTACGTAAAT
90718650 AATACAAAGTTTATTATTTAAATTAC----AAAAAACTCCTAAAATTAATAACTGAAATAACAAA
1 AATACAAAG-TTA-TATTTAAATTACAAAAAAAAAACTCCTAAAATTAATAACTGAAATAACAAA
90718711 AAAGTCATTACATA
64 AAAGTCATTACATA
* * **
90718725 AATACAAAGTTGACTATTTAAATTGCAAAAAAAAAAC-CCATAAAATTAATAACTTAAATGGCAA
1 AATACAAAGTT-A-TATTTAAATTACAAAAAAAAAACTCC-TAAAATTAATAACTGAAATAACAA
*
90718789 AAAAGTCATTATATA
63 AAAAGTCATTACATA
**
90718804 AATATGAAG-T-TATTTAAATTACAAA
1 AATACAAAGTTATATTTAAATTACAAA
90718829 CCCCCCTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
74 2 0.02
75 35 0.39
78 3 0.03
79 49 0.55
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (77 bp):
AATACAAAGTTATATTTAAATTACAAAAAAAAAACTCCTAAAATTAATAACTGAAATAACAAAAA
AGTCATTACATA
Found at i:90721096 original size:16 final size:16
Alignment explanation
Indices: 90721071--90721105 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
90721061 AAATAAAAAT
90721071 AAAATTACATT-ATAA
1 AAAATTACATTAATAA
90721086 AAAACTTACATTAATAA
1 AAAA-TTACATTAATAA
90721103 AAA
1 AAA
90721106 TCACAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:90721189 original size:100 final size:100
Alignment explanation
Indices: 90721069--90721291 Score: 283
Period size: 101 Copynumber: 2.2 Consensus size: 100
90721059 TCAAATAAAA
* *
90721069 ATAAAATTACATTATAAAAA-ACTTACATTAAT-AAAAATCACAAAACAC-TAAACTAAACACTA
1 ATAAAATT--ATTTTAAAAAGA-TTAAATTAATAAAAAATCAC-AAAC-CTTAAACTAAACACTA
*
90721131 ACAATTTATATAACCTAATCATAAATTACTAACAAAA-AACT
61 AC-A-GTATATAACCTAATCATAAATTACTAACAAAATAACT
*
90721172 ATAAAATTATTTTAAAAAGATTAAATTACTAAAAAATCACAAACCTTAAACTAAACACTAACAGT
1 ATAAAATTATTTTAAAAAGATTAAATTAATAAAAAATCACAAACCTTAAACTAAACACTAACAGT
* *
90721237 CTATAACCTAATCATAAATTACTAATAAAATAACT
66 ATATAACCTAATCATAAATTACTAACAAAATAACT
* *
90721272 ATAACATTTTTTTAAAAAGA
1 ATAAAATTATTTTAAAAAGA
90721292 ATTTACATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
99 29 0.27
100 24 0.22
101 37 0.34
102 10 0.09
103 8 0.07
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (100 bp):
ATAAAATTATTTTAAAAAGATTAAATTAATAAAAAATCACAAACCTTAAACTAAACACTAACAGT
ATATAACCTAATCATAAATTACTAACAAAATAACT
Found at i:90721261 original size:99 final size:104
Alignment explanation
Indices: 90721101--90721316 Score: 300
Period size: 99 Copynumber: 2.1 Consensus size: 104
90721091 TTACATTAAT
*
90721101 AAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACAA
1 AAAAATCAC-AAACACTAAACTAAACACTAACAATGTATATAACCTAATCATAAATTACTAACAA
90721166 AA-AACTATAAAATTATTTTAAAAAG-A-TTAAATTACTA
65 AATAACTATAAAATTATTTTAAAAAGAATTTAAATTACTA
* *
90721203 AAAAATCACAAAC-CTTAAACTAAACACTAAC-A-GTCTATAACCTAATCATAAATTACTAATAA
1 AAAAATCACAAACAC-TAAACTAAACACTAACAATGTATATAACCTAATCATAAATTACTAACAA
* * *
90721265 AATAACTATAACATTTTTTTAAAAAGAATTTACATTACTA
65 AATAACTATAAAATTATTTTAAAAAGAATTTAAATTACTA
* *
90721305 ATAAGTCACAAA
1 AAAAATCACAAA
90721317 ATACAAAACA
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
99 29 0.28
100 23 0.23
101 21 0.21
102 29 0.28
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (104 bp):
AAAAATCACAAACACTAAACTAAACACTAACAATGTATATAACCTAATCATAAATTACTAACAAA
ATAACTATAAAATTATTTTAAAAAGAATTTAAATTACTA
Found at i:90721324 original size:7 final size:7
Alignment explanation
Indices: 90721311--90721355 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
90721301 ACTAATAAGT
90721311 CACAAAA
1 CACAAAA
*
90721318 TACAAAA
1 CACAAAA
90721325 CACAAAA
1 CACAAAA
90721332 CACAAAA
1 CACAAAA
90721339 CACAAAA
1 CACAAAA
90721346 CACAAAA
1 CACAAAA
90721353 CAC
1 CAC
90721356 TAACAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.02
Consensus pattern (7 bp):
CACAAAA
Found at i:90721378 original size:126 final size:127
Alignment explanation
Indices: 90721224--90721454 Score: 331
Period size: 126 Copynumber: 1.8 Consensus size: 127
90721214 ACCTTAAACT
* * *
90721224 AAACACTAACAGTCTATAACCTAATCATAAATTACTAATAAAATAACTAT-AACAT-TTTTTTAA
1 AAACACTAACAATCTATAAACTAATCATAAATTACTAATAAAATAACTATAAAAATATTTTTT-A
* * *
90721287 AAAGAATTTACATTACTAATAAGTCACAAAATACAAAACACAAAACACAAAACACAAAACACA
65 AAAGAATTTACATTACTAAAAAATCACAAAACACAAAACACAAAACACAAAACACAAAACACA
* * *
90721350 AAACACTAACAATTTATAAACTAATCATAGATTACTAATAAAATAACTATAAAAATATTTTTTTA
1 AAACACTAACAATCTATAAACTAATCATAAATTACTAATAAAATAACTATAAAAATATTTTTTAA
* * *
90721415 AATATTTTATATTACTAAAAAATCACAAAACACAAAACAC
66 AAGAATTTACATTACTAAAAAATCACAAAACACAAAACAC
90721455 TAACATAAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
126 46 0.51
127 39 0.43
128 6 0.07
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (127 bp):
AAACACTAACAATCTATAAACTAATCATAAATTACTAATAAAATAACTATAAAAATATTTTTTAA
AAGAATTTACATTACTAAAAAATCACAAAACACAAAACACAAAACACAAAACACAAAACACA
Found at i:90721483 original size:12 final size:12
Alignment explanation
Indices: 90721468--90721492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90721458 CATAAATTAC
90721468 TAACAAAATAAT
1 TAACAAAATAAT
90721480 TAACAAAATAAT
1 TAACAAAATAAT
90721492 T
1 T
90721493 TTACATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TAACAAAATAAT
Found at i:90721529 original size:14 final size:15
Alignment explanation
Indices: 90721505--90721533 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
90721495 ACATTAATAA
90721505 AAAATCACAAAACAC
1 AAAATCACAAAACAC
90721520 AAAA-CACAAAACAC
1 AAAATCACAAAACAC
90721534 TAACAATTTA
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:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAATCACAAAACAC
Found at i:90721577 original size:95 final size:92
Alignment explanation
Indices: 90721454--90721660 Score: 299
Period size: 95 Copynumber: 2.2 Consensus size: 92
90721444 ACACAAAACA
90721454 CTAA-CATAAATTACTAACAAAATAATTAACAAAATAATTTTACATTAATAAAAAATCACAAAAC
1 CTAATCATAAATTACTAACAAAATAATTAACAAAATAATTTTACATTAATAAAAAATCACAAAAC
90721518 ACAAAACACAAAACACTAACAATTTATAAC
66 AC-AAA-ACAAAACAC-AACAATTTATAAC
* * **
90721548 CTAATCATAAATTACTAACAAAATGATTAAGAAAATAATTTTACATTAATAAAAAATCACAAATT
1 CTAATCATAAATTACTAACAAAATAATTAACAAAATAATTTTACATTAATAAAAAATCACAAAAC
* * *
90721613 ACTAAACTAAATACAACAATTTATAAC
66 ACAAAACAAAACACAACAATTTATAAC
* *
90721640 ATAATCCTAAATTACTAACAA
1 CTAATCATAAATTACTAACAA
90721661 GACAATTTTA
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
92 32 0.31
93 7 0.07
94 6 0.06
95 58 0.56
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.27
Consensus pattern (92 bp):
CTAATCATAAATTACTAACAAAATAATTAACAAAATAATTTTACATTAATAAAAAATCACAAAAC
ACAAAACAAAACACAACAATTTATAAC
Found at i:90722389 original size:21 final size:21
Alignment explanation
Indices: 90722359--90722399 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
90722349 TAACAGAATT
90722359 GCTGACGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
*
90722380 GCTGATGTGGCAAGTTAACT
1 GCTGACGTGGCAAGTTAACT
90722400 TGCCACGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:90722821 original size:14 final size:15
Alignment explanation
Indices: 90722802--90722830 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
90722792 CACCAAAAAC
90722802 CAGAGGAA-AAGAAG
1 CAGAGGAAGAAGAAG
90722816 CAGAGGAAGAAGAAG
1 CAGAGGAAGAAGAAG
90722831 ATGATGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.38, T:0.00
Consensus pattern (15 bp):
CAGAGGAAGAAGAAG
Found at i:90723769 original size:3 final size:3
Alignment explanation
Indices: 90723756--90723902 Score: 94
Period size: 3 Copynumber: 51.0 Consensus size: 3
90723746 TTCCATTTTC
* * * *
90723756 TCT TAT TCT TCT TCT CCT TCT CCT CCT TC- TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * * *
90723803 TCT TTT TCT TCT TCT TCT TTT TC- TCC TCC TCC TCT TCC TCC TCT TCC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
90723850 TCT TCAT T-T TCT TCT T-T GT-T TCT TC- TCT TGT TCT T-T TTT TCT
1 TCT TC-T TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT
90723892 T-T TCT TCT TCT
1 TCT TCT TCT TCT
90723903 ACTGCCCAGG
Statistics
Matches: 117, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
2 14 0.12
3 101 0.86
4 2 0.02
ACGTcount: A:0.01, C:0.34, G:0.01, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:90723885 original size:19 final size:19
Alignment explanation
Indices: 90723858--90723902 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
90723848 CCTCTTCATT
90723858 TTCTTCTTTGTTTCTTCTC
1 TTCTTCTTTGTTTCTTCTC
* * *
90723877 TTGTTCTTTTTTTCTTTTC
1 TTCTTCTTTGTTTCTTCTC
90723896 TTCTTCT
1 TTCTTCT
90723903 ACTGCCCAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.73
Consensus pattern (19 bp):
TTCTTCTTTGTTTCTTCTC
Found at i:90724288 original size:18 final size:17
Alignment explanation
Indices: 90724265--90724298 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
90724255 TAAATTGACC
90724265 TATATATA-ATTTTTTA
1 TATATATATATTTTTTA
90724281 TATATATATATTTTTTA
1 TATATATATATTTTTTA
90724298 T
1 T
90724299 CCCCTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATATATTTTTTA
Found at i:90724543 original size:2 final size:2
Alignment explanation
Indices: 90724536--90724567 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
90724526 CTACAAATTA
*
90724536 AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
90724568 GAGTTATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:90725724 original size:6 final size:6
Alignment explanation
Indices: 90725713--90725741 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
90725703 AAATGTTAAC
90725713 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
90725742 ATTAACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:90734290 original size:27 final size:27
Alignment explanation
Indices: 90734237--90734290 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
90734227 TCGATTGGAT
* *
90734237 ATATTTAAGTATGGTATATATTAATAA
1 ATATTTAACTATGGTATATAGTAATAA
*
90734264 ATATTTAACTATTG-ATATAGTAGATAA
1 ATATTTAACTATGGTATATAGTA-ATAA
90734291 TTATGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (27 bp):
ATATTTAACTATGGTATATAGTAATAA
Found at i:90737451 original size:21 final size:21
Alignment explanation
Indices: 90737425--90737465 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90737415 ATCTGCTCAA
* *
90737425 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
90737446 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
90737466 TCGCTTGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:90742610 original size:13 final size:13
Alignment explanation
Indices: 90742594--90742621 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
90742584 TTGAAAAATA
90742594 TTTTTGAGAAGTT
1 TTTTTGAGAAGTT
90742607 TTTTTGAGAAGTT
1 TTTTTGAGAAGTT
90742620 TT
1 TT
90742622 GTTTAAAATT
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:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (13 bp):
TTTTTGAGAAGTT
Found at i:90744622 original size:29 final size:29
Alignment explanation
Indices: 90744582--90744684 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
90744572 GTTGAGAGAT
*
90744582 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
90744611 TGGCACTAAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
* **
90744640 TGGCACTAAGTGTGCGAG-TTTAAAGTATA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
90744669 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
90744685 CGGCTGATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 5 0.07
29 64 0.93
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATGCA
Found at i:90748061 original size:41 final size:41
Alignment explanation
Indices: 90747953--90748063 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
90747943 GACTATGTTT
* * * *
90747953 GGCACTTAGTGTGCGA-TTTGAGATAGCTTTGGCTATATAT
1 GGCACTTAGTGTGCGAGATTGAGATAGCTTTGACTATAAAA
* *
90747993 GGCACTTAGTGTGTGAGACTGAGATAGCTTTGACTATAAAA
1 GGCACTTAGTGTGCGAGATTGAGATAGCTTTGACTATAAAA
* * *
90748034 GGCACTTAGTGTACGAGATTAAAATAGCTT
1 GGCACTTAGTGTGCGAGATTGAGATAGCTT
90748064 CAGCTATGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
40 15 0.25
41 44 0.75
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (41 bp):
GGCACTTAGTGTGCGAGATTGAGATAGCTTTGACTATAAAA
Found at i:90750278 original size:19 final size:19
Alignment explanation
Indices: 90750254--90750293 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
90750244 TGAGTCATCA
90750254 TAAATTCATAGGCATAACT
1 TAAATTCATAGGCATAACT
*
90750273 TAAATTTATAGGCATAACT
1 TAAATTCATAGGCATAACT
90750292 TA
1 TA
90750294 CATATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGGCATAACT
Found at i:90758019 original size:20 final size:19
Alignment explanation
Indices: 90757995--90758062 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
90757985 AAAAATTATT
90757995 TAAAAATTTA-TAAAAAATA
1 TAAAAA-TTAGTAAAAAATA
*
90758014 TGAAAATTAGTAAAAAAATA
1 TAAAAATTAGT-AAAAAATA
*
90758034 TAAATAATTATTAAAAAATTA
1 TAAA-AATTAGTAAAAAA-TA
90758055 CTAAAAAT
1 -TAAAAAT
90758063 ACATGTTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.07
19 6 0.15
20 17 0.41
21 11 0.27
22 4 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAAATTAGTAAAAAATA
Found at i:90758030 original size:11 final size:10
Alignment explanation
Indices: 90757985--90758061 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 10
90757975 CAAATATCTT
90757985 AAAAATTATTTA
1 AAAAATTA--TA
*
90757997 AAAATTTATA
1 AAAAATTATA
90758007 AAAAA-TAT-
1 AAAAATTATA
*
90758015 GAAAATTAGTA
1 AAAAATTA-TA
*
90758026 AAAAAATATA
1 AAAAATTATA
*
90758036 AATAATTATTA
1 AAAAATTA-TA
90758047 AAAAATTACTA
1 AAAAATTA-TA
90758058 AAAA
1 AAAA
90758062 TACATGTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
8 4 0.08
9 5 0.10
10 15 0.29
11 21 0.40
12 7 0.13
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:90758030 original size:21 final size:21
Alignment explanation
Indices: 90758006--90758051 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
90757996 AAAAATTTAT
*
90758006 AAAAAATATGAA-AATTAGTA
1 AAAAAATATAAATAATTAGTA
*
90758026 AAAAAATATAAATAATTATTA
1 AAAAAATATAAATAATTAGTA
90758047 AAAAA
1 AAAAA
90758052 TTACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
AAAAAATATAAATAATTAGTA
Found at i:90758151 original size:19 final size:20
Alignment explanation
Indices: 90758127--90758166 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
90758117 GTTTTTGAAT
90758127 ATTAT-AAAT-ATTACTTAAA
1 ATTATAAAATAATTA-TTAAA
90758146 ATTATAAAATAATTATTAAA
1 ATTATAAAATAATTATTAAA
90758166 A
1 A
90758167 ATCTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTATAAAATAATTATTAAA
Found at i:90758177 original size:21 final size:21
Alignment explanation
Indices: 90758132--90758177 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
90758122 TGAATATTAT
*
90758132 AAAT-ATTACTTAAAATTATA
1 AAATAATTACTTAAAAATATA
*
90758152 AAATAATTA-TTAAAAATCTA
1 AAATAATTACTTAAAAATATA
90758172 ATAATA
1 A-AATA
90758178 TATAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAATTACTTAAAAATATA
Found at i:90760652 original size:23 final size:23
Alignment explanation
Indices: 90760624--90760672 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
90760614 TAATAATGTC
90760624 AATATAAATTGTGACAAATTGAT
1 AATATAAATTGTGACAAATTGAT
90760647 AATATAAATTGTGACAAATTGAT
1 AATATAAATTGTGACAAATTGAT
90760670 AAT
1 AAT
90760673 CTTACTGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (23 bp):
AATATAAATTGTGACAAATTGAT
Found at i:90762989 original size:25 final size:26
Alignment explanation
Indices: 90762958--90763014 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
90762948 GTTACAGTAC
*
90762958 TTTTAAA-TTATACTTTTCAAT-ATTT
1 TTTTAAATTTA-AATTTTCAATAATTT
*
90762983 TTTTAAATTTAAATTTTTAATAATTT
1 TTTTAAATTTAAATTTTCAATAATTT
90763009 TTTTAA
1 TTTTAA
90763015 TATATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTAAATTTAAATTTTCAATAATTT
Found at i:90763013 original size:12 final size:13
Alignment explanation
Indices: 90762977--90763023 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
90762967 ATACTTTTCA
90762977 ATATTTTTTTAAAT
1 ATATTTTTTT-AAT
* **
90762991 TTAAATTTTTAAT
1 ATATTTTTTTAAT
90763004 A-ATTTTTTTAAT
1 ATATTTTTTTAAT
90763016 ATATTTTT
1 ATATTTTT
90763024 ACCATTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
12 10 0.38
13 9 0.35
14 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTTTTTTAAT
Found at i:90763031 original size:20 final size:20
Alignment explanation
Indices: 90763009--90763045 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
90762999 TTAATAATTT
90763009 TTTTAA-TATATTTTTACCA
1 TTTTAATTATATTTTTACCA
*
90763028 TTTTAATTTTATTTTTAC
1 TTTTAATTATATTTTTAC
90763046 AATATTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTAATTATATTTTTACCA
Found at i:90767210 original size:17 final size:17
Alignment explanation
Indices: 90767172--90767212 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
90767162 ATATATATTC
90767172 TAAAAA-AAATAAAAGT
1 TAAAAAGAAATAAAAGT
90767188 TCAAAAAGAATATAAAAG-
1 T-AAAAAGAA-ATAAAAGT
90767206 TAAAAAG
1 TAAAAAG
90767213 TAGTTAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
18 3 0.14
19 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (17 bp):
TAAAAAGAAATAAAAGT
Found at i:90767405 original size:23 final size:22
Alignment explanation
Indices: 90767379--90767421 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
90767369 AGTTCACATA
90767379 TAATTTATGTTAATTTTTTAATT
1 TAATTTAT-TTAATTTTTTAATT
*
90767402 TAATTTATTTTATTTTTTAA
1 TAATTTATTTAATTTTTTAA
90767422 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TAATTTATTTAATTTTTTAATT
Done.