Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_pilon, whole genome shotgun sequence
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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 33
Found at i:3799283 original size:309 final size:309
Alignment explanation
Indices: 3798724--3799343 Score: 1132
Period size: 309 Copynumber: 2.0 Consensus size: 309
3798714 GCTTTAATCT
*
3798724 TAAAATGTTTTTGAAACAATTTTCACAAAGTATTTAGAACAAAAAACGAGCCAAAAATTCAATTT
1 TAAAATGTTTTTGAAACAATTTTCACAAAGTATTTAGAACAAAAAACAAGCCAAAAATTCAATTT
*
3798789 TCAAAGAGATGTACCGATACACTAGTCCATGCATCGATGCACTAGTCCATACATCGATGCACTCT
66 TCAAAGAGATGTACCGATACACTAGTCCATGCATCAATGCACTAGTCCATACATCGATGCACTCT
3798854 TAATTAAATTGAATTTCGAATGCATTTAGTGTACCGATGCACTCTCTATGCATCGATGCACTCTT
131 TAATTAAATTGAATTTCGAATGCATTTAGTGTACCGATGCACTCTCTATGCATCGATGCACTCTT
* *
3798919 GAACAAATAGAAACATCGAATGCATTCAATGCACTATTGCACAAGTTATGCATCGATGCACTCAG
196 GAACAAATAGAAACATCGAATGCATTCAATGCACTAATGCACAAGCTATGCATCGATGCACTCAG
**
3798984 GCTATTTTAAAACACCTAATGTATTTTATGCATTGATGCACCCTCAATG
261 GCTATTTTAAAACACCTAATGTATTTTATGCACCGATGCACCCTCAATG
* *
3799033 TAAAATGTTTTTGATACAATTTTCACAAAGTATTTCGAACAAAAAACAAGCCAAAAATTCAATTT
1 TAAAATGTTTTTGAAACAATTTTCACAAAGTATTTAGAACAAAAAACAAGCCAAAAATTCAATTT
* * *
3799098 TCAAAGAGATGTATCGATACACTAGTTCATGCATCAATGCACTAGTCCATGCATCGATGCACTCT
66 TCAAAGAGATGTACCGATACACTAGTCCATGCATCAATGCACTAGTCCATACATCGATGCACTCT
*
3799163 TAATTAAATTGAATTTCGAATGCATTTAGTGTACCGATGCACTCTCTATGCATCGTTGCACTCTT
131 TAATTAAATTGAATTTCGAATGCATTTAGTGTACCGATGCACTCTCTATGCATCGATGCACTCTT
3799228 GAACAAATAGAAACATCGAATGCATTCAATGCACTAATGCACAAGCTATGCATCGATGCACTCAG
196 GAACAAATAGAAACATCGAATGCATTCAATGCACTAATGCACAAGCTATGCATCGATGCACTCAG
3799293 GCTATTTTAAAACACCTAATGTATTTTATGCACCGATGCACCCTCAATG
261 GCTATTTTAAAACACCTAATGTATTTTATGCACCGATGCACCCTCAATG
3799342 TA
1 TA
3799344 CAGATGCACT
Statistics
Matches: 299, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
309 299 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (309 bp):
TAAAATGTTTTTGAAACAATTTTCACAAAGTATTTAGAACAAAAAACAAGCCAAAAATTCAATTT
TCAAAGAGATGTACCGATACACTAGTCCATGCATCAATGCACTAGTCCATACATCGATGCACTCT
TAATTAAATTGAATTTCGAATGCATTTAGTGTACCGATGCACTCTCTATGCATCGATGCACTCTT
GAACAAATAGAAACATCGAATGCATTCAATGCACTAATGCACAAGCTATGCATCGATGCACTCAG
GCTATTTTAAAACACCTAATGTATTTTATGCACCGATGCACCCTCAATG
Found at i:3805160 original size:44 final size:43
Alignment explanation
Indices: 3805101--3805218 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 43
3805091 TGCATAATGT
*
3805101 ATCGATACACTATGAAGTGCATCGATGCA-TCCCTTTAAATGTGC
1 ATCGATACACAATGAAGTGCATCGATGCACT-CC-TTAAATGTGC
* *
3805145 ATCGATACATC-ATGAAGATGCACCGATGCACTCCTTGAATGTGC
1 ATCGATACA-CAATGAAG-TGCATCGATGCACTCCTTAAATGTGC
*
3805189 ATCGATGCACAATGACA-TGCATCGATGCAC
1 ATCGATACACAATGA-AGTGCATCGATGCAC
3805219 AATGACATGC
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
43 13 0.20
44 36 0.55
45 15 0.23
46 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
ATCGATACACAATGAAGTGCATCGATGCACTCCTTAAATGTGC
Found at i:3805228 original size:12 final size:14
Alignment explanation
Indices: 3805193--3805297 Score: 50
Period size: 12 Copynumber: 7.9 Consensus size: 14
3805183 ATGTGCATCG
3805193 ATGCACAATG-AC-
1 ATGCACAATGCACA
*
3805205 ATGCATCGATGCACA
1 ATGCA-CAATGCACA
*
3805220 ATG-AC-ATGCATCG
1 ATGCACAATGCA-CA
3805233 ATGCACAATG-AC-
1 ATGCACAATGCACA
*
3805245 ATGCATCGATGCACA
1 ATGCA-CAATGCACA
*
3805260 ATG-AC-ATGCATCG
1 ATGCACAATGCA-CA
*
3805273 ATGCATAATG-AC-
1 ATGCACAATGCACA
3805285 ATGCATCAATGCA
1 ATGCA-CAATGCA
3805298 TCCGTCGGGT
Statistics
Matches: 73, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
12 25 0.34
13 24 0.33
14 12 0.16
15 12 0.16
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (14 bp):
ATGCACAATGCACA
Found at i:3805298 original size:20 final size:20
Alignment explanation
Indices: 3805186--3805297 Score: 206
Period size: 20 Copynumber: 5.6 Consensus size: 20
3805176 TCCTTGAATG
3805186 TGCATCGATGCACAATGACA
1 TGCATCGATGCACAATGACA
3805206 TGCATCGATGCACAATGACA
1 TGCATCGATGCACAATGACA
3805226 TGCATCGATGCACAATGACA
1 TGCATCGATGCACAATGACA
3805246 TGCATCGATGCACAATGACA
1 TGCATCGATGCACAATGACA
*
3805266 TGCATCGATGCATAATGACA
1 TGCATCGATGCACAATGACA
*
3805286 TGCATCAATGCA
1 TGCATCGATGCA
3805298 TCCGTCGGGT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACAATGACA
Found at i:3812946 original size:14 final size:14
Alignment explanation
Indices: 3812927--3812966 Score: 66
Period size: 13 Copynumber: 3.0 Consensus size: 14
3812917 CATAAATTAT
3812927 TATATTTTAAAAAA
1 TATATTTTAAAAAA
3812941 TATATTTT-AAAAA
1 TATATTTTAAAAAA
3812954 -ATATTTTAAAAAA
1 TATATTTTAAAAAA
3812967 AAATCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 10 0.40
14 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATTTTAAAAAA
Found at i:3812965 original size:12 final size:12
Alignment explanation
Indices: 3812928--3812966 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
3812918 ATAAATTATT
3812928 ATATTTTAAAAAA
1 ATATTTT-AAAAA
3812941 TATATTTTAAAAA
1 -ATATTTTAAAAA
3812954 ATATTTTAAAAA
1 ATATTTTAAAAA
3812966 A
1 A
3812967 AAATCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 13 0.52
13 5 0.20
14 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTTTAAAAA
Found at i:3812967 original size:14 final size:14
Alignment explanation
Indices: 3812928--3812968 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
3812918 ATAAATTATT
*
3812928 ATATTTTAAAAAAT
1 ATATTTTAAAAAAA
3812942 ATATTTT--AAAAA
1 ATATTTTAAAAAAA
3812954 ATATTTTAAAAAAA
1 ATATTTTAAAAAAA
3812968 A
1 A
3812969 ATCCTTTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTTTAAAAAAA
Found at i:3814224 original size:24 final size:24
Alignment explanation
Indices: 3814196--3814243 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3814186 TGTTTATATT
3814196 TAATTT-TTATATTTTTATT-TTAAA
1 TAATTTCTTA-ATTTTT-TTCTTAAA
3814220 TAATTTCTTAATTTTTTTCTTAAA
1 TAATTTCTTAATTTTTTTCTTAAA
3814244 AAGTAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.09
24 17 0.77
25 3 0.14
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TAATTTCTTAATTTTTTTCTTAAA
Found at i:3816314 original size:21 final size:21
Alignment explanation
Indices: 3816282--3816324 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
3816272 TAAAAATTCC
3816282 TTATGTAGGCGTTTGGTTCGT
1 TTATGTAGGCGTTTGGTTCGT
3816303 TTATGGTA-GCGTTTGGTTCGT
1 TTAT-GTAGGCGTTTGGTTCGT
3816324 T
1 T
3816325 AGAATCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.09, C:0.09, G:0.33, T:0.49
Consensus pattern (21 bp):
TTATGTAGGCGTTTGGTTCGT
Found at i:3822273 original size:21 final size:22
Alignment explanation
Indices: 3822235--3822280 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3822225 ATCTGCTGAA
* **
3822235 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3822256 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3822278 ACT
1 ACT
3822281 TGTCTGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:3835898 original size:17 final size:17
Alignment explanation
Indices: 3835876--3835914 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3835866 GTAGACATAT
3835876 AGTTGAAAAGAAATCAA
1 AGTTGAAAAGAAATCAA
3835893 AGTTGAAAAGAAATCAA
1 AGTTGAAAAGAAATCAA
3835910 AGTTG
1 AGTTG
3835915 CAAGACTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (17 bp):
AGTTGAAAAGAAATCAA
Found at i:3836569 original size:65 final size:64
Alignment explanation
Indices: 3836458--3836586 Score: 231
Period size: 65 Copynumber: 2.0 Consensus size: 64
3836448 CTAATTTTAT
*
3836458 TTTATAAGATATGATTTTTGAAATAAGGCAAGATTAGGAAATTTCATATTCTGAGTATACGAAA
1 TTTATAAGATATGATTTTTGAAATAAGGCAAGATTAGGAAATTTCATATTCCGAGTATACGAAA
*
3836522 TTTATAAGATATGATTTTTGAAATTAAGGCAAGATTAGGAAATTTCATATTCCGAGTATATGAAA
1 TTTATAAGATATGATTTTTGAAA-TAAGGCAAGATTAGGAAATTTCATATTCCGAGTATACGAAA
3836587 ACAACAACCA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 23 0.37
65 39 0.63
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (64 bp):
TTTATAAGATATGATTTTTGAAATAAGGCAAGATTAGGAAATTTCATATTCCGAGTATACGAAA
Found at i:3843532 original size:2 final size:2
Alignment explanation
Indices: 3843527--3843562 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3843517 ATATATACAT
3843527 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3843563 GGACAGTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3875060 original size:13 final size:13
Alignment explanation
Indices: 3875042--3875077 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3875032 TGCGTCATAA
*
3875042 ATTTATGACGCGT
1 ATTTATGACGCGC
*
3875055 ATTTATGACACGC
1 ATTTATGACGCGC
3875068 ATTTATGACG
1 ATTTATGACG
3875078 TTCATTGCGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:3875219 original size:85 final size:85
Alignment explanation
Indices: 3875055--3875220 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 85
3875045 TATGACGCGT
* * * *
3875055 ATTTATGACACGCATTTATGACGTTCATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATGTATGACGTTCATTGCGCGTCATTGAAGCACACGTCATAAATAAAGATGA
*
3875120 CACATATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
*
3875140 ATTTATGACACGCATGTATGAC-TTACATTGCGTGTCATTGAAGCACACGTCATTAAA-AAAGAT
1 ATTTATGACACGCATGTATGACGTT-CATTGCGCGTCATTGAAGCACACGTCA-TAAATAAAGAT
3875203 GACACACATTCT-TGTGTC
64 GACACACATT-TGTGTGTC
3875221 GTGATTGTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
84 2 0.03
85 65 0.90
86 5 0.07
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACGTTCATTGCGCGTCATTGAAGCACACGTCATAAATAAAGATGA
CACACATTTGTGTGTCATAA
Found at i:3877030 original size:27 final size:27
Alignment explanation
Indices: 3876992--3877051 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
3876982 TTCAATATAC
3876992 TCGGTTTAGATGGCTTAACCAGTTAAT
1 TCGGTTTAGATGGCTTAACCAGTTAAT
3877019 TCGGTTTAGATGGCTTAACCAGTTAAT
1 TCGGTTTAGATGGCTTAACCAGTTAAT
3877046 TCGGTT
1 TCGGTT
3877052 ATAGGAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
TCGGTTTAGATGGCTTAACCAGTTAAT
Found at i:3879123 original size:15 final size:15
Alignment explanation
Indices: 3879089--3879117 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3879079 GGACTGCTGC
3879089 AAAGAGAAAAAGGGA
1 AAAGAGAAAAAGGGA
3879104 AAAGAGAAAAAGGG
1 AAAGAGAAAAAGGG
3879118 GGAAGAAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAAGAGAAAAAGGGA
Found at i:3884287 original size:17 final size:16
Alignment explanation
Indices: 3884256--3884289 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3884246 CAAGTGAGGA
3884256 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3884272 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3884289 T
1 T
3884290 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3890693 original size:20 final size:20
Alignment explanation
Indices: 3890651--3890699 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3890641 TTCTTTTATC
*
3890651 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
3890671 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
3890690 TTTTACCTTT
1 TTTTATCTTT
3890700 TCTATTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:3894554 original size:17 final size:16
Alignment explanation
Indices: 3894523--3894556 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3894513 CACGTGAGGA
3894523 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3894539 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3894556 T
1 T
3894557 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3901510 original size:14 final size:14
Alignment explanation
Indices: 3901493--3901528 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3901483 CAACCAAACT
3901493 GAGTCAACTCA-TCC
1 GAGTCAACTCACT-C
3901507 GAGTCAACTCACTC
1 GAGTCAACTCACTC
3901521 GAGTCAAC
1 GAGTCAAC
3901529 CAGTTGACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (14 bp):
GAGTCAACTCACTC
Found at i:3903221 original size:67 final size:67
Alignment explanation
Indices: 3903112--3903247 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 67
3903102 TGCTTAAATA
* *
3903112 ATGGAACACTCATGTTATTTCTAAATCTTCAATAAATATGATGTAAAAGATTATGAATGCCCTCC
1 ATGGAACACTCATGTTACTTCTAAATCTTCAATAAATATGATGTAAAAAATTATGAATGCCCTCC
3903177 TG
66 TG
* *
3903179 ATGGAACACTCATGTTACTTCTAAATCTTCAATAAATCTGATGTAAAAAATTATGAATGCCTTCC
1 ATGGAACACTCATGTTACTTCTAAATCTTCAATAAATATGATGTAAAAAATTATGAATGCCCTCC
3903244 TG
66 TG
3903246 AT
1 AT
3903248 TACTCAATTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (67 bp):
ATGGAACACTCATGTTACTTCTAAATCTTCAATAAATATGATGTAAAAAATTATGAATGCCCTCC
TG
Found at i:3904154 original size:24 final size:24
Alignment explanation
Indices: 3904099--3904154 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3904089 ACTAAAAATT
* * * *
3904099 ATAATTGAAATTTTTTAAAACATAT
1 ATAATT-AAATTTATAAAAAAATAA
*
3904124 ATTATTAAATTTATAAAAAAATAA
1 ATAATTAAATTTATAAAAAAATAA
3904148 ATAATTA
1 ATAATTA
3904155 TTTTTTTATG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
ATAATTAAATTTATAAAAAAATAA
Found at i:3906370 original size:14 final size:14
Alignment explanation
Indices: 3906351--3906381 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3906341 TATTTTTACT
3906351 AATTGTGTTTATAA
1 AATTGTGTTTATAA
*
3906365 AATTGTGTTTATCA
1 AATTGTGTTTATAA
3906379 AAT
1 AAT
3906382 ATCATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (14 bp):
AATTGTGTTTATAA
Found at i:3907752 original size:17 final size:17
Alignment explanation
Indices: 3907730--3907772 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
3907720 ATTCAAGAAT
3907730 TATGGTGAATTATAAGA
1 TATGGTGAATTATAAGA
3907747 TATGGTGAATTATAAGA
1 TATGGTGAATTATAAGA
3907764 TATGGTGAA
1 TATGGTGAA
3907773 GTGTTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.35
Consensus pattern (17 bp):
TATGGTGAATTATAAGA
Found at i:3913810 original size:2 final size:2
Alignment explanation
Indices: 3913803--3913845 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3913793 CCCTTTTTAA
3913803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3913845 A
1 A
3913846 AAGTGTCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3922699 original size:19 final size:20
Alignment explanation
Indices: 3922675--3922722 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3922665 AATGATTTTC
* * *
3922675 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
3922694 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
3922714 TTTTGAAAA
1 TTTTGAAAA
3922723 ATGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:3923903 original size:26 final size:26
Alignment explanation
Indices: 3923869--3923979 Score: 213
Period size: 26 Copynumber: 4.3 Consensus size: 26
3923859 TAAGGGGAGG
*
3923869 TTTGCTAAAAACAATTTTTCAAATGT
1 TTTGTTAAAAACAATTTTTCAAATGT
3923895 TTTGTTAAAAACAATTTTTCAAATGT
1 TTTGTTAAAAACAATTTTTCAAATGT
3923921 TTTGTTAAAAACAATTTTTCAAATGT
1 TTTGTTAAAAACAATTTTTCAAATGT
3923947 TTTGTTAAAAACAATTTTTCAAATGT
1 TTTGTTAAAAACAATTTTTCAAATGT
3923973 TTTGTTA
1 TTTGTTA
3923980 TATCAAAAAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 84 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTGTTAAAAACAATTTTTCAAATGT
Found at i:3930766 original size:2 final size:2
Alignment explanation
Indices: 3930759--3930832 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
3930749 AATAACAATA
3930759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3930801 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3930833 TATTATAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3930901 original size:23 final size:23
Alignment explanation
Indices: 3930872--3930979 Score: 117
Period size: 23 Copynumber: 4.5 Consensus size: 23
3930862 TTCAAAAATG
3930872 TGTTTTCAAAACTATATATTATA
1 TGTTTTCAAAACTATATATTATA
* ** * *
3930895 TGTTTTCAAAAATACGTTTTCAAAAA
1 TGTTTTCAAAACTATATATT---ATA
* *
3930921 TATTTTAAAAACTATATATTATA
1 TGTTTTCAAAACTATATATTATA
3930944 TGTTTTCAAAACTATATATTATA
1 TGTTTTCAAAACTATATATTATA
3930967 TGTTTTCCAAAAC
1 TGTTTT-CAAAAC
3930980 CGATTTTTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
23 45 0.67
24 6 0.09
26 16 0.24
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (23 bp):
TGTTTTCAAAACTATATATTATA
Found at i:3930915 original size:14 final size:14
Alignment explanation
Indices: 3930896--3930922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3930886 TATATTATAT
3930896 GTTTTCAAAAATAC
1 GTTTTCAAAAATAC
3930910 GTTTTCAAAAATA
1 GTTTTCAAAAATA
3930923 TTTTAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (14 bp):
GTTTTCAAAAATAC
Found at i:3931152 original size:38 final size:35
Alignment explanation
Indices: 3930944--3931159 Score: 148
Period size: 37 Copynumber: 5.7 Consensus size: 35
3930934 ATATATTATA
* *
3930944 TGTTTTCAAAACTATATATTATATGTTTTCCAAAAC
1 TGTTTTTAAAACTATATATTATATGATTT-CAAAAC
* * *
3930980 CGATTTTTTAAAAAACTATATATTATATATGCTTTCAAAAATA
1 TG--TTTTT--AAAACTATATA-T-TATATGATTTC-AAAA-C
* * * *
3931023 TGTTTTTAAAACTATATATTATACGTTTTAAAAAA
1 TGTTTTTAAAACTATATATTATATGATTTCAAAAC
*
3931058 TGTGTTTTCAAAACCATAT-TATATAT-ATTTTCAAAATC
1 TGT-TTTT-AAAACTATATAT-TATATGA-TTTCAAAA-C
* *
3931096 TATTTTTTTAAACTATATATTATATGATTTCAGAAAC
1 T-GTTTTTAAAACTATATATTATATGATTTCA-AAAC
3931133 TGTTTTCTAAAAACTATATATTATATG
1 TGTTTT-T-AAAACTATATATTATATG
3931160 TGTGTTTTCA
Statistics
Matches: 143, Mismatches: 18, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
35 4 0.03
36 14 0.10
37 49 0.34
38 32 0.22
39 12 0.08
40 11 0.08
41 7 0.05
42 13 0.09
43 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (35 bp):
TGTTTTTAAAACTATATATTATATGATTTCAAAAC
Found at i:3932218 original size:42 final size:43
Alignment explanation
Indices: 3932113--3932228 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
3932103 AAGCTTTACC
* * * * *
3932113 GCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGATATCTATA
1 GCGGCGTTTGTGTAAAAAACGCCGCAAAAGGTCGAGACCTATA
* *
3932156 GCGGCGTTTTTGTAACAAACGCCGCAAAAGGTC-AGACCTATA
1 GCGGCGTTTGTGTAAAAAACGCCGCAAAAGGTCGAGACCTATA
3932198 GCGGCGTTTGT-TACAAAAACGCCGCGAAAAG
1 GCGGCGTTTGTGTA-AAAAACGCCGC-AAAAG
3932229 AAAGATCTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.03
42 27 0.41
43 37 0.56
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (43 bp):
GCGGCGTTTGTGTAAAAAACGCCGCAAAAGGTCGAGACCTATA
Found at i:3932218 original size:85 final size:85
Alignment explanation
Indices: 3932114--3932350 Score: 223
Period size: 85 Copynumber: 2.8 Consensus size: 85
3932104 AGCTTTACCG
* * *
3932114 CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGTAACAAACGCC
1 CGGCG-TTTTGGAAAAAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAACAAACGCC
* *
3932179 GCAAAAGGTC-AGACCTATAG
65 GCAAAAAGTCAAGACCTATAA
* * * **
3932199 CGGCG-TTTGTTACAAAAACGCCGCGAAAA-G-AAAGATCTATAGTTGCGTTTTTGGAACAAAC-
1 CGGCGTTTTG-GA-AAAAACGCCGC-AAAAGGTCAATATCTATAGCGGCGTTTTTGGAACAAACG
* * *
3932260 ACGTCAAAAAGTCAATATCTATAA
63 CCG-CAAAAAGTCAAGACCTATAA
* * * * *
3932284 TGGCGTTTTGGAACAAACGCCACAAAAGGTCAATATCTATAACGGCGTTTGTGGATACAAACGCC
1 CGGCGTTTTGGAAAAAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGA-ACAAACGCC
3932349 GC
65 GC
3932351 TAATTACATT
Statistics
Matches: 118, Mismatches: 24, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
83 10 0.08
84 44 0.37
85 47 0.40
86 15 0.13
87 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (85 bp):
CGGCGTTTTGGAAAAAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAACAAACGCCG
CAAAAAGTCAAGACCTATAA
Found at i:3932310 original size:42 final size:43
Alignment explanation
Indices: 3932113--3932350 Score: 245
Period size: 42 Copynumber: 5.6 Consensus size: 43
3932103 AAGCTTTACC
*
3932113 GCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGATATCTATA
1 GCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATA
* * *
3932156 GCGGCGTTTTTGTAACAAACGCCGCAAAAGGTC-AGACCTATA
1 GCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATA
** * *
3932198 GCGGCGTTTGTTACAA-AAACGCCGCGAAAA-G-AAAGATCTATA
1 GCGGCGTTT-TTGGAACAAACGCCGC-AAAAGGTCAATATCTATA
** * *
3932240 GTTGCGTTTTTGGAACAAAC-ACGTCAAAAAGTCAATATCTATA
1 GCGGCGTTTTTGGAACAAACGCCG-CAAAAGGTCAATATCTATA
** *
3932283 ATGGCG-TTTTGGAACAAACGCCACAAAAGGTCAATATCTATA
1 GCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATA
* *
3932325 ACGGCGTTTGTGGATACAAACGCCGC
1 GCGGCGTTTTTGGA-ACAAACGCCGC
3932351 TAATTACATT
Statistics
Matches: 163, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
41 10 0.06
42 83 0.51
43 60 0.37
44 10 0.06
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (43 bp):
GCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATA
Found at i:3935424 original size:41 final size:41
Alignment explanation
Indices: 3935365--3935702 Score: 333
Period size: 41 Copynumber: 8.2 Consensus size: 41
3935355 GTTTACAAAT
* *
3935365 GCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTGTAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * *
3935406 GCCACTGAAGTACGAGTCTTTAGCGACATTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * *
3935447 GCCACTGAAGTATGATTCTATT-GCGGCGTTTATATAAAAAC
1 GCCACTAAAGTACGAGTCT-TTAGCGGCGTTTGTATAAAAAC
* * *
3935488 GCCACTAAATTACGAGTCTTTAGTAGG-GTTTGTAAACACAAAC
1 GCCACTAAAGTACGAGTCTTTAG-CGGCGTTTGTATA-A-AAAC
*
3935531 GCCACTAAAGTACGAGTCGTTAGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * *
3935572 GCCACTAAA-TAACTAGTTTTTAGCAGCGTTTGTACAAAAAC
1 GCCACTAAAGT-ACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * ** * *
3935613 GCCACTAATGAACTCGTTTTTAGCGGCGTTTGTACAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * *
3935654 TGCCACTAAAATATGAGTATTTAGCGGCGTTT-TAAAAAAAAC
1 -GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT-ATAAAAAC
*
3935696 ACCACTA
1 GCCACTA
3935703 TAGCACGTTT
Statistics
Matches: 248, Mismatches: 39, Indels: 20
0.81 0.13 0.07
Matches are distributed among these distances:
40 3 0.01
41 173 0.70
42 39 0.16
43 33 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
Found at i:3935635 original size:125 final size:122
Alignment explanation
Indices: 3935365--3935702 Score: 312
Period size: 125 Copynumber: 2.7 Consensus size: 122
3935355 GTTTACAAAT
* * ** *
3935365 GCCACTAAAGT-ACAAGTCTTTAGCGGCGTTTGTGTAAAAACGCCACTGAAGTACGAGTCTTTAG
1 GCCACTAAA-TAACGAGTCTTTAGAGGCGTTTGTACAAAAACGCCACTAAAGTACGAGTCTTTAG
* * * * *
3935429 CGACATTTGTATAAAAACGCCACTGAAGTATGATTCTATTGCGGCGTTTATATAAAAAC
65 CGGCGTTTGTATAAAAACGCCACT-AAATATGATTCTATTGCAGCGTTTATACAAAAAC
* * *
3935488 GCCACTAAATTACGAGTCTTTAGTAGG-GTTTGTAAACACAAACGCCACTAAAGTACGAGTCGTT
1 GCCACTAAATAACGAGTCTTTAG-AGGCGTTTGT--ACAAAAACGCCACTAAAGTACGAGTCTTT
*
3935552 AGCGGCGTTTGTATAAAAACGCCACTAAATAACT-AGTT-T-TTAGCAGCGTTTGTACAAAAAC
63 AGCGGCGTTTGTATAAAAACGCCACTAAAT-A-TGA-TTCTATT-GCAGCGTTTATACAAAAAC
** * * * * *
3935613 GCCACT-AATGAACTCGTTTTTAGCGGCGTTTGTACAAAAACTGCCACTAAAATATGAGTATTTA
1 GCCACTAAAT-AACGAGTCTTTAGAGGCGTTTGTACAAAAAC-GCCACTAAAGTACGAGTCTTTA
* *
3935677 GCGGCGTTT-TAAAAAAAACACCACTA
64 GCGGCGTTTGT-ATAAAAACGCCACTA
3935703 TAGCACGTTT
Statistics
Matches: 178, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
122 1 0.01
123 34 0.19
124 52 0.29
125 88 0.49
126 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (122 bp):
GCCACTAAATAACGAGTCTTTAGAGGCGTTTGTACAAAAACGCCACTAAAGTACGAGTCTTTAGC
GGCGTTTGTATAAAAACGCCACTAAATATGATTCTATTGCAGCGTTTATACAAAAAC
Found at i:3935641 original size:166 final size:167
Alignment explanation
Indices: 3935359--3935677 Score: 400
Period size: 166 Copynumber: 1.9 Consensus size: 167
3935349 GTTTGTGTTT
* * * *
3935359 ACAAATGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTGTAAAAACGCCACTGAAGTACGAGTC
1 ACAAACGCCACTAAAGTACAAGTCGTTAGCGGCGTTTGTATAAAAACGCCACTGAAATACGAGTC
* * *
3935424 TTTAGCGACATTTGTATAAAAACGCCACTGAAGTATGATTCTATTGCGGCGTTTATATAAAAAC-
66 TTTAGCGACATTTGTACAAAAACGCCACTGAAGAATGATTCTATTGCGGCGTTTATACAAAAACT
* *
3935488 GCCACTAAATTACGAGTCTTTAGTAGGGTTTGTAAAC
131 GCCACTAAAATACGAGTATTTAGTAGGGTTTGTAAAC
* *
3935525 ACAAACGCCACTAAAGTACGAGTCGTTAGCGGCGTTTGTATAAAAACGCCACT-AAATAACTAGT
1 ACAAACGCCACTAAAGTACAAGTCGTTAGCGGCGTTTGTATAAAAACGCCACTGAAAT-ACGAGT
* * *
3935589 TTTTAGC-AGCGTTTGTACAAAAACGCCACT-AATGAACTCG-TT-T-TTAGCGGCGTTTGTACA
65 CTTTAGCGA-CATTTGTACAAAAACGCCACTGAA-GAA-T-GATTCTATT-GCGGCGTTTATACA
*
3935649 AAAACTGCCACTAAAATATGAGTATTTAG
125 AAAACTGCCACTAAAATACGAGTATTTAG
3935678 CGGCGTTTTA
Statistics
Matches: 131, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
165 8 0.06
166 99 0.76
167 23 0.18
168 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (167 bp):
ACAAACGCCACTAAAGTACAAGTCGTTAGCGGCGTTTGTATAAAAACGCCACTGAAATACGAGTC
TTTAGCGACATTTGTACAAAAACGCCACTGAAGAATGATTCTATTGCGGCGTTTATACAAAAACT
GCCACTAAAATACGAGTATTTAGTAGGGTTTGTAAAC
Found at i:3935702 original size:83 final size:82
Alignment explanation
Indices: 3935469--3935702 Score: 222
Period size: 84 Copynumber: 2.8 Consensus size: 82
3935459 TGATTCTATT
* * * * * * * *
3935469 GCGGCGTTTATATAAAAACGCCACTAAATTACGAGTCTTTAGTAGGGTTTGTAAACACAAACGCC
1 GCGGCGTTTGTACAAAAACGCCACTAAATAACTAGTATTTAGCAGCGTTTGTAAA-A-AAACACC
* * ** **
3935534 ACTAAAGTACGAGTCGTTA
64 ACTAATGAACTCGTTTTTA
* * * *
3935553 GCGGCGTTTGTATAAAAACGCCACTAAATAACTAGTTTTTAGCAGCGTTTGTACAAAAACGCCAC
1 GCGGCGTTTGTACAAAAACGCCACTAAATAACTAGTATTTAGCAGCGTTTGTAAAAAAACACCAC
3935618 TAATGAACTCGTTTTTA
66 TAATGAACTCGTTTTTA
*
3935635 GCGGCGTTTGTACAAAAACTGCCACTAAA-ATA-TGAGTATTTAGCGGCGTTT-TAAAAAAAACA
1 GCGGCGTTTGTACAAAAAC-GCCACTAAATA-ACT-AGTATTTAGCAGCGTTTGT-AAAAAAACA
3935697 CCACTA
62 CCACTA
3935703 TAGCACGTTT
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
82 41 0.32
83 39 0.30
84 48 0.38
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (82 bp):
GCGGCGTTTGTACAAAAACGCCACTAAATAACTAGTATTTAGCAGCGTTTGTAAAAAAACACCAC
TAATGAACTCGTTTTTA
Found at i:3939117 original size:3 final size:3
Alignment explanation
Indices: 3939109--3939179 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
3939099 TTTTTACCCA
3939109 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3939157 TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
3939180 AATATATATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3940524 original size:13 final size:13
Alignment explanation
Indices: 3940506--3940533 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3940496 TGATTAATTA
3940506 TAAATTAGATTTT
1 TAAATTAGATTTT
3940519 TAAATTAGATTTT
1 TAAATTAGATTTT
3940532 TA
1 TA
3940534 CTATAATTTA
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:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
TAAATTAGATTTT
Found at i:3940647 original size:19 final size:20
Alignment explanation
Indices: 3940615--3940652 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3940605 ATTTTATTTG
**
3940615 TTTATATTTTTAAA-ATATT
1 TTTATATTCATAAATATATT
3940634 TTTATATTCATAAATATAT
1 TTTATATTCATAAATATAT
3940653 ATATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATATTCATAAATATATT
Found at i:3941396 original size:18 final size:18
Alignment explanation
Indices: 3941354--3941397 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3941344 TTGTCAAATT
3941354 TTTTATTTATTATTTTTA
1 TTTTATTTATTATTTTTA
**
3941372 TAATATTTA-TATGTTTTA
1 TTTTATTTATTAT-TTTTA
3941390 TTTTATTT
1 TTTTATTT
3941398 GCAAGTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATTTATTATTTTTA
Found at i:3944690 original size:15 final size:15
Alignment explanation
Indices: 3944667--3944698 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3944657 TTTGGGATCA
*
3944667 ATACCTTTTGCATAC
1 ATACATTTTGCATAC
3944682 ATACATTTTGCATAC
1 ATACATTTTGCATAC
3944697 AT
1 AT
3944699 TCATCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (15 bp):
ATACATTTTGCATAC
Found at i:3953344 original size:83 final size:83
Alignment explanation
Indices: 3953205--3953821 Score: 1055
Period size: 83 Copynumber: 7.5 Consensus size: 83
3953195 AATTTGCCAA
* * *
3953205 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACAAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
3953270 GAAGATGAATGTGTTCAT
66 GAAGATGAATGTGTTCAT
3953288 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
*
3953353 GAAGATGAATGTGCTCAT
66 GAAGATGAATGTGTTCAT
*
3953371 AGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TGGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
3953435 GAAGATGAATGTGTTCAT
66 GAAGATGAATGTGTTCAT
*
3953453 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGAC--AACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
3953516 GAAGATGAATGTGTTCAT
66 GAAGATGAATGTGTTCAT
* *
3953534 AGCA--TTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
3953597 GAAGATGAATGTGTTCAT
66 GAAGATGAATGTGTTCAT
* * * *
3953615 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACAAATCATTGAATTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
*
3953680 GAAAATGAATGTGTTCAT
66 GAAGATGAATGTGTTCAT
*
3953698 AGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
3953763 GAAGATGAATGTGTTCAT
66 GAAGATGAATGTGTTCAT
* *
3953781 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATTTGGTT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
3953822 TGGTAAGAAC
Statistics
Matches: 506, Mismatches: 23, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
79 36 0.07
81 80 0.16
82 79 0.16
83 311 0.61
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTG
GAAGATGAATGTGTTCAT
Found at i:3954958 original size:111 final size:113
Alignment explanation
Indices: 3954574--3955195 Score: 1059
Period size: 112 Copynumber: 5.6 Consensus size: 113
3954564 ATTGACATTT
3954574 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAA
1 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3954638 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
66 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
3954686 CAGAGAAGGTTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3954750 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGA-TATTTTTGC
66 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
3954797 C--AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG-A
1 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3954859 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTA-TTTTGC
66 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
3954906 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3954971 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTA-TTTTGC
66 TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
*
3955018 CAGAGAAAGTTCATAATGAG-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * **
3955082 TTTGTTCAACCTTTTG-CTCAAATCTATTACTTGATGGGTTATTTTTTTT
66 TTTGTTCAACCTTTTGTCTGAATTC-ATCACTTGATGGATTA-TTTTTGC
* *
3955131 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG-AGAAAGTTCATAATGAGAAGA
1 CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGA
3955195 A
65 A
3955196 CTCATCAAAG
Statistics
Matches: 491, Mismatches: 8, Indels: 20
0.95 0.02 0.04
Matches are distributed among these distances:
109 76 0.15
110 37 0.08
111 150 0.31
112 162 0.33
113 26 0.05
114 40 0.08
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (113 bp):
CAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGC
Found at i:3954960 original size:221 final size:224
Alignment explanation
Indices: 3954577--3955195 Score: 1049
Period size: 221 Copynumber: 2.8 Consensus size: 224
3954567 GACATTTCAG
3954577 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTT
1 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
3954641 GTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAG
66 GTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAG
3954706 AAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
3954770 AATTCATCACTTGATGGA-TATTTTTGCC-
196 AATTCATCACTTGATGGATTA-TTTTGCCA
3954798 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG-ATTT
1 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
3954862 GTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTA-TTTTGCCAGAGAAGGTTCATAATGAG
66 GTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAG
3954926 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
3954991 AATTCATCACTTGATGGATTATTTTGCCA
196 AATTCATCACTTGATGGATTATTTTGCCA
*
3955020 GAGAAAGTTCATAATGAG-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
1 -AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
* * * * ** *
3955084 TGTTCAACCTTTTG-CTCAAATCTATTACTTGATGGGTTATTTTTTTTCAGAGAAAGTTCATAAT
65 TGTTCAACCTTTTGTCTGAATTC-ATCACTTGATGGATTA-TTTTTGCCAGAGAAGGTTCATAAT
*
3955148 GAGAAGAACTCATCTGAAGAAAGAAG-AGAAAGTTCATAATGAGAAGAA
128 GAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
3955196 CTCATCAAAG
Statistics
Matches: 379, Mismatches: 9, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
220 39 0.10
221 155 0.41
222 72 0.19
223 47 0.12
224 2 0.01
225 64 0.17
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (224 bp):
AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
GTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAG
AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
AATTCATCACTTGATGGATTATTTTGCCA
Found at i:3955449 original size:3 final size:3
Alignment explanation
Indices: 3955441--3955513 Score: 89
Period size: 3 Copynumber: 24.7 Consensus size: 3
3955431 TTTTTACCCA
3955441 TAT TAT TAT TAT TAT TAT ATAT TAT TA- TAT T-T ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
3955486 TAA TAT TAT T-T CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3955514 AATATATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
2 4 0.07
3 53 0.87
4 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3955501 original size:14 final size:15
Alignment explanation
Indices: 3955444--3955513 Score: 90
Period size: 14 Copynumber: 4.7 Consensus size: 15
3955434 TTACCCATAT
3955444 TATTATTATTATTATA
1 TATTATTATTATTA-A
*
3955460 TATTATTA-TATTTA
1 TATTATTATTATTAA
3955474 TATTATTATTATTAA
1 TATTATTATTATTAA
* *
3955489 TATTATT-TCATTAT
1 TATTATTATTATTAA
3955503 TATTATTATTA
1 TATTATTATTA
3955514 AATATATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
14 21 0.45
15 18 0.38
16 8 0.17
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:3961902 original size:22 final size:22
Alignment explanation
Indices: 3961876--3961921 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3961866 AAACGTTAAG
3961876 TATTATTTTGAAAACAAATAAA
1 TATTATTTTGAAAACAAATAAA
3961898 TATTATTTTGAAAACAAATAAA
1 TATTATTTTGAAAACAAATAAA
3961920 TA
1 TA
3961922 CCGAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (22 bp):
TATTATTTTGAAAACAAATAAA
Found at i:3962714 original size:7 final size:7
Alignment explanation
Indices: 3962663--3962694 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3962653 AAAATTTAAA
3962663 AAAATAC
1 AAAATAC
3962670 AAAATAC
1 AAAATAC
3962677 AAAATAC
1 AAAATAC
3962684 AAAATAC
1 AAAATAC
3962691 AAAA
1 AAAA
3962695 ATATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAC
Found at i:3962716 original size:29 final size:29
Alignment explanation
Indices: 3962662--3962727 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
3962652 TAAAATTTAA
*
3962662 AAAAATACAAAATACAAAATACAAAATAC
1 AAAAATACAAAATACAAAATAAAAAATAC
* *
3962691 AAAAATATAATATA-AAATATAAAAAATA-
1 AAAAATACAAAATACAAA-ATAAAAAATAC
*
3962719 AGAAATACA
1 AAAAATACA
3962728 GACTGTAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.18
Consensus pattern (29 bp):
AAAAATACAAAATACAAAATAAAAAATAC
Found at i:3962719 original size:7 final size:7
Alignment explanation
Indices: 3962661--3962725 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
3962651 TTAAAATTTA
3962661 AAAAAAT
1 AAAAAAT
*
3962668 ACAAAAT
1 AAAAAAT
*
3962675 ACAAAAT
1 AAAAAAT
*
3962682 ACAAAAT
1 AAAAAAT
3962689 ACAAAAAT
1 A-AAAAAT
* *
3962697 ATAATAT
1 AAAAAAT
*
3962704 AAAATAT
1 AAAAAAT
3962711 AAAAAAT
1 AAAAAAT
*
3962718 AAGAAAT
1 AAAAAAT
3962725 A
1 A
3962726 CAGACTGTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
7 44 0.88
8 6 0.12
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:3963491 original size:64 final size:64
Alignment explanation
Indices: 3963409--3963542 Score: 259
Period size: 64 Copynumber: 2.1 Consensus size: 64
3963399 TATTATCTCT
*
3963409 TTGTTAGCCCGTGTACACTTTTGAGAACTATAGATATGTAAGTCTATTGAGGTTGTGCACTATG
1 TTGTCAGCCCGTGTACACTTTTGAGAACTATAGATATGTAAGTCTATTGAGGTTGTGCACTATG
3963473 TTGTCAGCCCGTGTACACTTTTGAGAACTATAGATATGTAAGTCTATTGAGGTTGTGCACTATG
1 TTGTCAGCCCGTGTACACTTTTGAGAACTATAGATATGTAAGTCTATTGAGGTTGTGCACTATG
3963537 TTGTCA
1 TTGTCA
3963543 CCATAGCTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (64 bp):
TTGTCAGCCCGTGTACACTTTTGAGAACTATAGATATGTAAGTCTATTGAGGTTGTGCACTATG
Found at i:3963660 original size:31 final size:31
Alignment explanation
Indices: 3963619--3963727 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
3963609 TAGGTCTCGA
* *
3963619 AGAACCTAGGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCCT
* * *
3963650 AGAATATAGGTATACTGTCCATATG-TCCCG
1 AGAACATAGGTAAACTGTCCATATGTTCCCT
* * * *
3963680 AAAGACATAGGTAATTCTTTCCATATGTTCCGT
1 AGA-ACATAGGTAA-ACTGTCCATATGTTCCCT
3963713 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
3963728 CATCGACTCT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
30 5 0.08
31 31 0.51
32 20 0.33
33 5 0.08
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCCT
Found at i:3963716 original size:63 final size:62
Alignment explanation
Indices: 3963601--3963724 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 62
3963591 AACCTCGGCA
* * * *
3963601 ACTGTCCATAGGTCTCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAATATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
3963663 ACTGTCCATATGTCCCGAA-AGACATAGGTAATTCTTTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTA
3963725 AACCATCGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 1 0.02
62 26 0.49
63 26 0.49
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:3965927 original size:64 final size:64
Alignment explanation
Indices: 3965799--3965935 Score: 152
Period size: 64 Copynumber: 2.1 Consensus size: 64
3965789 CCTTAACATA
* *
3965799 TGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTAATCTTAAGGGGG
1 TGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCAATCTTAAGGGGG
* * * * ** * *
3965863 TGTATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAA-GGG
1 TGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTT-CAATCTTAAGGGG
3965926 G
64 G
3965927 TGCATCGAT
1 TGCATCGAT
3965936 ACACACTGAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 52 0.87
65 6 0.10
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCAATCTTAAGGGGG
Found at i:3967962 original size:15 final size:15
Alignment explanation
Indices: 3967939--3967973 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3967929 TACCATTAAG
*
3967939 TTAATTTATAAAATA
1 TTAAATTATAAAATA
3967954 TTAAATTATAAAATA
1 TTAAATTATAAAATA
3967969 TTAAA
1 TTAAA
3967974 CGTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATTATAAAATA
Found at i:3968962 original size:14 final size:15
Alignment explanation
Indices: 3968929--3968965 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3968919 TGACCCAATC
*
3968929 GAGTCAACTCAGTTT
1 GAGTCAACTCAGTCT
3968944 GAGTCAACTC-GTCT
1 GAGTCAACTCAGTCT
3968958 GAGTCAAC
1 GAGTCAAC
3968966 CTGTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (15 bp):
GAGTCAACTCAGTCT
Found at i:3970460 original size:25 final size:25
Alignment explanation
Indices: 3970432--3970479 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3970422 AATAAGAAGT
**
3970432 GAATAATTGTGAAGTATCACAGTCC
1 GAATAATTGACAAGTATCACAGTCC
*
3970457 GAATGATTGACAAGTATCACAGT
1 GAATAATTGACAAGTATCACAGT
3970480 GTTAGGATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (25 bp):
GAATAATTGACAAGTATCACAGTCC
Found at i:3971166 original size:95 final size:96
Alignment explanation
Indices: 3970968--3971166 Score: 271
Period size: 96 Copynumber: 2.1 Consensus size: 96
3970958 ATCACTGATT
* * * *
3970968 TATTGGTTTATGAACTATGATTACCTGAAATGTGTTATTAGGTTTCATGTTTTCACTGGAAAATA
1 TATTGGTTTATGAACTATGATTACATGAAAGGTATTATTAGGTTTCATGTTTTCACTGGAAAAAA
*
3971033 TGATTGTTCCTAATTTATGAATCATAGAGTC
66 TGATTGTTCCTAATTTATGAATCATAGAATC
3971064 TATTGGTTTATGAACTAT-AGTTACATGAAAGGTATTATCT-GGTTTTC-TGTTTTCACT-GAAA
1 TATTGGTTTATGAACTATGA-TTACATGAAAGGTATTAT-TAGG-TTTCATGTTTTCACTGGAAA
* * *
3971125 AAATGATTGTTCCTGATTTATGGATCATGGAATC
63 AAATGATTGTTCCTAATTTATGAATCATAGAATC
3971159 TATTGGTT
1 TATTGGTT
3971167 ACTACTTGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
95 42 0.46
96 45 0.49
97 5 0.05
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (96 bp):
TATTGGTTTATGAACTATGATTACATGAAAGGTATTATTAGGTTTCATGTTTTCACTGGAAAAAA
TGATTGTTCCTAATTTATGAATCATAGAATC
Found at i:3973418 original size:2 final size:2
Alignment explanation
Indices: 3973399--3973458 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
3973389 ATCAATCAAT
*
3973399 TA TA -A TA T- TA TA -A TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3973438 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
3973459 TATCGTATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3973710 original size:60 final size:60
Alignment explanation
Indices: 3973614--3973732 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
3973604 TAAGTCTTGG
3973614 GTTCAAACCCCACTAGCAATAGTTATTGATTGAATTTATTTTATATTCATTCAATTGGTA
1 GTTCAAACCCCACTAGCAATAGTTATTGATTGAATTTATTTTATATTCATTCAATTGGTA
*
3973674 GTTCAAACCCCACTAGCAATAGTTATTGATTTAATTTATTTTATATTCATTCAATTGGT
1 GTTCAAACCCCACTAGCAATAGTTATTGATTGAATTTATTTTATATTCATTCAATTGGT
3973733 GATATGTGAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (60 bp):
GTTCAAACCCCACTAGCAATAGTTATTGATTGAATTTATTTTATATTCATTCAATTGGTA
Found at i:3974008 original size:31 final size:30
Alignment explanation
Indices: 3973964--3974029 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
3973954 TATTTAGCGA
* *
3973964 TAGGTGACTTGATTGACAATATTTAAATAAT
1 TAGGTGACTTGATTGACAAAATTGAAA-AAT
3973995 TAGGTGA-TCTGATTGACAAAATTGAAAAAT
1 TAGGTGACT-TGATTGACAAAATTGAAAAAT
3974025 T-GGTG
1 TAGGTG
3974030 GTAAAGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 5 0.16
31 23 0.72
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (30 bp):
TAGGTGACTTGATTGACAAAATTGAAAAAT
Found at i:3974550 original size:31 final size:30
Alignment explanation
Indices: 3974515--3974581 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
3974505 GCTTAAAATT
* *
3974515 TTAGGTGA-CTTGATTGACAATATTTAAATAA
1 TTAGGTGATC-TGATTGACAAAATTGAAA-AA
*
3974546 TTAGGCGATCTGATTGACAAAATTGAAAAA
1 TTAGGTGATCTGATTGACAAAATTGAAAAA
3974576 TT-GGTG
1 TTAGGTG
3974582 GTAAAGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 23 0.74
32 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.34
Consensus pattern (30 bp):
TTAGGTGATCTGATTGACAAAATTGAAAAA
Found at i:3975011 original size:555 final size:552
Alignment explanation
Indices: 3973964--3975071 Score: 2162
Period size: 555 Copynumber: 2.0 Consensus size: 552
3973954 TATTTAGCGA
*
3973964 TAGGTGACTTGATTGACAATATTTAAATAATTAGGTGATCTGATTGACAAAATTGAAAAATTGGT
1 TAGGTGACTTGATTGACAATATTTAAATAATTAGGCGATCTGATTGACAAAATTGAAAAATTGGT
3974029 GGTAAAGTAAAAGGTGGTCAATGATATAGTTTATCCTAAAAACTAATGTTTTATAAATATTATAT
66 GGTAAAGTAAAAGGTGGTCAATGATATAGTTTATCCTAAAAACTAATGTTTTATAAATATTATAT
3974094 TTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTATACGTTTAATACTTTATAATAAT
131 TTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTATACGTTTAATACTTTATAATAAT
3974159 ATTTACAAATTAATTTAATGATCTTCATCATTAACAGAACTCATCCACGCTCGACGAATGTTGTA
196 ATTTACAAATTAATTTAATGATCTTCATCATTAACAGAACTCATCCACGCTCGACGAATGTTGTA
3974224 AAATTTTTCATAAAATAAAGAATTGCAAATAATAAAAACAAATTTAATAAAATCTTAAAAAGTTA
261 AAATTTTTCATAAAATAAAGAATTGCAAATAATAAAAACAAATTTAATAAAATCTTAAAAAGTTA
3974289 TAAGTTTTGCTTCAATTTTTTAAAACTTGAAAATATTTTCTGTTTTTCATAATGGATCTATATTT
326 TAAGTTTTGCTTCAATTTTTTAAAACTTGAAAATATTTTCTGTTTTTCATAATGGATCTATATTT
3974354 ATTGAAATTCATTGATAGTTTATTTATGTATCGTTGGTTTATAATAAAAACCTTTCATAATGGTT
391 ATTGAAATTCATTGATAGTTTATTTATGTATCGTTGGTTTATAATAAAAACCTTTCATAATGGTT
3974419 ATCTCATCACAATATTAACCATTTTAAAAAGTAATTATAAAAAAATTGAAGCAAAACTAAGTTTG
456 ATCTCATCACAATATTAACCATTTTAAAAAGTAATTATAAAAAAATTGAAGCAAAACTAAGTTTG
3974484 ACTCGACTAAAAAATTCATAAGCTTAAAATTT
521 ACTCGACTAAAAAATTCATAAGCTTAAAATTT
3974516 TAGGTGACTTGATTGACAATATTTAAATAATTAGGCGATCTGATTGACAAAATTGAAAAATTGGT
1 TAGGTGACTTGATTGACAATATTTAAATAATTAGGCGATCTGATTGACAAAATTGAAAAATTGGT
3974581 GGTAAAGTAAAAGGTGGTCAATGATATAGTTTATCCTAAAAACTAATGTTTTATAAATATTATAT
66 GGTAAAGTAAAAGGTGGTCAATGATATAGTTTATCCTAAAAACTAATGTTTTATAAATATTATAT
3974646 TTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTATACGTTTAATACTTTATAATATA
131 TTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTATACGTTTAATACTTTAT-A-ATA
3974711 ATATTTTACAAATTAATTTAATGATCTTCATCATTAACAGAACTCATCCACGCTCGACGAATGTT
194 ATA-TTTACAAATTAATTTAATGATCTTCATCATTAACAGAACTCATCCACGCTCGACGAATGTT
*
3974776 GTAAAATTTTTCATAAAATAAAGAATTGCGAATAATAAAAACAAATTTAATAAAATCTTAAAAAG
258 GTAAAATTTTTCATAAAATAAAGAATTGCAAATAATAAAAACAAATTTAATAAAATCTTAAAAAG
3974841 TTATAAGTTTTGCTTCAATTTTTTAAAACTTGAAAATATTTTCTGTTTTTCATAATGGATCTATA
323 TTATAAGTTTTGCTTCAATTTTTTAAAACTTGAAAATATTTTCTGTTTTTCATAATGGATCTATA
*
3974906 TTTATTGAAATTCATTGATAGTTTATTTATGTATCGTTGGTTTATAATAAAAACTTTTCATAATG
388 TTTATTGAAATTCATTGATAGTTTATTTATGTATCGTTGGTTTATAATAAAAACCTTTCATAATG
3974971 GTTATCTCATCACAATATTAACCATTTTAAAAAGTAATTATAAAAAAATTGAAGCAAAACTAAGT
453 GTTATCTCATCACAATATTAACCATTTTAAAAAGTAATTATAAAAAAATTGAAGCAAAACTAAGT
3975036 TTGACTCGACTAAAAAATTCATAAGCTTAAAATTT
518 TTGACTCGACTAAAAAATTCATAAGCTTAAAATTT
3975071 T
1 T
3975072 CAAGTTTGAC
Statistics
Matches: 550, Mismatches: 3, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
552 188 0.34
553 1 0.00
554 6 0.01
555 355 0.65
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (552 bp):
TAGGTGACTTGATTGACAATATTTAAATAATTAGGCGATCTGATTGACAAAATTGAAAAATTGGT
GGTAAAGTAAAAGGTGGTCAATGATATAGTTTATCCTAAAAACTAATGTTTTATAAATATTATAT
TTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTATACGTTTAATACTTTATAATAAT
ATTTACAAATTAATTTAATGATCTTCATCATTAACAGAACTCATCCACGCTCGACGAATGTTGTA
AAATTTTTCATAAAATAAAGAATTGCAAATAATAAAAACAAATTTAATAAAATCTTAAAAAGTTA
TAAGTTTTGCTTCAATTTTTTAAAACTTGAAAATATTTTCTGTTTTTCATAATGGATCTATATTT
ATTGAAATTCATTGATAGTTTATTTATGTATCGTTGGTTTATAATAAAAACCTTTCATAATGGTT
ATCTCATCACAATATTAACCATTTTAAAAAGTAATTATAAAAAAATTGAAGCAAAACTAAGTTTG
ACTCGACTAAAAAATTCATAAGCTTAAAATTT
Found at i:3977488 original size:18 final size:18
Alignment explanation
Indices: 3977467--3977522 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
3977457 CTCTGCTACA
* *
3977467 CAAAACGAGTCTGATACT
1 CAAAACGAGTCTAATACC
* *
3977485 CAAAATGAGTGTAATACC
1 CAAAACGAGTCTAATACC
3977503 CAAAACGAGTCTAATACC
1 CAAAACGAGTCTAATACC
3977521 CA
1 CA
3977523 TGAAACTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (18 bp):
CAAAACGAGTCTAATACC
Found at i:3985217 original size:21 final size:22
Alignment explanation
Indices: 3985170--3985217 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
3985160 ATTTTTCATT
3985170 TTAA-AATTATTATAATTATAA
1 TTAATAATTATTATAATTATAA
*
3985191 TT-ATAATTATTAT-ATTATTA
1 TTAATAATTATTATAATTATAA
3985211 TTAATAA
1 TTAATAA
3985218 ATAAATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATAATTATTATAATTATAA
Found at i:3986458 original size:94 final size:95
Alignment explanation
Indices: 3986287--3986459 Score: 212
Period size: 94 Copynumber: 1.8 Consensus size: 95
3986277 ATATTTAGTC
* * *
3986287 CCTTATAATTTTTATAATTTATATTTTAACCCGAATTAATTAATTAAGGCTAAATTACATTATTA
1 CCTTATAATTTTAATAATTTATATTTTAACCCGAATTAATTAATTAAGGATAAATTACAGTATTA
* *
3986352 GCACTTAGATTTTTTTTATTCGAGTTAAAG
66 GAAATTAGATTTTTTTTATTCGAGTTAAAG
*
3986382 CCTT-TAATTTTAATAA-TTATTATTTTAATCACTG-ATTAA-TAATTAAGGGAT-AATTACAGT
1 CCTTATAATTTTAATAATTTA-TATTTTAA-C-CCGAATTAATTAATTAA-GGATAAATTACAGT
*
3986442 ATTAGAAATTATATTTTT
62 ATTAGAAATTAGATTTTT
3986460 ATAATAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
93 3 0.04
94 49 0.73
95 13 0.19
96 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (95 bp):
CCTTATAATTTTAATAATTTATATTTTAACCCGAATTAATTAATTAAGGATAAATTACAGTATTA
GAAATTAGATTTTTTTTATTCGAGTTAAAG
Found at i:3986605 original size:2 final size:2
Alignment explanation
Indices: 3986598--3986628 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3986588 ATTTTATTCG
3986598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3986629 TTGATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3995907 original size:22 final size:22
Alignment explanation
Indices: 3995882--3995947 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
3995872 TCTACATCTA
* *
3995882 CACTCTTCAAATATGACAGATT
1 CACTCTTCAAAGATGAAAGATT
*
3995904 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGAAAGATT
* *
3995926 CTCTTTTCAAAGATGAAAGATT
1 CACTCTTCAAAGATGAAAGATT
3995948 TATTGGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (22 bp):
CACTCTTCAAAGATGAAAGATT
Found at i:3996679 original size:45 final size:45
Alignment explanation
Indices: 3996615--3997134 Score: 817
Period size: 45 Copynumber: 11.6 Consensus size: 45
3996605 ATTTTCTACG
3996615 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* * *
3996660 TCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTTA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
3996705 TCTGTAAGCCCTTCATTGCATGATGTTTTCAAAACTTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
3996750 TCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAATCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
3996795 TCGGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
3996840 TTTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* * *
3996885 TCTATAAGCCCTTTAGTGCATGATATTTTCAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
*
3996930 TCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
*
3996975 TCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
3997020 TCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGTTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* * *
3997065 TCTGTAAGACCTTCAGTGCATGATGTTTTCAAAAGCTCCGGGTCA
1 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
3997110 TCTGTAAGACCTAT-AGTGCAAGATG
1 TCTGTAAGCCCT-TCAGTGCATGATG
3997135 ATAAGACCTC
Statistics
Matches: 436, Mismatches: 38, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
45 435 1.00
46 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (45 bp):
TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
Found at i:3997762 original size:25 final size:26
Alignment explanation
Indices: 3997715--3997763 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3997705 AAAATGGGGT
* *
3997715 TTTAAGTGAAATTTGGAATATAAAGG
1 TTTAAATGAAATTTGGAAGATAAAGG
*
3997741 TTTAAATG-AATTTGGAGGATAAA
1 TTTAAATGAAATTTGGAAGATAAA
3997764 TTTGACTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (26 bp):
TTTAAATGAAATTTGGAAGATAAAGG
Found at i:3998851 original size:13 final size:13
Alignment explanation
Indices: 3998833--3998862 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3998823 AGAGTTGAAT
3998833 TTTTAAATTTAAA
1 TTTTAAATTTAAA
3998846 TTTTAAATTTAAA
1 TTTTAAATTTAAA
3998859 TTTT
1 TTTT
3998863 CATGATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATTTAAA
Found at i:4002949 original size:240 final size:240
Alignment explanation
Indices: 4002652--4003162 Score: 869
Period size: 240 Copynumber: 2.1 Consensus size: 240
4002642 CAATACTTGG
* * *
4002652 ATTTCAACTTCACGACGAAGGATATCATGCTAACTCTAGATTGGATTTCAACTTCACGATGAAGG
1 ATTTCAACTTCACGACGAAGGATATCGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGG
** *
4002717 ATATCCAATTCAAAGCTCAACTTCACGGTGAAGGGGTTTCCCAGTTTCATTCAGAGCCAATTTCA
66 ATATCCAATTCAAAGCTCAACTTCACGGCAAAGGGGCTTCCCAGTTTCATTCAGAGCCAATTTCA
*
4002782 ACTTCACGGCGAAAGATATTGGACTCGAAACAATACAAGCTTGGATTTGAACTTCACGACGAAGG
131 ACTTCACGGCGAAAGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
*
4002847 ATATTCTAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACA
196 ATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACA
*
4002892 ATTTCAACTTCACGATGAAGGATATCGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACGACGAAGGATATCGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGG
* *
4002957 ATATCCAATTCAAAGCTCAACTTCATGGCAAAGGGGCTTCCCAGTTTCATTCAGAGCCAATTTTA
66 ATATCCAATTCAAAGCTCAACTTCACGGCAAAGGGGCTTCCCAGTTTCATTCAGAGCCAATTTCA
*
4003022 ACTTCACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
131 ACTTCACGGCGAAAGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
* **
4003087 ATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGCCATCCATG
196 ATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACA
* *
4003132 GTTTCAACTTCACGACGAATGATATCGTGCC
1 ATTTCAACTTCACGACGAAGGATATCGTGCC
4003163 CACAAGCTGC
Statistics
Matches: 253, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
240 253 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (240 bp):
ATTTCAACTTCACGACGAAGGATATCGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGG
ATATCCAATTCAAAGCTCAACTTCACGGCAAAGGGGCTTCCCAGTTTCATTCAGAGCCAATTTCA
ACTTCACGGCGAAAGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
ATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACA
Found at i:4003365 original size:121 final size:124
Alignment explanation
Indices: 4003057--4003402 Score: 509
Period size: 124 Copynumber: 2.8 Consensus size: 124
4003047 CGAAACAATA
* * * * *
4003057 CAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGG
1 CAAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGA
* * **
4003122 GCCATCCATGGTTTCAACTTCACGACGAATGATATCGTGCCCACAAGCTGCATCCACCT
66 GCCATCCATGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACATCCACCT
* * *
4003181 CTAGATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAGGCTCAACTTCACAATGAATGA
1 CAAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGA
* *
4003246 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAAC-T-TA-CT
66 GCCATCCATGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACATCCACCT
* *
4003302 CAAGATTGGATTTCAACTTCATGACGAATTATATCCAATTCAAGGCTCAACTTCACAACGAATGA
1 CAAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGA
* *
4003367 GCCATCTATGATTTTAACTTCACGACGAAGGATATC
66 GCCATCCATGATTTCAACTTCACGACGAAGGATATC
4003403 ATACCCAAAA
Statistics
Matches: 200, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
121 95 0.47
122 1 0.00
123 1 0.00
124 103 0.51
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (124 bp):
CAAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGA
GCCATCCATGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACATCCACCT
Found at i:4003831 original size:3 final size:3
Alignment explanation
Indices: 4003787--4003853 Score: 77
Period size: 3 Copynumber: 22.3 Consensus size: 3
4003777 TTTACAAAAA
*
4003787 TAT TA- TAT TA- TAT TA- TAT TATT TATT TATT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT
4003832 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
4003854 TATTTTTTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.10
3 41 0.71
4 11 0.19
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4005353 original size:10 final size:9
Alignment explanation
Indices: 4005336--4005406 Score: 54
Period size: 10 Copynumber: 7.4 Consensus size: 9
4005326 AATGTTTATA
4005336 ATTTTATTT
1 ATTTTATTT
4005345 ATCTTTATTT
1 AT-TTTATTT
4005355 A-TTTATTT
1 ATTTTATTT
*
4005363 ATTTATTTTT
1 ATTT-TATTT
*
4005373 ATTTGATTTT
1 ATTTTA-TTT
*
4005383 ATTCTTTTTT
1 ATT-TTATTT
*
4005393 ATATTTATAT
1 AT-TTTATTT
4005403 ATTT
1 ATTT
4005407 CATCATTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
8 8 0.16
9 6 0.12
10 33 0.67
11 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (9 bp):
ATTTTATTT
Found at i:4005355 original size:22 final size:22
Alignment explanation
Indices: 4005330--4005406 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
4005320 TTTTTAAATG
4005330 TTTATA-ATTTTATTTATCTTTA
1 TTTATATA-TTTATTTATCTTTA
* *
4005352 TTTATTTATTTATTTATTTTTA
1 TTTATATATTTATTTATCTTTA
* * *
4005374 TTT-GAT-TTTATTCTTTTTTATA
1 TTTATATATTTATT-TATCTT-TA
4005396 TTTATATATTT
1 TTTATATATTT
4005407 CATCATTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.14
21 6 0.14
22 26 0.59
23 3 0.07
24 3 0.07
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (22 bp):
TTTATATATTTATTTATCTTTA
Found at i:4012348 original size:2 final size:2
Alignment explanation
Indices: 4012337--4012380 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
4012327 AAATTTATTA
* *
4012337 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4012378 AT A
1 AT A
4012381 ATAATTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4012526 original size:36 final size:36
Alignment explanation
Indices: 4012448--4012526 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
4012438 TTACTAAACC
*
4012448 CGTCCCCGTCCCCGTTTAACATAAACAATTTTTCCT
1 CGTCCCCATCCCCGTTTAACATAAACAATTTTTCCT
** * * ** *
4012484 AATCCCCATCCCCGTTTAGCTTAAACGGTTTTTTCT
1 CGTCCCCATCCCCGTTTAACATAAACAATTTTTCCT
4012520 CGTCCCC
1 CGTCCCC
4012527 GTTTAATTCG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.37, G:0.10, T:0.34
Consensus pattern (36 bp):
CGTCCCCATCCCCGTTTAACATAAACAATTTTTCCT
Found at i:4015510 original size:25 final size:20
Alignment explanation
Indices: 4015452--4015502 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
4015442 CTCTAAATCA
4015452 TTTTTCAAAATTTTATTTTG
1 TTTTTCAAAATTTTATTTTG
4015472 TTTTTCAAAATTTTATTTTG
1 TTTTTCAAAATTTTATTTTG
4015492 TTTTTCAAAAT
1 TTTTTCAAAAT
4015503 AAACTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTCAAAATTTTATTTTG
Found at i:4017939 original size:54 final size:54
Alignment explanation
Indices: 4017818--4018127 Score: 405
Period size: 54 Copynumber: 5.8 Consensus size: 54
4017808 TCCGTATGGG
* * *
4017818 CACTATGTGTGCAACTCATGGAATTCATCATATGTT--TGAACAATCGTTTC-A
1 CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGA
*
4017869 GCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGCTTCGA
1 -CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGA
* *
4017924 CACTATGTGTACAACTCACGAAATTCATCATATGTTGATGAACAACTGTTTCGA
1 CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGA
* * * *
4017978 CACTATGTGTGCAACTCACAAAATTCATCATATATTGATGAGCAACCGTTTCGG
1 CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGA
* *
4018032 CACTATGTGTGCAACTCAC-AGAATTCATCATATGTTGATGAACAACTGTTTTGGA
1 CACTATGTGTGCAACTCACGA-AATTCATCATATGTTGATGAACAACCG-TTTCGA
* * * * *
4018087 -ACTATGTGTGCAACCCACGGAATTTATAATATGTTTATGAA
1 CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAA
4018128 TGACCGTATA
Statistics
Matches: 229, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
52 34 0.15
53 1 0.00
54 189 0.83
55 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (54 bp):
CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGA
Found at i:4021805 original size:18 final size:16
Alignment explanation
Indices: 4021768--4021809 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4021758 ATATACGATC
4021768 TATGTGAATGCATGTA
1 TATGTGAATGCATGTA
* *
4021784 TATGTGATTGCATGTC
1 TATGTGAATGCATGTA
*
4021800 TATATGAATG
1 TATGTGAATG
4021810 TCAGAAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (16 bp):
TATGTGAATGCATGTA
Found at i:4024953 original size:20 final size:20
Alignment explanation
Indices: 4024930--4024968 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
4024920 AGTGAAATCT
4024930 TGAGAAAGAGTTAGAAATAC
1 TGAGAAAGAGTTAGAAATAC
4024950 TGAGAAAGAGTTAGAAATA
1 TGAGAAAGAGTTAGAAATA
4024969 TGTTTTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.21
Consensus pattern (20 bp):
TGAGAAAGAGTTAGAAATAC
Found at i:4026113 original size:18 final size:16
Alignment explanation
Indices: 4026076--4026117 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4026066 ATATGTGATC
4026076 TATGTGAATGCATGTA
1 TATGTGAATGCATGTA
* *
4026092 TATGTGATTGCATGTC
1 TATGTGAATGCATGTA
*
4026108 TATATGAATG
1 TATGTGAATG
4026118 TCAGAAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (16 bp):
TATGTGAATGCATGTA
Found at i:4026182 original size:259 final size:247
Alignment explanation
Indices: 4025765--4026274 Score: 810
Period size: 246 Copynumber: 2.0 Consensus size: 247
4025755 ATATAGTGAT
4025765 ATGATGCTAGATGTATATGATTAAATGCATATATTTAGATGTTAAGTGCATATCCATATGTGATC
1 ATGATGCTAGATGTATATGATTAAATGCATATATTTAGATGTTAAGTGCATATCCATATGTGATC
** *
4025830 TATGTGAATGCATCTTGATATGATGTCATGAATGTCTATGAGAAAATGTGACTCTATGATGACAT
66 TATGTGAATGCATCTTGATATGATGTCATGAATGAATATCAGAAAATGTGACTCTATGATGACAT
4025895 ATATATATATATGAACATGTGATATGTGAACATAAGAAATTAAGTGACATGATCTATGTAACCAT
131 ATATATATATATGAACATGTGATATGTGAACATAAGAAATTAAGTGACATGATCTATGTAACCAT
4025960 -TGAAAGCAAGAACATGTGATATGAGATACATGATCAAAGATATGAAACTCC
196 ATGAAAGCAAGAACATGTGATATGAGATACATGATCAAAGATATGAAACTCC
4026011 ATGATGCTAGATGTATATGATTAAATGCATATATTTAGATGTTAAGTGCATATCCATATGTGATC
1 ATGATGCTAGATGTATATGATTAAATGCATATATTTAGATGTTAAGTGCATATCCATATGTGATC
* * *
4026076 TATGTGAATGCATGTAT-ATGTGAT-TGCATGTCTATATGAATGTCAGAAAATGTGACTCTATGA
66 TATGTGAATGCATCT-TGATATGATGT-CATG---A-ATGAATATCAGAAAATGTGACTCTAT--
4026139 GAATGTTATACCATATATATATGATATGAACATGTGATATGTGAACATAAGAAATTAAGTGACAT
123 G-ATG----A-CATATATATAT-ATATGAACATGTGATATGTGAACATAAGAAATTAAGTGACAT
4026204 GATCTATGTAACCATATGAAAGCAAGAACATGTGATATGAGATACATGATCAAAGATATGAAACT
181 GATCTATGTAACCATATGAAAGCAAGAACATGTGATATGAGATACATGATCAAAGATATGAAACT
4026269 CC
246 CC
4026271 ATGA
1 ATGA
4026275 GAGTATTACA
Statistics
Matches: 242, Mismatches: 6, Indels: 18
0.91 0.02 0.07
Matches are distributed among these distances:
245 1 0.00
246 89 0.37
247 1 0.00
249 1 0.00
250 22 0.09
252 1 0.00
253 3 0.01
257 1 0.00
258 11 0.05
259 57 0.24
260 55 0.23
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (247 bp):
ATGATGCTAGATGTATATGATTAAATGCATATATTTAGATGTTAAGTGCATATCCATATGTGATC
TATGTGAATGCATCTTGATATGATGTCATGAATGAATATCAGAAAATGTGACTCTATGATGACAT
ATATATATATATGAACATGTGATATGTGAACATAAGAAATTAAGTGACATGATCTATGTAACCAT
ATGAAAGCAAGAACATGTGATATGAGATACATGATCAAAGATATGAAACTCC
Found at i:4033526 original size:23 final size:22
Alignment explanation
Indices: 4033493--4033577 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
4033483 TTTAGTGCAG
*
4033493 AGGGAATCGATACCCCCCTTGAA
1 AGGGAACCGAT-CCCCCCTTGAA
* * *
4033516 AGGGAACCGATTCTCCCTTTAA
1 AGGGAACCGATCCCCCCTTGAA
* *
4033538 AGGGGAACCGATTCCCCC-TGTA
1 A-GGGAACCGATCCCCCCTTGAA
* *
4033560 AGGGAATCGATACCCCCT
1 AGGGAACCGATCCCCCCT
4033578 GGAGTTCTGG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.27
22 12 0.24
23 25 0.49
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATCCCCCCTTGAA
Found at i:4033539 original size:22 final size:22
Alignment explanation
Indices: 4033506--4033577 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 22
4033496 GAATCGATAC
*
4033506 CCCCCTTGAAAGGGAACCGATT
1 CCCCCTTTAAAGGGAACCGATT
*
4033528 CTCCCTTTAAAGGGGAACCGATT
1 CCCCCTTTAAA-GGGAACCGATT
* * *
4033551 CCCCCTGT-AAGGGAATCGATA
1 CCCCCTTTAAAGGGAACCGATT
4033572 CCCCCT
1 CCCCCT
4033578 GGAGTTCTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
21 15 0.35
22 11 0.26
23 17 0.40
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (22 bp):
CCCCCTTTAAAGGGAACCGATT
Found at i:4033564 original size:21 final size:21
Alignment explanation
Indices: 4033506--4033578 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
4033496 GAATCGATAC
*
4033506 CCCCCTTGAAAGGGAACCGATT
1 CCCCC-TGTAAGGGAACCGATT
* *
4033528 CTCCCTTTAAAGGGGAACCGATT
1 CCCCCTGT-AA-GGGAACCGATT
* *
4033551 CCCCCTGTAAGGGAATCGATA
1 CCCCCTGTAAGGGAACCGATT
4033572 CCCCCTG
1 CCCCCTG
4033579 GAGTTCTGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 17 0.40
22 8 0.19
23 17 0.40
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.21
Consensus pattern (21 bp):
CCCCCTGTAAGGGAACCGATT
Found at i:4040717 original size:22 final size:21
Alignment explanation
Indices: 4040662--4040732 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 21
4040652 TACATAAATG
*
4040662 GTATCGATACCGTA--ATAGA
1 GTATCGATACCATAGTATAGA
*
4040681 GTATC-AGTACTATAGTATAGTA
1 GTATCGA-TACCATAGTATAG-A
* *
4040703 GTATCGATACCATAGTA-GGG
1 GTATCGATACCATAGTATAGA
4040723 GTATCGATAC
1 GTATCGATAC
4040733 TATTGAGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.02
19 10 0.24
20 10 0.24
21 5 0.12
22 15 0.36
23 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATAGTATAGA
Found at i:4041362 original size:56 final size:54
Alignment explanation
Indices: 4041115--4041370 Score: 304
Period size: 54 Copynumber: 4.7 Consensus size: 54
4041105 GTATGGGCAT
*
4041115 TATGTGTGCAACTCACGGAATTCATCATATGTT-ATGAAAAAACGTTCCG-T-CAC
1 TATGTGTGCAACTCACGGAATTCATCATATGTTGATGAAAAACCGTT--GTTGCAC
* * * * *
4041168 TATGTGTGCAACTCACAGAATTCATCATATATTGGTGAACAACCGTTGTTGCAT
1 TATGTGTGCAACTCACGGAATTCATCATATGTTGATGAAAAACCGTTGTTGCAC
* * * *
4041222 TATGTGTGCAACTCACAGAATTCATCATATGGTGGTGAACAACCGTTGTTGCAC
1 TATGTGTGCAACTCACGGAATTCATCATATGTTGATGAAAAACCGTTGTTGCAC
* *
4041276 TATATGTGCAACTCACGGAATTCATCATATGTTGATGAAAAACTGTT-TTGGCAC
1 TATGTGTGCAACTCACGGAATTCATCATATGTTGATGAAAAACCGTTGTT-GCAC
* * *
4041330 TATGTGTGTGCAACCCACGGAATTCATAATATGTTTATGAA
1 TA--TGTGTGCAACTCACGGAATTCATCATATGTTGATGAA
4041371 TGATCGTATA
Statistics
Matches: 178, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
52 1 0.01
53 34 0.19
54 110 0.62
56 33 0.19
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (54 bp):
TATGTGTGCAACTCACGGAATTCATCATATGTTGATGAAAAACCGTTGTTGCAC
Found at i:4042478 original size:28 final size:28
Alignment explanation
Indices: 4042407--4042566 Score: 158
Period size: 29 Copynumber: 5.6 Consensus size: 28
4042397 TTGTTGTTAG
* * * *
4042407 GTGATATTCTGGGAAATATTTCGATAAA
1 GTGACATTTTGGGAATTATTTCGAAAAA
*
4042435 GATGACATTTTGGGAATTATTTTGAAAAA
1 G-TGACATTTTGGGAATTATTTCGAAAAA
* *
4042464 GTGACATTTTAGGAAATATTTCGAAAAA
1 GTGACATTTTGGGAATTATTTCGAAAAA
* *
4042492 GGTAACATATTGGGAATTATTTCGAAAAA
1 -GTGACATTTTGGGAATTATTTCGAAAAA
* * * * **
4042521 GGTAACACTCTGAGAATTATTTAAAAAAA
1 -GTGACATTTTGGGAATTATTTCGAAAAA
4042550 GTGACATTTTGGGAATT
1 GTGACATTTTGGGAATT
4042567 GTCAAATGTT
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 38 0.35
29 70 0.65
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (28 bp):
GTGACATTTTGGGAATTATTTCGAAAAA
Found at i:4042548 original size:57 final size:57
Alignment explanation
Indices: 4042414--4042566 Score: 143
Period size: 57 Copynumber: 2.7 Consensus size: 57
4042404 TAGGTGATAT
* * * * *
4042414 TCTG-GGAAATATTTC-GATAAAGATGACATTTTGGGAATTATTTTGAAAAAGTGACA
1 TCTGAGGAAATATTTCAAAAAAAG-TAACATTTTGGGAATTATTTCGAAAAAGTAACA
* * * * *
4042470 TTTTAGGAAATATTTCGAAAAAGGTAACATATTGGGAATTATTTCGAAAAAGGTAACA
1 TCTGAGGAAATATTTCAAAAAAAGTAACATTTTGGGAATTATTTCGAAAAA-GTAACA
* *
4042528 CTCTGA-GAATTATTT-AAAAAAAGTGACATTTTGGGAATT
1 -TCTGAGGAAATATTTCAAAAAAAGTAACATTTTGGGAATT
4042567 GTCAAATGTT
Statistics
Matches: 77, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
56 2 0.03
57 55 0.71
58 17 0.22
59 3 0.04
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (57 bp):
TCTGAGGAAATATTTCAAAAAAAGTAACATTTTGGGAATTATTTCGAAAAAGTAACA
Found at i:4049063 original size:29 final size:28
Alignment explanation
Indices: 4049031--4049189 Score: 122
Period size: 28 Copynumber: 5.6 Consensus size: 28
4049021 AATTGTTGTT
* *
4049031 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATTATGGGAAATATTTCGA-AA
* * *
4049060 AGGTGACATTTTGGGAATTATTTTGAAA
1 AGGTGACATTATGGGAAATATTTCGAAA
* *
4049088 AAGTGACATTATGGGAAATATTTCAAAA
1 AGGTGACATTATGGGAAATATTTCGAAA
* *
4049116 AGGTAACA-TATTGGAAATTATTTCGTAAA
1 AGGTGACATTATGGGAAA-TATTTCG-AAA
* * * * * **
4049145 AGGTAACACTCTGAGAATTATTTTAAAA
1 AGGTGACATTATGGGAAATATTTCGAAA
* *
4049173 AAGTGACATTTTGGGAA
1 AGGTGACATTATGGGAA
4049190 TTGTCAAATG
Statistics
Matches: 103, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
27 8 0.08
28 52 0.50
29 38 0.37
30 5 0.05
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (28 bp):
AGGTGACATTATGGGAAATATTTCGAAA
Found at i:4049108 original size:57 final size:57
Alignment explanation
Indices: 4049033--4049191 Score: 176
Period size: 57 Copynumber: 2.8 Consensus size: 57
4049023 TTGTTGTTAG
* * *
4049033 GTGATATTCTGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTG-AAAAA
1 GTGACATTCTGGGAAATATTTC-AAAAAGGTGACATTTTGGGAATTATTTCGTAAAAA
* * * * *
4049090 GTGACATTATGGGAAATATTTCAAAAAGGTAACATATTGGAAATTATTTCGTAAAAG
1 GTGACATTCTGGGAAATATTTCAAAAAGGTGACATTTTGGGAATTATTTCGTAAAAA
* * * * * *
4049147 GTAACACTCTGAGAATTATTTTAAAAAAGTGACATTTTGGGAATT
1 GTGACATTCTGGGAAATATTTCAAAAAGGTGACATTTTGGGAATT
4049192 GTCAAATGTT
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
56 24 0.29
57 59 0.71
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (57 bp):
GTGACATTCTGGGAAATATTTCAAAAAGGTGACATTTTGGGAATTATTTCGTAAAAA
Found at i:4049146 original size:56 final size:57
Alignment explanation
Indices: 4049033--4049146 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 57
4049023 TTGTTGTTAG
* * * * * * *
4049033 GTGATATTCTGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGAAAAA
1 GTGACATTATGGGAAATATTTCGAAAAAGGTAACATATTGGAAATTATTTCGAAAAA
*
4049090 GTGACATTATGGGAAATATTTC-AAAAAGGTAACATATTGGAAATTATTTCGTAAAA
1 GTGACATTATGGGAAATATTTCGAAAAAGGTAACATATTGGAAATTATTTCGAAAAA
4049146 G
1 G
4049147 GTAACACTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
56 29 0.59
57 20 0.41
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (57 bp):
GTGACATTATGGGAAATATTTCGAAAAAGGTAACATATTGGAAATTATTTCGAAAAA
Found at i:4058017 original size:6 final size:6
Alignment explanation
Indices: 4058006--4058037 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
4057996 TCGGCTCGCC
4058006 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
4058038 TTAGTGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:4058901 original size:5 final size:5
Alignment explanation
Indices: 4058891--4058949 Score: 100
Period size: 5 Copynumber: 11.8 Consensus size: 5
4058881 GTCCGTCCGT
* *
4058891 CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
4058941 CTCGG CTCG
1 CTCGG CTCG
4058950 TGGTCGTGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.03, C:0.41, G:0.39, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:4058958 original size:6 final size:6
Alignment explanation
Indices: 4058947--4059013 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
4058937 TCGGCTCGGC
* *
4058947 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
4058995 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
4059014 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:4059318 original size:22 final size:21
Alignment explanation
Indices: 4059293--4059341 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
4059283 AGTTACAGGA
* *
4059293 GTTATTTGATTTAATTCTAGGG
1 GTTATATGATATAATT-TAGGG
* *
4059315 GTTACATGATATAATTTCGGG
1 GTTATATGATATAATTTAGGG
4059336 GTTATA
1 GTTATA
4059342 ACAGCTGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (21 bp):
GTTATATGATATAATTTAGGG
Found at i:4061306 original size:5 final size:5
Alignment explanation
Indices: 4061296--4061344 Score: 80
Period size: 5 Copynumber: 9.8 Consensus size: 5
4061286 GTCCGTCCGT
* *
4061296 CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
4061345 TGGTCGTGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.04, C:0.41, G:0.39, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:4061353 original size:6 final size:6
Alignment explanation
Indices: 4061342--4061408 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
4061332 TCGGCTCGGC
* *
4061342 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
4061390 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
4061409 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:4061719 original size:22 final size:21
Alignment explanation
Indices: 4061694--4061734 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4061684 AGGAGTTATT
*
4061694 TGATTTAATTCTAGGGGTTACA
1 TGATATAATT-TAGGGGTTACA
*
4061716 TGATATAATTTCGGGGTTA
1 TGATATAATTTAGGGGTTA
4061735 TAACAGCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (21 bp):
TGATATAATTTAGGGGTTACA
Found at i:4063704 original size:5 final size:5
Alignment explanation
Indices: 4063694--4063737 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
4063684 GTCCGTCCGT
* * *
4063694 CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
4063738 TGGTCGTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.07, C:0.41, G:0.39, T:0.14
Consensus pattern (5 bp):
CTCGG
Found at i:4063746 original size:6 final size:6
Alignment explanation
Indices: 4063735--4063855 Score: 215
Period size: 6 Copynumber: 20.2 Consensus size: 6
4063725 TCGGCTCGGC
* * *
4063735 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTTG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
4063783 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
4063831 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
4063856 AATACGTGTC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 111 1.00
ACGTcount: A:0.02, C:0.17, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:4069729 original size:5 final size:5
Alignment explanation
Indices: 4069719--4069762 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
4069709 GTCCGTCCGT
* * * *
4069719 CTCGG CTCGG CACGG CACGG CACGG CTTGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
4069763 TGGTCGTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.07, C:0.39, G:0.39, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:4069771 original size:6 final size:6
Alignment explanation
Indices: 4069760--4069844 Score: 152
Period size: 6 Copynumber: 14.2 Consensus size: 6
4069750 TCGGCTCGGC
* *
4069760 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
4069808 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
4069845 AATACGTGTC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:4074841 original size:51 final size:51
Alignment explanation
Indices: 4074765--4074867 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
4074755 ATCCAACAAT
*
4074765 GTTCTAATCTTATATAATAATGTTTATTACATACAAGACACAAGAGTTTAA
1 GTTCTAATCTTATATAATAATGTTTATTACATACAAGACACAAGAATTTAA
*
4074816 GTTCTAATCTTATATAATAATGTTTATTACATACAGGACACAAGAATTTAA
1 GTTCTAATCTTATATAATAATGTTTATTACATACAAGACACAAGAATTTAA
4074867 G
1 G
4074868 AATAATAAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (51 bp):
GTTCTAATCTTATATAATAATGTTTATTACATACAAGACACAAGAATTTAA
Found at i:4080552 original size:23 final size:23
Alignment explanation
Indices: 4080507--4080552 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4080497 CATTATCAAA
* *
4080507 ATTAATTTTTAGAATAATTTAAT
1 ATTAATTTTTAAAATAATATAAT
4080530 ATTAATTTTATAAAAT-ATATAAT
1 ATTAATTTT-TAAAATAATATAAT
4080553 TAATTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTAATTTTTAAAATAATATAAT
Found at i:4082017 original size:2 final size:2
Alignment explanation
Indices: 4082010--4082037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4082000 CTTTTGTAAC
4082010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4082038 AAAAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4082241 original size:2 final size:2
Alignment explanation
Indices: 4082234--4082261 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4082224 CAAAATTAAC
4082234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4082262 GAAACTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4092301 original size:24 final size:24
Alignment explanation
Indices: 4092269--4092339 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
4092259 ACATTACCTT
* *
4092269 AATTTTGTTCTGATTTCTGATATG
1 AATTCTGTTATGATTTCTGATATG
* ** *
4092293 GATTCTGTTATGACATCTGATCTG
1 AATTCTGTTATGATTTCTGATATG
*
4092317 AATTCTGTTTTGATTTCTGATAT
1 AATTCTGTTATGATTTCTGATAT
4092340 CTCCGTTTAC
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.51
Consensus pattern (24 bp):
AATTCTGTTATGATTTCTGATATG
Found at i:4097752 original size:23 final size:23
Alignment explanation
Indices: 4097725--4097787 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
4097715 CAATAAAGCA
4097725 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
**
4097748 CTACCTATTACA-TATATAAGTG
1 CTACCTATTACATTATATAAACG
*
4097770 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
4097788 TTTTTACCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:4098236 original size:23 final size:23
Alignment explanation
Indices: 4098190--4098260 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 23
4098180 ATACTTTACA
*
4098190 ATATAAGCACTACCTA-TACATT
1 ATATAAGCGCTACCTATTACATT
*
4098212 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
4098235 ATATAAGTG-TACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
4098257 ATAT
1 ATAT
4098261 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 30 0.70
23 13 0.30
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:4098460 original size:470 final size:475
Alignment explanation
Indices: 4097324--4098519 Score: 1942
Period size: 470 Copynumber: 2.5 Consensus size: 475
4097314 ACATAATATG
4097324 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAA-TTATGT
1 TTGAAAGTGTC-ATAC-TTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
4097388 TTCAA-TTTTTTAATAGTG-TTCATGTTTTCA-CTACAATATTAATTTAATAATTTCATTTGCAC
64 TTCAATTTTTTTAATAGTGTTTCATGTTTTCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
4097450 AAAAAATTATTTGATTGTTTTGATATTTTAT-AAATAATATTTATAATTTAAATTTAACAATATT
129 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
* *
4097514 AACCAAAGATAATAATAATATGTAATATATATGTTTTATTTTTTAATTTAATGATAATATATACC
194 AACCAAAGATAATAATAA-A--T-ATATATATGTTTTATGTTTTAATTTAATAATAATATATA-C
* * *
4097579 GTAACATAAAAAATAAATCATTAAATACATATAATTACTAAATTGATATCTTAAAACTCACTCAA
254 -TAACATAAAAAATAAATCATT-AAGACACATAATTACTAAATTAATATCTTAAAACTCACTCAA
*
4097644 AAGATAACTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACCTTTTATAAAAATGATAGAT
317 AAGATAACTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACCTTTTATAAAAAGGATAGAT
4097709 ACTTTACAATAAAGCACTACCTATTACATTATATAAACGCTACCTATTACATATATAAGTGCTAC
382 ACTTTACAATAAAGCACTACCTATTACATTATATAAACGCTACCTATTACATATATAAGTGCTAC
*
4097774 CTATTACATCATATTTTTTACCTGTTATA
447 CTATTACATCATATTTTTTACCTATTATA
*
4097803 TTGAAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATATAATTTATGT
1 TTGAAAGTGT-CATACTTTTTATAAAAAA-GATCGATACTTTTTTTAAAGTTATGTAATTTATGT
4097868 TTCAATTTTTTTAATAGTGTTTCATGTTTTCACCTACAATATTAATTTAATAATTTCATTTGCAC
64 TTCAATTTTTTTAATAGTGTTTCATGTTTTCACCTACAATATTAATTTAATAATTTCATTTGCAC
4097933 -AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
129 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
* *
4097997 AACCAAAGATAATAATAAATATA-ATATG-TTTATGTTTTAATTTATTAATAATATATA-TAACG
194 AACCAAAGATAATAATAAATATATATATGTTTTATGTTTTAATTTAATAATAATATATACTAACA
* *
4098059 TAAAAAATAAATCATT-AGACGCCTAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
259 TAAAAAATAAATCATTAAGACACATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
4098123 CCTTAAATTAATGTTTTCCACAGTGAAA-AAGTATGGACACTTTTATAAAAAGGATAGATACTTT
324 -CTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGAC-CTTTTATAAAAAGGATAGATACTTT
4098187 ACAATATAAGCACTACCTA-TACATTATATAAACGCTACCTATTACATTATATAAGTG-TACCTA
387 ACAATA-AAGCACTACCTATTACATTATATAAACGCTACCTATTACA-TATATAAGTGCTACCTA
4098250 TTACATCATA-TTTTTACCTATTATA
450 TTACATCATATTTTTTACCTATTATA
*
4098275 TTGAAAGTGTCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTA-GTTT
1 TTGAAAGTGTCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
4098339 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA-TTAATAATTTCATTTGCACA
66 CAATTTTTTTAATAGTGTTTCATGTTTT-CACCTACAATATTAATTTAATAATTTCATTTGCACA
4098403 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
130 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
4098468 ACCAAAGATAAT-ATAAATATGTAATATATG-TTTATTGTTTTTAATATTAATA
195 ACCAAAGATAATAATAAATA--T-ATATATGTTTTA-TG-TTTTAAT-TTAATA
4098520 TCGCTACACT
Statistics
Matches: 681, Mismatches: 16, Indels: 43
0.92 0.02 0.06
Matches are distributed among these distances:
469 58 0.09
470 123 0.18
471 18 0.03
472 78 0.11
473 109 0.16
474 44 0.06
475 7 0.01
476 5 0.01
477 26 0.04
478 18 0.03
479 44 0.06
480 13 0.02
481 13 0.02
482 43 0.06
483 82 0.12
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (475 bp):
TTGAAAGTGTCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
CAATTTTTTTAATAGTGTTTCATGTTTTCACCTACAATATTAATTTAATAATTTCATTTGCACAA
AAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAA
CCAAAGATAATAATAAATATATATATGTTTTATGTTTTAATTTAATAATAATATATACTAACATA
AAAAATAAATCATTAAGACACATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACT
TAAATTAATGTTTTCCACAGTGAAATAAGTATGGACCTTTTATAAAAAGGATAGATACTTTACAA
TAAAGCACTACCTATTACATTATATAAACGCTACCTATTACATATATAAGTGCTACCTATTACAT
CATATTTTTTACCTATTATA
Found at i:4099671 original size:175 final size:175
Alignment explanation
Indices: 4099358--4099915 Score: 660
Period size: 194 Copynumber: 3.1 Consensus size: 175
4099348 TTTTATATAT
* *
4099358 GGATCGACACTTTATTGTTGCAACCCTGTTTGCCATTCATTTTGGACCAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCAACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAAC
*
4099423 TAAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCTAAAACCGTATACTTGTACCGGTTAG
66 TAAAAAAAGTGTCGACACATTATTTAGACATATTATCTCTAAAACCGTATACTTGTACCGGTTAG
4099488 ATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG-TTATG
131 ATTGAAAAA-TACAT-TTACATTATACTTTT-GGTTTCGATGTTTATG
*
4099535 GGATCGACACTTTATGGTTGC-ACCCTGTTTGCCATTCATTCTGGACCAAAATATCGATAC-AAC
1 GGATCGACACTTTATGGTTGCAACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAAC
* *
4099598 T-ACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATACTTGTACCGGTTA
66 TAAAAAAAGTGTCGACACATTATTTAGACATATTATCTC-TAAAACCGTATACTTGTACCGGTTA
*
4099662 GATTGAAAAATATATTTACATTATACTTTTGGTTTCGATGTTTATG
130 GATTGAAAAATACATTTACATTATACTTTTGGTTTCGATGTTTATG
* *
4099708 GGATCGAAACTTTTTATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGAC
1 GGATCGACAC---TT-TATGG-TTG-CA----A------C--CCTGTTTGCCATTCATTCTGGAC
* * * *
4099773 CAGAAATATCGACACAAACT-ACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAAC
48 CA-AAATATCGACACAAACTAAAAAAAGTGTCGACACATTATTTAGACATATTATCTC-TAAAAC
* * * * * * *
4099837 TGATATACTTGCACCGATTAGATTGAAAATTACCTATTACATTATACTTTGGGTTTCGATGTTTT
111 CG-TATACTTGTACCGGTTAGATTGAAAAATACAT-TTACATTATACTTTTGGTTTCGATGTTTA
4099902 TG
174 TG
4099904 GG-TCGACACTTT
1 GGATCGACACTTT
4099916 TATATATGGA
Statistics
Matches: 335, Mismatches: 21, Indels: 36
0.85 0.05 0.09
Matches are distributed among these distances:
172 10 0.03
173 29 0.09
174 38 0.11
175 39 0.12
176 39 0.12
177 25 0.07
178 2 0.01
179 1 0.00
184 1 0.00
190 1 0.00
191 1 0.00
192 27 0.08
193 11 0.03
194 47 0.14
195 33 0.10
196 31 0.09
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (175 bp):
GGATCGACACTTTATGGTTGCAACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAAC
TAAAAAAAGTGTCGACACATTATTTAGACATATTATCTCTAAAACCGTATACTTGTACCGGTTAG
ATTGAAAAATACATTTACATTATACTTTTGGTTTCGATGTTTATG
Found at i:4099919 original size:194 final size:193
Alignment explanation
Indices: 4099535--4099956 Score: 663
Period size: 195 Copynumber: 2.2 Consensus size: 193
4099525 CGATGTTATG
*
4099535 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAATATCGATACAACTA
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAACTA
* *
4099600 CAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATACTTGTACCGGTTAGAT
66 CAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATACTTGCACCGATTAGAT
*
4099665 TGAAAAATATATTTACATTATACTTTTGGTTTCGATGTTTATGGGATCGAAACTTTT-TATAT
131 TGAAAAATATATTTACATTATACTTTGGGTTTCGATGTTTATGGGATCGAAACTTTTATATAT
*
4099727 GGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCA-AAATATCGACAC-AAC
* * *
4099792 TACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACTGATATACTTGCACCGATTA
64 TACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG-TATACTTGCACCGATTA
* * *
4099857 GATTGAAAATTACCTA-TTACATTATACTTTGGGTTTCGATGTTTTTGGG-TCGACACTTTTATA
128 GATTGAAAAATA--TATTTACATTATACTTTGGGTTTCGATGTTTATGGGATCGAAACTTTTATA
4099920 TAT
191 TAT
*
4099923 GGATCGACACTTTAT-GTTGCACCCTGGTTGCCAT
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
4099957 ATTGTAAATT
Statistics
Matches: 211, Mismatches: 13, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
192 47 0.22
193 11 0.05
194 47 0.22
195 53 0.25
196 51 0.24
197 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (193 bp):
GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAACTA
CAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATACTTGCACCGATTAGAT
TGAAAAATATATTTACATTATACTTTGGGTTTCGATGTTTATGGGATCGAAACTTTTATATAT
Found at i:4100095 original size:18 final size:18
Alignment explanation
Indices: 4100069--4100115 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
4100059 TTATATTCAC
4100069 ATACAAAATTATAAATCGT
1 ATAC-AAATTATAAATCGT
*
4100088 ATACAAATTATAAATCTT
1 ATACAAATTATAAATCGT
4100106 ATACAAATTA
1 ATACAAATTA
4100116 ACCCTACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
ATACAAATTATAAATCGT
Found at i:4101331 original size:173 final size:174
Alignment explanation
Indices: 4101042--4101386 Score: 683
Period size: 173 Copynumber: 2.0 Consensus size: 174
4101032 TTACCGTCTA
4101042 AACACTACTTATCTCCATTTATTAATTTAACTCACCGCTAAGTGGTATGGAAGGTAGCCAATCCT
1 AACACTACTTATCTCCATTTATTAATTTAACTCACCGCTAAGTGGTATGGAAGGTAGCCAATCCT
4101107 CCGGAGTGACTTCTGAGAATCGTAGCATACTGTCCAGGCGAGCAAATCAATAACCTAACAAAATT
66 CCGGAGTGACTTCTGAGAATCGTAGCATACTGTCCAGGCGAGCAAATCAATAACCTAACAAAATT
4101172 AATTACATAATCAGAACATA-TCAATAAGTTTTAACATTTTCAT
131 AATTACATAATCAGAACATATTCAATAAGTTTTAACATTTTCAT
4101215 AACACTACTTATCTCCATTTATTAATTTAACTCACCGCTAAGTGGTATGGAAGGTAGCCAATCCT
1 AACACTACTTATCTCCATTTATTAATTTAACTCACCGCTAAGTGGTATGGAAGGTAGCCAATCCT
4101280 CCGGAGTGACTTCTGAGAATCGTAGCATACTGTCCAGGCGAGCAAATCAATAACCTAACAAAATT
66 CCGGAGTGACTTCTGAGAATCGTAGCATACTGTCCAGGCGAGCAAATCAATAACCTAACAAAATT
4101345 AATTACATAATCAGAACATATTCAATAAGTTTTAACATTTTC
131 AATTACATAATCAGAACATATTCAATAAGTTTTAACATTTTC
4101387 TACTTTCTAC
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 150 0.88
174 21 0.12
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (174 bp):
AACACTACTTATCTCCATTTATTAATTTAACTCACCGCTAAGTGGTATGGAAGGTAGCCAATCCT
CCGGAGTGACTTCTGAGAATCGTAGCATACTGTCCAGGCGAGCAAATCAATAACCTAACAAAATT
AATTACATAATCAGAACATATTCAATAAGTTTTAACATTTTCAT
Done.