Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 26 of 27
Found at i:3961333 original size:41 final size:41
Alignment explanation
Indices: 3961269--3961385 Score: 162
Period size: 41 Copynumber: 2.8 Consensus size: 41
3961259 AATAAAGCAA
* *
3961269 GCCCACGCCTTATTAAATGAGAGCTTCTGTTTTATTAACGT
1 GCCCACGCCTTATAAAATAAGAGCTTCTGTTTTATTAACGT
* * *
3961310 GCCCGCGCCTTATCAAACAAGAGCTTCTGTTTTATTAACGT
1 GCCCACGCCTTATAAAATAAGAGCTTCTGTTTTATTAACGT
* *
3961351 GCCCACACCTTATAAAATAAGAGTTTCTGATTTTA
1 GCCCACGCCTTATAAAATAAGAGCTTCTG-TTTTA
3961386 ATTTGAATGC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 61 0.92
42 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (41 bp):
GCCCACGCCTTATAAAATAAGAGCTTCTGTTTTATTAACGT
Found at i:3962554 original size:13 final size:13
Alignment explanation
Indices: 3962536--3962560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3962526 CATTTTATGG
3962536 TGTATCGATACAA
1 TGTATCGATACAA
3962549 TGTATCGATACA
1 TGTATCGATACA
3962561 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3962576 original size:32 final size:33
Alignment explanation
Indices: 3962513--3962580 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
3962503 CGTTACAAGC
**
3962513 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
3962546 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
3962578 CAA
1 CAA
3962581 GTTTAACTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:3962658 original size:20 final size:21
Alignment explanation
Indices: 3962612--3962664 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3962602 GCCAATGACT
**
3962612 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
3962633 TATATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
3962653 TGTATCGATACA
1 TGTATCGATACA
3962665 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:3962942 original size:12 final size:13
Alignment explanation
Indices: 3962925--3962959 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
3962915 CCATTTCATA
3962925 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
3962937 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
3962950 TTTCTTTCTT
1 TTT-TTTCTT
3962960 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 3 0.14
14 6 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:3964264 original size:32 final size:32
Alignment explanation
Indices: 3964215--3965073 Score: 1445
Period size: 32 Copynumber: 26.8 Consensus size: 32
3964205 AAAATGGTGA
* * *
3964215 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3964247 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964279 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
3964311 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964343 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964375 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
3964407 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964439 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964471 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964503 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
** *
3964535 TTTGAAAAAGGTTGCCACCGACTTGTGTGCGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964567 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964599 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
3964631 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964663 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964695 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
3964727 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3964759 TTTGAAATGGGTTGCCACCTACTTGTGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964791 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
3964823 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3964855 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964887 TTTGAAATGGGTTGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964919 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964951 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3964983 TTTAAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3965015 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3965047 TTTGGAATGGGTTGCCACCGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
3965074 AATTTAAAAG
Statistics
Matches: 782, Mismatches: 39, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
31 3 0.00
32 776 0.99
33 3 0.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:3965097 original size:27 final size:27
Alignment explanation
Indices: 3965059--3965692 Score: 899
Period size: 27 Copynumber: 22.9 Consensus size: 27
3965049 TGGAATGGGT
* * * *
3965059 TGCCACCGAGTTGTGAATTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
3965086 TGCCACGGAGTTGTGGACTTAAAAGGC
1 TGCCACGGAGTTGTGGACTTAAAAGGG
3965113 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
3965140 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
3965168 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
3965196 TGCCACAGAATTGTGGACTTAAAAGAGA
1 TGCCACGGAGTTGTGGACTTAAAAG-GG
*
3965224 TGCCACGGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
3965251 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
3965278 TGCCACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
3965305 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
3965333 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
3965360 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
3965388 TGCCACGGAGTTATGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
3965416 TGCCACAGAATTGTGGACTTAAAAGAGA
1 TGCCACGGAGTTGTGGACTTAAAAG-GG
*
3965444 TGCCACGGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
3965471 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
3965498 TGCCACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
3965525 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
3965553 TGCCACAGAGTTGTGGAATTAAAAGAGA
1 TGCCACGGAGTTGTGGACTTAAAAG-GG
*
3965581 TGCCACGGAGTTATGGACTTAAAAGGGTGCGG
1 TGCCACGGAGTTGTGGACTTAAAA----G-GG
3965613 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
3965640 TGCCACAGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
3965667 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
3965693 AAAATACCAT
Statistics
Matches: 551, Mismatches: 44, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
27 295 0.54
28 231 0.42
32 25 0.05
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.24
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:3965349 original size:165 final size:164
Alignment explanation
Indices: 3965059--3965692 Score: 905
Period size: 165 Copynumber: 3.8 Consensus size: 164
3965049 TGGAATGGGT
* * * * * *
3965059 TGCCACCGAGTTGTGAATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG-GCTGCCACGGAG
1 TGCCACGGAGTTATGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGAGGTGCCACGGAG
*
3965123 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
66 TTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-T
* * *
3965188 TAAAAGGGTGCCACAGAATTGTGGAC-TTAAAAGAGA
129 TAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG-GG
*
3965224 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCACGGAG
1 TGCCACGGAGTTATGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGAGGTGCCACGGAG
* *
3965288 TTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
66 TTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT
3965353 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
130 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
* * *
3965388 TGCCACGGAGTTATGGACTTTAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGA
1 TGCCACGGAGTTATGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGAGGTGCCACGGA
* *
3965453 GTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTT
65 GTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
3965518 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
130 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
* * * * * *
3965553 TGCCACAGAGTTGTGGAATTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCGGTGCCA
1 TGCCACGGAGTTATGGACTTAAAAG-GATGCCACAGAGTTGTGGACTTAAAA----GAGGTGCCA
* * *
3965618 CGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGATGCCACAGAGTTGTGG
61 CGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG
3965683 ACTTTAAAAG
126 AC-TTAAAAG
3965693 AAAATACCAT
Statistics
Matches: 429, Mismatches: 31, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
164 51 0.12
165 259 0.60
166 43 0.10
169 69 0.16
170 7 0.02
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.24
Consensus pattern (164 bp):
TGCCACGGAGTTATGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGAGGTGCCACGGAG
TTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
AAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
Found at i:3965447 original size:220 final size:220
Alignment explanation
Indices: 3965059--3965692 Score: 1053
Period size: 220 Copynumber: 2.9 Consensus size: 220
3965049 TGGAATGGGT
* * * *
3965059 TGCCACCGAGTTGTGAAT-TTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGCTGCCACGGA
1 TGCCACGGAGTTGTG-GTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGA
3965122 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
65 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
3965187 TTAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGT
130 TTAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGT
3965252 GCCACAGAGTTGTGGACTTAAAAGGG
195 GCCACAGAGTTGTGGACTTAAAAGGG
3965278 TGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAG
*
3965343 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTT
66 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
3965408 TAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTG
131 TAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTG
3965473 CCACAGAGTTGTGGACTTAAAAGGG
196 CCACAGAGTTGTGGACTTAAAAGGG
*
3965498 TGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAG
1 TGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAG
* * *
3965563 TTGTGGAATTAAAAGAGATGCCACGGAGTTATGGAC-TTAAAAGGGTGCGGTGCCACGGAGTTGT
66 TTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTTAAAA----G-GGTGCCACGGAGTTGT
* * *
3965627 GGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA-AGATGCCACAGAGTTGTGGACTTTAA
125 GGACTTTAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGAGTTATGGAC-TTAA
3965690 AAG
189 AAG
3965693 AAAATACCAT
Statistics
Matches: 393, Mismatches: 13, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
218 1 0.00
219 40 0.10
220 256 0.65
221 18 0.05
223 19 0.05
224 40 0.10
225 19 0.05
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.24
Consensus pattern (220 bp):
TGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAG
TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
TAAAAGGGTGCCACAGAATTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTG
CCACAGAGTTGTGGACTTAAAAGGG
Found at i:3971581 original size:12 final size:12
Alignment explanation
Indices: 3971564--3971588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3971554 AATAATCATC
3971564 ATAATGACAAGT
1 ATAATGACAAGT
3971576 ATAATGACAAGT
1 ATAATGACAAGT
3971588 A
1 A
3971589 AAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATAATGACAAGT
Found at i:3972963 original size:23 final size:24
Alignment explanation
Indices: 3972915--3972964 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
3972905 ATATTTTTTA
* *
3972915 TTTTTTAAAACAAATAAAGATCAT
1 TTTTTTAAAACAAATAAACATAAT
*
3972939 TTTTTTAAAA-AAA-AAACATAAA
1 TTTTTTAAAACAAATAAACATAAT
3972961 TTTT
1 TTTT
3972965 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 3 0.13
24 10 0.43
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTTTTAAAACAAATAAACATAAT
Found at i:3973508 original size:12 final size:13
Alignment explanation
Indices: 3973491--3973525 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
3973481 CCATTTCATA
3973491 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
3973503 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
3973516 TTTCTTTCTT
1 TTT-TTTCTT
3973526 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 3 0.14
14 6 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:3976144 original size:41 final size:41
Alignment explanation
Indices: 3976080--3976196 Score: 162
Period size: 41 Copynumber: 2.8 Consensus size: 41
3976070 AATAAAGCAA
* *
3976080 GCCCACGCCTTATTAAACGAGAGCTTCTGTTTTATTAACGT
1 GCCCACGCCTTATAAAACAAGAGCTTCTGTTTTATTAACGT
* *
3976121 GCCCGCGCCTTATCAAACAAGAGCTTCTGTTTTATTAACGT
1 GCCCACGCCTTATAAAACAAGAGCTTCTGTTTTATTAACGT
* * *
3976162 GCCCACACCTTATAAAATAAGAGTTTCTGATTTTA
1 GCCCACGCCTTATAAAACAAGAGCTTCTG-TTTTA
3976197 ATTTGAATGC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 62 0.93
42 5 0.07
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (41 bp):
GCCCACGCCTTATAAAACAAGAGCTTCTGTTTTATTAACGT
Found at i:3977364 original size:13 final size:13
Alignment explanation
Indices: 3977346--3977370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3977336 CATTTTATGG
3977346 TGTATCGATACAA
1 TGTATCGATACAA
3977359 TGTATCGATACA
1 TGTATCGATACA
3977371 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3977386 original size:32 final size:33
Alignment explanation
Indices: 3977323--3977390 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
3977313 CGTTACAAGC
**
3977323 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
3977356 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
3977388 CAA
1 CAA
3977391 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:3977480 original size:13 final size:13
Alignment explanation
Indices: 3977462--3977490 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3977452 ACATTTGGTC
3977462 ATGTATCGATACA
1 ATGTATCGATACA
3977475 ATGTATCGATACA
1 ATGTATCGATACA
3977488 ATG
1 ATG
3977491 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3977501 original size:20 final size:20
Alignment explanation
Indices: 3977476--3977526 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3977466 ATCGATACAA
*
3977476 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
3977496 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
3977516 TGTATCGATAC
1 TGTATCGATAC
3977527 TTTTTAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:3978083 original size:22 final size:21
Alignment explanation
Indices: 3978041--3978084 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3978031 TTTTCTTTTC
*
3978041 TCTCCCCCTTAATCAAAAATT
1 TCTCCCCCTTAATAAAAAATT
*
3978062 TCTCCCCCTTAGTAAAACAATT
1 TCTCCCCCTTAATAAAA-AATT
3978084 T
1 T
3978085 AACACTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:3978134 original size:19 final size:19
Alignment explanation
Indices: 3978110--3978147 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3978100 TAACCATTTC
3978110 TTTCTCCCCCTTAATCATA
1 TTTCTCCCCCTTAATCATA
3978129 TTTCTCCCCCTTAATCATA
1 TTTCTCCCCCTTAATCATA
3978148 AAATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTCTCCCCCTTAATCATA
Found at i:3979818 original size:20 final size:21
Alignment explanation
Indices: 3979789--3979829 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3979779 TGTTTTTGAT
3979789 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
3979808 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
3979830 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:3979979 original size:13 final size:13
Alignment explanation
Indices: 3979961--3979985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3979951 ATAATCCCTT
3979961 TGTATCGATACAA
1 TGTATCGATACAA
3979974 TGTATCGATACA
1 TGTATCGATACA
3979986 GAAAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3982081 original size:15 final size:15
Alignment explanation
Indices: 3982061--3982101 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3982051 GTTCATCAAT
3982061 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
3982076 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
3982091 CTCAATTTGGA
1 TTC-ATTTGGA
3982102 CGTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:3985617 original size:33 final size:32
Alignment explanation
Indices: 3985580--3985647 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
3985570 CGTTACAAGC
**
3985580 CAATGTATCAATACATTTTATGGTGTATCGATA
1 CAATGTATCAATACATACTAT-GTGTATCGATA
* *
3985613 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCAATACATACTATGTGTATCGATA
3985645 CAA
1 CAA
3985648 GTTTAGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATACTATGTGTATCGATA
Found at i:3985621 original size:13 final size:13
Alignment explanation
Indices: 3985603--3985627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3985593 CATTTTATGG
3985603 TGTATCGATACAA
1 TGTATCGATACAA
3985616 TGTATCGATACA
1 TGTATCGATACA
3985628 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3985705 original size:21 final size:20
Alignment explanation
Indices: 3985679--3985731 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3985669 GCCAATGACT
**
3985679 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATT-TGGTCA
*
3985700 TGTATCGATATATTTGGTCA
1 TGTATCGATACATTTGGTCA
3985720 TGTATCGATACA
1 TGTATCGATACA
3985732 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTGGTCA
Found at i:3985737 original size:13 final size:13
Alignment explanation
Indices: 3985719--3985747 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3985709 ATATTTGGTC
3985719 ATGTATCGATACA
1 ATGTATCGATACA
3985732 ATGTATCGATACA
1 ATGTATCGATACA
3985745 ATG
1 ATG
3985748 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3985758 original size:20 final size:20
Alignment explanation
Indices: 3985733--3985783 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3985723 ATCGATACAA
*
3985733 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
3985753 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
3985773 TGTATCGATAC
1 TGTATCGATAC
3985784 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:3986663 original size:16 final size:16
Alignment explanation
Indices: 3986642--3986740 Score: 53
Period size: 16 Copynumber: 5.9 Consensus size: 16
3986632 TTGATTTTTT
3986642 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAATG
* *
3986658 AAAAAAAT-AAGAAGTA
1 AAAAAAATGAA-AAATG
*
3986674 AAAAAAATAAGAAACAAAAG
1 AAAAAAAT--G-AA-AAATG
*
3986694 AAAAAAA-GAAAATTG
1 AAAAAAATGAAAAATG
3986709 AAAAGAAAATTG-AAAA-G
1 -AAA-AAAA-TGAAAAATG
3986726 AAAAAAAGTGAAAAA
1 AAAAAAA-TGAAAAA
3986741 AATTATTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
15 11 0.17
16 31 0.49
17 6 0.10
18 3 0.05
19 1 0.02
20 11 0.17
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:3986714 original size:12 final size:12
Alignment explanation
Indices: 3986697--3986729 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3986687 ACAAAAGAAA
3986697 AAAAGAAAATTG
1 AAAAGAAAATTG
3986709 AAAAGAAAATTG
1 AAAAGAAAATTG
3986721 AAAAGAAAA
1 AAAAGAAAA
3986730 AAAGTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (12 bp):
AAAAGAAAATTG
Found at i:3989770 original size:20 final size:20
Alignment explanation
Indices: 3989712--3989772 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3989702 TATACAACAG
*
3989712 TAATAATGAGATTAATTATTA
1 TAATAATGAGATTAA-AATTA
*
3989733 TAATATATAAGATT-AAATTA
1 TAATA-ATGAGATTAAAATTA
*
3989753 TAATGATGAGATTAAAATTA
1 TAATAATGAGATTAAAATTA
3989773 ATGGTGAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 7 0.21
20 14 0.41
21 6 0.18
22 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (20 bp):
TAATAATGAGATTAAAATTA
Found at i:3989780 original size:18 final size:19
Alignment explanation
Indices: 3989742--3989783 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
3989732 ATAATATATA
*
3989742 AGATTAAATTATAATGATG
1 AGATTAAAATATAATGATG
*
3989761 AGATTAAAAT-TAATGGTG
1 AGATTAAAATATAATGATG
3989779 AGATT
1 AGATT
3989784 TGTACTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (19 bp):
AGATTAAAATATAATGATG
Found at i:3992883 original size:16 final size:16
Alignment explanation
Indices: 3992862--3992894 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3992852 ACTCATTCTT
3992862 TCTGTTCTTTAAGGTC
1 TCTGTTCTTTAAGGTC
3992878 TCTGTTCTTTAAGGTC
1 TCTGTTCTTTAAGGTC
3992894 T
1 T
3992895 TGACATGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.52
Consensus pattern (16 bp):
TCTGTTCTTTAAGGTC
Found at i:3993506 original size:22 final size:22
Alignment explanation
Indices: 3993480--3993564 Score: 62
Period size: 26 Copynumber: 3.5 Consensus size: 22
3993470 AGATTATGTA
3993480 AAAAATAATTAAAATATAATAT
1 AAAAATAATTAAAATATAATAT
*
3993502 AAAAATAAAATAAATATGATAAATAT
1 AAAAAT-AATTAAA-AT-AT-AATAT
* * *
3993528 ATAAATATATTTAAATTTATATAAT
1 AAAAATA-ATTAAAATATA-AT-AT
*
3993553 AAAAATTATTAA
1 AAAAATAATTAA
3993565 TAATGTGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
22 6 0.12
23 7 0.15
24 9 0.19
25 12 0.25
26 14 0.29
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
AAAAATAATTAAAATATAATAT
Found at i:3993678 original size:3 final size:3
Alignment explanation
Indices: 3993670--3993712 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
3993660 CGAGATTATA
3993670 TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3993713 CGGAATAAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3996822 original size:2 final size:2
Alignment explanation
Indices: 3996815--3996840 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3996805 CACCTTGTAA
3996815 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
3996841 GTACGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3998197 original size:4 final size:4
Alignment explanation
Indices: 3998188--3998214 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3998178 TTCTTAATGT
3998188 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3998215 TTGTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3998583 original size:16 final size:17
Alignment explanation
Indices: 3998549--3998586 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3998539 TTTTTATAAT
3998549 AAAATAAAGCTAAACTA
1 AAAATAAAGCTAAACTA
**
3998566 AAAATAAATTTAAA-TA
1 AAAATAAAGCTAAACTA
3998582 AAAAT
1 AAAAT
3998587 TTGTGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATAAAGCTAAACTA
Found at i:3998753 original size:18 final size:18
Alignment explanation
Indices: 3998706--3998755 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3998696 AAGTTAAATG
3998706 ATTTAAA-TT-ATTATTT
1 ATTTAAATTTAATTATTT
**
3998722 ATTT-AATAAAAATTATTT
1 ATTTAAAT-TTAATTATTT
3998740 ATTTAAATTTAATTAT
1 ATTTAAATTTAATTAT
3998756 AAAAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 2 0.08
16 4 0.15
18 17 0.65
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAAATTTAATTATTT
Found at i:3998779 original size:14 final size:15
Alignment explanation
Indices: 3998760--3998793 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
3998750 AATTATAAAA
3998760 AATATAAAAATA-TT
1 AATATAAAAATATTT
3998774 AATATAAAAATATTT
1 AATATAAAAATATTT
3998789 AATAT
1 AATAT
3998794 TTTAATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAAAATATTT
Found at i:3998798 original size:23 final size:22
Alignment explanation
Indices: 3998739--3998799 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
3998729 AAAAATTATT
3998739 TATTTAAA-TTTAATTATAAAAAA
1 TATTTAAATTTTAA-TAT-AAAAA
** *
3998762 TATAAAAATATTAATATAAAAA
1 TATTTAAATTTTAATATAAAAA
3998784 TATTTAATATTTTAAT
1 TATTTAA-ATTTTAAT
3998800 TTCTTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 10 0.33
23 16 0.53
24 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTTAAATTTTAATATAAAAA
Found at i:3999022 original size:2 final size:2
Alignment explanation
Indices: 3999015--3999052 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3999005 TAGCATGATC
3999015 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
3999053 TCAATTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4003340 original size:24 final size:22
Alignment explanation
Indices: 4003313--4003374 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
4003303 AAATAAAATT
*
4003313 ATAATTATTATTGTAAGAATATAC
1 ATAATTA-TATTATAA-AATATAC
*
4003337 ATAATTATATTATAAAATATAA
1 ATAATTATATTATAAAATATAC
* *
4003359 AT-TTTATATTAAAAAA
1 ATAATTATATTATAAAA
4003375 ATATTATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.35
22 8 0.24
23 7 0.21
24 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (22 bp):
ATAATTATATTATAAAATATAC
Found at i:4004498 original size:3 final size:3
Alignment explanation
Indices: 4004490--4004526 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4004480 TACTAACAAT
4004490 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4004527 TTATTTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4007544 original size:2 final size:2
Alignment explanation
Indices: 4007537--4007577 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4007527 TCTGTATGTG
*
4007537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4007578 GTCAACGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4010389 original size:2 final size:2
Alignment explanation
Indices: 4010382--4010412 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4010372 TTCACTCTTC
4010382 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
4010413 CTTTCCTATT
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:4012134 original size:21 final size:18
Alignment explanation
Indices: 4012110--4012165 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
4012100 ATATGTGTAT
4012110 AAATAATAAATAAATATA
1 AAATAATAAATAAATATA
*
4012128 AACA-AATATATAAAAATGATA
1 AA-ATAATA-A-ATAAAT-ATA
4012149 AAATAATAAATAAATAT
1 AAATAATAAATAAATAT
4012166 TGATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
18 8 0.26
19 7 0.23
20 7 0.23
21 9 0.29
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAATAAATAAATATA
Found at i:4012406 original size:41 final size:41
Alignment explanation
Indices: 4012313--4012408 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
4012303 ATATAAATTG
* *
4012313 AACAAGTTTTATTTGAAATTAACTGATTTAGTAGATGAACA
1 AACAAATTTTGTTTGAAATTAACTGATTTAGTAGATGAACA
* *
4012354 AACAAACTTTGTTTGAAATTGACTGATTTAGTAGATGAAC-
1 AACAAATTTTGTTTGAAATTAACTGATTTAGTAGATGAACA
*
4012394 AGCATAATTTTGTTT
1 AACA-AATTTTGTTT
4012409 AACTTGATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 3 0.06
41 45 0.94
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (41 bp):
AACAAATTTTGTTTGAAATTAACTGATTTAGTAGATGAACA
Found at i:4012627 original size:16 final size:15
Alignment explanation
Indices: 4012608--4012650 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
4012598 AAAAATAACC
4012608 CAAACTTGAAATAATT
1 CAAACTT-AAATAATT
*
4012624 CAAATTTAAAATAATT
1 CAAACTT-AAATAATT
4012640 CAAACTTAAAT
1 CAAACTTAAAT
4012651 TTACCTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (15 bp):
CAAACTTAAATAATT
Found at i:4013707 original size:32 final size:32
Alignment explanation
Indices: 4013661--4013725 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
4013651 TACTTGTGGG
4013661 ACACAAAAAAGTAATGGCCAAGTGTGGTTATA
1 ACACAAAAAAGTAATGGCCAAGTGTGGTTATA
*
4013693 ACACCAAAAAGTAATGGCCAAGTGTGGTTATA
1 ACACAAAAAAGTAATGGCCAAGTGTGGTTATA
4013725 A
1 A
4013726 ACTTACGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (32 bp):
ACACAAAAAAGTAATGGCCAAGTGTGGTTATA
Found at i:4013905 original size:2 final size:2
Alignment explanation
Indices: 4013898--4013932 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4013888 ATGCCTTTTC
4013898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4013933 CACACATGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4014765 original size:94 final size:94
Alignment explanation
Indices: 4014604--4014791 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
4014594 TAGTGGAGGT
4014604 TATCTGAATGCACTTTTCATTTCCAACAAGAACATCTTTCGCTGAAGCAAACAACTTAGAAAAAA
1 TATCTGAATGCACTTTTCATTTCCAACAAGAACATCTTTCGCTGAAGCAAACAACTTAGAAAAAA
4014669 GTGATAAACATTAAAATACAACAGTAAGA
66 GTGATAAACATTAAAATACAACAGTAAGA
* * *
4014698 TATCTGAATGCACTTTTCATTTCCAACAAGAACATCTTTTGTTGCAGCAAACAACTTAGAAAAAA
1 TATCTGAATGCACTTTTCATTTCCAACAAGAACATCTTTCGCTGAAGCAAACAACTTAGAAAAAA
*
4014763 GTGATAAACATTAATATACAACAGTAAGA
66 GTGATAAACATTAAAATACAACAGTAAGA
4014792 CTACCGGAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.27
Consensus pattern (94 bp):
TATCTGAATGCACTTTTCATTTCCAACAAGAACATCTTTCGCTGAAGCAAACAACTTAGAAAAAA
GTGATAAACATTAAAATACAACAGTAAGA
Found at i:4016469 original size:2 final size:2
Alignment explanation
Indices: 4016462--4016501 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4016452 TTCTTTTCTA
4016462 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
4016502 TACTATACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4017018 original size:11 final size:11
Alignment explanation
Indices: 4016978--4017020 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4016968 CCTTGAAGTC
*
4016978 TTTTTAAATTA
1 TTTTAAAATTA
*
4016989 TTTTAAATATAA
1 TTTTAAA-ATTA
*
4017001 ATTTAAAATTA
1 TTTTAAAATTA
4017012 TTTTAAAAT
1 TTTTAAAAT
4017021 ATACATAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:4017801 original size:20 final size:20
Alignment explanation
Indices: 4017758--4017807 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
4017748 TATAAAAATA
*
4017758 ATTAAATTATA-TCATATTT
1 ATTAAATTATATTCATATTC
* *
4017777 GTTAAATTATATTTATATTC
1 ATTAAATTATATTCATATTC
4017797 ATTAAA-TATAT
1 ATTAAATTATAT
4017808 GGGACATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAAATTATATTCATATTC
Found at i:4018022 original size:21 final size:22
Alignment explanation
Indices: 4017979--4018044 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
4017969 GATATTAACA
* *
4017979 TAATAAAAATTATAATTAAAATT
1 TAATAAAAATAATAA-AAAAATT
*
4018002 TAATATAAAT-ATAAAAAAA-T
1 TAATAAAAATAATAAAAAAATT
*
4018022 TAATAAAAATAATAAAAATATT
1 TAATAAAAATAATAAAAAAATT
4018044 T
1 T
4018045 TAAAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.27
21 12 0.32
22 6 0.16
23 9 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATAAAAATAATAAAAAAATT
Found at i:4018024 original size:20 final size:21
Alignment explanation
Indices: 4017979--4018039 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
4017969 GATATTAACA
* *
4017979 TAATAAAAATTATAATTAAAATT
1 TAATAAAAATAATAA--AAAAAT
*
4018002 TAATATAAAT-ATAAAAAAAT
1 TAATAAAAATAATAAAAAAAT
4018022 TAATAAAAATAATAAAAA
1 TAATAAAAATAATAAAAA
4018040 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.41
21 7 0.21
22 4 0.12
23 9 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAATAAAAATAATAAAAAAAT
Found at i:4018127 original size:20 final size:21
Alignment explanation
Indices: 4018105--4018152 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
4018095 ATAATATTTT
4018105 AAATATAATTATAATATAATA
1 AAATATAATTATAATATAATA
4018126 AAATAT-A-TA-AATATAATTAA
1 AAATATAATTATAATATAA-T-A
4018146 AAATATA
1 AAATATA
4018153 TTAGTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.29
19 3 0.12
20 8 0.33
21 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATAATTATAATATAATA
Found at i:4018153 original size:20 final size:18
Alignment explanation
Indices: 4018117--4018152 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4018107 ATATAATTAT
4018117 AATATAATAAAATATATA
1 AATATAATAAAATATATA
4018135 AATATAATTAAAA-ATATA
1 AATATAA-TAAAATATATA
4018153 TTAGTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:4018290 original size:20 final size:21
Alignment explanation
Indices: 4018249--4018294 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
4018239 TAAATTTAAC
* *
4018249 TTATTT-AATAATTTAAATTA
1 TTATTTAAATAATTAAAAATA
4018269 TTATTTAAAT-ATTAAAAATA
1 TTATTTAAATAATTAAAAATA
4018289 TT-TTTA
1 TTATTTA
4018295 TATTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTTAAATAATTAAAAATA
Found at i:4018297 original size:17 final size:17
Alignment explanation
Indices: 4018277--4018318 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4018267 TATTATTTAA
4018277 ATATTAAAAATATTTTT
1 ATATTAAAAATATTTTT
*
4018294 ATATTAATATATATTTTT
1 ATATTAA-AAATATTTTT
4018312 A-ATTAAA
1 ATATTAAA
4018319 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 12 0.52
18 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTAAAAATATTTTT
Found at i:4031381 original size:2 final size:2
Alignment explanation
Indices: 4031374--4031404 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4031364 CACGAGCACA
4031374 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4031405 TCCCCTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4032475 original size:27 final size:27
Alignment explanation
Indices: 4032445--4032505 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
4032435 GGGTTTAGGG
4032445 TTATAAAAAAAATTTATAAAAATAAAA
1 TTATAAAAAAAATTTATAAAAATAAAA
* * * * *
4032472 TTATTATATAAATTTATTAAATTAAAA
1 TTATAAAAAAAATTTATAAAAATAAAA
*
4032499 TTTTAAA
1 TTATAAA
4032506 GTTTTTTATT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TTATAAAAAAAATTTATAAAAATAAAA
Found at i:4032482 original size:13 final size:13
Alignment explanation
Indices: 4032464--4032505 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
4032454 AAATTTATAA
4032464 AAATAAAATTATT
1 AAATAAAATTATT
* *
4032477 ATATAAATTTATT
1 AAATAAAATTATT
4032490 AAATTAAAATT-TT
1 AAA-TAAAATTATT
4032503 AAA
1 AAA
4032506 GTTTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATAAAATTATT
Found at i:4034238 original size:15 final size:15
Alignment explanation
Indices: 4034218--4034257 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
4034208 AAGTTACTTT
4034218 TTATTTTTTAAAATA
1 TTATTTTTTAAAATA
*
4034233 TTATTTTTAAAAATA
1 TTATTTTTTAAAATA
4034248 TTATTTTTTA
1 TTATTTTTTA
4034258 CTCAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTTTTAAAATA
Found at i:4038351 original size:2 final size:2
Alignment explanation
Indices: 4038344--4038382 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4038334 GGAATGAGTT
4038344 TA TA TA TA 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 TA TA TA TA T
4038383 TTTGTCTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4040708 original size:24 final size:24
Alignment explanation
Indices: 4040676--4040725 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4040666 TAATTATTAT
*
4040676 TTTAGTAATATTAT-TTTATTAAAA
1 TTTAGTAAT-TTATATTTATAAAAA
* *
4040700 TTTATTAATTTTTATTTATAAAAA
1 TTTAGTAATTTATATTTATAAAAA
4040724 TT
1 TT
4040726 ATTGATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTAGTAATTTATATTTATAAAAA
Found at i:4043542 original size:15 final size:14
Alignment explanation
Indices: 4043514--4043548 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4043504 AAGATATACA
*
4043514 AAAAATAAATAAAT
1 AAAAATAAAAAAAT
4043528 AAAAATCAAAAAAAT
1 AAAAAT-AAAAAAAT
4043543 AAAAAT
1 AAAAAT
4043549 TGGAGGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:4045031 original size:32 final size:30
Alignment explanation
Indices: 4044978--4045066 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 30
4044968 TTGTATGAGT
*
4044978 TAAATTATTAT-T-TAATAATAATTTTTTAA
1 TAAAATATTATATATAA-AATAATTTTTTAA
*
4045007 TTATAAATATTA-ATATAAATATAATATTTTAA
1 -TA-AAATATTATATATAAA-ATAATTTTTTAA
*
4045039 TAATATATTATATATAAAATGAATTTTT
1 TAAAATATTATATATAAAAT-AATTTTT
4045067 CGAACCAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
30 11 0.22
31 24 0.49
32 14 0.29
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TAAAATATTATATATAAAATAATTTTTTAA
Found at i:4045046 original size:18 final size:18
Alignment explanation
Indices: 4045004--4045053 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
4044994 AATAATTTTT
4045004 TAAT-TATAA-ATATTAA
1 TAATATATAATATATTAA
* *
4045020 TATAAATATAATATTTTAA
1 TA-ATATATAATATATTAA
*
4045039 TAATATATTATATAT
1 TAATATATAATATAT
4045054 AAAATGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 15 0.58
19 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATATATAATATATTAA
Found at i:4048787 original size:3 final size:3
Alignment explanation
Indices: 4048779--4048808 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4048769 TCCGAAGGAC
4048779 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4048809 ATATTGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4050408 original size:2 final size:2
Alignment explanation
Indices: 4050403--4050427 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4050393 GTACGTAGTA
4050403 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4050428 GAGGCAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4050707 original size:23 final size:22
Alignment explanation
Indices: 4050680--4050758 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
4050670 CTAAACACGA
4050680 ATATTATATATATATATATAAAT
1 ATATTATAT-TATATATATAAAT
* *
4050703 ATATTAAATT-TATTATTATAATT
1 ATATTATATTATA-TA-TATAAAT
4050726 ATATTA-ATTATAT-T-TAAAT
1 ATATTATATTATATATATAAAT
4050745 ATATTATATTATAT
1 ATATTATATTATAT
4050759 TAATTATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 10 0.20
20 8 0.16
21 2 0.04
22 7 0.14
23 22 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTATATTATATATATAAAT
Found at i:4050710 original size:9 final size:9
Alignment explanation
Indices: 4050691--4050769 Score: 59
Period size: 10 Copynumber: 7.9 Consensus size: 9
4050681 TATTATATAT
4050691 ATATATATAA
1 ATATAT-TAA
4050701 ATATATTAA
1 ATATATTAA
4050710 ATTTATTATTATA
1 A--TA-TATTA-A
4050723 ATTATATTAA
1 A-TATATTAA
*
4050733 TTATATTTAA
1 ATATA-TTAA
4050743 ATATATTATA
1 ATATATTA-A
*
4050753 TTATATTAA
1 ATATATTAA
*
4050762 TTATATTA
1 ATATATTA
4050770 TTTTTATATT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
9 20 0.33
10 23 0.38
11 7 0.12
12 8 0.13
13 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATATTAA
Found at i:4050722 original size:29 final size:29
Alignment explanation
Indices: 4050686--4050769 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 29
4050676 ACGAATATTA
* *
4050686 TATATATATATATAAATATATTAAATTTAT
1 TATATATATAT-TAATTATATTAAATATAT
4050716 TATTATAATTATATTAATTATATTTAAATATAT
1 TA-TAT-A-TATATTAATTATA-TTAAATATAT
4050749 TATAT-TATATTAATTATATTA
1 TATATATATATTAATTATATTA
4050770 TTTTTATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 3 0.06
29 13 0.27
30 2 0.04
31 3 0.06
32 11 0.23
33 16 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATATATATTAATTATATTAAATATAT
Found at i:4050799 original size:17 final size:17
Alignment explanation
Indices: 4050701--4050799 Score: 71
Period size: 17 Copynumber: 5.8 Consensus size: 17
4050691 ATATATATAA
*
4050701 ATATATTAAATTTATTATT
1 ATAT-TTAAAATTA-TATT
* *
4050720 ATAATT-ATATTA-ATT
1 ATATTTAAAATTATATT
4050735 ATATTT-AAA-TATATT
1 ATATTTAAAATTATATT
*
4050750 ATATTATATTAATTATATT
1 ATATT-TA-AAATTATATT
* * *
4050769 ATTTTTATATTTATATT
1 ATATTTAAAATTATATT
4050786 ATATTTAAAATTAT
1 ATATTTAAAATTAT
4050800 CACATCTAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
14 2 0.03
15 18 0.28
16 1 0.02
17 24 0.38
18 6 0.09
19 13 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTAAAATTATATT
Found at i:4053351 original size:32 final size:31
Alignment explanation
Indices: 4053311--4053402 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
4053301 TAATATGAAT
*
4053311 ATATTAATATATTAAAATTTATATAAAATAA
1 ATATTAATATATTAAAATATATATAAAATAA
* *
4053342 ACTATTAATATATTAAAAAATATAT-AAATAT
1 A-TATTAATATATTAAAATATATATAAAATAA
* *
4053373 ATAATAATATAATTATAATATATA-AAAATA
1 ATATTAATAT-ATTAAAATATATATAAAATA
4053403 TATAAATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
30 8 0.15
31 23 0.44
32 21 0.40
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
ATATTAATATATTAAAATATATATAAAATAA
Found at i:4053358 original size:16 final size:16
Alignment explanation
Indices: 4053311--4053359 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
4053301 TAATATGAAT
4053311 ATATTAATATATTAAA
1 ATATTAATATATTAAA
* *
4053327 AT-TTATATAAAATAAA
1 ATATTA-ATATATTAAA
*
4053343 CTATTAATATATTAAA
1 ATATTAATATATTAAA
4053359 A
1 A
4053360 AATATATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTAATATATTAAA
Found at i:4053374 original size:10 final size:10
Alignment explanation
Indices: 4053309--4053418 Score: 61
Period size: 10 Copynumber: 10.8 Consensus size: 10
4053299 TATAATATGA
*
4053309 ATATATTAAT
1 ATATATAAAT
4053319 ATAT-TAAAAT
1 ATATAT-AAAT
*
4053329 TTATATAAAAT
1 ATATAT-AAAT
* *
4053340 AAACTATTAAT
1 ATA-TATAAAT
*
4053351 ATAT-TAAAAA
1 ATATAT-AAAT
4053361 ATATATAAAT
1 ATATATAAAT
4053371 ATATA-ATAAT
1 ATATATA-AAT
4053381 ATA-ATTATAAT
1 ATATA-TA-AAT
4053392 ATATA-AAA-
1 ATATATAAAT
4053400 ATATATAAAT
1 ATATATAAAT
4053410 ATAATATAA
1 AT-ATATAA
4053419 TAGACGGATT
Statistics
Matches: 79, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
8 5 0.06
9 9 0.11
10 34 0.43
11 27 0.34
12 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATAAAT
Found at i:4053398 original size:29 final size:28
Alignment explanation
Indices: 4053360--4053420 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
4053350 TATATTAAAA
*
4053360 AATATATAAATATATA-ATAATATAATTAT
1 AATATATAAAAATATATA-AATATAA-TAT
4053389 AATATATAAAAATATATAAATATAATAT
1 AATATATAAAAATATATAAATATAATAT
4053417 AATA
1 AATA
4053421 GACGGATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.23
29 22 0.73
30 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AATATATAAAAATATATAAATATAATAT
Found at i:4053408 original size:39 final size:41
Alignment explanation
Indices: 4053330--4053420 Score: 120
Period size: 39 Copynumber: 2.3 Consensus size: 41
4053320 TATTAAAATT
4053330 TATATAA-AATAAACTATTAATATATTAAAAAATATATAAA
1 TATATAATAATAAACTATTAATATATTAAAAAATATATAAA
*
4053370 TATATAATAATATAATTA-TAATATA-T-AAAAATATATAAA
1 TATATAATAATA-AACTATTAATATATTAAAAAATATATAAA
4053409 TATA-ATATAATA
1 TATATA-ATAATA
4053421 GACGGATTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
38 1 0.02
39 23 0.49
40 8 0.17
41 11 0.23
42 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (41 bp):
TATATAATAATAAACTATTAATATATTAAAAAATATATAAA
Found at i:4053574 original size:2 final size:2
Alignment explanation
Indices: 4053567--4053615 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
4053557 CTTCTTTCTT
* *
4053567 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4053609 TA TA TA T
1 TA TA TA T
4053616 TTGTTTCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4054514 original size:2 final size:2
Alignment explanation
Indices: 4054507--4054543 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4054497 AAAATAATCC
4054507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4054544 CACACACACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4055831 original size:15 final size:15
Alignment explanation
Indices: 4055811--4055858 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
4055801 TATGGATATT
4055811 TAAAAATTTATATAA
1 TAAAAATTTATATAA
4055826 TAAAAA-TTATTAATATA
1 TAAAAATTTA-T-ATA-A
*
4055843 TTAAAATTTATATAA
1 TAAAAATTTATATAA
4055858 T
1 T
4055859 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 6 0.21
17 7 0.25
18 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAAATTTATATAA
Found at i:4055863 original size:17 final size:17
Alignment explanation
Indices: 4055808--4055866 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
4055798 ATATATGGAT
*
4055808 ATTTAAAAATTTATATA
1 ATTTTAAAATTTATATA
*
4055825 A---TAAAAATTAT-TA
1 ATTTTAAAATTTATATA
4055838 ATATATTAAAATTTATATA
1 AT-T-TTAAAATTTATATA
4055857 ATTTTAAAAT
1 ATTTTAAAAT
4055867 ATCTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
17 8 0.24
18 10 0.30
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTAAAATTTATATA
Found at i:4060320 original size:4 final size:4
Alignment explanation
Indices: 4060311--4060336 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4060301 AATTTAATTT
4060311 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
4060337 AATCAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:4060412 original size:6 final size:6
Alignment explanation
Indices: 4060403--4060429 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4060393 CCCCCCCCCC
4060403 CTCTTT CTCTTT CTCTTT CTCTTT CTC
1 CTCTTT CTCTTT CTCTTT CTCTTT CTC
4060430 AACGCCTCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (6 bp):
CTCTTT
Found at i:4063289 original size:15 final size:15
Alignment explanation
Indices: 4063269--4063319 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
4063259 ATTTTGACTA
4063269 AAATTTATATTATTT
1 AAATTTATATTATTT
4063284 AAATTTATATTATTT
1 AAATTTATATTATTT
* *
4063299 GAGTTTGAT-TTATTT
1 AAATTT-ATATTATTT
4063314 AAATTT
1 AAATTT
4063320 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
AAATTTATATTATTT
Found at i:4063325 original size:15 final size:15
Alignment explanation
Indices: 4063269--4063325 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
4063259 ATTTTGACTA
*
4063269 AAATTTATATTATTT
1 AAATTTATTTTATTT
*
4063284 AAATTTATATTATTT
1 AAATTTATTTTATTT
* *
4063299 GAGTTTGA-TTTATTT
1 AAATTT-ATTTTATTT
*
4063314 AAATTTTTTTTA
1 AAATTTATTTTA
4063326 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 33 0.97
16 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
AAATTTATTTTATTT
Found at i:4063343 original size:23 final size:26
Alignment explanation
Indices: 4063315--4063364 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
4063305 GATTTATTTA
4063315 AATTTT-TTTTAAAA-AA-TTAAATT
1 AATTTTATTTTAAAATAATTTAAATT
4063338 AATTTTAATTTTAAAATAATTTAAATT
1 AATTTT-ATTTTAAAATAATTTAAATT
4063365 TTAAACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
25 8 0.35
26 2 0.09
27 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AATTTTATTTTAAAATAATTTAAATT
Found at i:4063357 original size:17 final size:17
Alignment explanation
Indices: 4063331--4063369 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4063321 TTTTAAAAAA
* *
4063331 TTAAATTAATTTTAATT
1 TTAAAATAATTTAAATT
4063348 TTAAAATAATTTAAATT
1 TTAAAATAATTTAAATT
4063365 TTAAA
1 TTAAA
4063370 CATATAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAATAATTTAAATT
Found at i:4064189 original size:20 final size:21
Alignment explanation
Indices: 4064151--4064192 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
4064141 TATAATCTAA
4064151 TATAATAAATAATTTAAAATT
1 TATAATAAATAATTTAAAATT
4064172 TATAAT-AA-AATATTAAAATT
1 TATAATAAATAAT-TTAAAATT
4064192 T
1 T
4064193 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 11 0.55
21 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATAAATAATTTAAAATT
Found at i:4065309 original size:19 final size:21
Alignment explanation
Indices: 4065263--4065309 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
4065253 TATTTAAGAT
4065263 AGAAAAATTAAGGAAATTTATA
1 AGAAAAATTAAGGAAA-TTATA
*
4065285 ATGAAAAATTAATGAAA-TA-A
1 A-GAAAAATTAAGGAAATTATA
4065305 AGAAA
1 AGAAA
4065310 TTATTTGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 2 0.09
21 2 0.09
22 1 0.04
23 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (21 bp):
AGAAAAATTAAGGAAATTATA
Found at i:4065867 original size:2 final size:2
Alignment explanation
Indices: 4065860--4065889 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4065850 CTTCACATTC
4065860 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
4065890 TGATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4067991 original size:3 final size:3
Alignment explanation
Indices: 4067985--4068044 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
4067975 TCATATGATG
4067985 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4068033 ATA ATA ATA ATA
1 ATA ATA ATA ATA
4068045 TAAGATTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4068385 original size:19 final size:19
Alignment explanation
Indices: 4068361--4068397 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4068351 TTATTGTATA
*
4068361 TAAATAAGTTATTAATTTT
1 TAAATAAATTATTAATTTT
*
4068380 TAAATAAATTTTTAATTT
1 TAAATAAATTATTAATTT
4068398 AAATTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TAAATAAATTATTAATTTT
Found at i:4068391 original size:12 final size:13
Alignment explanation
Indices: 4068374--4068406 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4068364 ATAAGTTATT
4068374 AATTTTTAA-ATA
1 AATTTTTAATATA
*
4068386 AATTTTTAATTTA
1 AATTTTTAATATA
4068399 AATTTTTA
1 AATTTTTA
4068407 TTTAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATTTTTAATATA
Found at i:4068400 original size:13 final size:13
Alignment explanation
Indices: 4068374--4068413 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
4068364 ATAAGTTATT
*
4068374 AATTTTTAA-ATA
1 AATTTTTAATTTA
4068386 AATTTTTAATTTA
1 AATTTTTAATTTA
4068399 AATTTTT-ATTTA
1 AATTTTTAATTTA
4068411 AAT
1 AAT
4068414 AAATATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTTTAATTTA
Found at i:4068400 original size:17 final size:17
Alignment explanation
Indices: 4068378--4068424 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 17
4068368 GTTATTAATT
4068378 TTTAAATAAATTTTTAA
1 TTTAAATAAATTTTTAA
4068395 -TT---TAAATTTTT-A
1 TTTAAATAAATTTTTAA
*
4068407 TTTAAATAAATATTTAA
1 TTTAAATAAATTTTTAA
4068424 T
1 T
4068425 ATTTAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 10
0.69 0.03 0.29
Matches are distributed among these distances:
12 1 0.04
13 11 0.46
16 10 0.42
17 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAATAAATTTTTAA
Found at i:4068443 original size:30 final size:29
Alignment explanation
Indices: 4068380--4068463 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 29
4068370 TATTAATTTT
* * *
4068380 TAAATAAATTTTTAATTTAAATTTTTATT
1 TAAATAAATTTTTAATTTTAATTTGTATC
*
4068409 TAAATAAATATTTAATATTTAATTTGTATC
1 TAAATAAATTTTTAAT-TTTAATTTGTATC
4068439 TAAATAAATTTTTAATCTTTAATTT
1 TAAATAAATTTTTAAT-TTTAATTT
4068464 ATACCAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (29 bp):
TAAATAAATTTTTAATTTTAATTTGTATC
Found at i:4071074 original size:2 final size:2
Alignment explanation
Indices: 4071069--4071095 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4071059 TAAAAAAAAG
4071069 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4071096 TAATCATCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4072773 original size:3 final size:3
Alignment explanation
Indices: 4072761--4072791 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4072751 ACAATGTTTG
4072761 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4072792 TAAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4074254 original size:32 final size:32
Alignment explanation
Indices: 4074201--4074291 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
4074191 ATCATATTTA
* *
4074201 TAATATTTTATGATTATATAAATTTTAATACAT
1 TAATAATTTAT-ATTATATAAATTTTAAAACAT
* *
4074234 TAATAATTTATATTATATAAAATTTAAAATAT
1 TAATAATTTATATTATATAAATTTTAAAACAT
* *
4074266 TTAT-A-TTATATTATATTATATTTTAA
1 TAATAATTTATATTATA-TAAATTTTAA
4074292 CTAATTTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 10 0.20
31 9 0.18
32 21 0.42
33 10 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
TAATAATTTATATTATATAAATTTTAAAACAT
Found at i:4074257 original size:16 final size:17
Alignment explanation
Indices: 4074194--4074259 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 17
4074184 TATTTAAATC
*
4074194 ATATT-TATAATATTTT
1 ATATTATATAATAATTT
4074210 ATGATTATAT-A-AATTT
1 AT-ATTATATAATAATTT
* *
4074226 -TAATACATTAATAATTT
1 ATATTATA-TAATAATTT
4074243 ATATTATATAA-AATTT
1 ATATTATATAATAATTT
4074259 A
1 A
4074260 AAATATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 4 0.10
15 2 0.05
16 13 0.33
17 12 0.31
18 8 0.21
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATATTATATAATAATTT
Found at i:4075252 original size:2 final size:2
Alignment explanation
Indices: 4075245--4075275 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4075235 CAGTGTCCAA
4075245 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4075276 TCCTATATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4076008 original size:2 final size:2
Alignment explanation
Indices: 4076001--4076029 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4075991 TTAGCTTGCC
4076001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4076030 CAAAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4079782 original size:147 final size:147
Alignment explanation
Indices: 4079515--4079811 Score: 594
Period size: 147 Copynumber: 2.0 Consensus size: 147
4079505 GATTTACGAA
4079515 CTTTAAAGCTCTAAAATAAAATAGAGGAAAGCGTCTGCACATTGTTATGTTGATTAGGAAAATTC
1 CTTTAAAGCTCTAAAATAAAATAGAGGAAAGCGTCTGCACATTGTTATGTTGATTAGGAAAATTC
4079580 GGTATAGAGGCACACATCTAGTCTATAGGAGGTACTAATGGTCCTATACATATATTAGATTAAAC
66 GGTATAGAGGCACACATCTAGTCTATAGGAGGTACTAATGGTCCTATACATATATTAGATTAAAC
4079645 CACACTCATGGAGCTAC
131 CACACTCATGGAGCTAC
4079662 CTTTAAAGCTCTAAAATAAAATAGAGGAAAGCGTCTGCACATTGTTATGTTGATTAGGAAAATTC
1 CTTTAAAGCTCTAAAATAAAATAGAGGAAAGCGTCTGCACATTGTTATGTTGATTAGGAAAATTC
4079727 GGTATAGAGGCACACATCTAGTCTATAGGAGGTACTAATGGTCCTATACATATATTAGATTAAAC
66 GGTATAGAGGCACACATCTAGTCTATAGGAGGTACTAATGGTCCTATACATATATTAGATTAAAC
4079792 CACACTCATGGAGCTAC
131 CACACTCATGGAGCTAC
4079809 CTT
1 CTT
4079812 CTTTTTGATG
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (147 bp):
CTTTAAAGCTCTAAAATAAAATAGAGGAAAGCGTCTGCACATTGTTATGTTGATTAGGAAAATTC
GGTATAGAGGCACACATCTAGTCTATAGGAGGTACTAATGGTCCTATACATATATTAGATTAAAC
CACACTCATGGAGCTAC
Found at i:4082722 original size:16 final size:16
Alignment explanation
Indices: 4082696--4082735 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4082686 ATTAATTATT
4082696 AAAATTTTAAC-ATTA
1 AAAATTTTAACAATTA
4082711 AAAATATTTAACAATT-
1 AAAAT-TTTAACAATTA
4082727 AAAATTTTA
1 AAAATTTTA
4082736 TCATTTATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 11 0.48
17 3 0.13
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTTTAACAATTA
Found at i:4083128 original size:165 final size:166
Alignment explanation
Indices: 4082804--4083131 Score: 489
Period size: 165 Copynumber: 2.0 Consensus size: 166
4082794 TTAGCATGAC
* * *
4082804 TCTCACGAACTAGGGATTTTCTAGCCAGATTTCTTCTTTATTCGGCATTTTCATTGCTGATTTCA
1 TCTCACGAACTAGGGATTTTCTAGCCAAATTTCTCCTTTATTCGGCATATTCATTGCTGATTTCA
*
4082869 AGTTCTAATTCTGATTCCACTGCTGCTAACTACAAATCTCATTGTTTACTGAAACTTTGAACATC
66 AGTACTAATTCTGATTCCACTGCTGCTAACTACAAATCTCATTGTTTACTGAAACTTTGAACATC
* *
4082934 TTGGTGCGATTTTTCTTTTCGCAAATGGAAAACGAA
131 TTGATGCAATTTTTCTTTTCGCAAATGGAAAACGAA
* * *
4082970 TCTCATGAACTAGGGATTTTCT-GCCAAATTTCTCCTTTCTTTGGCATATTCATTGCTGATTTCA
1 TCTCACGAACTAGGGATTTTCTAGCCAAATTTCTCCTTTATTCGGCATATTCATTGCTGATTTCA
* * * * *
4083034 AGTACTGATTCTGATTCCACTGCTGCTAACTGC-AATCTCATTGTTTTCTGAATCTTTTAACATC
66 AGTACTAATTCTGATTCCACTGCTGCTAACTACAAATCTCATTGTTTACTGAAACTTTGAACATC
* *
4083098 TTGATGCAATTTTTTTTTCTCGCGAATGGAAAAC
131 TTGATGCAATTTTTCTTT-TCGCAAATGGAAAAC
4083132 TTGCCACTGT
Statistics
Matches: 145, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
164 43 0.30
165 81 0.56
166 21 0.14
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (166 bp):
TCTCACGAACTAGGGATTTTCTAGCCAAATTTCTCCTTTATTCGGCATATTCATTGCTGATTTCA
AGTACTAATTCTGATTCCACTGCTGCTAACTACAAATCTCATTGTTTACTGAAACTTTGAACATC
TTGATGCAATTTTTCTTTTCGCAAATGGAAAACGAA
Found at i:4086354 original size:32 final size:33
Alignment explanation
Indices: 4086297--4086360 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
4086287 TGCAAGCCAA
**
4086297 TGTATCGATACAATTTTTTGTGTATCAATACAT
1 TGTATCGATACAATACTTTGTGTATCAATACAT
*
4086330 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCAATACA
4086361 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCAATACAT
Found at i:4090759 original size:2 final size:2
Alignment explanation
Indices: 4090752--4090780 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4090742 AAAGCAAAGA
4090752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4090781 CCTTATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4094124 original size:18 final size:20
Alignment explanation
Indices: 4094071--4094130 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
4094061 AGGGCACGAA
4094071 ACAACATAAAACATATATATT
1 ACAACA-AAAACATATATATT
* * *
4094092 AC-A-ATAAATATATATTTT
1 ACAACAAAAACATATATATT
*
4094110 ACAACAAAAACATATAGATT
1 ACAACAAAAACATATATATT
4094130 A
1 A
4094131 GATTTAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 13 0.43
19 2 0.07
20 13 0.43
21 2 0.07
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.30
Consensus pattern (20 bp):
ACAACAAAAACATATATATT
Found at i:4098488 original size:2 final size:2
Alignment explanation
Indices: 4098481--4098512 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4098471 ATGTTGAACT
4098481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4098513 GAATTATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4103889 original size:43 final size:43
Alignment explanation
Indices: 4103828--4103911 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
4103818 GTTCACTATG
*
4103828 ATGATGTATAAAGTAACTTAAAATTAAAATCAGTAAGACTACA
1 ATGATGCATAAAGTAACTTAAAATTAAAATCAGTAAGACTACA
4103871 ATGATGCATAAAGTAACTTAAAATTAAAATCAGTAAGACTA
1 ATGATGCATAAAGTAACTTAAAATTAAAATCAGTAAGACTA
4103912 AAAGAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (43 bp):
ATGATGCATAAAGTAACTTAAAATTAAAATCAGTAAGACTACA
Found at i:4105475 original size:15 final size:16
Alignment explanation
Indices: 4105455--4105487 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4105445 GAAAATTTAT
4105455 TTTATTAT-TTAAAAA
1 TTTATTATATTAAAAA
4105470 TTTATTATATTAAAAA
1 TTTATTATATTAAAAA
4105486 TT
1 TT
4105488 AATTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATTATATTAAAAA
Found at i:4105569 original size:10 final size:10
Alignment explanation
Indices: 4105550--4105582 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
4105540 ATATAAATAA
4105550 TAATTTAAAT
1 TAATTTAAAT
4105560 T-ATATTAAAT
1 TAAT-TTAAAT
4105570 TAATTTAAAT
1 TAATTTAAAT
4105580 TAA
1 TAA
4105583 AAATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.10
10 17 0.81
11 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:4106059 original size:22 final size:24
Alignment explanation
Indices: 4106016--4106073 Score: 88
Period size: 22 Copynumber: 2.6 Consensus size: 24
4106006 ATTCAGTTAA
4106016 ATTATTATTTAA-TAATTAAAAAT
1 ATTATTATTTAATTAATTAAAAAT
4106039 ATTATTA-TTAATTAATT-AAAAT
1 ATTATTATTTAATTAATTAAAAAT
4106061 A-TATTATTTAATT
1 ATTATTATTTAATT
4106074 TTTTATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.15
22 16 0.48
23 12 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATTATTTAATTAATTAAAAAT
Found at i:4106232 original size:23 final size:24
Alignment explanation
Indices: 4106201--4106277 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 24
4106191 TAATAATATG
4106201 TAAATAAAATAATAAATAATTTTTT
1 TAAA-AAAATAATAAATAATTTTTT
*
4106226 TAAAAAAAGTATGATTAAAT-ATTTAATT
1 TAAAAAAA-TA--A-TAAATAATTT-TTT
* *
4106254 T-AATAATTAATAAATAATTTTTT
1 TAAAAAAATAATAAATAATTTTTT
4106277 T
1 T
4106278 TCATAAAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
23 8 0.19
24 9 0.21
25 6 0.14
26 2 0.05
27 9 0.21
28 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
TAAAAAAATAATAAATAATTTTTT
Found at i:4106604 original size:22 final size:21
Alignment explanation
Indices: 4106576--4106619 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
4106566 AATATAAAAA
4106576 ATATATTTT-TATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
4106598 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
4106619 A
1 A
4106620 AATAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:4107501 original size:22 final size:20
Alignment explanation
Indices: 4107475--4107526 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
4107465 TTTATATTCA
4107475 TATATTTTAATTAGATTATAAT
1 TATATTTTAATTA-ATTA-AAT
*
4107497 TATA-TTTAA-TATTTAAAT
1 TATATTTTAATTAATTAAAT
4107515 TA-ATTTTAATTA
1 TATATTTTAATTA
4107527 TTATTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 5 0.19
20 2 0.07
21 5 0.19
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATTTTAATTAATTAAAT
Found at i:4107524 original size:28 final size:30
Alignment explanation
Indices: 4107466--4107527 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
4107456 CGTTTTTTTT
*
4107466 TTATATTCATATATTTTAATTAGATTATAA
1 TTATATTCATATATTTAAATTAGATTATAA
* *
4107496 TTATATTTA-ATATTTAAATTA-ATTTTAA
1 TTATATTCATATATTTAAATTAGATTATAA
4107524 TTAT
1 TTAT
4107528 TATTAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.34
29 11 0.38
30 8 0.28
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTATATTCATATATTTAAATTAGATTATAA
Done.