Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 50
Found at i:3700226 original size:12 final size:12
Alignment explanation
Indices: 3700199--3700233 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3700189 TTAAATTTTT
*
3700199 ATTTATATTA-A
1 ATTTTTATTATA
3700210 ATTTTTATTATA
1 ATTTTTATTATA
3700222 ATTTTTATTATA
1 ATTTTTATTATA
3700234 TTAATTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTTTTATTATA
Found at i:3702513 original size:30 final size:30
Alignment explanation
Indices: 3702468--3702568 Score: 112
Period size: 33 Copynumber: 3.1 Consensus size: 30
3702458 TGTCTCTTTT
* *
3702468 GTAAACTTGGACATGTTGCAATCTTTTGTAA
1 GTAAAATT-GACATGTTGCCATCTTTTGTAA
3702499 GTAAAATTGACATGTTGCTGCCATCTTTTGTAA
1 GTAAAATTGACATG-T--TGCCATCTTTTGTAA
*
3702532 GTAAAATTGACATATTGCTGCCATCTTTTGTAA
1 GTAAAATTGAC--A-TGTTGCCATCTTTTGTAA
3702565 GTAA
1 GTAA
3702569 GCTTAATTGG
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
30 6 0.10
31 8 0.13
33 44 0.72
35 1 0.02
36 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (30 bp):
GTAAAATTGACATGTTGCCATCTTTTGTAA
Found at i:3702530 original size:33 final size:33
Alignment explanation
Indices: 3702488--3702568 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
3702478 ACATGTTGCA
*
3702488 ATCTTTTGTAAGTAAAATTGACATGTTGCTGCC
1 ATCTTTTGTAAGTAAAATTGACATATTGCTGCC
3702521 ATCTTTTGTAAGTAAAATTGACATATTGCTGCC
1 ATCTTTTGTAAGTAAAATTGACATATTGCTGCC
3702554 ATCTTTTGTAAGTAA
1 ATCTTTTGTAAGTAA
3702569 GCTTAATTGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
ATCTTTTGTAAGTAAAATTGACATATTGCTGCC
Found at i:3703370 original size:17 final size:17
Alignment explanation
Indices: 3703348--3703384 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3703338 ATTCGAGTTT
3703348 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
3703365 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
3703382 GAG
1 GAG
3703385 CTCAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:3703427 original size:24 final size:24
Alignment explanation
Indices: 3703363--3703458 Score: 133
Period size: 24 Copynumber: 4.1 Consensus size: 24
3703353 CGAGCTTGAA
*
3703363 TCGAGT-TCGAGCTTGAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
*** *
3703386 TC-AAAATCAAGCTTCAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
3703409 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
3703433 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGTCTCGAGCTTCAATCGAGC
3703457 TC
1 TC
3703459 TTGAAATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.02
23 19 0.30
24 43 0.68
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (24 bp):
TCGAGTCTCGAGCTTCAATCGAGC
Found at i:3705658 original size:25 final size:27
Alignment explanation
Indices: 3705619--3705668 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
3705609 ATGAGATTTG
*
3705619 TAAACAAAATAATTGGGAAGGTTGTAA
1 TAAACAAAATAATTGGAAAGGTTGTAA
3705646 TAAA-AAAA-AATTGGAAAGGTTGT
1 TAAACAAAATAATTGGAAAGGTTGT
3705669 GTTGCTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 4 0.18
27 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.22, T:0.26
Consensus pattern (27 bp):
TAAACAAAATAATTGGAAAGGTTGTAA
Found at i:3711317 original size:20 final size:20
Alignment explanation
Indices: 3711292--3711343 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3711282 TAACCTTTGA
3711292 GTATCGATACTCCACCTAGG
1 GTATCGATACTCCACCTAGG
3711312 GTATCGATACTCCACCTAGG
1 GTATCGATACTCCACCTAGG
3711332 GTATCGATACTC
1 GTATCGATACTC
3711344 TACTACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCCACCTAGG
Found at i:3719923 original size:40 final size:40
Alignment explanation
Indices: 3719862--3719941 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
3719852 ATAGGAGTCA
* * *
3719862 AATATTGCACAATAGTTCTGAGGTC-GAGCCTTGCTCACCT
1 AATAATGCACAATAGTGCTGAGGTCGGA-CCTTGCCCACCT
*
3719902 AATAATGCACCATAGTGCTGAGGTCGGACCTTGCCCACCT
1 AATAATGCACAATAGTGCTGAGGTCGGACCTTGCCCACCT
3719942 GACTTGTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
AATAATGCACAATAGTGCTGAGGTCGGACCTTGCCCACCT
Found at i:3727069 original size:61 final size:60
Alignment explanation
Indices: 3726997--3727121 Score: 178
Period size: 61 Copynumber: 2.1 Consensus size: 60
3726987 AAAATATATG
* * * *
3726997 AAAAAAATATTATAAATTATAGTTAATAAATAAAAACTAAGAATTATTTCTTTCATTAAT
1 AAAAAAATATTATAAATTATAATTAATAAATAAAAACTAACAATTATTTCTTCCATTAAC
* * *
3727057 AAAAAATATATTATAAATTGTAATTAATAAATAAAAAGTAACTATTATTTCTTCCATTAAC
1 AAAAAA-ATATTATAAATTATAATTAATAAATAAAAACTAACAATTATTTCTTCCATTAAC
3727118 AAAA
1 AAAA
3727122 GTTAAAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 6 0.11
61 51 0.89
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (60 bp):
AAAAAAATATTATAAATTATAATTAATAAATAAAAACTAACAATTATTTCTTCCATTAAC
Found at i:3727104 original size:139 final size:140
Alignment explanation
Indices: 3726941--3727200 Score: 387
Period size: 140 Copynumber: 1.9 Consensus size: 140
3726931 TAAATTAAAG
* *
3726941 TTAATAAATAAAAATTAACAATTATTTCTTTCATTAACAAAAACTAAAAATATAT-GAAAAAAAT
1 TTAATAAATAAAAAGTAACAATTATTTCTTCCATTAACAAAAACTAAAAATATATAGAAAAAAAT
* * * * *
3727005 ATTATAAATTATAGTTAATAAATAAAAACTAAGAATTATTTCTTTCATTAATAAAAAATATATTA
66 ATTATAAACTACAGTTAATAAATAAAAACTAAGAATCATTTCTTCCATTAACAAAAAATATATTA
3727070 TAAATTGTAA
131 TAAATTGTAA
* ** *
3727080 TTAATAAATAAAAAGTAACTATTATTTCTTCCATTAACAAAAGTTAAAAATATATATAAAAAAAT
1 TTAATAAATAAAAAGTAACAATTATTTCTTCCATTAACAAAAACTAAAAATATATAGAAAAAAAT
* * *
3727145 ATTGTAAACTACGGTTAATAAATAAAAATTAAGAATCATTTCTTCCATTAACAAAA
66 ATTATAAACTACAGTTAATAAATAAAAACTAAGAATCATTTCTTCCATTAACAAAA
3727201 TTTAAAAACA
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
139 50 0.47
140 56 0.53
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (140 bp):
TTAATAAATAAAAAGTAACAATTATTTCTTCCATTAACAAAAACTAAAAATATATAGAAAAAAAT
ATTATAAACTACAGTTAATAAATAAAAACTAAGAATCATTTCTTCCATTAACAAAAAATATATTA
TAAATTGTAA
Found at i:3727147 original size:79 final size:80
Alignment explanation
Indices: 3727055--3727218 Score: 206
Period size: 79 Copynumber: 2.1 Consensus size: 80
3727045 TCTTTCATTA
* ** * *
3727055 ATAAAAAATATATTATAAATTGTAATTAATAAATAAAAAGTAACTATTATTTCTTCCATTAACAA
1 ATAAAAAATATATTATAAACTACAATTAATAAATAAAAAGTAACAATCATTTCTTCCATTAACAA
*
3727120 AAGTTAAAAATATAT
66 AAGTTAAAAACATAT
* ** * *
3727135 ATAAAAAA-ATATTGTAAACTACGGTTAATAAATAAAAATTAAGAATCATTTCTTCCATTAACAA
1 ATAAAAAATATATTATAAACTACAATTAATAAATAAAAAGTAACAATCATTTCTTCCATTAACAA
*
3727199 AATTTAAAAACATAT
66 AAGTTAAAAACATAT
3727214 A-AAAA
1 ATAAAA
3727219 TGTTGTAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 4 0.06
79 60 0.83
80 8 0.11
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (80 bp):
ATAAAAAATATATTATAAACTACAATTAATAAATAAAAAGTAACAATCATTTCTTCCATTAACAA
AAGTTAAAAACATAT
Found at i:3727240 original size:75 final size:74
Alignment explanation
Indices: 3727054--3727309 Score: 244
Period size: 75 Copynumber: 3.4 Consensus size: 74
3727044 TTCTTTCATT
* * * * * ** *
3727054 AATAAAAAATATATTATAAATTGTAATTAATAAATAAAAAGTAACTATTATTTCTTCCATTAACA
1 AATATAAAA-ATATTGTAAATTATATTTAATAAATAAAAATTAAAAATAATTTCTTCCATTAACA
*
3727119 AAAGTTAAAAA
65 AAA-TTTAAAA
* *** * *
3727130 TATATATAAAAAAATATTGTAAACTACGGTTAATAAATAAAAATTAAGAATCATTTCTTCCATTA
1 -A-ATAT--AAAAATATTGTAAATTATATTTAATAAATAAAAATTAAAAATAATTTCTTCCATTA
3727195 ACAAAATTTAAAA
62 ACAAAATTTAAAA
* * * *
3727208 ACATATAAAAATGTTGTAAATTATATTTAATAAATAATAATTAAAAATAAATTCTTCC-TGTAAT
1 A-ATATAAAAATATTGTAAATTATATTTAATAAATAAAAATTAAAAATAATTTCTTCCAT-TAAC
3727272 AAAATTTAAAA
64 AAAATTTAAAA
*
3727283 AATACAAAAAATATTGTAAATTATATT
1 AATA-TAAAAATATTGTAAATTATATT
3727310 CAAATATGTG
Statistics
Matches: 149, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
74 4 0.03
75 78 0.52
77 6 0.04
78 9 0.06
79 48 0.32
80 4 0.03
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (74 bp):
AATATAAAAATATTGTAAATTATATTTAATAAATAAAAATTAAAAATAATTTCTTCCATTAACAA
AATTTAAAA
Found at i:3727894 original size:14 final size:13
Alignment explanation
Indices: 3727858--3727894 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3727848 TTTAAATTAT
3727858 ACTTTTAAAAAAC
1 ACTTTTAAAAAAC
*
3727871 ACTTTTAAAAATC
1 ACTTTTAAAAAAC
*
3727884 ACTTTTCAAAA
1 ACTTTTAAAAA
3727895 CTAATACCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
ACTTTTAAAAAAC
Found at i:3731702 original size:215 final size:215
Alignment explanation
Indices: 3731331--3731727 Score: 758
Period size: 215 Copynumber: 1.8 Consensus size: 215
3731321 AAGGCTACGC
3731331 CTTTTAGTTAGTAGAAAGTCCCATGTTGGGTTTTGTTCTTTATGAGAAAATGTTTTAAAGAGAGA
1 CTTTTAGTTAGTAGAAAGTCCCATGTTGGGTTTTGTTCTTTATGAGAAAATGTTTTAAAGAGAGA
* *
3731396 TGAGATGCTAACATTGAATCTCAAGTTTCCCATAATTTTGGAGCTTTTTGTGGTTTTGTGTTAGA
66 TGAGATGCTAACATTGAATCTCAAGTTTCCCATAATTTGGGAACTTTTTGTGGTTTTGTGTTAGA
3731461 TCTCATCCCCTTTTGATTTTGTTTGAAATGTTGTTTTGGGTGATTGATTCTGGTGGTTGATCACT
131 TCTCATCCCCTTTTGATTTTGTTTGAAATGTTGTTTTGGGTGATTGATTCTGGTGGTTGATCACT
3731526 GGAACATTACTTCTTATATG
196 GGAACATTACTTCTTATATG
3731546 CTTTTAGTTAGTAGAAAGTCCCATGTTGGGTTTTGTTCTTTATGAGAAAATGTTTTAAAGAGAGA
1 CTTTTAGTTAGTAGAAAGTCCCATGTTGGGTTTTGTTCTTTATGAGAAAATGTTTTAAAGAGAGA
* *
3731611 TGAGTTGCTAACATTGAATCTCAAGTTTCCCATAATTTGGGAATTTTTTGTGGTTTTGTGTTAGA
66 TGAGATGCTAACATTGAATCTCAAGTTTCCCATAATTTGGGAACTTTTTGTGGTTTTGTGTTAGA
3731676 TCTCATCCCCTTTTGATTTTGTTTGAAATGTTGTTTTGGGTGATTGATTCTG
131 TCTCATCCCCTTTTGATTTTGTTTGAAATGTTGTTTTGGGTGATTGATTCTG
3731728 TTAGTTCCTG
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
215 178 1.00
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (215 bp):
CTTTTAGTTAGTAGAAAGTCCCATGTTGGGTTTTGTTCTTTATGAGAAAATGTTTTAAAGAGAGA
TGAGATGCTAACATTGAATCTCAAGTTTCCCATAATTTGGGAACTTTTTGTGGTTTTGTGTTAGA
TCTCATCCCCTTTTGATTTTGTTTGAAATGTTGTTTTGGGTGATTGATTCTGGTGGTTGATCACT
GGAACATTACTTCTTATATG
Found at i:3738210 original size:20 final size:21
Alignment explanation
Indices: 3738156--3738216 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
3738146 TTTCTATGAA
*
3738156 AATAATAATAATATAAATTATT
1 AATAATAA-AATATATATTATT
* *
3738178 AATAAT-TATTATATATTATT
1 AATAATAAAATATATATTATT
*
3738198 AA-AATAAAATATATCTTAT
1 AATAATAAAATATATATTAT
3738217 ATTATTATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.09
20 23 0.72
22 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATAAAATATATATTATT
Found at i:3738264 original size:21 final size:22
Alignment explanation
Indices: 3738240--3738296 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
3738230 ATTGATTATT
3738240 TATTATAATATTAA-AAATATA
1 TATTATAATATTAATAAATATA
3738261 TATTATTAGAATATTAATAAATATA
1 TATTA-T--AATATTAATAAATATA
*
3738286 TTTTA-AATATT
1 TATTATAATATT
3738297 TTAATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
24 8 0.26
25 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATAATATTAATAAATATA
Found at i:3738266 original size:24 final size:25
Alignment explanation
Indices: 3738239--3738286 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
3738229 AATTGATTAT
*
3738239 TTATTATAATATTAA-AAATATATA
1 TTATTAGAATATTAATAAATATATA
3738263 TTATTAGAATATTAATAAATATAT
1 TTATTAGAATATTAATAAATATAT
3738287 TTTAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TTATTAGAATATTAATAAATATATA
Found at i:3738303 original size:23 final size:22
Alignment explanation
Indices: 3738246--3738296 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
3738236 TATTTATTAT
*
3738246 AATATTAAAAATATATATTATTAG
1 AATATTAATAA-ATATATT-TTAG
3738270 AATATTAATAAATATATTTTA-
1 AATATTAATAAATATATTTTAG
3738291 AATATT
1 AATATT
3738297 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 7 0.27
24 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATATTAATAAATATATTTTAG
Found at i:3738395 original size:2 final size:2
Alignment explanation
Indices: 3738388--3738424 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
3738378 AAATTTCATA
3738388 AT AT AT AT AT AT AT AT AT AT -T AT GA- 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
3738425 TATGAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3738418 original size:17 final size:17
Alignment explanation
Indices: 3738396--3738430 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3738386 TAATATATAT
3738396 ATATATATATATTATGA
1 ATATATATATATTATGA
3738413 ATATATATATATTATGA
1 ATATATATATATTATGA
3738430 A
1 A
3738431 ATTTAGCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATATATATATATTATGA
Found at i:3739164 original size:36 final size:36
Alignment explanation
Indices: 3739118--3739187 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
3739108 AACATTAGAG
*
3739118 TTTTATTAGGATTCAAACTCCTAAAAATAGGATAAA
1 TTTTACTAGGATTCAAACTCCTAAAAATAGGATAAA
*
3739154 TTTTACTAGGATTCAATCTCCTAAAAATAGGATA
1 TTTTACTAGGATTCAAACTCCTAAAAATAGGATA
3739188 GAGTTCTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (36 bp):
TTTTACTAGGATTCAAACTCCTAAAAATAGGATAAA
Found at i:3739756 original size:19 final size:18
Alignment explanation
Indices: 3739732--3739781 Score: 75
Period size: 19 Copynumber: 2.8 Consensus size: 18
3739722 TTTACTTTAG
3739732 TATATATATATATTACATA
1 TATATATATATATTA-ATA
*
3739751 TATATATATATATTATTA
1 TATATATATATATTAATA
3739769 TATAT-TATATATT
1 TATATATATATATT
3739782 GTTTTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 8 0.27
18 7 0.23
19 15 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATATATATTAATA
Found at i:3739778 original size:27 final size:26
Alignment explanation
Indices: 3739738--3739841 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 26
3739728 TTAGTATATA
3739738 TATATATTACATATATATATATATATTAT
1 TATATATT--ATATATAT-TATATATTAT
*
3739767 TATATA-T-TATATATTGT-T-TTAT
1 TATATATTATATATATTATATATTAT
* *
3739789 TA-AT-TTATATATATTTTACTATTTT
1 TATATATTATATATATTATA-TATTAT
* * *
3739814 TATGTTTTATTTATATATATATATTAT
1 TATATATTATATATAT-TATATATTAT
3739841 T
1 T
3739842 TTTACTTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
21 3 0.05
22 15 0.25
23 1 0.02
24 3 0.05
25 12 0.20
26 1 0.02
27 15 0.25
28 4 0.07
29 6 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TATATATTATATATATTATATATTAT
Found at i:3739799 original size:2 final size:2
Alignment explanation
Indices: 3739732--3739780 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
3739722 TTTACTTTAG
*
3739732 TA TA TA TA TA TA T- TA CA TA TA TA TA TA TA TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3739771 TA T- TA TA TA T
1 TA TA TA TA TA T
3739781 TGTTTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3739802 original size:31 final size:32
Alignment explanation
Indices: 3739763--3739835 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 32
3739753 TATATATATA
3739763 TTAT-TATATATTATA-TATTGTTT-T-ATTAAT
1 TTATATATATATT-TACTATT-TTTATGATTAAT
* *
3739793 TTATATATAT-TTTACTATTTTTATGTTTTAT
1 TTATATATATATTTACTATTTTTATGATTAAT
3739824 TTATATATATAT
1 TTATATATATAT
3739836 ATTATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 5 0.14
30 11 0.31
31 19 0.53
32 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (32 bp):
TTATATATATATTTACTATTTTTATGATTAAT
Found at i:3739861 original size:49 final size:45
Alignment explanation
Indices: 3739808--3739918 Score: 116
Period size: 53 Copynumber: 2.3 Consensus size: 45
3739798 TATATTTTAC
*
3739808 TATTTTTATGTTTTATTTATATATATATATTATTTTTACTTTTTATTAT
1 TATTTTTATATTTTATTTATATATATATATT-TTTTT-CTTTTT-TT-T
* *
3739857 TATTTTATTTATTTATTTATTTATATTTATATATTTTTTTCTTTTTTTT
1 TA--TT-TTTATAT-TTTATTTATATATATATATTTTTTTCTTTTTTTT
3739906 T-TTTTTATATTTT
1 TATTTTTATATTTT
3739919 TACTCACATT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
44 3 0.05
45 6 0.11
46 2 0.04
49 4 0.07
50 2 0.04
51 8 0.15
52 11 0.20
53 19 0.35
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.75
Consensus pattern (45 bp):
TATTTTTATATTTTATTTATATATATATATTTTTTTCTTTTTTTT
Found at i:3739865 original size:24 final size:23
Alignment explanation
Indices: 3739751--3739882 Score: 72
Period size: 24 Copynumber: 5.4 Consensus size: 23
3739741 ATATTACATA
* *
3739751 TATATATATATATTA-TTATATAT
1 TATATATATATTTTATTTTTAT-T
* *
3739774 TATATAT-TGTTTTATTAATTTATA
1 TATATATATATTTTATT--TTTATT
*
3739798 TATATTTTACTATTTTTATGTTTTATT
1 TATA-TATA-TA-TTTTAT-TTTTATT
*
3739825 TATATATATATATTATTTTTACTT
1 TATATATATATTTTATTTTTA-TT
*
3739849 TTTAT-TATTATTTTATTTATTTATT
1 TATATATA-TATTTTA-TT-TTTATT
*
3739874 TATTTATAT
1 TATATATAT
3739883 TTATATATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
22 5 0.06
23 15 0.18
24 21 0.25
25 16 0.19
26 9 0.11
27 10 0.12
28 6 0.07
29 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TATATATATATTTTATTTTTATT
Found at i:3739886 original size:33 final size:33
Alignment explanation
Indices: 3739849--3739917 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3739839 ATTTTTACTT
3739849 TTTAT-TATTATTTTATTTATTTATTTATTTATA
1 TTTATATATTATTTTATTT-TTTATTTATTTATA
* * * *
3739882 TTTATATATTTTTTTCTTTTTTTTTTTTTTATA
1 TTTATATATTATTTTATTTTTTATTTATTTATA
3739915 TTT
1 TTT
3739918 TTACTCACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.78
Consensus pattern (33 bp):
TTTATATATTATTTTATTTTTTATTTATTTATA
Found at i:3739998 original size:9 final size:9
Alignment explanation
Indices: 3739986--3740010 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3739976 TTTCTTCATT
3739986 TTAATTTAA
1 TTAATTTAA
3739995 TTAATTTAA
1 TTAATTTAA
3740004 TTAATTT
1 TTAATTT
3740011 TTACCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTAATTTAA
Found at i:3741881 original size:16 final size:15
Alignment explanation
Indices: 3741841--3741881 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3741831 CATTTAAACA
3741841 TATTTTACATTTTGT
1 TATTTTACATTTTGT
3741856 TATTTT-CATTTCT-T
1 TATTTTACATTT-TGT
3741870 TATATTTACATT
1 TAT-TTTACATT
3741882 ATTTTTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.39
15 10 0.43
16 4 0.17
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (15 bp):
TATTTTACATTTTGT
Found at i:3742884 original size:95 final size:94
Alignment explanation
Indices: 3742712--3742896 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 94
3742702 AGATTATAAT
* *
3742712 ATTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGCTAAACGCCCCGGCTCTATG
1 ATTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGCTAAACGCACCGACTCTATG
* * *
3742777 GATAATATTCAGCTAGCATGATAAATGTA
66 GATAAGACTCAGCTAACATGATAAATGTA
* * *
3742806 ATTATACTATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCATCGACTTTA
1 ATTATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGCTAAACGCACCGACTCTA
*
3742870 TGGATAAGACTCAGCTAACCTGATAAA
64 TGGATAAGACTCAGCTAACATGATAAA
3742897 GGTGTTTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
94 7 0.09
95 73 0.91
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (94 bp):
ATTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGCTAAACGCACCGACTCTATG
GATAAGACTCAGCTAACATGATAAATGTA
Found at i:3744327 original size:165 final size:165
Alignment explanation
Indices: 3744046--3744737 Score: 1032
Period size: 165 Copynumber: 4.2 Consensus size: 165
3744036 TTAAATACAA
* * * * * *
3744046 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
3744111 GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
3744176 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* ** *
3744211 CATTTACATCATAACTCAAGGCTAGAAGGGTTATCTATC-ACCAAAAGACTTTCGAGTTCGACTA
1 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* *
3744275 CGCTCAGCTCCAAGACACCTCATTTGCAGCATAGCTTAACTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * *
3744340 CCTCAAGTTTGATTACACTCAGCTTCGAGGGCATAT
130 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * * * *
3744376 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTCCGAGTTTGACTAC
1 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
3744441 GCTCAGCTCCAAGGCACATCATTTTCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
3744506 CTCGAGTTCGATTACACTCAGCTT--TGGGCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* **
3744539 CATTTACAACATAAATCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTA
1 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
*
3744603 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
*
3744668 CCTCGAGTTCGATTACATTCAGCTTCGAGGGCACAT
130 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * *
3744704 AATTTACAGCATAACTCAAGGCTATAAGGGTTAT
1 CATTTACAACATAACTCAAGGCTAGAAGGGTTAT
3744738 GCAACGCTTT
Statistics
Matches: 470, Mismatches: 52, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
162 3 0.01
163 144 0.31
164 3 0.01
165 317 0.67
166 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
Found at i:3744487 original size:84 final size:82
Alignment explanation
Indices: 3744046--3744719 Score: 578
Period size: 84 Copynumber: 8.2 Consensus size: 82
3744036 TTAAATACAA
* *
3744046 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAA-ACC-TCGAGTTCGACTAC
*
3744111 GCTCAGCTCCAAGACACAT
64 GCTCAGCTCCAAGGCACAT
* * * * *
3744130 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA--AGACCCTCGAGTTCGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAACCTCGAGTTCGACTACGC
* *
3744193 TCAGCTTCGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* * * * * * ** *
3744211 CATTTACATCATAACTCAAGGCTAGAAGGGTTATCTATC-ACCAAAAGACTTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACC-AAA-AC-CTCGAGTTCGACTA
* *
3744275 CGCTCAGCTCCAAGACACCT
63 CGCTCAGCTCCAAGGCACAT
* * * * * * * *
3744295 CATTTGCAGCATAGCTTAACTCGAGAAGGGCTATCTGCCAA--AGACCCTCAAGTTTGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAACCTCGAGTTCGACTACGC
* * *
3744358 TCAGCTTCGAGGGCATAT
66 TCAGC-TCCAAGGCACAT
* * *
3744376 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTCCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAA-ACCT-CGAGTTCGACTAC
3744441 GCTCAGCTCCAAGGCACAT
64 GCTCAGCTCCAAGGCACAT
* * * * * * *
3744460 CATTTTCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAA--AGACCCTCGAGTTCGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAACCTCGAGTTCGACTACGC
***
3744523 TCAGCT-TTGGGCACAT
66 TCAGCTCCAAGGCACAT
* * * * * * * **
3744539 CATTTACAACATAAATCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACC-AAA-ACC-TCGAGTTCGACTA
3744603 CGCTCAGCTCCAAGGCACAT
63 CGCTCAGCTCCAAGGCACAT
* * * * **
3744623 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA--AGACCCTCGAGTTCGATTACAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAACCTCGAGTTCGACTACGC
* *
3744686 TCAGCTTCGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* *
3744704 AATTTACAGCATAACT
1 CATTTGCAGCATAACT
3744720 CAAGGCTATA
Statistics
Matches: 457, Mismatches: 113, Indels: 43
0.75 0.18 0.07
Matches are distributed among these distances:
78 1 0.00
79 35 0.08
80 72 0.16
81 116 0.25
82 10 0.02
83 24 0.05
84 161 0.35
85 38 0.08
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (82 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAACCTCGAGTTCGACTACGC
TCAGCTCCAAGGCACAT
Found at i:3744692 original size:328 final size:329
Alignment explanation
Indices: 3744046--3744737 Score: 1125
Period size: 328 Copynumber: 2.1 Consensus size: 329
3744036 TTAAATACAA
**
3744046 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCCGAGTTCGACTAC
*
3744111 GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACC
* *
3744176 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGG
131 CTCGAGTTCGATTACACTCAGCTTC-AGGGCACATCATTTACAACATAAATCAAGGCTAGAAGGG
* *
3744241 TTATCTATCACCAAAAGACTTTCGAGTTCGACTACGCTCAGCTCCAAGACACCTCATTTGCAGCA
195 TTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCA
*
3744306 TAGCTTAACTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTTGATTACACTCAGCTTCGAGGG
260 TAGCTTAACTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGG
*
3744371 CATAT
325 CACAT
* * *
3744376 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTCCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCCGAGTTCGACTAC
* *
3744441 GCTCAGCTCCAAGGCACATCATTTTCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACC
*
3744506 CTCGAGTTCGATTACACTCAGCTT-TGGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGT
131 CTCGAGTTCGATTACACTCAGCTTCAGGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGT
* * *
3744570 TATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAT
196 TATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCAT
* * *
3744635 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACATTCAGCTTCGAGGGC
261 AGCTTAACTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGC
3744700 ACAT
326 ACAT
* * * * * *
3744704 AATTTACAGCATAACTCAAGGCTATAAGGGTTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
3744738 GCAACGCTTT
Statistics
Matches: 334, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
328 188 0.56
330 146 0.44
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (329 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCCGAGTTCGACTAC
GCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACC
CTCGAGTTCGATTACACTCAGCTTCAGGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGT
TATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCAT
AGCTTAACTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGC
ACAT
Found at i:3747663 original size:5 final size:5
Alignment explanation
Indices: 3747639--3747689 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
3747629 TGCAAAAATC
* *
3747639 ATAAA CATAAA AT-AA TTAAA ATAAA ATCAA ATGAAA ATAAA ATAAA A-AAA
1 ATAAA -ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA ATAAA ATAAA
3747689 A
1 A
3747690 AAATCTATCG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 7 0.18
5 23 0.59
6 9 0.23
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:3750661 original size:16 final size:16
Alignment explanation
Indices: 3750640--3750702 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
3750630 ATTTTAAATT
3750640 TTAAATATAAAATTAA
1 TTAAATATAAAATTAA
3750656 TTAAATATTTAAAA--AA
1 TTAAATA--TAAAATTAA
* *
3750672 TTAAATATAAAAATAC
1 TTAAATATAAAATTAA
*
3750688 TAAAATA-AAAATTAA
1 TTAAATATAAAATTAA
3750703 ATTACTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.13
15 6 0.15
16 23 0.59
18 5 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAATATAAAATTAA
Found at i:3750713 original size:16 final size:18
Alignment explanation
Indices: 3750694--3750733 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
3750684 ATACTAAAAT
3750694 AAAAATTAAAT-TAC-TA
1 AAAAATTAAATATACATA
3750710 AAAAATTAAATATACATA
1 AAAAATTAAATATACATA
3750728 AAAAAT
1 AAAAAT
3750734 ACTAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAATTAAATATACATA
Found at i:3751015 original size:13 final size:13
Alignment explanation
Indices: 3750997--3751022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3750987 TTATCTTTTA
3750997 GAGAAAATAACTT
1 GAGAAAATAACTT
3751010 GAGAAAATAACTT
1 GAGAAAATAACTT
3751023 ATAAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
GAGAAAATAACTT
Found at i:3753108 original size:20 final size:20
Alignment explanation
Indices: 3753083--3753179 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
3753073 CGTAACTCGA
*
3753083 TTTCGAGTTGTGAATTTCAT
1 TTTCGAGTTGCGAATTTCAT
3753103 TTTCGAGTTGCGAA-TTCGAT
1 TTTCGAGTTGCGAATTTC-AT
*
3753123 TTTCGAGTTGCGATTTTCAT
1 TTTCGAGTTGCGAATTTCAT
* * **
3753143 GTTGCGAATTGCGAATTGAAT
1 -TTTCGAGTTGCGAATTTCAT
* *
3753164 TTTCGTGTTACGAATT
1 TTTCGAGTTGCGAATT
3753180 GCGAATTCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.67
21 18 0.29
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTCAT
Found at i:3753177 original size:27 final size:27
Alignment explanation
Indices: 3753135--3753186 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3753125 TCGAGTTGCG
*
3753135 ATTTTCATGTTGCGAATTGCGAATTGA
1 ATTTTCATGTTACGAATTGCGAATTGA
*
3753162 ATTTTCGTGTTACGAATTGCGAATT
1 ATTTTCATGTTACGAATTGCGAATT
3753187 CATAATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (27 bp):
ATTTTCATGTTACGAATTGCGAATTGA
Found at i:3755428 original size:24 final size:24
Alignment explanation
Indices: 3755401--3755471 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
3755391 CCAAATCCGA
* *
3755401 GTATTGACTAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAATTTCGG
*
3755425 GTATAGACCAAGATCAAATTTCGG
1 GTATTGACCAAGATCAAATTTCGG
3755449 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAATTTCG
3755472 AATACTGACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAATTTCGG
Found at i:3755480 original size:24 final size:24
Alignment explanation
Indices: 3755430--3755480 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3755420 TTCGGGTATA
** *
3755430 GACCAAGATCAAATTTCGGGTATT
1 GACCAAGATCAAATTTCGAATACT
3755454 GACCAAGATCAAATTTCGAATACT
1 GACCAAGATCAAATTTCGAATACT
3755478 GAC
1 GAC
3755481 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GACCAAGATCAAATTTCGAATACT
Found at i:3756464 original size:20 final size:20
Alignment explanation
Indices: 3756386--3756468 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
3756376 ATTCACGTAG
*
3756386 GAATTCAAAAATCGAGTTGC
1 GAATTTAAAAATCGAGTTGC
** * * * *
3756406 GAAAATGAAACTCGTGTTAC
1 GAATTTAAAAATCGAGTTGC
**
3756426 GAA-TTAGAAAATCTTGTTGC
1 GAATTTA-AAAATCGAGTTGC
3756446 GAATTTAAAAATCGAGTTGC
1 GAATTTAAAAATCGAGTTGC
3756466 GAA
1 GAA
3756469 AAAGAAATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
19 1 0.02
20 43 0.91
21 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (20 bp):
GAATTTAAAAATCGAGTTGC
Found at i:3756475 original size:40 final size:42
Alignment explanation
Indices: 3756431--3756510 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
3756421 GTTACGAATT
3756431 AGAAAATCTTGTTGCG-AATT-TAAAAATCGAGTTGCGAAAA
1 AGAAAATCTTGTTGCGAAATTGTAAAAATCGAGTTGCGAAAA
* * *
3756471 AGAAATTCTTGTTGCGAAATTGTCAAATTCGAGTTGCGAA
1 AGAAAATCTTGTTGCGAAATTGTAAAAATCGAGTTGCGAA
3756511 TTCGACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 15 0.43
41 4 0.11
42 16 0.46
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (42 bp):
AGAAAATCTTGTTGCGAAATTGTAAAAATCGAGTTGCGAAAA
Found at i:3756528 original size:20 final size:19
Alignment explanation
Indices: 3756503--3756593 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 19
3756493 TCAAATTCGA
**
3756503 GTTGCGAATTCGACTTTTGT
1 GTTGCGAATTCGA-AATTGT
*
3756523 GTTGCGAATTCGAAAACTGT
1 GTTGCGAATTCG-AAATTGT
*
3756543 GTTGCGAAATT-GGAATTCGT
1 GTTGCG-AATTCGAAATT-GT
*
3756563 GTTGCGAATTCGAAATTGA
1 GTTGCGAATTCGAAATTGT
3756582 GTTGCGAATTCG
1 GTTGCGAATTCG
3756594 TTGGTTATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 20 0.33
20 35 0.58
21 5 0.08
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCGAAATTGT
Found at i:3756529 original size:82 final size:79
Alignment explanation
Indices: 3756440--3756593 Score: 186
Period size: 82 Copynumber: 1.9 Consensus size: 79
3756430 TAGAAAATCT
* *
3756440 TGTTGCGAATTTAAAAA-TCGAGTTGCGAAAAAGAAATTCTTGTTGCGAAATT-GTCAAATTCGA
1 TGTTGCGAATTCAAAAACT-GAGTTGCGAAAAAGAAATTCGTGTTGCG-AATTCG--AAATT-GA
3756503 GTTGCGAATTCGACTTTTG
61 GTTGCGAATTCGACTTTTG
* * ** *
3756522 TGTTGCGAATTCGAAAACTGTGTTGCGAAATTGGAATTCGTGTTGCGAATTCGAAATTGAGTTGC
1 TGTTGCGAATTCAAAAACTGAGTTGCGAAAAAGAAATTCGTGTTGCGAATTCGAAATTGAGTTGC
3756587 GAATTCG
66 GAATTCG
3756594 TTGGTTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 14 0.22
80 5 0.08
81 4 0.06
82 39 0.62
83 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (79 bp):
TGTTGCGAATTCAAAAACTGAGTTGCGAAAAAGAAATTCGTGTTGCGAATTCGAAATTGAGTTGC
GAATTCGACTTTTG
Found at i:3756921 original size:2 final size:2
Alignment explanation
Indices: 3756914--3756944 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3756904 TATAACCTAT
3756914 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
3756945 TCAATTTTTA
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:3778853 original size:20 final size:21
Alignment explanation
Indices: 3778816--3778859 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3778806 TTTAGCAAAC
*
3778816 TTTATTTTCATTATATTT-AT
1 TTTATTTTAATTATATTTAAT
3778836 TTTATTTTTAATTA-ATTTAAT
1 TTTA-TTTTAATTATATTTAAT
3778857 TTT
1 TTT
3778860 TCTTTGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTTTAATTATATTTAAT
Found at i:3780706 original size:73 final size:75
Alignment explanation
Indices: 3780511--3780717 Score: 258
Period size: 76 Copynumber: 2.8 Consensus size: 75
3780501 ACATTATATT
* * * * *
3780511 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAATTTAATTAAGTTTTAGGATATT
1 TTATCATTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGAATATT
* *
3780576 ATTTTTATATT
65 ATTTTTAAATA
** *
3780587 TTATCATTGTTTTAAATATTTTAGTCTAAATAAGTTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATCATTGTTTTAGGTATTTTAGTTTAAAT-AGTTTTAGTATTTTAATTAGGATTTAGAATATT
3780652 A-TTTTAAATA
65 ATTTTTAAATA
* *
3780662 TTATTA-T-TTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATCATTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
3780718 AGATGTTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
72 6 0.05
73 38 0.33
74 1 0.01
75 12 0.11
76 56 0.49
77 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (75 bp):
TTATCATTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAATATTA
TTTTTAAATA
Found at i:3781318 original size:17 final size:17
Alignment explanation
Indices: 3781293--3781326 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3781283 ATTTATCCCA
*
3781293 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
3781310 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
3781327 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:3781416 original size:30 final size:29
Alignment explanation
Indices: 3781380--3781444 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
3781370 TCTTTATTAC
* *
3781380 TATTTTTAATTCATTATTTATTATTTTATT
1 TATTTTTAATTCATAATTAATTA-TTTATT
* *
3781410 TTTTTTTAATTTATAATTAATTATTTATT
1 TATTTTTAATTCATAATTAATTATTTATT
3781439 TATTTT
1 TATTTT
3781445 ATACCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (29 bp):
TATTTTTAATTCATAATTAATTATTTATT
Found at i:3789705 original size:83 final size:84
Alignment explanation
Indices: 3789578--3789815 Score: 243
Period size: 83 Copynumber: 2.9 Consensus size: 84
3789568 ACGCTGCGGA
* * *
3789578 TTAATCTATAGTGGCATTTTTTTCAACAAATGCCGCAACAGAGTAGTACTTTAG-ATGCGTTGTT
1 TTAATATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCA-GCGTTGTT
* *
3789642 ATACAAACGCCGTAATAGGG
65 ATACAAACACCATAATAGGG
* ** *
3789662 TTAATATATAGTGGCA-TTTTTTCAACAAATGCCGTAATTGAGTAGTAATTTAGCAGCGTTTTTA
1 TTAATATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCAGCGTTGTTA
*
3789726 TACAAATACCATAATAGGG
66 TACAAACACCATAATAGGG
* * ** * * * * *
3789745 TTCATCA-ATAGTGG-AGTTTTTTTAACAAACACTGCAATAGACTAGTACTTTAGC-GTCGTTTT
1 TTAAT-ATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCAG-CGTTGT
3789807 TATACAAAC
64 TATACAAAC
3789816 GTAGCAATGA
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
82 2 0.02
83 112 0.85
84 17 0.13
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (84 bp):
TTAATATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCAGCGTTGTTA
TACAAACACCATAATAGGG
Found at i:3790001 original size:39 final size:39
Alignment explanation
Indices: 3789927--3790005 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
3789917 TTTTTTGATC
* * *
3789927 AAACGCCGCAAAAGACTCTTACTTTACTGGTGTTTGTAT
1 AAACGCCGCAAAAGACTCTAAATTTACTGGCGTTTGTAT
* *
3789966 AAACGCCGCTAAAGACTC-AAATTTTCGTGGCGTTTGTAT
1 AAACGCCGCAAAAGACTCTAAATTTAC-TGGCGTTTGTAT
3790005 A
1 A
3790006 CAAACGCTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (39 bp):
AAACGCCGCAAAAGACTCTAAATTTACTGGCGTTTGTAT
Found at i:3790047 original size:41 final size:41
Alignment explanation
Indices: 3789992--3790115 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 41
3789982 TCAAATTTTC
* *
3789992 GTGGCGTTTGTATACAAACGCTGCTATAAACTCGTACTTTA
1 GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
* *
3790033 GTGGAGTTTTTATACAAACACTGCTATAGACTCGTACTTTA
1 GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
* * * * *
3790074 GTGGCGCTTTTATATAAACACCGCTATATACTTGTACTTTA
1 GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
3790115 G
1 G
3790116 CAATTTGTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
Found at i:3804020 original size:91 final size:91
Alignment explanation
Indices: 3803862--3804031 Score: 252
Period size: 91 Copynumber: 1.9 Consensus size: 91
3803852 TTGTTTATGA
*
3803862 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTATTTGACATCTTT
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTATTTGACATCATT
3803927 TGTTGATGTATTTTATGATCTTTAAT
66 TGTTGATGTATTTTATGATCTTTAAT
* * * * *
3803953 TCTTTTATGTAGGCCTTAAACAAATATGTTAAGTA-TATATTCCTTGTCAACTGTTTTACATCAT
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTA-ATTCCATGTCAACTATTTGACATCAT
* *
3804017 TTGTTGCTGTTTTTT
65 TTGTTGATGTATTTT
3804032 TCTTAAGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
90 2 0.03
91 68 0.97
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.48
Consensus pattern (91 bp):
TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTATTTGACATCATT
TGTTGATGTATTTTATGATCTTTAAT
Found at i:3807752 original size:15 final size:15
Alignment explanation
Indices: 3807728--3807758 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3807718 TGTCAATCAA
3807728 ATATAAATTATATAT
1 ATATAAATTATATAT
*
3807743 ATATATATTATATAT
1 ATATAAATTATATAT
3807758 A
1 A
3807759 ATTTACGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAAATTATATAT
Found at i:3807936 original size:82 final size:82
Alignment explanation
Indices: 3807786--3807939 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 82
3807776 ACGACCCCTG
* * * **
3807786 AATGTGTGTCATCTTTTTATTGACGGGAGCTTCAATGACGCTCAATGTAAGTCATACATGCGTGT
1 AATGTGTGTCATCTTTTTATTGACGGGAGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCAT
3807851 CATAAATTTATGACACA
66 CATAAATTTATGACACA
**
3807868 AATGTGTGTCATCTTAATTTA-TGACGGG-GCTTCAATGACGCTCAATGCGCGTCATAAATGAGC
1 AATGTGTGTCATCTT--TTTATTGACGGGAGCTTCAATGACGCTCAATGCAAGTCATAAATGAGC
3807931 ATCATAAAT
64 ATCATAAAT
3807940 GCGTGTCATA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
82 52 0.83
83 7 0.11
84 4 0.06
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (82 bp):
AATGTGTGTCATCTTTTTATTGACGGGAGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCAT
CATAAATTTATGACACA
Found at i:3807948 original size:13 final size:13
Alignment explanation
Indices: 3807911--3807962 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
3807901 AATGACGCTC
3807911 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
3807924 AATGAGCATCATA
1 AATGCGCGTCATA
*
3807937 AATGCGTGTCATA
1 AATGCGCGTCATA
3807950 AATGCGCGTCATA
1 AATGCGCGTCATA
3807963 GATTTATGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:3807961 original size:82 final size:82
Alignment explanation
Indices: 3807793--3807961 Score: 180
Period size: 82 Copynumber: 2.1 Consensus size: 82
3807783 CTGAATGTGT
* * * **
3807793 GTCATCTTTTTATTGACGGGAGCTTCAATGACGCTCAATGTAAGTCATACATGCGTGTCATAAAT
1 GTCATCTTTTTATTGACGGGAGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCATCATAAAT
** * *
3807858 TTATGACACAAATGTGT
66 GCATGACACAAATGCGC
**
3807875 GTCATCTTAATTTA-TGACGGG-GCTTCAATGACGCTCAATGCGCGTCATAAATGAGCATCATAA
1 GTCATCTT--TTTATTGACGGGAGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCATCATAA
* * *
3807938 ATGCGTGTCATAAATGCGC
64 ATGCATGACACAAATGCGC
3807957 GTCAT
1 GTCAT
3807962 AGATTTATGA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
82 60 0.85
83 7 0.10
84 4 0.06
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (82 bp):
GTCATCTTTTTATTGACGGGAGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCATCATAAAT
GCATGACACAAATGCGC
Found at i:3810884 original size:18 final size:18
Alignment explanation
Indices: 3810861--3810897 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3810851 CTACCCAAGG
3810861 GTATCCTTAGGTCCGTAA
1 GTATCCTTAGGTCCGTAA
3810879 GTATCCTTAGGTCCGTAA
1 GTATCCTTAGGTCCGTAA
3810897 G
1 G
3810898 GTCTTTCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (18 bp):
GTATCCTTAGGTCCGTAA
Found at i:3817904 original size:17 final size:17
Alignment explanation
Indices: 3817879--3817918 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3817869 GTATGTTGTT
*
3817879 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
3817896 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
3817913 CATTTA
1 CATTTA
3817919 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:3821538 original size:17 final size:17
Alignment explanation
Indices: 3821513--3821552 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3821503 GTAAGTTGTT
*
3821513 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
3821530 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
3821547 CATTTA
1 CATTTA
3821553 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:3823461 original size:30 final size:30
Alignment explanation
Indices: 3823416--3823486 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
3823406 CTATCTAAAG
3823416 AAATATTATTCTGTATTAATATACACACTTA
1 AAAT-TTATTCTGTATTAATATACACACTTA
*
3823447 AAATTTATTTTGTATTAATATACACACTTA
1 AAATTTATTCTGTATTAATATACACACTTA
*
3823477 AAAATTATTC
1 AAATTTATTC
3823487 CGTTTATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTATTCTGTATTAATATACACACTTA
Found at i:3827294 original size:33 final size:33
Alignment explanation
Indices: 3827256--3827326 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
3827246 ACAAATTTTA
*
3827256 TTGTACAAAAATAAAATCATATAGTGACATGTT
1 TTGTACAAAAACAAAATCATATAGTGACATGTT
3827289 TTGTACAAAAACAAAATCATATAGTGACATGTT
1 TTGTACAAAAACAAAATCATATAGTGACATGTT
3827322 TTGTA
1 TTGTA
3827327 ACTATAAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTACAAAAACAAAATCATATAGTGACATGTT
Found at i:3831708 original size:22 final size:20
Alignment explanation
Indices: 3831680--3831732 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
3831670 TATTAATATA
3831680 ATATTTAAGAAAATATATTAAT
1 ATATTTAAGAAAATAT-TT-AT
3831702 ATATTTATA-AAAATATTTAT
1 ATATTTA-AGAAAATATTTAT
*
3831722 TTATTT-AGAAA
1 ATATTTAAGAAA
3831733 TATCAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 7 0.25
21 2 0.07
22 14 0.50
23 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
ATATTTAAGAAAATATTTAT
Found at i:3831717 original size:20 final size:21
Alignment explanation
Indices: 3831680--3831728 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3831670 TATTAATATA
*
3831680 ATATTTAAGAAAATATATTAAT
1 ATATTT-ATAAAATATATTAAT
*
3831702 ATATTTATAAAA-ATATTTAT
1 ATATTTATAAAATATATTAAT
*
3831722 TTATTTA
1 ATATTTA
3831729 GAAATATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
21 5 0.21
22 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATTTATAAAATATATTAAT
Found at i:3834159 original size:16 final size:16
Alignment explanation
Indices: 3834140--3834189 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
3834130 CATATTTATT
3834140 AATAATAATATAATAA
1 AATAATAATATAATAA
3834156 AATAATAATA-ACAT-A
1 AATAATAATATA-ATAA
*
3834171 AATAAAAATATAAATAA
1 AATAATAATAT-AATAA
3834188 AA
1 AA
3834190 ATAAATGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 11 0.38
16 14 0.48
17 4 0.14
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAATAATATAATAA
Found at i:3834161 original size:19 final size:20
Alignment explanation
Indices: 3834139--3834177 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3834129 TCATATTTAT
*
3834139 TAATAATAATAT-AATAAAA
1 TAATAATAACATAAATAAAA
3834158 TAATAATAACATAAATAAAA
1 TAATAATAACATAAATAAAA
3834178 ATATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
TAATAATAACATAAATAAAA
Found at i:3834183 original size:12 final size:12
Alignment explanation
Indices: 3834168--3834192 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3834158 TAATAATAAC
3834168 ATAAATAAAAAT
1 ATAAATAAAAAT
3834180 ATAAATAAAAAT
1 ATAAATAAAAAT
3834192 A
1 A
3834193 AATGGATGAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAATAAAAAT
Found at i:3834299 original size:7 final size:7
Alignment explanation
Indices: 3834284--3834316 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
3834274 AGATAATAAG
3834284 TTTTT-T
1 TTTTTAT
3834290 TTTTTAT
1 TTTTTAT
3834297 TTTTTAT
1 TTTTTAT
3834304 TTTTTAT
1 TTTTTAT
3834311 TTTTTA
1 TTTTTA
3834317 ATGTTGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:3834986 original size:113 final size:113
Alignment explanation
Indices: 3834650--3835155 Score: 545
Period size: 113 Copynumber: 4.3 Consensus size: 113
3834640 CGATAGAGTC
* * *
3834650 GAGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATT-ATC-CTCTTCAGATGAGTTCTT
1 GAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTT
**** * * *
3834712 CTCATTATGAACTTTTTCTGGAAATGTTGATCCATCGAATGATGAA-TT
65 CTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
* * * *
3834760 CACGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAGTTCTT
1 GA-GCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTT
3834825 CTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
65 CTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
3834874 GAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 GAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
3834939 TCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
66 TCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
* * * * * * ****
3834987 GTTCAACTTTTGATGAATTTGAGCGAAAAGTTGAACAAATTCTTC-TCATTATGAACTTCTTCTT
1 G---AGC----GA-AAAGTTGA---ACAAGTT---C---TTC-TCATTATGAACTTCTTCTTC--
*
3835051 TTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAA
46 TTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAA
3835116 TTT
111 TTT
*
3835119 GAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACT
1 GAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
3835156 CGACCTGGCA
Statistics
Matches: 333, Mismatches: 37, Indels: 47
0.80 0.09 0.11
Matches are distributed among these distances:
110 1 0.00
111 32 0.10
112 6 0.02
113 165 0.50
114 5 0.02
115 7 0.02
116 2 0.01
118 1 0.00
120 2 0.01
121 11 0.03
124 12 0.04
125 2 0.01
127 1 0.00
129 2 0.01
130 14 0.04
131 2 0.01
132 68 0.20
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (113 bp):
GAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
TCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
Found at i:3835103 original size:132 final size:133
Alignment explanation
Indices: 3834864--3835119 Score: 487
Period size: 132 Copynumber: 1.9 Consensus size: 133
3834854 ATCCATCGAG
*
3834864 TGATGAATTTGAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGA
1 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGA
*
3834929 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGTTCAAC
66 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGTTCAAC
3834994 TTT
131 TTT
3834997 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-TTTCTTCAGA
1 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGA
3835061 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTG
66 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTG
3835120 AGCGAAAAGT
Statistics
Matches: 121, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
132 68 0.56
133 53 0.44
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (133 bp):
TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGTTCAAC
TTT
Found at i:3835191 original size:73 final size:73
Alignment explanation
Indices: 3835065--3835228 Score: 310
Period size: 73 Copynumber: 2.2 Consensus size: 73
3835055 TTCAGATGAG
*
3835065 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGAGCGAAAAGT
1 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATCAATTTGAGCGAAAAGT
3835130 TGAACAAA
66 TGAACAAA
*
3835138 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTTGAGCGAAAAGT
1 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATCAATTTGAGCGAAAAGT
3835203 TGAACAAA
66 TGAACAAA
3835211 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
3835229 TCTTCTTCTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 89 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (73 bp):
TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATCAATTTGAGCGAAAAGT
TGAACAAA
Found at i:3835310 original size:186 final size:185
Alignment explanation
Indices: 3834997--3835341 Score: 654
Period size: 186 Copynumber: 1.9 Consensus size: 185
3834987 GTTCAACTTT
3834997 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTTTCTTCAGAT
1 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTTTCTTCAGAT
3835062 GAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGAGCGAAA
66 GAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGAGCGAAA
3835127 AGTTGAACAAATTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAA
131 AGTTGAACAAATTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAA
3835182 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGA
1 TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-TTTCTTCAGA
*
3835247 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAA
65 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGAGCGAA
* *
3835312 ACGTTGAACAAGTTCTTCTCATTATGAACT
130 AAGTTGAACAAATTCTTCTCATTATGAACT
3835342 TGTTCTTCTT
Statistics
Matches: 156, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
185 54 0.35
186 102 0.65
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (185 bp):
TGATGAATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTTTCTTCAGAT
GAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATCAATTTGAGCGAAA
AGTTGAACAAATTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAA
Found at i:3835336 original size:113 final size:113
Alignment explanation
Indices: 3835138--3835462 Score: 614
Period size: 113 Copynumber: 2.9 Consensus size: 113
3835128 GTTGAACAAA
*
3835138 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTTGAGCGAAAAGT
1 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAAAAGT
3835203 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
*
3835251 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAAACGT
1 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAAAAGT
* *
3835316 TGAACAAGTTCTTCTCATTATGAACTTGTTCTTCTTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
3835364 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAAAAGT
1 TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAAAAGT
3835429 TGAACAAATTCTTCTCATTATGAACTTCTTCTTC
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTC
3835463 AGATGAGTTC
Statistics
Matches: 205, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 205 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTTGAGCGAAAAGT
TGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
Found at i:3836003 original size:22 final size:22
Alignment explanation
Indices: 3835925--3836001 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
3835915 TATAAAGCTT
*
3835925 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
3835947 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3835969 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3835991 TCATCTTTGAA
1 TCATCTTTGAA
3836002 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3836435 original size:50 final size:54
Alignment explanation
Indices: 3836373--3836514 Score: 170
Period size: 50 Copynumber: 2.7 Consensus size: 54
3836363 CACTGGTTCA
* *
3836373 TAAAACATTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTG-TC-GA-GAT-G
1 TAAAACATTTGACAATACATTCATCCTTTT-ATGTGGCTTCTGCTCAGATGATCG
* * *
3836423 TAAAACACTTGACAACACATTCATCCTTTTATGTGGCTTCTGCTCAGATGTTCG
1 TAAAACATTTGACAATACATTCATCCTTTTATGTGGCTTCTGCTCAGATGATCG
* *
3836477 TAAAGCATTTGACAATACATTCATCCTTTT-TTTGGCTT
1 TAAAACATTTGACAATACATTCATCCTTTTATGTGGCTT
3836515 ATGCCAAGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
50 32 0.41
51 7 0.09
52 2 0.03
53 9 0.12
54 28 0.36
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (54 bp):
TAAAACATTTGACAATACATTCATCCTTTTATGTGGCTTCTGCTCAGATGATCG
Found at i:3838785 original size:114 final size:114
Alignment explanation
Indices: 3838585--3838810 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 114
3838575 GATCATGCAG
* * * * *
3838585 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
3838650 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
3838699 TTCATCTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAATA
1 TTCATCTTTCAAATCCAATGATCAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
3838764 ACACTTCCAGAGGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
3838811 CATGGCACTT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:3841496 original size:22 final size:20
Alignment explanation
Indices: 3841468--3841520 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
3841458 TATTAATATA
3841468 ATATTTAAGAAAATATATTAAT
1 ATATTTAAGAAAATAT-TT-AT
3841490 ATATTTATA-AAAATATTTAT
1 ATATTTA-AGAAAATATTTAT
*
3841510 TTATTT-AGAAA
1 ATATTTAAGAAA
3841521 TATCAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 7 0.25
21 2 0.07
22 14 0.50
23 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
ATATTTAAGAAAATATTTAT
Found at i:3841505 original size:20 final size:21
Alignment explanation
Indices: 3841468--3841516 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3841458 TATTAATATA
*
3841468 ATATTTAAGAAAATATATTAAT
1 ATATTT-ATAAAATATATTAAT
*
3841490 ATATTTATAAAA-ATATTTAT
1 ATATTTATAAAATATATTAAT
*
3841510 TTATTTA
1 ATATTTA
3841517 GAAATATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
21 5 0.21
22 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATTTATAAAATATATTAAT
Found at i:3841622 original size:21 final size:22
Alignment explanation
Indices: 3841598--3841644 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3841588 AAACATTTTC
3841598 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
3841619 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
3841641 TTAA
1 TTAA
3841645 AAAAATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:3843313 original size:17 final size:17
Alignment explanation
Indices: 3843283--3843322 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3843273 ATGCTGGATC
*
3843283 CGGGTTGGGCTTGTAAA
1 CGGGTCGGGCTTGTAAA
*
3843300 CGGGTCGGGTTTGTAAA
1 CGGGTCGGGCTTGTAAA
*
3843317 TGGGTC
1 CGGGTC
3843323 ATCTGGACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.42, T:0.30
Consensus pattern (17 bp):
CGGGTCGGGCTTGTAAA
Found at i:3843541 original size:23 final size:23
Alignment explanation
Indices: 3843497--3843541 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3843487 TAACAAAATG
* * * *
3843497 ATTTAGTCACAATAACACGTTAA
1 ATTTAATCAAAATAAAAAGTTAA
3843520 ATTTAATCAAAATAAAAAGTTA
1 ATTTAATCAAAATAAAAAGTTA
3843542 TGTCAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATTTAATCAAAATAAAAAGTTAA
Found at i:3843705 original size:31 final size:31
Alignment explanation
Indices: 3843669--3843731 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3843659 TAATATTCTT
* * *
3843669 TCACAATAACAAA-TTGTAACAAATTATTTAG
1 TCACAATAA-AAAGTTATAAAAAAATATTTAG
3843700 TCACAATAAAAAGTTATAAAAAAATATTTAG
1 TCACAATAAAAAGTTATAAAAAAATATTTAG
3843731 T
1 T
3843732 AACGAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (31 bp):
TCACAATAAAAAGTTATAAAAAAATATTTAG
Found at i:3845685 original size:18 final size:19
Alignment explanation
Indices: 3845664--3845703 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3845654 GTACTATTGA
3845664 ATTTTAAGATT-T-TATTTG
1 ATTTTAA-ATTATATATTTG
3845682 ATTTTAAATTATATATTTG
1 ATTTTAAATTATATATTTG
3845701 ATT
1 ATT
3845704 AAATTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.15
18 8 0.40
19 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTTTAAATTATATATTTG
Found at i:3845885 original size:20 final size:20
Alignment explanation
Indices: 3845860--3845914 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3845850 TTTTACAAAG
3845860 GGATGTACCGATACACTCTT
1 GGATGTACCGATACACTCTT
3845880 GGATGTACCGATACACTCTT
1 GGATGTACCGATACACTCTT
*
3845900 GGATGTATCGATACA
1 GGATGTACCGATACA
3845915 GACCCAACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (20 bp):
GGATGTACCGATACACTCTT
Found at i:3849878 original size:38 final size:42
Alignment explanation
Indices: 3849824--3850000 Score: 155
Period size: 47 Copynumber: 4.0 Consensus size: 42
3849814 GGTTTATTGG
*
3849824 TTAATAAATGGTAAG-TAT-G-AAAATAAGCTTACGAGCTTA
1 TTAATAAATGGAAAGATATGGAAAAATAAGCTTACGAGCTTA
3849863 TTAAT-AATGGAAAGTATATGGATAAAATAAGCTTACGAGCTTA
1 TTAATAAATGGAAAG-ATATGGA-AAAATAAGCTTACGAGCTTA
* *
3849906 TGGAATTTAAATGGCAAGTATATGGATAAAATAAGCTTACGAGCTTA
1 T-TAA--TAAATGGAAAG-ATATGGA-AAAATAAGCTTACGAGCTTA
* * * *
3849953 TGGAATTTAAATGGTAAGTATTTTGATAAAATAAGCTTACGAGCTTA
1 T-TAA--TAAATGGAAAG-ATATGGA-AAAATAAGCTTACGAGCTTA
3850000 T
1 T
3850001 GGGATAAATG
Statistics
Matches: 123, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
38 8 0.07
39 5 0.04
40 3 0.02
41 1 0.01
43 21 0.17
44 2 0.02
46 1 0.01
47 82 0.67
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.32
Consensus pattern (42 bp):
TTAATAAATGGAAAGATATGGAAAAATAAGCTTACGAGCTTA
Found at i:3849908 original size:25 final size:25
Alignment explanation
Indices: 3849879--3849956 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
3849869 ATGGAAAGTA
3849879 TATGGATAAAATAAGCTTACGAGCT
1 TATGGATAAAATAAGCTTACGAGCT
* *
3849904 TATGGAATTTAAAT-GGC--A--AG-T
1 TATGG-A-TAAAATAAGCTTACGAGCT
3849925 ATATGGATAAAATAAGCTTACGAGCT
1 -TATGGATAAAATAAGCTTACGAGCT
3849951 TATGGA
1 TATGGA
3849957 ATTTAAATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
20 5 0.12
21 4 0.10
22 7 0.17
23 1 0.03
24 1 0.03
25 13 0.32
26 4 0.10
27 5 0.12
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (25 bp):
TATGGATAAAATAAGCTTACGAGCT
Found at i:3849936 original size:47 final size:47
Alignment explanation
Indices: 3849843--3850002 Score: 247
Period size: 47 Copynumber: 3.5 Consensus size: 47
3849833 GGTAAGTATG
*
3849843 AAAATAAGCTTACGAGCTTAT-TAA--T-AATGGAAAGTATATGGAT
1 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGAAAGTATATGGAT
*
3849886 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATATGGAT
1 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGAAAGTATATGGAT
* * *
3849933 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGAT
1 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGAAAGTATATGGAT
3849980 AAAATAAGCTTACGAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
3850003 GATAAATGGT
Statistics
Matches: 108, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
43 21 0.19
44 2 0.02
46 1 0.01
47 84 0.78
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (47 bp):
AAAATAAGCTTACGAGCTTATGGAATTTAAATGGAAAGTATATGGAT
Found at i:3856451 original size:21 final size:22
Alignment explanation
Indices: 3856427--3856480 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
3856417 ACCCTCGCTA
3856427 TGTATCGATACA-CTATGAATG
1 TGTATCGATACATCTATGAATG
* * *
3856448 TGTACCGATACATTTTTTGAATG
1 TGTATCGATACA-TCTATGAATG
3856471 TGTATCGATA
1 TGTATCGATA
3856481 AACTCAGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 11 0.41
23 16 0.59
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (22 bp):
TGTATCGATACATCTATGAATG
Found at i:3856926 original size:20 final size:19
Alignment explanation
Indices: 3856894--3856940 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3856884 TGGAAAAAAA
3856894 TGTTTTATTTTTAAA-ATTGT
1 TGTTTT-TTTTTAAATA-TGT
*
3856914 TGTTTTTTATTTAATTATGT
1 TGTTTTTT-TTTAAATATGT
3856934 TGTTTTT
1 TGTTTTT
3856941 ATGAAAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (19 bp):
TGTTTTTTTTTAAATATGT
Found at i:3856993 original size:12 final size:13
Alignment explanation
Indices: 3856964--3856996 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3856954 GTATTATGAT
*
3856964 TTTTCAAACATTG
1 TTTTCAAACATAG
3856977 TTTTCAAA-ATAG
1 TTTTCAAACATAG
3856989 TTTTCAAA
1 TTTTCAAA
3856997 TTATGCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:3858857 original size:19 final size:18
Alignment explanation
Indices: 3858821--3858859 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
3858811 GTACTATTGA
3858821 ATTTTAAGATTTTATTCG
1 ATTTTAAGATTTTATTCG
3858839 ATTTTAA-ATTATATATTCG
1 ATTTTAAGATT-T-TATTCG
3858858 AT
1 AT
3858860 AAAATTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (18 bp):
ATTTTAAGATTTTATTCG
Found at i:3865759 original size:13 final size:13
Alignment explanation
Indices: 3865737--3865766 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3865727 ACTAAACACC
3865737 TTTC-ACATACCT
1 TTTCAACATACCT
3865749 TTTCAACATACCT
1 TTTCAACATACCT
3865762 TTTCA
1 TTTCA
3865767 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:3872140 original size:20 final size:20
Alignment explanation
Indices: 3872115--3872156 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3872105 ATTCCACTAC
3872115 ATGCAACTATATG-ACCCTAA
1 ATGCAACTATATGTA-CCTAA
*
3872135 ATGCAACTTTATGTACCTAA
1 ATGCAACTATATGTACCTAA
3872155 AT
1 AT
3872157 ACATCTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
ATGCAACTATATGTACCTAA
Found at i:3888716 original size:21 final size:21
Alignment explanation
Indices: 3888687--3888762 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
3888677 CAAGGAGTGC
*
3888687 ATCGGTGCATATTCATGATGT
1 ATCGATGCATATTCATGATGT
* * *
3888708 ATCGATGCACATTCAAAGGGATGC
1 ATCGATGCATATTC--A-TGATGT
*
3888732 ATTGATGCATATTCAT-AGTGT
1 ATCGATGCATATTCATGA-TGT
3888753 ATCGATGCAT
1 ATCGATGCAT
3888763 TATGCACAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 1 0.02
21 23 0.55
22 1 0.02
23 1 0.02
24 16 0.38
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (21 bp):
ATCGATGCATATTCATGATGT
Found at i:3888744 original size:45 final size:44
Alignment explanation
Indices: 3888641--3888761 Score: 131
Period size: 45 Copynumber: 2.8 Consensus size: 44
3888631 ACCCAACGGA
** * * *
3888641 TGCATCGATGCAT-GGCATTGTGCATTGATGCACATTCAAGGAG
1 TGCATCGATGCATATTCATAGTGTATCGATGCACATTCAAGGAG
*
3888684 TGCATCGGTGCATATTCAT-GATGTATCGATGCACATTCAAAGG-G
1 TGCATCGATGCATATTCATAG-TGTATCGATGCACATTC-AAGGAG
*
3888728 ATGCATTGATGCATATTCATAGTGTATCGATGCA
1 -TGCATCGATGCATATTCATAGTGTATCGATGCA
3888762 TTATGCACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
43 13 0.20
44 19 0.29
45 33 0.50
46 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (44 bp):
TGCATCGATGCATATTCATAGTGTATCGATGCACATTCAAGGAG
Found at i:3897191 original size:17 final size:17
Alignment explanation
Indices: 3897169--3897202 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3897159 GGGCTCCACA
3897169 TAGATGAGGACTACACG
1 TAGATGAGGACTACACG
*
3897186 TAGATGAGGACTCCACG
1 TAGATGAGGACTACACG
3897203 ATCAGGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (17 bp):
TAGATGAGGACTACACG
Found at i:3900865 original size:31 final size:31
Alignment explanation
Indices: 3900827--3900894 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
3900817 GTGCATTTCA
3900827 GCATAAAAGGTGCCACTAATGAAAGTTAAAT
1 GCATAAAAGGTGCCACTAATGAAAGTTAAAT
3900858 GCATAAAAGGTGCCACTAATGAAAGTTAAAT
1 GCATAAAAGGTGCCACTAATGAAAGTTAAAT
3900889 GCATAA
1 GCATAA
3900895 CAGAGAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (31 bp):
GCATAAAAGGTGCCACTAATGAAAGTTAAAT
Found at i:3900905 original size:80 final size:80
Alignment explanation
Indices: 3900795--3900943 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 80
3900785 AATGCTGTAA
* * * * *
3900795 AATGAAACTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGC
1 AATGAAACTTAAATGCATAACAGAGAATTTCAGCATAAAAGGTACCACAAATGAAAGTTAAATGC
3900860 ATAAAAGGTGCCACT
66 ATAAAAGGTGCCACT
* * *
3900875 AATGAAAGTTAAATGCATAACAGAGAATTTCGGCATAAAATGTACCACAAATGAAAGTTAAATGC
1 AATGAAACTTAAATGCATAACAGAGAATTTCAGCATAAAAGGTACCACAAATGAAAGTTAAATGC
3900940 ATAA
66 ATAA
3900944 CGGTGCATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (80 bp):
AATGAAACTTAAATGCATAACAGAGAATTTCAGCATAAAAGGTACCACAAATGAAAGTTAAATGC
ATAAAAGGTGCCACT
Found at i:3900911 original size:49 final size:49
Alignment explanation
Indices: 3900858--3901021 Score: 256
Period size: 49 Copynumber: 3.3 Consensus size: 49
3900848 AAAGTTAAAT
* * *
3900858 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACAGAGAATTTCG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * *
3900907 GCATAAAATGTACCACAAATGAAAGTTAAATGCATAACGGTGCATTTCG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
*
3900956 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
*
3901005 GCATAAAAGATGCCACT
1 GCATAAAAGGTGCCACT
3901022 CATGGTATTC
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 104 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (49 bp):
GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
Found at i:3907529 original size:49 final size:49
Alignment explanation
Indices: 3907476--3907569 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
3907466 AATGCTCTAA
3907476 AATGAAAGTTAAATGCATAACGGTGAATTT-CGACATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGAATTTCCG-CATAAAAGGTGCCACT
* * *
3907525 AATGACAGTTAAATGCATAATGGTGCATTTCCGCATAAAAGGTGC
1 AATGAAAGTTAAATGCATAACGGTGAATTTCCGCATAAAAGGTGC
3907570 AACTCATGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 39 0.95
50 2 0.05
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGAATTTCCGCATAAAAGGTGCCACT
Found at i:3914028 original size:2 final size:2
Alignment explanation
Indices: 3914021--3914046 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3914011 GTTAATATTA
3914021 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
3914047 GCACGTGTAA
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:3918486 original size:25 final size:25
Alignment explanation
Indices: 3918465--3918547 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 25
3918455 ATATATTTTT
3918465 AAATATATATATATATGCTATTTGA
1 AAATATATATATATATGCTATTTGA
*
3918490 AAATATATATATATA---TATTGGA
1 AAATATATATATATATGCTATTTGA
*
3918512 AACATATATA-ATATA-G-TTTTTGA
1 AA-ATATATATATATATGCTATTTGA
*
3918535 AAATATGTATATA
1 AAATATATATATA
3918548 GTTTTTGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
22 19 0.37
23 17 0.33
25 15 0.29
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (25 bp):
AAATATATATATATATGCTATTTGA
Found at i:3918497 original size:21 final size:21
Alignment explanation
Indices: 3918469--3918561 Score: 98
Period size: 21 Copynumber: 4.2 Consensus size: 21
3918459 ATTTTTAAAT
3918469 ATATATATATATGCTATTTGAAA
1 ATATATATATA-G-TATTTGAAA
3918492 ATATATATATA-TATATTGGAAA
1 ATATATATATAGTAT-TT-GAAA
*
3918514 CATATATAATATAGTTTTTGAAA
1 -ATATAT-ATATAGTATTTGAAA
* *
3918537 ATATGTATATAGTTTTTGAAA
1 ATATATATATAGTATTTGAAA
3918558 ATAT
1 ATAT
3918562 TTTTTGAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
20 3 0.05
21 21 0.33
22 9 0.14
23 21 0.33
24 7 0.11
25 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (21 bp):
ATATATATATAGTATTTGAAA
Found at i:3918499 original size:23 final size:22
Alignment explanation
Indices: 3918454--3918561 Score: 100
Period size: 23 Copynumber: 5.0 Consensus size: 22
3918444 ATATACGTAT
3918454 TATATAT-T-TTT-AAATATATA
1 TATATATGTATTTGAAA-ATATA
3918474 TATATATGCTATTTGAAAATATA
1 TATATATG-TATTTGAAAATATA
* *
3918497 TATATATATATTGGAAACATATA
1 TATATATGTATTTGAAA-ATATA
* *
3918520 TA-ATATAGTTTTTGAAAATATG
1 TATATAT-GTATTTGAAAATATA
*
3918542 TATATA-GTTTTTGAAAATAT
1 TATATATGTATTTGAAAATAT
3918562 TTTTTGAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
20 7 0.09
21 14 0.19
22 19 0.25
23 32 0.43
24 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (22 bp):
TATATATGTATTTGAAAATATA
Found at i:3918588 original size:22 final size:23
Alignment explanation
Indices: 3918563--3918611 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
3918553 TGAAAATATT
* *
3918563 TTTTGAAAACATATTATATA-AG
1 TTTTAAAAACATATTACATATAG
3918585 TTTTAAAAACATATTACATATAG
1 TTTTAAAAACATATTACATATAG
3918608 TTTT
1 TTTT
3918612 TGATGATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (23 bp):
TTTTAAAAACATATTACATATAG
Found at i:3918668 original size:10 final size:10
Alignment explanation
Indices: 3918653--3918691 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3918643 TAAGTACTAC
3918653 TATTATTATT
1 TATTATTATT
3918663 TATTATTATT
1 TATTATTATT
*
3918673 TATCATTA-T
1 TATTATTATT
*
3918682 TATTTTTATT
1 TATTATTATT
3918692 AATTCATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTATTATT
Found at i:3918671 original size:13 final size:12
Alignment explanation
Indices: 3918653--3918692 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
3918643 TAAGTACTAC
3918653 TATTATTATTTAT
1 TATTATT-TTTAT
*
3918666 TATTATTTATCAT
1 TATTATTT-TTAT
3918679 TATTATTTTTAT
1 TATTATTTTTAT
3918691 TA
1 TA
3918693 ATTCATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTATTTTTAT
Found at i:3919261 original size:22 final size:21
Alignment explanation
Indices: 3919235--3919275 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3919225 ATCAGTGAAT
3919235 ATGGTAACCAAATTAGAATAGG
1 ATGGTAACCAAATTA-AATAGG
*
3919257 ATGGTAACCGAATTAAATA
1 ATGGTAACCAAATTAAATA
3919276 AGACCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGGTAACCAAATTAAATAGG
Found at i:3934223 original size:18 final size:17
Alignment explanation
Indices: 3934200--3934238 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
3934190 GACCGGTCAC
3934200 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
*
3934218 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
3934235 GACC
1 GACC
3934239 GTTGACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:3939721 original size:24 final size:22
Alignment explanation
Indices: 3939689--3939759 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
3939679 TGTAGTTTAT
3939689 TTTAAAACATATAAATATATAG
1 TTTAAAACATATAAATATATAG
3939711 CTTTGAAAACATAT-AATATAGT-G
1 -TTT-AAAACATATAAATATA-TAG
* *
3939734 TTTAAAAAATATAAATATATAA
1 TTTAAAACATATAAATATATAG
3939756 TTTA
1 TTTA
3939760 TTTTAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 9 0.21
22 13 0.31
23 10 0.24
24 10 0.24
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (22 bp):
TTTAAAACATATAAATATATAG
Found at i:3945975 original size:21 final size:21
Alignment explanation
Indices: 3945948--3945997 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3945938 GCATTTGACT
3945948 ATTTTTTTC-TTTT-TTTTCAC
1 ATTTTTTTCGTTTTGTTTTC-C
*
3945968 ACTTTTTTCGTTTTGTTTTCC
1 ATTTTTTTCGTTTTGTTTTCC
3945989 ATTTTTTTC
1 ATTTTTTTC
3945998 ATGTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (21 bp):
ATTTTTTTCGTTTTGTTTTCC
Found at i:3956251 original size:24 final size:24
Alignment explanation
Indices: 3956219--3956278 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
3956209 TTTTGTTATA
*
3956219 ATACTTGACCTGGATTCTGATCTG
1 ATACTTGACCTGGATTCTGATATG
*
3956243 ATACTTGACTTGGATTCTGATATG
1 ATACTTGACCTGGATTCTGATATG
*
3956267 ATAGTTGACCTG
1 ATACTTGACCTG
3956279 AATTATGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATATG
Found at i:3956406 original size:76 final size:76
Alignment explanation
Indices: 3956280--3956431 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
3956270 GTTGACCTGA
3956280 ATTATGTTTTGATTTTTGATATATCCGTTTACAGACGGAACATGTTATTTTGGGGGTAATGTTGG
1 ATTATGTTTTGATTTTTGATATATCCGTTTACAGACGGAACATGTTATTTTGGGGGTAATGTTGG
3956345 AGGAAGTATAC
66 AGGAAGTATAC
3956356 ATTATGTTTTGATTTTTGATATATCCGTTTACAGACGGAACATGTTATTTTGGGGGTAATGTTGG
1 ATTATGTTTTGATTTTTGATATATCCGTTTACAGACGGAACATGTTATTTTGGGGGTAATGTTGG
3956421 AGGAAGTATAC
66 AGGAAGTATAC
3956432 CTGGAGGCTC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (76 bp):
ATTATGTTTTGATTTTTGATATATCCGTTTACAGACGGAACATGTTATTTTGGGGGTAATGTTGG
AGGAAGTATAC
Found at i:3958950 original size:25 final size:26
Alignment explanation
Indices: 3958897--3958958 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
3958887 GTTTTAGAGT
* *
3958897 TTTTAAAAATTTATCATCTTTTATAA
1 TTTTAAAAATTAATAATCTTTTATAA
* *
3958923 TTTTAATAATTAATAAT-TTTTATTA
1 TTTTAAAAATTAATAATCTTTTATAA
*
3958948 TTTTCAAAATT
1 TTTTAAAAATT
3958959 TTAAAAATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTAAAAATTAATAATCTTTTATAA
Found at i:3960225 original size:81 final size:82
Alignment explanation
Indices: 3960123--3960391 Score: 205
Period size: 75 Copynumber: 3.4 Consensus size: 82
3960113 CACAATATAG
** * * *
3960123 TAGTACTTTAGCGGCGTTTTTATAAAAACGCCGCAATA-TGTCCATCTATAGTGGCGTTTTTCAA
1 TAGTACTTTAGAAGCGTTTTTATAAAAACGCCGCAATAGGGTCCACCTATAGTGGCATTTTTCAA
*
3960187 TTAACACCGCAACATAT
66 TAAACACCGCAACATAT
* * * * * *
3960204 TAGTACTTTAGAAGTGTTTTTATACAAATGTCGTAATAGGGTTCACCTATAGTGGCATTTTTCAA
1 TAGTACTTTAGAAGCGTTTTTATAAAAACGCCGCAATAGGGTCCACCTATAGTGGCATTTTTCAA
*
3960269 TAAACGCCGCAAC----
66 TAAACACCGCAACATAT
* * * * * * * *
3960282 -A--ACTTTAG-CGACATTTTTATACAAATGTCGCAATAAGGTTCACCTATAGTGGCGTTTTTTC
1 TAGTACTTTAGAAG-CGTTTTTATAAAAACGCCGCAATAGGGTCCACCTATAGTGGC-ATTTTTC
*
3960343 AATAAACACCGCAATATAT
64 AATAAACACCGCAACATAT
* * ** * *
3960362 AAGAACTTTAGCGGCGTTTCTATACAAACG
1 TAGTACTTTAGAAGCGTTTTTATAAAAACG
3960392 TTGGTAAAGA
Statistics
Matches: 152, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
74 1 0.01
75 45 0.30
76 19 0.12
77 1 0.01
81 32 0.21
82 33 0.22
83 20 0.13
84 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (82 bp):
TAGTACTTTAGAAGCGTTTTTATAAAAACGCCGCAATAGGGTCCACCTATAGTGGCATTTTTCAA
TAAACACCGCAACATAT
Found at i:3960417 original size:158 final size:156
Alignment explanation
Indices: 3960127--3960423 Score: 337
Period size: 158 Copynumber: 1.9 Consensus size: 156
3960117 ATATAGTAGT
* * * * *
3960127 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATATGTCCATCTATAGTGGCGTTTTTCAATTAAC
1 ACTTTAGCGACATTTTTATAAAAACGCCGCAATAGGTCCACCTATAGTGGCGTTTTTCAATAAAC
* * * * * ** *
3960192 ACCGCAACATATTAGTACTTTAGAAGTGTTTTTATACAAATGTCGTAATAGGGTTCACCTATAGT
66 ACCGCAACATATAAGAACTTTAGAAGCGTTTCTATACAAACGTCGTAATAGACTTCAACTATAGT
3960257 GGCATTTTTCAATAAACGCCGCAACA
131 GGCATTTTTCAATAAACGCCGCAACA
* * * *
3960283 ACTTTAGCGACATTTTTATACAAATGTCGCAATAAGGTTCACCTATAGTGGCGTTTTTTCAATAA
1 ACTTTAGCGACATTTTTATAAAAACGCCGCAAT-AGGTCCACCTATAGTGGCG-TTTTTCAATAA
* ** * *
3960348 ACACCGCAATATATAAGAACTTTAGCGGCGTTTCTATACAAACGTTGGTAA-AGACTT-ATACTT
64 ACACCGCAACATATAAGAACTTTAGAAGCGTTTCTATACAAACG-TCGTAATAGACTTCA-ACTA
*
3960411 TTGTGGCATTTTT
127 TAGTGGCATTTTT
3960424 ATACAAACGC
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
156 28 0.25
157 17 0.15
158 64 0.56
159 5 0.04
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (156 bp):
ACTTTAGCGACATTTTTATAAAAACGCCGCAATAGGTCCACCTATAGTGGCGTTTTTCAATAAAC
ACCGCAACATATAAGAACTTTAGAAGCGTTTCTATACAAACGTCGTAATAGACTTCAACTATAGT
GGCATTTTTCAATAAACGCCGCAACA
Found at i:3964376 original size:29 final size:29
Alignment explanation
Indices: 3964334--3964506 Score: 116
Period size: 29 Copynumber: 5.9 Consensus size: 29
3964324 ACCATTGACC
* * * *
3964334 GGTGCTATTCTGGGAATTTATTC-AATTTT
1 GGTGCTATTTTGGGAATTAATTCGAA-ATG
3964363 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
** ** * *
3964392 GGTGCTATTTTGGTTATTTTTTTGAAA-A
1 GGTGCTATTTTGGGAATTAATTCGAAATG
** * ** ** *
3964420 AATGCAAAATTCGGGGAATTAATTCGATTTT
1 GGTGC--TATTTTGGGAATTAATTCGAAATG
* *
3964451 GGTGCTATTATGGGAATTAATTCAAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
*
3964480 GGTGCTATTTTGGTAATTAATTCGAAA
1 GGTGCTATTTTGGGAATTAATTCGAAA
3964507 AGGGGTACTA
Statistics
Matches: 105, Mismatches: 35, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
28 3 0.03
29 85 0.81
30 14 0.13
31 3 0.03
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:3964507 original size:88 final size:88
Alignment explanation
Indices: 3964340--3964507 Score: 255
Period size: 88 Copynumber: 1.9 Consensus size: 88
3964330 GACCGGTGCT
* * * *
3964340 ATTCTGGGAATTTATTCAATTTTGGTGCTATTTTGGGAATTAATTCGAAATGGGTGCTATTTTGG
1 ATTCGGGGAATTAATTCAATTTTGGTGCTATTATGGGAATTAATTCAAAATGGGTGCTATTTTGG
* ** *
3964405 TTATTTTTTTGAAAAAATGCAAA
66 TAATTAATTCGAAAAAATGCAAA
*
3964428 ATTCGGGGAATTAATTCGATTTTGGTGCTATTATGGGAATTAATTCAAAATGGGTGCTATTTTGG
1 ATTCGGGGAATTAATTCAATTTTGGTGCTATTATGGGAATTAATTCAAAATGGGTGCTATTTTGG
3964493 TAATTAATTCGAAAA
66 TAATTAATTCGAAAA
3964508 GGGGTACTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 71 1.00
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (88 bp):
ATTCGGGGAATTAATTCAATTTTGGTGCTATTATGGGAATTAATTCAAAATGGGTGCTATTTTGG
TAATTAATTCGAAAAAATGCAAA
Done.