Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 91 of 211
Found at i:28366550 original size:12 final size:12
Alignment explanation
Indices: 28366533--28366587 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
28366523 CTGCTCTCGA
28366533 TCTTTCTTTTCT
1 TCTTTCTTTTCT
28366545 TCTTTCTTTCTCAT
1 TCTTTCTTT-TC-T
*
28366559 T-TTTATTTTCT
1 TCTTTCTTTTCT
28366570 T-TTTCATTTTCT
1 TCTTTC-TTTTCT
28366582 CTCTTT
1 -TCTTT
28366588 TGTTCCATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 9 0.25
14 5 0.14
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTTCTTTTCT
Found at i:28367797 original size:15 final size:15
Alignment explanation
Indices: 28367755--28367802 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
28367745 AATAACAAAC
*
28367755 ACTTCACTTTTTTTT
1 ACTTCAATTTTTTTT
28367770 ACTTCGTATATTTTTTTT
1 ACTTC--A-ATTTTTTTT
28367788 ACTTCAATTTTTTTT
1 ACTTCAATTTTTTTT
28367803 TCAATTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
17 1 0.03
18 13 0.45
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.67
Consensus pattern (15 bp):
ACTTCAATTTTTTTT
Found at i:28367801 original size:18 final size:18
Alignment explanation
Indices: 28367762--28367803 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28367752 AACACTTCAC
*
28367762 TTTTTTTTACTTCGTATA
1 TTTTTTTTACTTCATATA
28367780 TTTTTTTTACTTCA-AT-
1 TTTTTTTTACTTCATATA
28367796 TTTTTTTT
1 TTTTTTTT
28367804 CAATTACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTTTTACTTCATATA
Found at i:28370203 original size:79 final size:82
Alignment explanation
Indices: 28370085--28370269 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
28370075 GCTACTCGTT
* * *
28370085 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28370148 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
28370165 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28370228 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28370245 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28370270 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28370269 original size:40 final size:40
Alignment explanation
Indices: 28370066--28370269 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
28370056 TCGAATTTAA
** *
28370066 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
28370106 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28370146 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28370185 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28370225 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28370265 CCGGA
1 CCGGA
28370270 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28380310 original size:20 final size:18
Alignment explanation
Indices: 28380285--28380321 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
28380275 ACCTAACATG
28380285 AATTAAATTTAAGACATATT
1 AATTAAA-TTAA-ACATATT
28380305 AATTAAATTAAACATAT
1 AATTAAATTAAACATAT
28380322 CAACATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:28388808 original size:79 final size:77
Alignment explanation
Indices: 28388672--28388893 Score: 211
Period size: 79 Copynumber: 2.8 Consensus size: 77
28388662 TTGAATGCTG
* * * * * *
28388672 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTA-AACCGGGCTAAG-TCCCGAAGGCAT
28388735 TTGTGCGAG-A-TACAA
62 TTGTGCGAGTATTA-AA
* * *
28388750 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA-CCGGGCTAAGTCCCGAAGGCAT
*
28388814 TCGTGCGAGTATTAAA
62 TTGTGCGAGTATTAAA
* * *
28388830 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAACCGGGCTAAGTCCCGAAGGCATTTG
28388894 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
77 22 0.18
78 28 0.23
79 45 0.37
80 23 0.19
81 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (77 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAACCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTATTAAA
Found at i:28388882 original size:38 final size:38
Alignment explanation
Indices: 28388672--28388891 Score: 198
Period size: 39 Copynumber: 5.6 Consensus size: 38
28388662 TTGAATGCTG
* * * * *
28388672 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGT-ATTAAA
**
28388712 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAG-A-TACAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTATTA-AA
*
28388750 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAA
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAG-TATTAAA
28388791 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTATTAAA
* *
28388830 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAG-TATTAAA
* *
28388869 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28388892 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 12, Indels: 28
0.79 0.06 0.14
Matches are distributed among these distances:
37 2 0.01
38 29 0.19
39 67 0.43
40 45 0.29
41 10 0.06
42 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTATTAAA
Found at i:28388915 original size:77 final size:79
Alignment explanation
Indices: 28388752--28388926 Score: 196
Period size: 77 Copynumber: 2.3 Consensus size: 79
28388742 AGATACAAGT
* * *
28388752 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTC
** * *
28388816 GTGCGAGTATTAAA
66 GAACGAGGACTAAA
* * * *
28388830 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAA-CCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTC
*
28388893 GAACGAGGAGCTATA
66 GAACGAGGA-CTAAA
*
28388908 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28388927 TACGTGATTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
77 42 0.51
78 32 0.39
79 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGACTAAA
Found at i:28396312 original size:79 final size:78
Alignment explanation
Indices: 28396176--28396399 Score: 206
Period size: 79 Copynumber: 2.8 Consensus size: 78
28396166 TTGAATGCTG
* * * * * * *
28396176 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
28396239 TTGTGCGAG-A-TACAA
63 TTGTGCGAGCATTA-AA
* * * *
28396254 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCAT
*
28396318 TCGTGCGAGTCATTAAA
63 TTGTGCGAG-CATTAAA
* * *
28396335 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
28396400 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
78 1 0.01
79 87 0.71
80 28 0.23
81 4 0.03
82 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGCATTAAA
Found at i:28396324 original size:40 final size:40
Alignment explanation
Indices: 28396176--28396399 Score: 210
Period size: 40 Copynumber: 5.7 Consensus size: 40
28396166 TTGAATGCTG
* * * *
28396176 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ATTAAA
** * *
28396216 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATATTAA-A
*
28396256 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
*
28396295 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAT-ATTAAA
* * *
28396335 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
* * *
28396374 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
28396400 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 18, Indels: 20
0.80 0.09 0.10
Matches are distributed among these distances:
39 65 0.42
40 80 0.51
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
Found at i:28396417 original size:79 final size:80
Alignment explanation
Indices: 28396256--28396432 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
28396246 AGATACAAGT
* * * *
28396256 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
28396320 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
28396335 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
28396399 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
28396414 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28396433 TATGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 16 0.20
79 58 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:28407420 original size:44 final size:44
Alignment explanation
Indices: 28407357--28407448 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
28407347 GCTAGTTGTC
* *
28407357 ACCAACCACCACAGGACCTTCGCCGACCACCATCGTCTGCCCCT
1 ACCAACCACCACAGAACCTTCGCCGACCACCACCGTCTGCCCCT
* *
28407401 ACCAACCACCACAGAACCTTCGCCGACCATCGCCGTCTGCCCCT
1 ACCAACCACCACAGAACCTTCGCCGACCACCACCGTCTGCCCCT
28407445 ACCA
1 ACCA
28407449 TCAATCACCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.24, C:0.50, G:0.13, T:0.13
Consensus pattern (44 bp):
ACCAACCACCACAGAACCTTCGCCGACCACCACCGTCTGCCCCT
Found at i:28414337 original size:11 final size:10
Alignment explanation
Indices: 28414319--28414370 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 10
28414309 ATCATATTTT
28414319 TTTAAAAAAA
1 TTTAAAAAAA
28414329 TTCTAAAAAAA
1 TT-TAAAAAAA
*
28414340 TTCTAAAAATA
1 TT-TAAAAAAA
*
28414351 TTTAAAGAAA
1 TTTAAAAAAA
*
28414361 GTTAAAAAAA
1 TTTAAAAAAA
28414371 ATAAAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
10 16 0.44
11 20 0.56
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:28414366 original size:20 final size:21
Alignment explanation
Indices: 28414320--28414370 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28414310 TCATATTTTT
*
28414320 TTAAAAAAATTCTAAAAAAAT
1 TTAAAAAAATTCTAAAAAAAG
* *
28414341 TCTAAAAATATT-TAAAGAAAG
1 T-TAAAAAAATTCTAAAAAAAG
28414362 TTAAAAAAA
1 TTAAAAAAA
28414371 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 9 0.36
22 9 0.36
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
TTAAAAAAATTCTAAAAAAAG
Found at i:28424198 original size:18 final size:18
Alignment explanation
Indices: 28424175--28424209 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28424165 TTATTTTATT
28424175 TTATTTTT-TAATATTTAG
1 TTATTTTTGTAAT-TTTAG
28424193 TTATTTTTGTAATTTTA
1 TTATTTTTGTAATTTTA
28424210 TCATATCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTATTTTTGTAATTTTAG
Found at i:28433294 original size:15 final size:15
Alignment explanation
Indices: 28433274--28433303 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28433264 CATCGTTAGG
*
28433274 CTTTCTCCCCTATCA
1 CTTTCTCCCCCATCA
28433289 CTTTCTCCCCCATCA
1 CTTTCTCCCCCATCA
28433304 ATTTTTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.00, T:0.37
Consensus pattern (15 bp):
CTTTCTCCCCCATCA
Found at i:28436406 original size:16 final size:17
Alignment explanation
Indices: 28436380--28436413 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28436370 TTTATTGTAT
*
28436380 TTAAGTTTTGTTTAAAA
1 TTAAGTTTTGTTAAAAA
28436397 TTAA-TTTTGTTAAAAA
1 TTAAGTTTTGTTAAAAA
28436413 T
1 T
28436414 AATATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TTAAGTTTTGTTAAAAA
Found at i:28437042 original size:26 final size:25
Alignment explanation
Indices: 28436995--28437043 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
28436985 TTTCTCATCC
*
28436995 CAATTTTACTCCAGTAAAATTTTAA
1 CAATTTTACCCCAGTAAAATTTTAA
*
28437020 CAATTTTACCCTCGGTAAAATTTT
1 CAATTTTACCC-CAGTAAAATTTT
28437044 GAGAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (25 bp):
CAATTTTACCCCAGTAAAATTTTAA
Found at i:28437515 original size:20 final size:20
Alignment explanation
Indices: 28437490--28437529 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28437480 CGTAAAATAA
*
28437490 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28437510 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28437530 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28437519 original size:34 final size:35
Alignment explanation
Indices: 28437475--28437541 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28437465 CAGTAAAATA
*
28437475 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
28437509 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
28437542 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:28447985 original size:285 final size:285
Alignment explanation
Indices: 28447469--28448012 Score: 1025
Period size: 285 Copynumber: 1.9 Consensus size: 285
28447459 AACCATATCT
28447469 TTTGCAGGATTATGCCTCAGATCATCCCTCTACTACTTTTTAATCCAATAAGTAAGTTGTGCGAA
1 TTTGCAGGATTATGCCTCAGATCATCCCTCTACTACTTTTTAATCCAATAAGTAAGTTGTGCGAA
*
28447534 AGGTGTTCACGTGTAAGTTGTGTTAGGCAAATTGTGTTCACAAGTCTATCTGTTAAATTATGGAT
66 AGGTGTTCACGTGTAAGTTGTATTAGGCAAATTGTGTTCACAAGTCTATCTGTTAAATTATGGAT
28447599 ACCCAATTACATGTGTTTGAAGTCTTAACTAAGTCAGTATCTCATGTACATTAAGACTGAGCAAG
131 ACCCAATTACATGTGTTTGAAGTCTTAACTAAGTCAGTATCTCATGTACATTAAGACTGAGCAAG
28447664 AATGCCTCCTCGTAAAGTGAATGCGAACTATGTGAATGAAGCTGCTAACCCCTCAAAAGGTAATT
196 AATGCCTCCTCGTAAAGTGAATGCGAACTATGTGAATGAAGCTGCTAACCCCTCAAAAGGTAATT
28447729 GGGCTTATGCCTCAGATTACATGTG
261 GGGCTTATGCCTCAGATTACATGTG
28447754 TTTGCAGGATTATGCCTCAGATCATCCCTCTACTACTTTTTAATCCAATAAGTAAGTTGTGCGAA
1 TTTGCAGGATTATGCCTCAGATCATCCCTCTACTACTTTTTAATCCAATAAGTAAGTTGTGCGAA
*
28447819 ATGTGTTCACGTGTAAGTTGTATTAGGCAAATTGTGTTCACAAGTCTATCTGTTAAATTATGGAT
66 AGGTGTTCACGTGTAAGTTGTATTAGGCAAATTGTGTTCACAAGTCTATCTGTTAAATTATGGAT
* * *
28447884 ACCCAGTTACGTGTGTTTGAAGTCTTAACTAAGTCAGTATCTCATGTACATTTAGACTGAGCAAG
131 ACCCAATTACATGTGTTTGAAGTCTTAACTAAGTCAGTATCTCATGTACATTAAGACTGAGCAAG
* *
28447949 AATGCCTTCTCGTAAAGTGAATGCGAACTGTGTGAATGAAGCTGCTAACCCCTCAAAAGGTAAT
196 AATGCCTCCTCGTAAAGTGAATGCGAACTATGTGAATGAAGCTGCTAACCCCTCAAAAGGTAAT
28448013 CGAGCTTTAG
Statistics
Matches: 252, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
285 252 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (285 bp):
TTTGCAGGATTATGCCTCAGATCATCCCTCTACTACTTTTTAATCCAATAAGTAAGTTGTGCGAA
AGGTGTTCACGTGTAAGTTGTATTAGGCAAATTGTGTTCACAAGTCTATCTGTTAAATTATGGAT
ACCCAATTACATGTGTTTGAAGTCTTAACTAAGTCAGTATCTCATGTACATTAAGACTGAGCAAG
AATGCCTCCTCGTAAAGTGAATGCGAACTATGTGAATGAAGCTGCTAACCCCTCAAAAGGTAATT
GGGCTTATGCCTCAGATTACATGTG
Found at i:28462016 original size:15 final size:15
Alignment explanation
Indices: 28461992--28462028 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28461982 GTATAGAAAC
*
28461992 ATAATATTTTAACCT
1 ATAATTTTTTAACCT
*
28462007 ATAATTTTTTATCCT
1 ATAATTTTTTAACCT
28462022 ATAATTT
1 ATAATTT
28462029 AACACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (15 bp):
ATAATTTTTTAACCT
Found at i:28462951 original size:6 final size:6
Alignment explanation
Indices: 28462942--28462976 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
28462932 CATATACAGA
28462942 CACATG CACATG CACATG CACATG CACATG CACAT
1 CACATG CACATG CACATG CACATG CACATG CACAT
28462977 ATGTACACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (6 bp):
CACATG
Found at i:28467182 original size:19 final size:18
Alignment explanation
Indices: 28467154--28467189 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28467144 AGTACATTTT
*
28467154 TTATATTTTAAATAAAAAA
1 TTATAATTTAAA-AAAAAA
28467173 TTATAATTTAAAAAAAA
1 TTATAATTTAAAAAAAA
28467190 TAAAAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTATAATTTAAAAAAAAA
Found at i:28467221 original size:6 final size:6
Alignment explanation
Indices: 28467210--28467239 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28467200 TTAAAATTCA
28467210 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
28467240 TATTTTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:28472131 original size:19 final size:19
Alignment explanation
Indices: 28472107--28472144 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28472097 GAGACATAGA
28472107 TGTCTAAATTCAAACTGAT
1 TGTCTAAATTCAAACTGAT
28472126 TGTCTAAATTCAAACTGAT
1 TGTCTAAATTCAAACTGAT
28472145 GATAAGTGGC
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:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TGTCTAAATTCAAACTGAT
Found at i:28472310 original size:246 final size:246
Alignment explanation
Indices: 28471876--28472355 Score: 960
Period size: 246 Copynumber: 2.0 Consensus size: 246
28471866 ATTAGCTCAT
28471876 TGATTGTCTAAATTCAAACTGATGATAAGTGGCTTAGTAAGAATGTTTACATTACAAGAAAGATA
1 TGATTGTCTAAATTCAAACTGATGATAAGTGGCTTAGTAAGAATGTTTACATTACAAGAAAGATA
28471941 ACTTACTTCAATAGATAATCTAAATGAGTCTGTAATCCCATAAAAGAATCAAACTGAACATTTGA
66 ACTTACTTCAATAGATAATCTAAATGAGTCTGTAATCCCATAAAAGAATCAAACTGAACATTTGA
28472006 TTCAAATACTTAGAAAGATTATTATGTCATCTACAATTCCAACTGAGGAGATGGCTAGTCTTGGC
131 TTCAAATACTTAGAAAGATTATTATGTCATCTACAATTCCAACTGAGGAGATGGCTAGTCTTGGC
28472071 TATCGGAGTAGTTGACTCCACAGGTAGAGACATAGATGTCTAAATTCAAAC
196 TATCGGAGTAGTTGACTCCACAGGTAGAGACATAGATGTCTAAATTCAAAC
28472122 TGATTGTCTAAATTCAAACTGATGATAAGTGGCTTAGTAAGAATGTTTACATTACAAGAAAGATA
1 TGATTGTCTAAATTCAAACTGATGATAAGTGGCTTAGTAAGAATGTTTACATTACAAGAAAGATA
28472187 ACTTACTTCAATAGATAATCTAAATGAGTCTGTAATCCCATAAAAGAATCAAACTGAACATTTGA
66 ACTTACTTCAATAGATAATCTAAATGAGTCTGTAATCCCATAAAAGAATCAAACTGAACATTTGA
28472252 TTCAAATACTTAGAAAGATTATTATGTCATCTACAATTCCAACTGAGGAGATGGCTAGTCTTGGC
131 TTCAAATACTTAGAAAGATTATTATGTCATCTACAATTCCAACTGAGGAGATGGCTAGTCTTGGC
28472317 TATCGGAGTAGTTGACTCCACAGGTAGAGACATAGATGT
196 TATCGGAGTAGTTGACTCCACAGGTAGAGACATAGATGT
28472356 ACTAGACCTA
Statistics
Matches: 234, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 234 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (246 bp):
TGATTGTCTAAATTCAAACTGATGATAAGTGGCTTAGTAAGAATGTTTACATTACAAGAAAGATA
ACTTACTTCAATAGATAATCTAAATGAGTCTGTAATCCCATAAAAGAATCAAACTGAACATTTGA
TTCAAATACTTAGAAAGATTATTATGTCATCTACAATTCCAACTGAGGAGATGGCTAGTCTTGGC
TATCGGAGTAGTTGACTCCACAGGTAGAGACATAGATGTCTAAATTCAAAC
Found at i:28476485 original size:25 final size:25
Alignment explanation
Indices: 28476457--28476535 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
28476447 TTCTTATACG
28476457 AGCTGTGAATCAGTATGCTCACTCA
1 AGCTGTGAATCAGTATGCTCACTCA
* * *
28476482 AGCTGTGAATCGGTATTCTCACTCG
1 AGCTGTGAATCAGTATGCTCACTCA
* *
28476507 AGCTGT-AGATCAGTATGCTCCCACA
1 AGCTGTGA-ATCAGTATGCTCACTCA
28476532 AGCT
1 AGCT
28476536 ATAAATTGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 1 0.02
25 44 0.98
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (25 bp):
AGCTGTGAATCAGTATGCTCACTCA
Found at i:28476519 original size:50 final size:50
Alignment explanation
Indices: 28476454--28476576 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
28476444 GTATTCTTAT
* * * *
28476454 ACGAGCTGT-GAATCAGTATGCTCACTCAAGCTGTGAATCGGTATTCTCAC
1 ACGAGCTGTAG-ATCAGTATGCTCACACAAGCTATAAATCGGTATGCTCAC
* * * *
28476504 TCGAGCTGTAGATCAGTATGCTCCCACAAGCTATAAATTGGTATGCTTAC
1 ACGAGCTGTAGATCAGTATGCTCACACAAGCTATAAATCGGTATGCTCAC
* * *
28476554 AAGAGCTATAGATCGGTATGCTC
1 ACGAGCTGTAGATCAGTATGCTC
28476577 TCACTAGTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (50 bp):
ACGAGCTGTAGATCAGTATGCTCACACAAGCTATAAATCGGTATGCTCAC
Found at i:28476547 original size:25 final size:25
Alignment explanation
Indices: 28476489--28476576 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
28476479 TCAAGCTGTG
* ** *
28476489 AATCGGTATTCTCACTCGAGCTGTA
1 AATCGGTATGCTCACAAGAGCTATA
* * *
28476514 GATCAGTATGCTCCCACA-AGCTATA
1 AATCGGTATGCTCACA-AGAGCTATA
* *
28476539 AATTGGTATGCTTACAAGAGCTATA
1 AATCGGTATGCTCACAAGAGCTATA
*
28476564 GATCGGTATGCTC
1 AATCGGTATGCTC
28476577 TCACTAGTTA
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
24 1 0.02
25 45 0.98
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (25 bp):
AATCGGTATGCTCACAAGAGCTATA
Found at i:28479423 original size:79 final size:81
Alignment explanation
Indices: 28479323--28479507 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
28479313 GCTACTCGTT
* * *
28479323 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28479386 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* * **
28479403 CAAATGCCTTTGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
28479467 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
28479483 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28479508 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:28479507 original size:40 final size:40
Alignment explanation
Indices: 28479323--28479507 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
28479313 GCTACTCGTT
* *
28479323 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
28479363 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28479403 CAAATGCCTTTGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
28479442 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
28479483 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28479508 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 77 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:28491411 original size:14 final size:14
Alignment explanation
Indices: 28491394--28491426 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28491384 CTTTTTTTTC
*
28491394 TTTTTTTTTC-AAA
1 TTTTTTTATCTAAA
28491407 TTTTTTTATCTAAA
1 TTTTTTTATCTAAA
28491421 TTTTTT
1 TTTTTT
28491427 AATAAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTTATCTAAA
Found at i:28491427 original size:13 final size:13
Alignment explanation
Indices: 28491394--28491435 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
28491384 CTTTTTTTTC
*
28491394 TTTTTTTTTCAAA
1 TTTTTTTATCAAA
28491407 TTTTTTTATCTAAA
1 TTTTTTTATC-AAA
*
28491421 TTTTTTAAT-AAA
1 TTTTTTTATCAAA
28491433 TTT
1 TTT
28491436 CAATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 11 0.42
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTTTATCAAA
Found at i:28496741 original size:17 final size:17
Alignment explanation
Indices: 28496716--28496750 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28496706 CAATCAAATT
*
28496716 GATAGCTCTCTATTGAA
1 GATAACTCTCTATTGAA
28496733 GATAACTCTCTATTGAA
1 GATAACTCTCTATTGAA
28496750 G
1 G
28496751 CACATTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (17 bp):
GATAACTCTCTATTGAA
Found at i:28505207 original size:19 final size:19
Alignment explanation
Indices: 28505185--28505235 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
28505175 TTTAAATAAC
*
28505185 TTTAATAATTTTCTATA-TT
1 TTTAATAATTTT-TAGAGTT
28505204 TTTAA-AATTTTTAGAGTT
1 TTTAATAATTTTTAGAGTT
28505222 TTTAATAAATTTTT
1 TTTAAT-AATTTTT
28505236 TAAATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 13 0.46
19 5 0.18
20 7 0.25
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTTTAGAGTT
Found at i:28507443 original size:20 final size:20
Alignment explanation
Indices: 28507418--28507457 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28507408 CGAAAAATGA
28507418 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28507438 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28507458 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28507535 original size:33 final size:32
Alignment explanation
Indices: 28507448--28507533 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
28507438 TTTCTGGAAA
* *
28507448 ATGATTTACTGAAAATATTTTCTGTTGTTTGG
1 ATGATTTCCTGAAAATATTTTCTGTTGTTTGC
* *
28507480 ATGA-ATCTGTGTAAAATATTTTCTGTTGTTTGCC
1 ATGATTTC-CTG-AAAATATTTTCTGTTGTTTG-C
28507514 A-GATTTCCTGAAAATATTTT
1 ATGATTTCCTGAAAATATTTT
28507534 TCGGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.02
32 16 0.36
33 24 0.55
34 3 0.07
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGTTGTTTGC
Found at i:28507578 original size:20 final size:20
Alignment explanation
Indices: 28507555--28507593 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28507545 ATTTTTACAT
28507555 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
28507575 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
28507594 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:28509592 original size:11 final size:12
Alignment explanation
Indices: 28509571--28509595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28509561 CATTTTACCC
28509571 TTTCTTTTTTTT
1 TTTCTTTTTTTT
28509583 TTTCTTTTTTTT
1 TTTCTTTTTTTT
28509595 T
1 T
28509596 GAATTTAACT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:28516331 original size:21 final size:23
Alignment explanation
Indices: 28516307--28516354 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
28516297 TTTAAATAAT
28516307 ATTTACTATTAAA-AA-AATTTA
1 ATTTACTATTAAACAAGAATTTA
*
28516328 ATTTATTATTAAACAAGTAATTTA
1 ATTTACTATTAAACAAG-AATTTA
28516352 ATT
1 ATT
28516355 AATTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
22 2 0.09
24 9 0.39
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTACTATTAAACAAGAATTTA
Found at i:28516353 original size:24 final size:21
Alignment explanation
Indices: 28516307--28516359 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
28516297 TTTAAATAAT
*
28516307 ATTTACTATTAAAAAAATTTA
1 ATTTATTATTAAAAAAATTTA
28516328 ATTTATTATTAAACAAGTAATTTA
1 ATTTATTATTAAA-AA--AATTTA
*
28516352 ATTAATTA
1 ATTTATTA
28516360 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 2 0.07
24 13 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTATTATTAAAAAAATTTA
Found at i:28528633 original size:59 final size:57
Alignment explanation
Indices: 28528569--28528757 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
28528559 AAATTATTAA
28528569 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
28528628 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
28528689 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
28528748 ATCATATATT
1 ATCATATATT
28528758 ATTATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:28528666 original size:66 final size:64
Alignment explanation
Indices: 28528596--28528794 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
28528586 AAATATATTT
*
28528596 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
28528661 G
64 G
* * * * **
28528662 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
* *
28528716 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
28528781 G
64 G
*
28528782 AATATTGATTATT
1 AATATTAATTATT
28528795 AAGAATTTTA
Statistics
Matches: 102, Mismatches: 17, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 9 0.09
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.26
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
Found at i:28528698 original size:61 final size:61
Alignment explanation
Indices: 28528631--28528818 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
28528621 TTATAGTATC
*
28528631 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
28528692 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATTATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
28528750 C
61 T
*
28528751 ATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
*
28528812 CTATATT
1 ATATATT
28528819 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 17 0.18
61 24 0.25
62 7 0.07
63 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:28528698 original size:120 final size:120
Alignment explanation
Indices: 28528562--28528855 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 120
28528552 TTATTTTAAA
* * * *
28528562 TTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTTTATA
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTTTATA
28528626 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
65 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
*
28528682 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAG
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATAG
* *
28528747 TATCATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATT
66 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
* *
28528802 TTATTAAATTCTATATTTTAATTATAATATATCTAATAATAATTATGTTTAAAT
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
28528856 ATGATTAAAT
Statistics
Matches: 162, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
120 155 0.96
121 7 0.04
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATAG
TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
Found at i:28528718 original size:15 final size:15
Alignment explanation
Indices: 28528683--28528734 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28528673 TTAAGAATTT
*
28528683 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28528697 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28528711 TATTTAATAATAAT-
1 TATTTAATTATAATA
28528725 TATGTTAATT
1 TAT-TTAATT
28528735 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28529090 original size:16 final size:16
Alignment explanation
Indices: 28529069--28529136 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
28529059 GATTTGCTAT
28529069 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28529085 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28529101 TACAACTCTAATCCAA
1 TACACCTCTAATCCAA
28529117 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28529133 TACA
1 TACA
28529137 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28537578 original size:25 final size:25
Alignment explanation
Indices: 28537550--28537602 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
28537540 TAAGGACATA
*
28537550 CATTCAAAATGGCTAAGTCCCTATG
1 CATTCAAAATGACTAAGTCCCTATG
28537575 CATTCAAAATGACTAAGTCCCTATG
1 CATTCAAAATGACTAAGTCCCTATG
28537600 CAT
1 CAT
28537603 GCCATAGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (25 bp):
CATTCAAAATGACTAAGTCCCTATG
Found at i:28538195 original size:50 final size:50
Alignment explanation
Indices: 28538073--28538307 Score: 204
Period size: 50 Copynumber: 4.6 Consensus size: 50
28538063 ACATGCTAAA
* * *
28538073 GCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGT-ACTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATCAGTGCCAAT
* * * * *
28538122 GACATATCCCAGATATGGTCTTACATAGGAGTTCTCATATCAGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCAGTGCCAAT
* ** ** * *
28538172 GCCATGTCCCAGACATGGCCTTACGGGGGACCTCTCATCTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCAGTGCCAAT
* * **
28538222 GCCATGTCCTAGACATGGTATTACATGGGACCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC-A-G-TGCCAAT
* *
28538278 GCCATGTTCCAGACATGGTGTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
28538308 TCTCATCACC
Statistics
Matches: 148, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 3 0.02
49 30 0.20
50 78 0.53
53 2 0.01
54 1 0.01
55 1 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCAGTGCCAAT
Found at i:28542344 original size:36 final size:36
Alignment explanation
Indices: 28542266--28542348 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
28542256 TGGTGTGCCT
28542266 AGCACTAGTCGAACGAATCAACAAATTATTGCGCCC
1 AGCACTAGTCGAACGAATCAACAAATTATTGCGCCC
* * * *
28542302 AACACTATTCGAACGAATCAACAAATTATTGTGCTC
1 AGCACTAGTCGAACGAATCAACAAATTATTGCGCCC
28542338 AGCACTAGTCG
1 AGCACTAGTCG
28542349 GATAACTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (36 bp):
AGCACTAGTCGAACGAATCAACAAATTATTGCGCCC
Found at i:28564834 original size:10 final size:10
Alignment explanation
Indices: 28564819--28564848 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28564809 ATATTAATTT
28564819 GAAAAAAAAG
1 GAAAAAAAAG
*
28564829 GAAAAAAAAA
1 GAAAAAAAAG
28564839 GAAAAAAAAG
1 GAAAAAAAAG
28564849 AATAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAG
Found at i:28572950 original size:17 final size:17
Alignment explanation
Indices: 28572928--28572961 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28572918 CACTGATATG
*
28572928 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
28572945 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
28572962 TATATTTATC
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:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:28573455 original size:21 final size:21
Alignment explanation
Indices: 28573413--28573466 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
28573403 TTCTCATTTT
* * *
28573413 CAGCAACTTCTTCTTTTTCAG
1 CAGCAACTTCCTCTTCTACAG
28573434 CAAG-AACTTCCTCTTCTACAG
1 C-AGCAACTTCCTCTTCTACAG
28573455 CAGCAACTTCCT
1 CAGCAACTTCCT
28573467 TCTCAACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (21 bp):
CAGCAACTTCCTCTTCTACAG
Found at i:28579847 original size:21 final size:20
Alignment explanation
Indices: 28579800--28579847 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
28579790 CTGTAATCAA
*
28579800 AAAGATTGATCACAAAATCT
1 AAAGATTGATAACAAAATCT
* *
28579820 ATCAGATTGATAACAAAGTCT
1 A-AAGATTGATAACAAAATCT
28579841 CAAAGAT
1 -AAAGAT
28579848 CGAGAAAACG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 20 0.91
22 1 0.05
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (20 bp):
AAAGATTGATAACAAAATCT
Found at i:28584475 original size:24 final size:24
Alignment explanation
Indices: 28584443--28584493 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
28584433 GTGAGTTTTA
28584443 AATTCTGACCTAAATTAATCTGCC
1 AATTCTGACCTAAATTAATCTGCC
28584467 AATTCTGACCTAAATTAATCTGCC
1 AATTCTGACCTAAATTAATCTGCC
28584491 AAT
1 AAT
28584494 GTTTTTCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (24 bp):
AATTCTGACCTAAATTAATCTGCC
Found at i:28586591 original size:12 final size:12
Alignment explanation
Indices: 28586574--28586598 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28586564 GTTATTGCTA
28586574 TAGCAGCTTCTG
1 TAGCAGCTTCTG
28586586 TAGCAGCTTCTG
1 TAGCAGCTTCTG
28586598 T
1 T
28586599 TTTTTGTATG
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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (12 bp):
TAGCAGCTTCTG
Found at i:28590693 original size:91 final size:91
Alignment explanation
Indices: 28590561--28590768 Score: 274
Period size: 91 Copynumber: 2.3 Consensus size: 91
28590551 TTGATTTTAG
* *
28590561 TAAATTCATATAAGAACATTTTATTATTAACAATTTCATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAACAATTTCATGAAATTATATATCACTATTAAATTAT
* *
28590626 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* * * * *
28590653 TAAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTTTATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAACAATTTCATGAAATTATATATCACTATTAAATTATA
28590718 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
28590744 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
28590769 GTTATAATTA
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
91 83 0.81
92 19 0.19
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAACAATTTCATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:28590817 original size:16 final size:17
Alignment explanation
Indices: 28590798--28590829 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28590788 TTATTAAATC
28590798 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
28590814 ATATATTTAATATTAA
1 ATATATTTAATATTAA
28590830 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:28594447 original size:13 final size:13
Alignment explanation
Indices: 28594431--28594456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28594421 TAAATTGGAC
28594431 TCATAAATATTTA
1 TCATAAATATTTA
28594444 TCATAAATATTTA
1 TCATAAATATTTA
28594457 CGAAGTTAGT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TCATAAATATTTA
Found at i:28594710 original size:5 final size:5
Alignment explanation
Indices: 28594692--28594753 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
28594682 AATAAATAAG
*
28594692 TATTA TATTA -ATTA TATTA TTATAA TATTA TA--A TATTA TATTA T-TATA
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TAT-TA
28594740 TATTA TATATA TAT
1 TATTA TAT-TA TAT
28594754 ATAAAAGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
3 3 0.06
4 5 0.10
5 30 0.62
6 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:28594715 original size:8 final size:8
Alignment explanation
Indices: 28594692--28594747 Score: 78
Period size: 8 Copynumber: 7.0 Consensus size: 8
28594682 AATAAATAAG
28594692 TATTATAT
1 TATTATAT
28594700 TAATTATAT
1 T-ATTATAT
*
28594709 TATTATAA
1 TATTATAT
*
28594717 TATTATAA
1 TATTATAT
28594725 TATTATAT
1 TATTATAT
28594733 TATTATA-
1 TATTATAT
28594740 TATTATAT
1 TATTATAT
28594748 ATATATATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.16
8 29 0.66
9 8 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTATAT
Found at i:28594721 original size:11 final size:12
Alignment explanation
Indices: 28594705--28594755 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
28594695 TATATTAATT
28594705 ATATTAT-TATA
1 ATATTATATATA
*
28594716 ATATTATAATATT
1 ATATTAT-ATATA
28594729 ATATTAT-TAT-
1 ATATTATATATA
28594739 ATATTATATATA
1 ATATTATATATA
28594751 TATAT
1 -ATAT
28594756 AAAAGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 7 0.21
11 13 0.38
13 14 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTATATATA
Found at i:28594753 original size:13 final size:14
Alignment explanation
Indices: 28594692--28594755 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 14
28594682 AATAAATAAG
28594692 TATTATATTAATTATA
1 TATTATA-T-ATTATA
28594708 TTATTATAATATTATAA
1 -TATTAT-ATATTAT-A
28594725 TATTATATTATTATA
1 TATTATA-TATTATA
28594740 TATTATATA-TATA
1 TATTATATATTATA
28594753 TAT
1 TAT
28594756 AAAAGAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.16
14 2 0.05
15 9 0.20
16 17 0.39
17 8 0.18
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATATATTATA
Found at i:28596081 original size:37 final size:39
Alignment explanation
Indices: 28596022--28596117 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
28596012 CGGATAGATT
* * * *
28596022 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
28596059 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
28596098 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
28596118 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:28599851 original size:19 final size:19
Alignment explanation
Indices: 28599827--28599864 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28599817 GTCGAAAGCA
28599827 AAGACTACAGCAAGTAATT
1 AAGACTACAGCAAGTAATT
*
28599846 AAGACTACAGCCAGTAATT
1 AAGACTACAGCAAGTAATT
28599865 CTTTCTCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (19 bp):
AAGACTACAGCAAGTAATT
Found at i:28608709 original size:37 final size:37
Alignment explanation
Indices: 28608659--28608774 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
28608649 TTATTACGAA
* * * *
28608659 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
28608696 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
28608733 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
28608770 GTCTT
1 GTCTT
28608775 TAGAGCTCGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
Found at i:28608978 original size:47 final size:47
Alignment explanation
Indices: 28608893--28609346 Score: 853
Period size: 47 Copynumber: 9.7 Consensus size: 47
28608883 CCCTTCGGGA
28608893 CTTATCAC--ATATACACTTTCACA-TCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28608937 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28608984 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28609031 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28609078 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28609125 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28609172 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28609219 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28609266 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28609313 CTTATCTCATATATGCA-TTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
28609347 AGAATCCTAA
Statistics
Matches: 404, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
44 8 0.02
46 31 0.08
47 365 0.90
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28612967 original size:40 final size:40
Alignment explanation
Indices: 28612910--28613092 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
28612900 CCAGCATGAT
* *
28612910 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
28612950 TGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
28612990 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
28613031 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
28613071 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
28613093 CATCATTCGA
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.03
40 97 0.82
41 19 0.16
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:28613434 original size:29 final size:29
Alignment explanation
Indices: 28613395--28613473 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
28613385 GCTTATAATC
*
28613395 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
28613425 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
28613454 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28613474 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:28613516 original size:43 final size:43
Alignment explanation
Indices: 28613455--28613557 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
28613445 TGCATTTCAA
28613455 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
28613498 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
28613541 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
28613558 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:28615536 original size:35 final size:32
Alignment explanation
Indices: 28615453--28615516 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
28615443 CAATCTTCGT
*
28615453 CACA-AGTATCGGGTCTTACCCGGACAAAATC
1 CACATAGTCTCGGGTCTTACCCGGACAAAATC
28615484 CACATAGTCTCGGGTCTTACCCGGACAAAATC
1 CACATAGTCTCGGGTCTTACCCGGACAAAATC
28615516 C
1 C
28615517 CGCACGTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (32 bp):
CACATAGTCTCGGGTCTTACCCGGACAAAATC
Found at i:28615765 original size:47 final size:47
Alignment explanation
Indices: 28615655--28616106 Score: 853
Period size: 47 Copynumber: 9.7 Consensus size: 47
28615645 CCCTTCGGGA
*
28615655 CTTATCACAT-TATACACTTTCACATTCATCACAT-GGCCA-TCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615699 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615746 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615793 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615840 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615887 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615934 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28615981 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28616028 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28616075 CTTATCACATATAT-CA-TTTCACA-TCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
28616107 AGATCCTATC
Statistics
Matches: 404, Mismatches: 1, Indels: 6
0.98 0.00 0.01
Matches are distributed among these distances:
44 19 0.05
45 31 0.08
46 7 0.02
47 347 0.86
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28616118 original size:22 final size:22
Alignment explanation
Indices: 28616078--28616120 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28616068 ATTAGGCCTT
* *
28616078 ATCACATATATCATTTCACATC
1 ATCACATAGATCATATCACATC
*
28616100 ATCACATAGATCCTATCACAT
1 ATCACATAGATCATATCACAT
28616121 ATAGATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (22 bp):
ATCACATAGATCATATCACATC
Found at i:28620806 original size:27 final size:26
Alignment explanation
Indices: 28620758--28620812 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 26
28620748 ACCATATCCG
28620758 GACTAAGATCCGAAGCATTTGT-CGA
1 GACTAAGATCCGAAGCATTTGTGCGA
28620783 GACTAAGAGTCCGAAGGCATTTGTGCGA
1 GACTAAGA-TCCGAA-GCATTTGTGCGA
28620811 GA
1 GA
28620813 TACTAATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 8 0.30
26 6 0.22
27 8 0.30
28 5 0.19
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (26 bp):
GACTAAGATCCGAAGCATTTGTGCGA
Found at i:28620822 original size:27 final size:26
Alignment explanation
Indices: 28620758--28620812 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
28620748 ACCATATCCG
28620758 GACTAAG-ATCCGAAGCATTTGTCGA
1 GACTAAGAATCCGAAGCATTTGTCGA
*
28620783 GACTAAGAGTCCGAAGGCATTTGTGCGA
1 GACTAAGAATCCGAA-GCATTTGT-CGA
28620811 GA
1 GA
28620813 TACTAATCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 7 0.27
26 6 0.23
27 8 0.31
28 5 0.19
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (26 bp):
GACTAAGAATCCGAAGCATTTGTCGA
Found at i:28620937 original size:40 final size:39
Alignment explanation
Indices: 28620793--28620923 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 39
28620783 GACTAAGAGT
* *
28620793 CCGAAGGCATTTGTGCGAGATACTAATCCGGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAAACCGGGCTAAGTC
*
28620831 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAA-CCGGGCTAAGTC
*
28620871 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AACCGGGCTAAGTC
28620911 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28620924 AACGAGTAGC
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
38 25 0.29
39 9 0.11
40 49 0.58
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTACTAAACCGGGCTAAGTC
Found at i:28620941 original size:80 final size:77
Alignment explanation
Indices: 28620793--28620956 Score: 213
Period size: 79 Copynumber: 2.1 Consensus size: 77
28620783 GACTAAGAGT
* **
28620793 CCGAAGGCATTTGTGCGAGATACTAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
*
28620858 TCCGGGTTAAGTC
66 TCC-GGTTAAATC
* *
28620871 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGATACTA-AACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CT
* *
28620935 ATATCCGGTTAAATT
63 AAATCCGGTTAAATC
28620950 CCGAAGG
1 CCGAAGG
28620957 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 24 0.32
79 26 0.35
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
TCCGGTTAAATC
Found at i:28628920 original size:39 final size:40
Alignment explanation
Indices: 28628664--28628887 Score: 312
Period size: 40 Copynumber: 5.7 Consensus size: 40
28628654 TTGAATGATG
* * * * *
28628664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
**
28628703 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28628743 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
28628783 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
28628823 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
** *
28628864 -CC-GACTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
28628888 AACGAGTAGC
Statistics
Matches: 171, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
39 38 0.22
40 131 0.77
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28636596 original size:9 final size:9
Alignment explanation
Indices: 28636579--28636615 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28636569 TGAGTTTTCG
28636579 AATTCGAAT
1 AATTCGAAT
*
28636588 AACTCGAAT
1 AATTCGAAT
28636597 AATTCGAAT
1 AATTCGAAT
*
28636606 TATTCGAAT
1 AATTCGAAT
28636615 A
1 A
28636616 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28636868 original size:30 final size:31
Alignment explanation
Indices: 28636834--28636893 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28636824 AAACATTTTA
*
28636834 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
28636864 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
28636894 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:28637134 original size:17 final size:17
Alignment explanation
Indices: 28637114--28637196 Score: 55
Period size: 17 Copynumber: 4.8 Consensus size: 17
28637104 ATTTATATCT
28637114 ATTATTTATATTATTAA
1 ATTATTTATATTATTAA
* * *
28637131 ATTAAATTTCACATT-TGAT
1 ATT--ATTT-ATATTATTAA
*
28637150 ATTATTTATATTATTGA
1 ATTATTTATATTATTAA
*
28637167 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTAA
28637185 A-TATTTATATTA
1 ATTATTTATATTA
28637197 AAATTGAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 22 0.42
18 8 0.15
19 10 0.19
20 4 0.08
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (17 bp):
ATTATTTATATTATTAA
Found at i:28637542 original size:5 final size:5
Alignment explanation
Indices: 28637532--28637578 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
28637522 GAACAAATAT
* *
28637532 ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG A
28637579 GAAAACTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (5 bp):
ATTCG
Found at i:28647101 original size:50 final size:50
Alignment explanation
Indices: 28646989--28647157 Score: 185
Period size: 50 Copynumber: 3.3 Consensus size: 50
28646979 AAAGAGATCT
* * *
28646989 CATGTAAGACCATGTATGGGGCATGGCATTGGCATCATTGAGATTATGATTGGTCC
1 CATGTAAGACCATGTCTGGGGCATGGCATTGGCA-C--CGAGATGA-GA--GGTCC
*
28647045 CATGTAAGACCATGTCTGGGGCATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGGCATGGCATTGGCACCGAGATGAGAGGTCC
* ** * * **
28647095 CCTGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGGCATGGCATTGGCACCGAGATGAGAGGTCC
28647145 CATGTAAGACCAT
1 CATGTAAGACCAT
28647158 ATTTGGGATA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
50 59 0.59
52 2 0.02
53 6 0.06
55 1 0.01
56 32 0.32
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGGCATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:28647165 original size:50 final size:50
Alignment explanation
Indices: 28647042--28647227 Score: 180
Period size: 50 Copynumber: 3.7 Consensus size: 50
28647032 TTATGATTGG
** * **
28647042 TCCCATGTAAGACCATGTCTGGGGCATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAAC
* * *
28647092 TCCCCTGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAAC
* * * * *
28647142 TCCCATGTAAGACCATATTTGGGATATGACATTGGCA--GTAAAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCG-AGATGAGAAC
* * * *
28647190 ATCCCATGTAAAACCATGTCTAGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
28647228 TGTTATTATC
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
48 4 0.04
49 34 0.30
50 74 0.66
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAAC
Found at i:28648115 original size:20 final size:20
Alignment explanation
Indices: 28648090--28648129 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28648080 CTGACTTTGG
28648090 AAAATAATTAAAAATTGTAA
1 AAAATAATTAAAAATTGTAA
* * *
28648110 AAAATATTTATAAGTTGTAA
1 AAAATAATTAAAAATTGTAA
28648130 TTTATAGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAATAATTAAAAATTGTAA
Found at i:28652125 original size:9 final size:9
Alignment explanation
Indices: 28652108--28652144 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28652098 TATAGTTTGA
*
28652108 TATTTGAAT
1 TATTCGAAT
28652117 TATTCGAAT
1 TATTCGAAT
*
28652126 TATTCGAGT
1 TATTCGAAT
28652135 TATTCGAAT
1 TATTCGAAT
28652144 T
1 T
28652145 CAAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28653527 original size:54 final size:54
Alignment explanation
Indices: 28653469--28653572 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
28653459 GTCTCCGCCC
* * * *
28653469 GTGTAACT-TACTAAGTTGGGCCACACGGCCGTGTCGTAGGCCATGTGCTACACG
1 GTGTAACTCT-CTAACTTGGGACACACGACCGTGTCGCAGGCCATGTGCTACACG
* * *
28653523 GTGTAACTCTCTGACTTGTGACACACGACCGTGTCGCAGGCCGTGTGCTA
1 GTGTAACTCTCTAACTTGGGACACACGACCGTGTCGCAGGCCATGTGCTA
28653573 GGCCATGTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (54 bp):
GTGTAACTCTCTAACTTGGGACACACGACCGTGTCGCAGGCCATGTGCTACACG
Found at i:28653582 original size:54 final size:54
Alignment explanation
Indices: 28653490--28653630 Score: 149
Period size: 54 Copynumber: 2.6 Consensus size: 54
28653480 TAAGTTGGGC
* * ** ** * * *
28653490 CACACGGCCGTGTCGTAGGCCATGTGCTACACGGTGTAACTCTCTGACTT-GTGA
1 CACACGACCGTGTCGCAGGCCATGTGCTAGGCCATGTAACACACTGACTTAAT-A
*
28653544 CACACGACCGTGTCGCAGGCCGTGTGCTAGGCCATGTAACACACTGACTTAATA
1 CACACGACCGTGTCGCAGGCCATGTGCTAGGCCATGTAACACACTGACTTAATA
* * *
28653598 CACACGACCGTGTGGCAGCCCATGTCCTAGGCC
1 CACACGACCGTGTCGCAGGCCATGTGCTAGGCC
28653631 GTGTGCACCT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (54 bp):
CACACGACCGTGTCGCAGGCCATGTGCTAGGCCATGTAACACACTGACTTAATA
Found at i:28654603 original size:37 final size:37
Alignment explanation
Indices: 28654539--28654627 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
28654529 GTACACAAGT
* ** *
28654539 AATCCAACC-AAAACACACCAATCACTCATAAGAGAG
1 AATCCAACCGATAACATGCCAAACACTCATAAGAGAG
* **
28654575 AATCCACCCGATAACATGCCAAACACTCATAAGAGCT
1 AATCCAACCGATAACATGCCAAACACTCATAAGAGAG
*
28654612 AATCCAATCGATAACA
1 AATCCAACCGATAACA
28654628 CACCACGACA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 8 0.19
37 35 0.81
ACGTcount: A:0.46, C:0.30, G:0.09, T:0.15
Consensus pattern (37 bp):
AATCCAACCGATAACATGCCAAACACTCATAAGAGAG
Found at i:28662934 original size:17 final size:17
Alignment explanation
Indices: 28662914--28662949 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28662904 TATTAAATTA
*
28662914 AATTAATTAATTTTCTC
1 AATTAAATAATTTTCTC
28662931 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
28662948 AA
1 AA
28662950 CCCAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:28676175 original size:26 final size:26
Alignment explanation
Indices: 28676118--28676211 Score: 107
Period size: 26 Copynumber: 3.6 Consensus size: 26
28676108 AAGTTTGAAA
* * *
28676118 CAAAGGCATTCTTTTCATATTCCACCG
1 CAAAGGCTTTC-TTTCATATTACGCCG
*
28676145 TAAAGGCTTTCTTTCATATTACGCCG
1 CAAAGGCTTTCTTTCATATTACGCCG
* * *
28676171 CAAAGGCTTTTTTTCATATTATGCCA
1 CAAAGGCTTTCTTTCATATTACGCCG
*
28676197 CAAAGGTTTTCTTTC
1 CAAAGGCTTTCTTTC
28676212 CTGATGTGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 48 0.84
27 9 0.16
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (26 bp):
CAAAGGCTTTCTTTCATATTACGCCG
Found at i:28677389 original size:26 final size:26
Alignment explanation
Indices: 28677359--28677425 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
28677349 ACGAAGTTTT
* *
28677359 CCATAAAGGCTTTCTTTCATATTATG
1 CCATAAAGGCTTTCTTTCAAATTACG
**
28677385 CCATAAATACTTTCTTTCAAATTACG
1 CCATAAAGGCTTTCTTTCAAATTACG
28677411 CCACT-AAGGCTTTCT
1 CCA-TAAAGGCTTTCT
28677426 GTCCTGACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 33 0.97
27 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (26 bp):
CCATAAAGGCTTTCTTTCAAATTACG
Found at i:28681134 original size:15 final size:15
Alignment explanation
Indices: 28681114--28681144 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28681104 TTTTAATGAT
28681114 TTTTTAACTGACGAA
1 TTTTTAACTGACGAA
28681129 TTTTTAACTGACGAA
1 TTTTTAACTGACGAA
28681144 T
1 T
28681145 GGACCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTTTTAACTGACGAA
Found at i:28683894 original size:26 final size:26
Alignment explanation
Indices: 28683865--28683949 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
28683855 TGAAAATTTG
28683865 AAGGCAAATTGATCACATAACTATTA
1 AAGGCAAATTGATCACATAACTATTA
** *
28683891 AAGGTGAATTAGGA-CACCACAGA-TATCTA
1 AAGGCAAATT--GATCA-CATA-ACTAT-TA
* *
28683920 AAGGCAAATTGATCAGATAACCATTA
1 AAGGCAAATTGATCACATAACTATTA
28683946 AAGG
1 AAGG
28683950 TGTATTTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
26 15 0.34
27 8 0.18
28 10 0.23
29 11 0.25
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (26 bp):
AAGGCAAATTGATCACATAACTATTA
Found at i:28683984 original size:55 final size:55
Alignment explanation
Indices: 28683865--28683968 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
28683855 TGAAAATTTG
*
28683865 AAGGCAAATTGATCACATAACTATTAAAGGTGAATTAGGACACCACAGATATCTA
1 AAGGCAAATTGATCACATAACCATTAAAGGTGAATTAGGACACCACAGATATCTA
* * **
28683920 AAGGCAAATTGATCAGATAACCATTAAAGGTGTATTTTGACACCACAGA
1 AAGGCAAATTGATCACATAACCATTAAAGGTGAATTAGGACACCACAGA
28683969 GTAATTGAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (55 bp):
AAGGCAAATTGATCACATAACCATTAAAGGTGAATTAGGACACCACAGATATCTA
Found at i:28684992 original size:36 final size:36
Alignment explanation
Indices: 28684883--28684992 Score: 166
Period size: 36 Copynumber: 3.1 Consensus size: 36
28684873 AAAAAATTCC
*
28684883 ATGACCGCAATAGTCTCCCTTAAGCCCACAATTGCG
1 ATGACCGCAATAGTCTCCCTTAAGCCCGCAATTGCG
* *
28684919 AAGACCGCAATAGTCTCCCTTAAACCCGCAATTGCG
1 ATGACCGCAATAGTCTCCCTTAAGCCCGCAATTGCG
* * *
28684955 ATGACCGCAGTAGTCTCCCTCAAGCCTGCAATTGCG
1 ATGACCGCAATAGTCTCCCTTAAGCCCGCAATTGCG
28684991 AT
1 AT
28684993 AAATGTGACA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (36 bp):
ATGACCGCAATAGTCTCCCTTAAGCCCGCAATTGCG
Found at i:28685146 original size:14 final size:14
Alignment explanation
Indices: 28685127--28685177 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
28685117 ATCCAATTCT
28685127 TAAAATAAATATTA
1 TAAAATAAATATTA
*
28685141 TAAAATAAA-ACTGAA
1 TAAAATAAATA-T-TA
*
28685156 GTAAAAAAAATATTA
1 -TAAAATAAATATTA
28685171 TAAAATA
1 TAAAATA
28685178 TATTAAGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 1 0.03
14 16 0.55
15 2 0.07
16 9 0.31
17 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (14 bp):
TAAAATAAATATTA
Found at i:28687264 original size:21 final size:21
Alignment explanation
Indices: 28687239--28687284 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28687229 ACGAGGCGAC
*
28687239 CTACTCCTC-CTCCGGCGATCT
1 CTACTCC-CACTCCGCCGATCT
*
28687260 CTACTCCCACTCCTCCGATCT
1 CTACTCCCACTCCGCCGATCT
28687281 CTAC
1 CTAC
28687285 GAGGCGACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.13, C:0.50, G:0.09, T:0.28
Consensus pattern (21 bp):
CTACTCCCACTCCGCCGATCT
Found at i:28691111 original size:28 final size:27
Alignment explanation
Indices: 28691077--28691273 Score: 98
Period size: 28 Copynumber: 7.1 Consensus size: 27
28691067 TTTAAACTGC
* *
28691077 GCCACAAAGGCGTTCCTTT-TCAGAGGTA
1 GCCACAAAGG-ATTCCTTTAT-AGAGATA
*
28691105 GCCACAAAGGATTCCTTTATAGAGATT
1 GCCACAAAGGATTCCTTTATAGAGATA
*
28691132 GCCACAAA-GACTTCTTTTAATAGAGATCA
1 GCCACAAAGGA-TTCCTTT-ATAGAGAT-A
* *
28691161 -CCACAGCAA--CTTCCTTTATAGAGATT
1 GCCACA--AAGGATTCCTTTATAGAGATA
** * * *
28691187 GCCACAAGAGTTTTCCTTAATAAAGATC
1 GCCACAA-AGGATTCCTTTATAGAGATA
** * * *
28691215 GCCACAAAGTTTTTCTTTAACAGAGATC
1 GCCACAAAGGATTCCTTT-ATAGAGATA
* * * *
28691243 TCCACAAAGGCTTCCTTTACAGAGATT
1 GCCACAAAGGATTCCTTTATAGAGATA
28691270 GCCA
1 GCCA
28691274 TAGAGGCATT
Statistics
Matches: 136, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.01
26 3 0.02
27 59 0.43
28 71 0.52
30 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (27 bp):
GCCACAAAGGATTCCTTTATAGAGATA
Found at i:28691219 original size:83 final size:82
Alignment explanation
Indices: 28691078--28691273 Score: 200
Period size: 83 Copynumber: 2.4 Consensus size: 82
28691068 TTAAACTGCG
* * * ** * * *
28691078 CCACAAAGGCGTTCCTTTTCAGAGGTAGCCACAA-AGGATTCCTTTATAGAGATTGCCACAAAGA
1 CCACAAA-GC-TTCCTTTACAGAGATTGCCACAAGAGTTTTCCTTAATAAAGATCGCCACAAAG-
*
28691142 CTTCT-TTTAATAGAGATCA
63 CTTCTCTTTAACAGAGATCA
* *
28691161 CCACAGCAA-CTTCCTTTATAGAGATTGCCACAAGAGTTTTCCTTAATAAAGATCGCCACAAAGT
1 CCACA--AAGCTTCCTTTACAGAGATTGCCACAAGAGTTTTCCTTAATAAAGATCGCCACAAAGC
* *
28691225 TTTTCTTTAACAGAGATCT
64 TTCTCTTTAACAGAGATCA
28691244 CCACAAAGGCTTCCTTTACAGAGATTGCCA
1 CCACAAA-GCTTCCTTTACAGAGATTGCCA
28691274 TAGAGGCATT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
81 2 0.02
82 22 0.24
83 67 0.72
85 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (82 bp):
CCACAAAGCTTCCTTTACAGAGATTGCCACAAGAGTTTTCCTTAATAAAGATCGCCACAAAGCTT
CTCTTTAACAGAGATCA
Found at i:28691233 original size:55 final size:54
Alignment explanation
Indices: 28691105--28691223 Score: 136
Period size: 55 Copynumber: 2.2 Consensus size: 54
28691095 TTCAGAGGTA
*
28691105 GCCACAAAGGATTCCTTTATAGAGATTGCCACAAAGACTTCTTTTAATAGAGATC
1 GCCACAAA-GATTCCTTTATAGAGATTGCCACAAAGACTTCTTTTAATAAAGATC
* * *
28691160 ACCACAGCAA-CTTCCTTTATAGAGATTGCCAC-AAGAGTT-TTCCTTAATAAAGATC
1 GCCACA--AAGATTCCTTTATAGAGATTGCCACAAAGACTTCTT--TTAATAAAGATC
28691215 GCCACAAAG
1 GCCACAAAG
28691224 TTTTTCTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
53 4 0.07
54 6 0.11
55 42 0.78
57 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (54 bp):
GCCACAAAGATTCCTTTATAGAGATTGCCACAAAGACTTCTTTTAATAAAGATC
Found at i:28692824 original size:40 final size:40
Alignment explanation
Indices: 28692787--28692972 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
28692777 GCTACTCGTT
* * *
28692787 CAAATGCCTTCGGGGCATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28692827 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28692867 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
28692907 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28692948 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28692973 CATCATTCAA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28695977 original size:779 final size:779
Alignment explanation
Indices: 28694480--28696040 Score: 3086
Period size: 779 Copynumber: 2.0 Consensus size: 779
28694470 CATTTCAAAA
28694480 TTTTCTCACATAAGTCTTATTTGATAAAATTCACTTACAATTAACAAAATTCAAACACGAAATTT
1 TTTTCTCACATAAGTCTTATTTGATAAAATTCACTTACAATTAACAAAATTCAAACACGAAATTT
28694545 TCACACATGCACATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGT
66 TCACACATGCACATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGT
28694610 TTAGTGGTCCCGAAACCACTTCCCGGCTAGGGTCAATTTTGGGCTGTCACAAAGATTGCCACGAA
131 TTAGTGGTCCCGAAACCACTTCCCGGCTAGGGTCAATTTTGGGCTGTCACAAAGATTGCCACGAA
28694675 GGCATCCACTTTCTTTCCACAAAGGCTTTTCTTTTAGAGATTGCCATAGCGGCGTTCTTTACAAA
196 GGCATCCACTTTCTTTCCACAAAGGCTTTTCTTTTAGAGATTGCCATAGCGGCGTTCTTTACAAA
*
28694740 GATTTCCACAAAGGCATCCCTCCTCTAGCATATTTACGCTAAGGATTTGCCTAAACTCGTATTAT
261 GATTTCCACAAAGGCATCCCTCCTCTAGCATATTTACGCTAAGGATTTGCCTAAACTCGTATTAC
*
28694805 GTGAGGTTTCCCCCTCATTGTTTGGGTCGCACGGAAATTACATTAGGTAATAACCTTCCTTTAGT
326 GTGAGGTTTCCCCCTCATTGTTTGGGTCGCACGAAAATTACATTAGGTAATAACCTTCCTTTAGT
28694870 TCTTCCCATATGACGCTATAGCCCAACTATGGTCTTACACGATATGTATTTTCTTTTAAAATGTC
391 TCTTCCCATATGACGCTATAGCCCAACTATGGTCTTACACGATATGTATTTTCTTTTAAAATGTC
28694935 ATGACCATTGAAATTTCCTTTTAGATACTCTTATTTAAAGTCCCGATGGACCCCTTTAGACGACT
456 ATGACCATTGAAATTTCCTTTTAGATACTCTTATTTAAAGTCCCGATGGACCCCTTTAGACGACT
28695000 TCAGAGATAGACACGGACTCACCATACATATACCCATCATACAATGACTTGCTCATGAGAGACAT
521 TCAGAGATAGACACGGACTCACCATACATATACCCATCATACAATGACTTGCTCATGAGAGACAT
28695065 ATTCATGCTTTCAGACTCATATACACACCTTAATCATTCAAATTCATGCCCTGTACTTAGACCAT
586 ATTCATGCTTTCAGACTCATATACACACCTTAATCATTCAAATTCATGCCCTGTACTTAGACCAT
28695130 CAAATTTCATGCAATCAATACACAAAAGTCCATAATATATACATTTCTCATAAGAATCATCACAT
651 CAAATTTCATGCAATCAATACACAAAAGTCCATAATATATACATTTCTCATAAGAATCATCACAT
28695195 CATACTATTCTAGCTTGAATCTCATTGTAAGGCCTTAAAAAGAGGTCTAGTAGTTTCGGGTAAG
716 CATACTATTCTAGCTTGAATCTCATTGTAAGGCCTTAAAAAGAGGTCTAGTAGTTTCGGGTAAG
28695259 TTTTCTCACATAAGTCTTATTTGATAAAATTCACTTACAATTAACAAAATTCAAACACGAAATTT
1 TTTTCTCACATAAGTCTTATTTGATAAAATTCACTTACAATTAACAAAATTCAAACACGAAATTT
28695324 TCACACATGCACATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGT
66 TCACACATGCACATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGT
28695389 TTAGTGGTCCCGAAACCACTTCCCGGCTAGGGTCAATTTTGGGCTGTCACAAAGATTGCCACGAA
131 TTAGTGGTCCCGAAACCACTTCCCGGCTAGGGTCAATTTTGGGCTGTCACAAAGATTGCCACGAA
28695454 GGCATCCACTTTCTTTCCACAAAGGCTTTTCTTTTAGAGATTGCCATAGCGGCGTTCTTTACAAA
196 GGCATCCACTTTCTTTCCACAAAGGCTTTTCTTTTAGAGATTGCCATAGCGGCGTTCTTTACAAA
28695519 GATTTCCACAAAGGCATCCCTCCTCTAGCATATTTACGCTAAGGATTTGCCTAAACTCGTATTAC
261 GATTTCCACAAAGGCATCCCTCCTCTAGCATATTTACGCTAAGGATTTGCCTAAACTCGTATTAC
28695584 GTGAGGTTTCCCCCTCATTGTTTGGGTCGCACGAAAATTACATTAGGTAATAACCTTCCTTTAGT
326 GTGAGGTTTCCCCCTCATTGTTTGGGTCGCACGAAAATTACATTAGGTAATAACCTTCCTTTAGT
*
28695649 TCTTCCCATATGACGCTATAGCCCAACTATGGTCTTACACGATATGTCTTTTCTTTTAAAATGTC
391 TCTTCCCATATGACGCTATAGCCCAACTATGGTCTTACACGATATGTATTTTCTTTTAAAATGTC
28695714 ATGACCATTGAAATTTCCTTTTAGATACTCTTATTTAAAGTCCCGATGGACCCCTTTAGACGACT
456 ATGACCATTGAAATTTCCTTTTAGATACTCTTATTTAAAGTCCCGATGGACCCCTTTAGACGACT
28695779 TCAGAGATAGACACGGACTCACCATACATATACCCATCATACAATGACTTGCTCATGAGAGACAT
521 TCAGAGATAGACACGGACTCACCATACATATACCCATCATACAATGACTTGCTCATGAGAGACAT
*
28695844 ATTCATGCTTTTAGACTCATATACACACCTTAATCATTCAAATTCATGCCCTGTACTTAGACCAT
586 ATTCATGCTTTCAGACTCATATACACACCTTAATCATTCAAATTCATGCCCTGTACTTAGACCAT
28695909 CAAATTTCATGCAATCAATACACAAAAGTCCATAATATATACATTTCTCATAAGAATCATCACAT
651 CAAATTTCATGCAATCAATACACAAAAGTCCATAATATATACATTTCTCATAAGAATCATCACAT
28695974 CATACTATTCTAGCTTGAATCTCATTGTAAGGCCTTAAAAAGAGGTCTAGTAGTTTCGGGTAAG
716 CATACTATTCTAGCTTGAATCTCATTGTAAGGCCTTAAAAAGAGGTCTAGTAGTTTCGGGTAAG
28696038 TTT
1 TTT
28696041 ACTGGGTTTC
Statistics
Matches: 778, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
779 778 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (779 bp):
TTTTCTCACATAAGTCTTATTTGATAAAATTCACTTACAATTAACAAAATTCAAACACGAAATTT
TCACACATGCACATGTACATATAATGAGCATCAATTATGACGGTTAATTATTTTTATGACTCGGT
TTAGTGGTCCCGAAACCACTTCCCGGCTAGGGTCAATTTTGGGCTGTCACAAAGATTGCCACGAA
GGCATCCACTTTCTTTCCACAAAGGCTTTTCTTTTAGAGATTGCCATAGCGGCGTTCTTTACAAA
GATTTCCACAAAGGCATCCCTCCTCTAGCATATTTACGCTAAGGATTTGCCTAAACTCGTATTAC
GTGAGGTTTCCCCCTCATTGTTTGGGTCGCACGAAAATTACATTAGGTAATAACCTTCCTTTAGT
TCTTCCCATATGACGCTATAGCCCAACTATGGTCTTACACGATATGTATTTTCTTTTAAAATGTC
ATGACCATTGAAATTTCCTTTTAGATACTCTTATTTAAAGTCCCGATGGACCCCTTTAGACGACT
TCAGAGATAGACACGGACTCACCATACATATACCCATCATACAATGACTTGCTCATGAGAGACAT
ATTCATGCTTTCAGACTCATATACACACCTTAATCATTCAAATTCATGCCCTGTACTTAGACCAT
CAAATTTCATGCAATCAATACACAAAAGTCCATAATATATACATTTCTCATAAGAATCATCACAT
CATACTATTCTAGCTTGAATCTCATTGTAAGGCCTTAAAAAGAGGTCTAGTAGTTTCGGGTAAG
Found at i:28699632 original size:44 final size:43
Alignment explanation
Indices: 28699580--28699892 Score: 121
Period size: 44 Copynumber: 7.3 Consensus size: 43
28699570 TGTAATTTCA
*
28699580 AGGG-GATAAGACTTGTCTTCTCAATCTACTCCACTGCAACCTC
1 AGGGAGATAAGACTTGTCTTCT-AATCCACTCCACTGCAACCTC
* * * * ** *
28699623 AGGGAGATAAGACCTG--ATGTGATCCACTTTACTGCAACTTC
1 AGGGAGATAAGACTTGTCTTCTAATCCACTCCACTGCAACCTC
* * * * *
28699664 AGAGAGATAAGATCTAT-TACTT-TAATCCGCTCCACTACAACTTT
1 AGGGAGATAAGA-CT-TGT-CTTCTAATCCACTCCACTGCAACCTC
* * * **
28699708 AGGGAGATAGGATTATCGACTTC-AATCTGCTCCACTGCAACCTC
1 AGGGAGATAAGACT-T-GTCTTCTAATCCACTCCACTGCAACCTC
* * * * * *
28699752 AGGGAGATAAGA-TT-TAATGC-GATCCACTCTACTGCAACTTT
1 AGGGAGATAAGACTTGT-CTTCTAATCCACTCCACTGCAACCTC
* * * *
28699793 AGAGAGATAAGATCTAT-TACTT-TAATCCGCTCCACTACAACTTC
1 AGGGAGATAAGA-CT-TGT-CTTCTAATCCACTCCACTGCAACCTC
* * ***
28699837 AGGGAGATAGGA-TTAACGGCTTC-AATTTGCTCCACTGCAACCTC
1 AGGGAGATAAGACTT---GTCTTCTAATCCACTCCACTGCAACCTC
28699881 AGGGAGATAAGA
1 AGGGAGATAAGA
28699893 TTTAATATGA
Statistics
Matches: 200, Mismatches: 51, Indels: 37
0.69 0.18 0.13
Matches are distributed among these distances:
41 56 0.28
42 5 0.03
43 10 0.05
44 128 0.64
45 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (43 bp):
AGGGAGATAAGACTTGTCTTCTAATCCACTCCACTGCAACCTC
Found at i:28699755 original size:129 final size:129
Alignment explanation
Indices: 28699600--28700271 Score: 567
Period size: 129 Copynumber: 5.3 Consensus size: 129
28699590 ACTTGTCTTC
* *
28699600 TCAATCTACTCCACTGCAACCTCAGGGAGATAAGACCTGATGTGATCCACTTTACTGCAACTTCA
1 TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCA
*
28699665 GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGACT
66 GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGACT
** * * *
28699729 TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTAATGCGATCCACTCTACTGCAACTTTA
1 TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCA
* *
28699794 GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAACGGCT
66 GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGACT
* ** * *
28699858 TCAATTTGCTCCACTGCAACCTCAGGGAGATAAGATTTAATATGATCCACTCTACTGCAACTTCA
1 TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCA
* * * * *** * * * * *
28699923 -AG-G---AGAT-T-GTAGCTTCAA-CTTGTTCTGTTTCAACTTTA--AAGATA--AGTCT-GA-
66 GAGAGATAAGATCTATTA-CTTTAATC-CGCTCCACTACAACTTCAGGGAGATAGGATTATCGAC
28699974 T
129 T
* * * * * * * * *
28699975 GT-AATCTGATCTACTGCAACTTCAGAGAGATGAGATCCATCG-TCTTAATCCGCTCCACTGCAA
1 -TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGA-CC-T-GAT-GTGATCCACTCTACTGCAA
* * * * *** * * * *
28700038 CTTCAGGGAAATAAGATTTGTGGTTTTCGATCTG-TCCCACTGCAACTTCAAGGG-GATAAGATC
61 CTTCAGAGAGATAAGATCTATTACTTT-AATCCGCT-CCACTACAACTTC-AGGGAGATAGGAT-
* *
28700101 T-GCTTACT
122 TATC-GACT
* ** * * * *
28700109 T-AGTCTGCTCTGCTGTAACCTTAGGGAGATAAGACCCGATGCGATCCACTCTACTGCAACTTCA
1 TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCA
28700173 GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATC-AGCT
66 GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGA-CT
*
28700237 TCAATCTGCTCCACTGCAACCTTAGGGAGATAAGA
1 TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGA
28700272 GTTGCCATCT
Statistics
Matches: 423, Mismatches: 88, Indels: 64
0.74 0.15 0.11
Matches are distributed among these distances:
117 28 0.07
118 2 0.00
119 4 0.01
120 20 0.05
121 6 0.01
122 3 0.01
123 17 0.04
124 4 0.01
125 4 0.01
126 4 0.01
127 13 0.03
128 12 0.03
129 237 0.56
130 36 0.09
131 2 0.00
132 3 0.01
133 27 0.06
134 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (129 bp):
TCAATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCA
GAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGACT
Found at i:28700217 original size:44 final size:44
Alignment explanation
Indices: 28699987--28700442 Score: 203
Period size: 44 Copynumber: 10.5 Consensus size: 44
28699977 AATCTGATCT
* * *
28699987 ACTGCAACTTCAGAGAGATGAGATCCATCGT-CTT-AATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTAT--TACTTCAATCCGCTCC
* * * * * *
28700031 ACTGCAACTTCAGGGAAATAAGATTTGTGGT-TTTCGATCTG-TCCC
1 ACTGCAACTTCAGGGAGATAAGATCTAT--TACTTCAATCCGCT-CC
* * * *
28700076 ACTGCAACTTCAAGGG-GATAAGATCTGCTTACTT-AGTCTGCTCT
1 ACTGCAACTTC-AGGGAGATAAGATCT-ATTACTTCAATCCGCTCC
* * *** * * * *
28700120 GCTGTAACCTT-AGGGAGATAAGA-C-CCGA-TGCGATCCACTCT
1 ACTGCAA-CTTCAGGGAGATAAGATCTATTACTTCAATCCGCTCC
* *
28700161 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCCGCTCC
* * * *
28700205 ACTACAACTTCAGGGAGATAGGAT-TATCAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCCGCTCC
* * *
28700249 ACTGCAACCTT-AGGGAGATAAGAGTTGCCA-T-CTTCGATCTG-TCC
1 ACTGCAA-CTTCAGGGAGATAAGA--T-CTATTACTTCAATCCGCTCC
* * * * *
28700293 TACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCTGCTCC
1 -ACTGCAACTTCAGGGAGATAAGATCT-ATTACTTCAATCCGCTCC
** * * * * * * *
28700338 GGTGCAACCTCAGGGAGACAAGACCTA--A-TGCGATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCCGCTCC
* * *
28700379 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCCGCTCC
*
28700423 ACTACAACTTCAGGGAGATA
1 ACTGCAACTTCAGGGAGATA
28700443 GGATTTGTGT
Statistics
Matches: 303, Mismatches: 80, Indels: 58
0.69 0.18 0.13
Matches are distributed among these distances:
40 4 0.01
41 52 0.17
42 2 0.01
43 11 0.04
44 162 0.53
45 65 0.21
46 6 0.02
48 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCCGCTCC
Found at i:28700371 original size:218 final size:218
Alignment explanation
Indices: 28700021--28700447 Score: 667
Period size: 218 Copynumber: 2.0 Consensus size: 218
28700011 CCATCGTCTT
* *** *
28700021 AATCCGCTCCACTGCAACTTCAGGGAAATAAGATTTGTGGTTTTCGATCTGTCCCACTGCAACTT
1 AATCCGCTCCACTGCAACTTCAGGGAAATAAGAGTTGCCATCTTCGATCTGTCCCACTGCAACTT
* * * * * * *
28700086 CAAGGGGATAAGATCTGCTTACTTAGTCTGCTCTGCTGTAACCTTAGGGAGATAAGACCCGATGC
66 CAAGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGGAGACAAGACCCAATGC
*
28700151 GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTC
131 GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTC
28700216 AGGGAGATAGGATTATCAGCTTC
196 AGGGAGATAGGATTATCAGCTTC
* * *
28700239 AATCTGCTCCACTGCAACCTT-AGGGAGATAAGAGTTGCCATCTTCGATCTGTCCTACTGCAACT
1 AATCCGCTCCACTGCAA-CTTCAGGGAAATAAGAGTTGCCATCTTCGATCTGTCCCACTGCAACT
* * *
28700303 TCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGGTGCAACCTCAGGGAGACAAGACCTAATG
65 TCAAGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGGAGACAAGACCCAATG
28700368 CGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTT
130 CGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTT
28700433 CAGGGAGATAGGATT
195 CAGGGAGATAGGATT
28700448 TGTGTCTTAA
Statistics
Matches: 189, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
218 186 0.98
219 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (218 bp):
AATCCGCTCCACTGCAACTTCAGGGAAATAAGAGTTGCCATCTTCGATCTGTCCCACTGCAACTT
CAAGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGGAGACAAGACCCAATGC
GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTC
AGGGAGATAGGATTATCAGCTTC
Found at i:28700586 original size:129 final size:129
Alignment explanation
Indices: 28700433--28700697 Score: 431
Period size: 129 Copynumber: 2.1 Consensus size: 129
28700423 ACTACAACTT
* * * *
28700433 CAGGGAGATAGGATTTGTGTCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTC
1 CAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCATCTTC
* *
28700498 GATCTGCTCCGCTACTGCTTAGGGGGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* *
28700562 CAGGGATATAGGACTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
1 CAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCATCTTC
* *
28700627 GATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTGATTTCCCAACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
*
28700691 TAGGGAG
1 CAGGGAG
28700698 CTAGTGTAAC
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (129 bp):
CAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCATCTTC
GATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
Found at i:28702497 original size:11 final size:11
Alignment explanation
Indices: 28702480--28702528 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
28702470 AATCATTTAT
28702480 TAATAAAATAA
1 TAATAAAATAA
* **
28702491 TACTAAAAATCT
1 TAAT-AAAATAA
28702503 TAATAAAATAA
1 TAATAAAATAA
*
28702514 TAATTAAATAA
1 TAATAAAATAA
28702525 TAAT
1 TAAT
28702529 TATCTAATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:28704523 original size:17 final size:17
Alignment explanation
Indices: 28704503--28704562 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 17
28704493 AGCCTCTCCA
28704503 TTTTTACTTTTTCATCAT
1 TTTTTA-TTTTTCATCAT
28704521 TTTTTATTTTTCATTTTCACT
1 TTTTTATTTTTCA---TCA-T
*
28704542 TTTTCATTTTTCA-CAT
1 TTTTTATTTTTCATCAT
28704558 TTTTT
1 TTTTT
28704563 TGACTCAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 5 0.14
17 9 0.25
18 6 0.17
20 3 0.08
21 13 0.36
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTATTTTTCATCAT
Found at i:28704530 original size:6 final size:7
Alignment explanation
Indices: 28704517--28704554 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
28704507 TACTTTTTCA
28704517 TCATTTT
1 TCATTTT
*
28704524 TTATTTT
1 TCATTTT
28704531 TCA-TTT
1 TCATTTT
28704537 TCACTTTT
1 TCA-TTTT
28704545 TCATTTT
1 TCATTTT
28704552 TCA
1 TCA
28704555 CATTTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.22
7 15 0.56
8 6 0.22
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (7 bp):
TCATTTT
Found at i:28704552 original size:15 final size:15
Alignment explanation
Indices: 28704517--28704561 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
28704507 TACTTTTTCA
*
28704517 TCATTTTTTA-TTTT
1 TCATTTTTCACTTTT
28704531 TCA-TTTTCACTTTT
1 TCATTTTTCACTTTT
28704545 TCATTTTTCACATTTT
1 TCATTTTTCAC-TTTT
28704561 T
1 T
28704562 TTGACTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 5 0.19
14 10 0.37
15 7 0.26
16 5 0.19
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (15 bp):
TCATTTTTCACTTTT
Found at i:28716180 original size:15 final size:15
Alignment explanation
Indices: 28716160--28716189 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28716150 ATTTGAGTTA
28716160 AAATTAAATTTAATT
1 AAATTAAATTTAATT
*
28716175 AAATTAGATTTAATT
1 AAATTAAATTTAATT
28716190 GTAAAATAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTAAATTTAATT
Found at i:28716606 original size:19 final size:19
Alignment explanation
Indices: 28716561--28716607 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
28716551 CAAGATTTTT
*
28716561 AATCAAAGGATTTAGAATG
1 AATCAAATGATTTAGAATG
28716580 AATCAAATGATTTAGAATG
1 AATCAAATGATTTAGAATG
28716599 AATCAAATG
1 AATCAAATG
28716608 TAATTGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (19 bp):
AATCAAATGATTTAGAATG
Found at i:28716662 original size:20 final size:20
Alignment explanation
Indices: 28716637--28716681 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28716627 TATTTTTATG
*
28716637 ATGATTAGAAGT-ATATTTAC
1 ATGATT-GAAGTGATAATTAC
*
28716657 ATGATTTAAGTGATAATTAC
1 ATGATTGAAGTGATAATTAC
28716677 ATGAT
1 ATGAT
28716682 CTTTTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (20 bp):
ATGATTGAAGTGATAATTAC
Found at i:28721771 original size:47 final size:47
Alignment explanation
Indices: 28721700--28722006 Score: 492
Period size: 47 Copynumber: 6.6 Consensus size: 47
28721690 CCCTTCGGGA
* * * * * *
28721700 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28721747 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28721794 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28721841 CTTATCACATATATACACTTTCACATTCATAACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28721888 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28721935 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28721982 CTTATCAC--ATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28722007 TATTCAAATA
Statistics
Matches: 243, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 17 0.07
47 226 0.93
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28726196 original size:40 final size:40
Alignment explanation
Indices: 28726121--28726392 Score: 411
Period size: 40 Copynumber: 6.8 Consensus size: 40
28726111 CCAGCATGAT
* * * *
28726121 TGCTCTTCGGGAC-TAGCACGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
28726160 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28726200 TGCTCTTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTC-TTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28726241 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28726281 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28726321 TGCTCTTCGGGACTTAGCCCAGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28726361 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
28726393 CTCAATTCTC
Statistics
Matches: 215, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 11 0.05
40 170 0.79
41 34 0.16
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28727884 original size:47 final size:47
Alignment explanation
Indices: 28727813--28728080 Score: 326
Period size: 47 Copynumber: 5.6 Consensus size: 47
28727803 CCCTTCGGGA
* * * *
28727813 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCA-TTAGGC
* * *
28727860 CCTATCACATATATACACTTTCACATTTATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
28727907 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
28727954 CTTATCACATATATACACTTTCACATTTTCACATTCATCATATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACA--TT--CA-TCA-CAT-T-GGCCATTAGGC
*
28728009 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
28728056 CTTATCAC--ATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28728081 TATTCAAATA
Statistics
Matches: 197, Mismatches: 15, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
45 17 0.09
46 2 0.01
47 122 0.62
48 1 0.01
49 5 0.03
50 3 0.02
51 4 0.02
52 2 0.01
53 5 0.03
55 36 0.18
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Done.