Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 173 of 216
Found at i:54200956 original size:44 final size:44
Alignment explanation
Indices: 54200908--54201046 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
54200898 AATAGCAGAT
54200908 CTTGCCTTCCTGCACCTACAGTGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCACCTACAGTGAAGCAGATCGAAGACACTAGC
* *** ** * * * *
54200952 CTTGCCTCCCTG-GGTTGTAGTGGAGCAGGAT-GAAAATAGC-AGAT
1 CTTGCCTTCCTGCACCTACAGTGAAGCA-GATCGAAGACA-CTAG-C
* * *
54200996 CTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCACCTACAGTGAAGCAGATCGAAGACACTAGC
54201040 CTTGCCT
1 CTTGCCT
54201047 CTCTGGGTTG
Statistics
Matches: 66, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
43 16 0.24
44 36 0.55
45 14 0.21
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.22
Consensus pattern (44 bp):
CTTGCCTTCCTGCACCTACAGTGAAGCAGATCGAAGACACTAGC
Found at i:54200960 original size:88 final size:88
Alignment explanation
Indices: 54200858--54201243 Score: 495
Period size: 88 Copynumber: 4.4 Consensus size: 88
54200848 CGAAGTAGAT
*
54200858 ACTAGCCTTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCAC
1 ACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCA-
*
54200923 CT-ACAGTGAAGCAGATCGAAGAC
65 CTGACAGCGAAGCAGATCGAAGAC
* * * * *
54200946 ACTAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGATGAAAATAGCAGATCTTGCCTTCTTGCAC
1 ACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCAC
*
54201011 CGACAGCGAAGCAGATCGAAGAC
66 TGACAGCGAAGCAGATCGAAGAC
* * * * * *
54201034 ACTAGCCTTGCCTCTCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAAATCTTGCCTTCCTGTAT
1 ACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCAC
* * * *
54201099 TGACAGTGAAGCAGATCAAAAAT
66 TGACAGCGAAGCAGATCGAAGAC
* * * * * * * *
54201122 ACTAGCCTTGCCTCCTTTGGTTGTAGCAGAGCAGGTTAAAGATGGCAGATCTTGCCTTCCTGTAT
1 ACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCAC
* *
54201187 TGGCAGCGAAGCAAATCGAAGAC
66 TGACAGCGAAGCAGATCGAAGAC
*
54201210 ACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAG
1 ACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAG
54201244 TTGCAATAGA
Statistics
Matches: 256, Mismatches: 41, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
87 1 0.00
88 255 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.23
Consensus pattern (88 bp):
ACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCAC
TGACAGCGAAGCAGATCGAAGAC
Found at i:54201345 original size:44 final size:45
Alignment explanation
Indices: 54201269--54201680 Score: 137
Period size: 44 Copynumber: 9.5 Consensus size: 45
54201259 TCGCATCAGG
* * * ** * *
54201269 TCTTATCTCCCTGAAGTTGTAGCGGAATAGACTGAATA-AGCAGA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAA
* * *
54201313 TTTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAA
* * * **
54201358 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA--ATAA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA-AA
* * * * * ** * *
54201402 TCCTATCTCCCTAAAGTTACAGCGGAGTGGA-TTAAAAT-G-ATAGA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA-A-A
* ** * ** * *
54201446 TCTTATCTCTTTGAGGTTGCA-AAGAGCAGA-TCG--CAT--CAGA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAGCAAA
* * * * *
54201486 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCG--CAT--CAAG
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAGCAAA
* * * **
54201526 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAATA-AGCAGG
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAA
* * * *
54201570 TCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAA
* * * * * **
54201615 TCTTATCTCCCTGAGGTTGCAGTCGAGCAGATTAAAGCCA--ATAA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA-AA
*
54201659 TCTTATCTCCCTGAAGTTGCAG
1 TCTTATCCCCCTGAAGTTGCAG
54201681 CAGAACGGAT
Statistics
Matches: 282, Mismatches: 71, Indels: 30
0.74 0.19 0.08
Matches are distributed among these distances:
40 56 0.20
41 8 0.03
42 4 0.01
43 14 0.05
44 132 0.47
45 68 0.24
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (45 bp):
TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAA
Found at i:54201488 original size:40 final size:40
Alignment explanation
Indices: 54201443--54201546 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
54201433 TTAAAATGAT
* *
54201443 AGATCTTATCTCTTTGAGGTTGCAAAGAGCAGATCGCATC
1 AGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATC
*
54201483 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
1 AGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATC
* *
54201523 A-AGTCTTATCTCCCTAAAGTTGCA
1 AGA-TCTTATCTCTCTGAAGTTGCA
54201547 GTGGAGCAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (40 bp):
AGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATC
Found at i:54201692 original size:44 final size:40
Alignment explanation
Indices: 54201613--54201719 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 40
54201603 GAAGATGGCG
* *
54201613 AATCTTATCTCCCTGAGGTTGCAGTCGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTCGAACAGATT-AA---AAT
*
54201657 AATCTTATCTCCCTGAAGTTGCAG-CAGAACGGATTAAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTC-GAACAGATTAAAAT
* *
54201697 GATCTTATCTCTCTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
54201720 AAGAGCAGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
40 24 0.42
43 3 0.05
44 30 0.53
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (40 bp):
AATCTTATCTCCCTGAAGTTGCAGTCGAACAGATTAAAAT
Found at i:54210667 original size:8 final size:8
Alignment explanation
Indices: 54210648--54210700 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
54210638 TTCAAAATTA
54210648 TTAAAAATT
1 TTAAAAA-T
54210657 TTAAAAAT
1 TTAAAAAT
54210665 TTAAAAA-
1 TTAAAAAT
*
54210672 CTAAAAA-
1 TTAAAAAT
*
54210679 CTAAAAAT
1 TTAAAAAT
54210687 TTAAAAAT
1 TTAAAAAT
54210695 TATAAA
1 T-TAAA
54210701 TATATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 13 0.32
8 16 0.40
9 11 0.28
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (8 bp):
TTAAAAAT
Found at i:54212494 original size:38 final size:38
Alignment explanation
Indices: 54212443--54212517 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
54212433 AGAAAATCTG
54212443 CCATTTACTTCCAAACTGGAATTGTAAGTCATTTCTTT
1 CCATTTACTTCCAAACTGGAATTGTAAGTCATTTCTTT
*
54212481 CCATTTACTTCCAAATTGGAATTGTAAGTCATTTCTT
1 CCATTTACTTCCAAACTGGAATTGTAAGTCATTTCTT
54212518 AAAAAATCGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.43
Consensus pattern (38 bp):
CCATTTACTTCCAAACTGGAATTGTAAGTCATTTCTTT
Found at i:54213943 original size:23 final size:22
Alignment explanation
Indices: 54213891--54213968 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
54213881 TCATGACATT
*
54213891 TAATGAA-ATAATAAC-ATAAA
1 TAATGAATAAAATAACAATAAA
* *
54213911 TAATAAAATAAAATGACAATAATA
1 TAAT-GAATAAAATAACAATAA-A
* *
54213935 TAATGAATACAATAATAATAAA
1 TAATGAATAAAATAACAATAAA
*
54213957 TAATGAAAAAAA
1 TAATGAATAAAA
54213969 ATATTCAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 4 0.09
21 2 0.04
22 17 0.38
23 17 0.38
24 5 0.11
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.24
Consensus pattern (22 bp):
TAATGAATAAAATAACAATAAA
Found at i:54215790 original size:14 final size:14
Alignment explanation
Indices: 54215771--54215798 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54215761 TAATTAATGG
54215771 ATTTATTTTTGTTT
1 ATTTATTTTTGTTT
54215785 ATTTATTTTTGTTT
1 ATTTATTTTTGTTT
54215799 GGGTCGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
ATTTATTTTTGTTT
Found at i:54216624 original size:19 final size:20
Alignment explanation
Indices: 54216595--54216636 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
54216585 TAGAAAATGA
*
54216595 TTTTTGAAAAATTATTTACT
1 TTTTTGAAAAATGATTTACT
54216615 TTTTTG-AAAATGATTTACT
1 TTTTTGAAAAATGATTTACT
54216634 TTT
1 TTT
54216637 CTAGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTTGAAAAATGATTTACT
Found at i:54228140 original size:19 final size:19
Alignment explanation
Indices: 54228100--54228142 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54228090 AATTCTGTAG
*
54228100 AGAAATGAAAATAAATCTA
1 AGAAATGAAAATAAATCAA
*
54228119 AGAAATGAAGATAAAAT-AA
1 AGAAATGAAAAT-AAATCAA
54228138 AGAAA
1 AGAAA
54228143 GATGTAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.16
Consensus pattern (19 bp):
AGAAATGAAAATAAATCAA
Found at i:54231110 original size:16 final size:16
Alignment explanation
Indices: 54231091--54231126 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
54231081 AAAGAAAAAC
54231091 ATATATAAA-TATAAA
1 ATATATAAATTATAAA
54231106 TATATATAAATTATAAA
1 -ATATATAAATTATAAA
54231123 ATAT
1 ATAT
54231127 GTGTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATAAATTATAAA
Found at i:54231309 original size:31 final size:29
Alignment explanation
Indices: 54231237--54231330 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
54231227 ATAAATATAT
* * *
54231237 TTACATGTACATATATAAAA-AAATAAATA
1 TTACATATATATATATAAAATAAA-AAAAA
*
54231266 TATACATATATATATA-AATTATAAAAAAAA
1 T-TACATATATATATATAA-AATAAAAAAAA
* *
54231296 TTACATATATATATATAAAATAATAATAA
1 TTACATATATATATATAAAATAAAAAAAA
54231325 TTACAT
1 TTACAT
54231331 TATTGAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
29 31 0.57
30 20 0.37
31 3 0.06
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (29 bp):
TTACATATATATATATAAAATAAAAAAAA
Found at i:54233078 original size:45 final size:45
Alignment explanation
Indices: 54233010--54233343 Score: 201
Period size: 45 Copynumber: 7.6 Consensus size: 45
54233000 TTAGTTTGCC
* * *
54233010 CCACTGCAACTTTAGGGGGATAAGACTTGCTTTCTTGAGTCTGCT
1 CCACTGCATCTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTGCT
* * *
54233055 CCACTGCATCTTCAGGGAAATAAGACTCGCTTTCTTGGGTCTGCT
1 CCACTGCATCTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTGCT
* *
54233100 CCACTGCATCTTCAGGGAGATAAGACCTGC--T-ATGA-TCTGCT
1 CCACTGCATCTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTGCT
* * * * * * *
54233141 -CTCTGCAACTTCAGAGAGATAAGA--T-CTATCACTTTAATCTTCT
1 CCACTGCATCTTCAGGGAGATAAGACTTGCT-T-TCTTGAGTCTGCT
* * * * * * * *
54233184 CCACTGCAACTTTAAGGAGATAGGA-TT-ATTGGCTTTAATCTGCT
1 CCACTGCATCTTCAGGGAGATAAGACTTGCTT-TCTTGAGTCTGCT
* * * ** *
54233228 CCACTGAAACCTCAGGGAGATAAGA-TTCGCCATCTTGGGTCTGCT
1 CCACTGCATCTTCAGGGAGATAAGACTT-GCTTTCTTGAGTCTGCT
* * *
54233273 CCACTGCGA-CTTCA-GGAGGATAAGACTTGCTTAC-TCAATCTGCT
1 CCACTGC-ATCTTCAGGGA-GATAAGACTTGCTTTCTTGAGTCTGCT
* **
54233317 CCACTGCAACTTCAATGAGATAAGACT
1 CCACTGCATCTTCAGGGAGATAAGACT
54233344 AGATGCGATC
Statistics
Matches: 226, Mismatches: 48, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
40 21 0.09
41 6 0.03
42 4 0.02
43 7 0.03
44 84 0.37
45 99 0.44
46 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (45 bp):
CCACTGCATCTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTGCT
Found at i:54233195 original size:44 final size:44
Alignment explanation
Indices: 54233143--54233470 Score: 189
Period size: 44 Copynumber: 7.5 Consensus size: 44
54233133 GATCTGCTCT
*
54233143 CTGCAACTTCAGAGAGATAAGATCTATCACTTTAATCTTCTCCA
1 CTGCAACTTCAGAGAGATAAGATCTATCACTTTAATCTACTCCA
* * ** *
54233187 CTGCAACTTTA-AGGAGATAGGAT-TATTGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGA-GAGATAAGATCTA-TCACTTTAATCTACTCCA
* * * ** *** *
54233231 CTGAAACCTCAGGGAGATAAGAT-TCGCCATCTTGGGTCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCT-ATCA-CTTTAATCTACTCCA
* * *
54233276 CTGCGACTTCAG-GAGGATAAGA-CT-TGCTTAC-TCAATCTGCTCCA
1 CTGCAACTTCAGAGA-GATAAGATCTAT-C--ACTTTAATCTACTCCA
* *** *
54233320 CTGCAACTTCA-ATGAGATAAGA-CTA-GA-TGCGATCTACT-CT
1 CTGCAACTTCAGA-GAGATAAGATCTATCACTTTAATCTACTCCA
*
54233360 CTGCAACTTCAGAGAGATAAGATCTATCACTTTAATCCACTCCA
1 CTGCAACTTCAGAGAGATAAGATCTATCACTTTAATCTACTCCA
* * **
54233404 TTGCAACTTCAGGGAGAT-AGAAT-TATTGGCTTTAATCTACTCCA
1 CTGCAACTTCAGAGAGATAAG-ATCTA-TCACTTTAATCTACTCCA
* *
54233448 TTGCAACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGAGAGATAAGAT
54233471 TCGCCATCTT
Statistics
Matches: 221, Mismatches: 41, Indels: 44
0.72 0.13 0.14
Matches are distributed among these distances:
40 21 0.10
41 12 0.05
42 1 0.00
43 14 0.06
44 138 0.62
45 34 0.15
46 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAGAGAGATAAGATCTATCACTTTAATCTACTCCA
Found at i:54233368 original size:217 final size:218
Alignment explanation
Indices: 54233042--54233497 Score: 632
Period size: 217 Copynumber: 2.1 Consensus size: 218
54233032 AGACTTGCTT
* ***
54233042 TCTTGAGTCTGCTCCACTGCATCTTCAGGGAAATAAGACTCGCTTTCTTGGGTCTGCTCCACTGC
1 TCTTGAGTCTGCTCCACTGCATCTTCAGGGAAATAAGACTCGCTTACTTCAATCTGCTCCACTGC
* * * * *
54233107 ATCTTCAGGGAGATAAGACCTGCTATGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTATCA
66 AACTTCAAGGAGATAAGACCTGATACGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTATCA
** * * *
54233172 CTTTAATCTTCTCCACTGCAACTTTAAGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGAAA
131 CTTTAATCCACTCCACTGCAACTTCAAGGAGATAGAATTATTGGCTTTAATCTACTCCACTGAAA
54233237 CCTCAGGGAGATAAGATTCGCCA
196 CCTCAGGGAGATAAGATTCGCCA
* * *
54233260 TCTTGGGTCTGCTCCACTGCGA-CTTCA-GGAGGATAAGACTTGCTTAC-TCAATCTGCTCCACT
1 TCTTGAGTCTGCTCCACTGC-ATCTTCAGGGA-AATAAGACTCGCTTACTTCAATCTGCTCCACT
* *
54233322 GCAACTTCAATGAGATAAGA-CTAGATGCGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTA
64 GCAACTTCAAGGAGATAAGACCT-GATACGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTA
* * *
54233386 TCACTTTAATCCACTCCATTGCAACTTCAGGGAGATAGAATTATTGGCTTTAATCTACTCCATTG
128 TCACTTTAATCCACTCCACTGCAACTTCAAGGAGATAGAATTATTGGCTTTAATCTACTCCACTG
* *
54233451 CAACTTCAGGGAGATAAGATTCGCCA
193 AAACCTCAGGGAGATAAGATTCGCCA
*
54233477 TCTTCAGTCTGCTCCACTGCA
1 TCTTGAGTCTGCTCCACTGCA
54233498 ATAGACCTGC
Statistics
Matches: 209, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
216 3 0.01
217 168 0.80
218 37 0.18
219 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (218 bp):
TCTTGAGTCTGCTCCACTGCATCTTCAGGGAAATAAGACTCGCTTACTTCAATCTGCTCCACTGC
AACTTCAAGGAGATAAGACCTGATACGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTATCA
CTTTAATCCACTCCACTGCAACTTCAAGGAGATAGAATTATTGGCTTTAATCTACTCCACTGAAA
CCTCAGGGAGATAAGATTCGCCA
Found at i:54233395 original size:173 final size:173
Alignment explanation
Indices: 54233049--54233422 Score: 397
Period size: 173 Copynumber: 2.2 Consensus size: 173
54233039 CTTTCTTGAG
* * **
54233049 TCTGCTCCACTGCATCTTCAGGGAAATAAGACTCGCTTTCTTGGGTCTGCTCCACTGCATCTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCCATCTTGGGTCTGCTCCACTGCATCTTCA
* * **
54233114 GGGAGATAAGACCTGCTATGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTATCACTTTAAT
66 GGGAGATAAGACCTGCTATAATCTGCTCACTGCAACTTCAGAGAGATAAGATCTATCACTGCAAT
* * * **
54233179 CTTCTCCACTGCAACTTTAAGGAGATAGGATTATTGGCTTTAA
131 CTACTCCACTGCAACTTCAAGGAGATAAGATTATTCACTTTAA
* * *
54233222 TCTGCTCCACTGAAACCTCAGGGAGATAAGATTCGCCATCTTGGGTCTGCTCCACTGCGA-CTTC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCCATCTTGGGTCTGCTCCACTGC-ATCTTC
* *
54233286 A-GGAGGATAAGACTTGCTTACTCAATCTGCTCCACTGCAACTTCA-ATGAGATAAGA-CTA-GA
65 AGGGA-GATAAGACCTGC-TA-T-AATCTGCT-CACTGCAACTTCAGA-GAGATAAGATCTATCA
* *
54233347 -TGCGATCTACT-CTCTGCAACTTC-AGAGAGATAAGATCTA-TCACTTTAA
124 CTGCAATCTACTCCACTGCAACTTCAAG-GAGATAAGAT-TATTCACTTTAA
** *
54233395 TCCACTCCATTGCAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
54233423 GAATTATTGG
Statistics
Matches: 167, Mismatches: 25, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
172 5 0.03
173 116 0.69
174 12 0.07
175 2 0.01
176 11 0.07
177 21 0.13
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (173 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCCATCTTGGGTCTGCTCCACTGCATCTTCA
GGGAGATAAGACCTGCTATAATCTGCTCACTGCAACTTCAGAGAGATAAGATCTATCACTGCAAT
CTACTCCACTGCAACTTCAAGGAGATAAGATTATTCACTTTAA
Found at i:54237806 original size:18 final size:18
Alignment explanation
Indices: 54237783--54237825 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54237773 ACCCAATCTA
**
54237783 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
54237801 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
54237819 AACCCAA
1 AACCCAA
54237826 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:54237965 original size:9 final size:9
Alignment explanation
Indices: 54237947--54238004 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
54237937 TCAATTTGGT
54237947 TAATTC-GG
1 TAATTCGGG
54237955 TAATTCGGG
1 TAATTCGGG
*
54237964 TAATTCGGT
1 TAATTCGGG
54237973 TAATTCGGG
1 TAATTCGGG
*
54237982 TAATTCGGT
1 TAATTCGGG
*
54237991 TAATTCGGT
1 TAATTCGGG
54238000 TAATT
1 TAATT
54238005 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
8 6 0.13
9 40 0.87
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:54237978 original size:18 final size:18
Alignment explanation
Indices: 54237947--54238004 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
54237937 TCAATTTGGT
54237947 TAATTCGG-TAATTCGGG
1 TAATTCGGTTAATTCGGG
54237964 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
54237982 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGGG
54238000 TAATT
1 TAATT
54238005 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
17 8 0.21
18 31 0.79
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:54237994 original size:27 final size:26
Alignment explanation
Indices: 54237939--54238004 Score: 105
Period size: 27 Copynumber: 2.5 Consensus size: 26
54237929 GTAGTGATTC
*
54237939 AATTTGGTTAATTCGGTAATTCGGGT
1 AATTCGGTTAATTCGGTAATTCGGGT
*
54237965 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTC-GGTAATTCGGGT
54237992 AATTCGGTTAATT
1 AATTCGGTTAATT
54238005 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
26 13 0.35
27 24 0.65
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (26 bp):
AATTCGGTTAATTCGGTAATTCGGGT
Found at i:54246245 original size:4 final size:4
Alignment explanation
Indices: 54246236--54246265 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
54246226 TATGAGAATC
54246236 TAAA TAAA TAAA TAAA TAAA CTAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA -TAAA TAAA T
54246266 GTCCAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:54247361 original size:3 final size:3
Alignment explanation
Indices: 54247353--54247382 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
54247343 TACTATGATT
54247353 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54247383 CTATATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54247653 original size:22 final size:23
Alignment explanation
Indices: 54247612--54247655 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
54247602 ACATGTACAT
* *
54247612 ATACATCTATTTTTATAATATTC
1 ATACATATATTTTTAAAATATTC
54247635 ATACATAT-TTTTTAAAATATT
1 ATACATATATTTTTAAAATATT
54247656 TATAAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
ATACATATATTTTTAAAATATTC
Found at i:54248896 original size:36 final size:35
Alignment explanation
Indices: 54248843--54248928 Score: 145
Period size: 36 Copynumber: 2.4 Consensus size: 35
54248833 TATTCATTAG
* *
54248843 AAAAAATATATAAATATATTTACATGTACATATAT
1 AAAAAATAAATATATATATTTACATGTACATATAT
54248878 AAAAAAATAAATATATATATTTACATGTACATATAT
1 -AAAAAATAAATATATATATTTACATGTACATATAT
54248914 AAAAAATAAATATAT
1 AAAAAATAAATATAT
54248929 GCATATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 15 0.31
36 33 0.69
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (35 bp):
AAAAAATAAATATATATATTTACATGTACATATAT
Found at i:54248974 original size:29 final size:27
Alignment explanation
Indices: 54248908--54248986 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
54248898 TTACATGTAC
* *
54248908 ATATATAAAAAATAAATAT-A-TGCAT
1 ATATATAAAAAATAAAAATAATTACAT
*
54248933 ATATA-AATTATAA-AAAAATAATTACAT
1 ATATATAA--AAAATAAAAATAATTACAT
*
54248960 ATATATAAAAAATAATAATAATTACAT
1 ATATATAAAAAATAAAAATAATTACAT
54248987 TCTTGAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
24 2 0.05
25 10 0.23
26 7 0.16
27 22 0.51
28 2 0.05
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (27 bp):
ATATATAAAAAATAAAAATAATTACAT
Found at i:54251413 original size:23 final size:22
Alignment explanation
Indices: 54251373--54251415 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
54251363 AAATTATAAA
*
54251373 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
54251395 ATATAAGAAAAATATATATGT
1 ATATAA-AAAAATATATATGT
54251416 GTGTGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:54252151 original size:23 final size:22
Alignment explanation
Indices: 54252108--54252165 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
54252098 AAAGGGTATC
* *
54252108 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
54252129 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
54252152 TGCATATCATATCT
1 TACAAATCATATCT
54252166 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:54255251 original size:25 final size:25
Alignment explanation
Indices: 54255223--54255385 Score: 97
Period size: 24 Copynumber: 6.6 Consensus size: 25
54255213 ATCCGGGCAA
54255223 TATAACGGGAAGCTCACAAAGAGCC
1 TATAACGGGAAGCTCACAAAGAGCC
*
54255248 TATAACGGGTAGCTC-CAAAGAG-C
1 TATAACGGGAAGCTCACAAAGAGCC
* * ** *
54255271 AATTAACGGGAAGCAC-CGGATAGCC
1 TA-TAACGGGAAGCTCACAAAGAGCC
* * **
54255296 ATATAATGGGAAGTTCA-AGCGAG-C
1 -TATAACGGGAAGCTCACAAAGAGCC
*
54255320 -ACTAACAGGAAGCTCACAAAGAGCC
1 TA-TAACGGGAAGCTCACAAAGAGCC
* * * *
54255345 TTTAATCGGAAAGCTCACGAAGAGTC
1 TATAA-CGGGAAGCTCACAAAGAGCC
*
54255371 -ATAACGGGATGCTCA
1 TATAACGGGAAGCTCA
54255386 TAAGAGCTGC
Statistics
Matches: 102, Mismatches: 27, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
22 1 0.01
23 13 0.13
24 36 0.35
25 35 0.34
26 17 0.17
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.16
Consensus pattern (25 bp):
TATAACGGGAAGCTCACAAAGAGCC
Found at i:54259857 original size:22 final size:22
Alignment explanation
Indices: 54259832--54259880 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
54259822 TGTTTTCTCC
*
54259832 TTATTTTGCTACCATTTCATTA
1 TTATTTTACTACCATTTCATTA
* * **
54259854 TTATGTTACTACTATTTTGTTA
1 TTATTTTACTACCATTTCATTA
54259876 TTATT
1 TTATT
54259881 GTTTGGATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.59
Consensus pattern (22 bp):
TTATTTTACTACCATTTCATTA
Found at i:54262573 original size:19 final size:20
Alignment explanation
Indices: 54262536--54262574 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54262526 GTAATTTTTG
* *
54262536 GAAAAATTAATTTTGATCAA
1 GAAAAATTAATATTAATCAA
54262556 GAAAAATTAA-ATTAATCAA
1 GAAAAATTAATATTAATCAA
54262575 ATCAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (20 bp):
GAAAAATTAATATTAATCAA
Found at i:54263076 original size:20 final size:20
Alignment explanation
Indices: 54263047--54263085 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54263037 ATAATATTTT
*
54263047 ATTATTTTAATACTAAATTG
1 ATTATATTAATACTAAATTG
*
54263067 ATTATATTAATATTAAATT
1 ATTATATTAATACTAAATT
54263086 AAATTTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTATATTAATACTAAATTG
Found at i:54266139 original size:20 final size:20
Alignment explanation
Indices: 54266101--54266140 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54266091 TCTTTCTTTC
*
54266101 TTCTTTTATTTACTTAATTA
1 TTCTTTTATTTACTAAATTA
*
54266121 TTCTTTTATTTGCTAAATTA
1 TTCTTTTATTTACTAAATTA
54266141 CTACTTTGGC
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:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (20 bp):
TTCTTTTATTTACTAAATTA
Found at i:54268439 original size:13 final size:12
Alignment explanation
Indices: 54268416--54268450 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
54268406 ATTATTTGTG
54268416 AAAATATAAAAAT
1 AAAA-ATAAAAAT
54268429 ATAAAATAAAAAT
1 A-AAAATAAAAAT
54268442 AAAAATAAA
1 AAAAATAAA
54268451 TTTAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 10 0.48
14 3 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:54268442 original size:6 final size:6
Alignment explanation
Indices: 54268416--54268450 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
54268406 ATTATTTGTG
54268416 AAAATAT AAAAAT ATAAAAT AAAAAT AAAAAT AAA
1 AAAA-AT AAAAAT A-AAAAT AAAAAT AAAAAT AAA
54268451 TTTAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 17 0.63
7 10 0.37
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:54269763 original size:23 final size:23
Alignment explanation
Indices: 54269737--54269780 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54269727 TAAGCTCCAC
*
54269737 CGATTTCGATCGTCGGCGATCGG
1 CGATTGCGATCGTCGGCGATCGG
* *
54269760 CGATTGGGATCGTTGGCGATC
1 CGATTGCGATCGTCGGCGATC
54269781 AAGCGGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.23, G:0.36, T:0.27
Consensus pattern (23 bp):
CGATTGCGATCGTCGGCGATCGG
Found at i:54275686 original size:14 final size:14
Alignment explanation
Indices: 54275660--54275699 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
54275650 AGTTGTGCCG
54275660 TTTTTATTT-TTTA
1 TTTTTATTTATTTA
54275673 TTTTTATTTATTTA
1 TTTTTATTTATTTA
**
54275687 TTTACATTTATTT
1 TTTTTATTTATTT
54275700 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:54288766 original size:24 final size:24
Alignment explanation
Indices: 54288730--54288780 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
54288720 AAAATCACAT
54288730 TGGATTGAACCTTGAAGATTACAG
1 TGGATTGAACCTTGAAGATTACAG
*
54288754 TGGATTGAGCCTTGAAGATTACAG
1 TGGATTGAACCTTGAAGATTACAG
54288778 TGG
1 TGG
54288781 GGGCAATCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (24 bp):
TGGATTGAACCTTGAAGATTACAG
Found at i:54289201 original size:51 final size:50
Alignment explanation
Indices: 54289125--54289579 Score: 415
Period size: 51 Copynumber: 9.2 Consensus size: 50
54289115 GCATCACAGT
* * *
54289125 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGTAATGGAAC
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTGG-AC
** * * **
54289176 AGATTAAAGCTGAAGGCAGAAAATCTTTTTTCCCTGGCGTTACAGT----
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTGGAC
* * * *
54289222 ATATTAAAGCTGAAGGCAGCGAATCTTTTTTTTCCTTAGCGTTGCAGTAGGAC
1 AGATTAAAGCTGAAGGCAGCGAATC--TTATTTCCCTAGCGTTGTAGT-GGAC
* *
54289275 AGATTAAAGTTGAAGGCAGCGAATCTT-TTTCCCTGGCGTTGTAGT----
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTGGAC
*
54289320 AGATTAAAGCTGAAGGCAGCGAATCTTACTTT-CCTAGCGTCGCT-GTGGAAC
1 AGATTAAAGCTGAAGGCAGCGAATCTTA-TTTCCCTAGCGTTG-TAGTGG-AC
* *
54289371 AGATTAATGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGAC
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGT-GGAC
* * *
54289422 AGATTAAAGTTGAAGGCAGCGAATCTT-TTTCCCTGGCGTTGCAGT----
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTGGAC
* * * *
54289467 AGATTAAAGTTGAAGGCAGCGAATCTTACTTT-CTTAGCATCGCT-GTGGAAC
1 AGATTAAAGCTGAAGGCAGCGAATCTTA-TTTCCCTAGCGTTG-TAGTGG-AC
* * * *
54289518 AGATTAAAGTTGAAGGCAGCGAATCTAATTTCCCTAGTGTTGTAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTGG-AC
54289569 AGATTAAAGCT
1 AGATTAAAGCT
54289580 ACAAGTTACG
Statistics
Matches: 337, Mismatches: 39, Indels: 56
0.78 0.09 0.13
Matches are distributed among these distances:
45 53 0.16
46 40 0.12
47 7 0.02
48 18 0.05
50 39 0.12
51 155 0.46
52 2 0.01
53 23 0.07
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTGGAC
Found at i:54289228 original size:97 final size:97
Alignment explanation
Indices: 54289071--54289579 Score: 475
Period size: 97 Copynumber: 5.2 Consensus size: 97
54289061 CTGGCGTGGC
* ** * *
54289071 AGTGGAACAGATTAAAGCTGAAGGTAGCGAATCTTATTTCATTGGCATCACAGTAGATTAAAGCT
1 AGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTACAGTAGATTAAAGCT
*
54289136 GAAGGCAGCGAATCTTATTTCCTTGGCGTTGT
66 GAAGGCAGCGAATCTTATTTCCTTAGCGTTGT
* ** * *
54289168 AATGGAACAGATTAAAGCTGAAGGCAGAAAATCTTTTTTCCCTGGCGTTACAGTATATTAAAGCT
1 AGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTACAGTAGATTAAAGCT
* *
54289233 GAAGGCAGCGAATCTTTTTTTTCCTTAGCGTTGC
66 GAAGGCAGCGAATC--TTATTTCCTTAGCGTTGT
* **
54289267 AGTAGG-ACAGATTAAAGTTGAAGGCAGCGAATCTT-TTTCCCTGGCGTTGTAGTAGATTAAAGC
1 AGT-GGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTACAGTAGATTAAAGC
*
54289330 TGAAGGCAGCGAATCTTACTTTCC-TAGCGTCGCT
65 TGAAGGCAGCGAATCTTA-TTTCCTTAGCGTTG-T
* * *
54289364 -GTGGAACAGATTAATGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGACAGATTA
1 AGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTACAGT-----AGATTA
* * * *
54289428 AAGTTGAAGGCAGCGAATCTT-TTTCCCTGGCGTTGC
61 AAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGT
* * * * *
54289464 AGT-----AGATTAAAGTTGAAGGCAGCGAATCTTACTTTCTTAGCATCGCTGTGGA-A-CAGAT
1 AGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTA-TTTC----CCTGGC-GT-TACAGTAGAT
* * * *
54289522 TAAAGTTGAAGGCAGCGAATCTAATTTCCCTAGTGTTGT
59 TAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGT
*
54289561 AGTGGAATAGATTAAAGCT
1 AGTGGAACAGATTAAAGCT
54289580 ACAAGTTACG
Statistics
Matches: 342, Mismatches: 43, Indels: 49
0.79 0.10 0.11
Matches are distributed among these distances:
95 2 0.01
96 90 0.26
97 109 0.32
98 40 0.12
99 43 0.13
100 7 0.02
101 12 0.04
102 39 0.11
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (97 bp):
AGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTACAGTAGATTAAAGCT
GAAGGCAGCGAATCTTATTTCCTTAGCGTTGT
Found at i:54289439 original size:147 final size:147
Alignment explanation
Indices: 54289224--54289577 Score: 564
Period size: 147 Copynumber: 2.4 Consensus size: 147
54289214 GTTACAGTAT
* * *
54289224 ATTAAAGCTGAAGGCAGCGAATCTTTTTTTTCCTTAGCGTTGCAGTAGGACAGATTAAAGTTGAA
1 ATTAAAGCTGAAGGCAGCGAATC--TTATTTCCCTAGCGTTGCAGTGGGACAGATTAAAGTTGAA
*
54289289 GGCAGCGAATCTTTTTCCCTGGCGTTGTAGTAGATTAAAGCTGAAGGCAGCGAATCTTACTTTCC
64 GGCAGCGAATCTTTTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCGAATCTTACTTTCC
*
54289354 TAGCGTCGCTGTGGAACAG
129 TAGCATCGCTGTGGAACAG
*
54289373 ATTAATGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGACAGATTAAAGTTGAAGG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGACAGATTAAAGTTGAAGG
* *
54289438 CAGCGAATCTTTTTCCCTGGCGTTGCAGTAGATTAAAGTTGAAGGCAGCGAATCTTACTTTCTTA
66 CAGCGAATCTTTTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCGAATCTTACTTTCCTA
54289503 GCATCGCTGTGGAACAG
131 GCATCGCTGTGGAACAG
* * * * * *
54289520 ATTAAAGTTGAAGGCAGCGAATCTAATTTCCCTAGTGTTGTAGTGGAATAGATTAAAG
1 ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGACAGATTAAAG
54289578 CTACAAGTTA
Statistics
Matches: 190, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
147 168 0.88
149 22 0.12
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (147 bp):
ATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGACAGATTAAAGTTGAAGG
CAGCGAATCTTTTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCGAATCTTACTTTCCTA
GCATCGCTGTGGAACAG
Found at i:54289520 original size:96 final size:97
Alignment explanation
Indices: 54289371--54289552 Score: 269
Period size: 96 Copynumber: 1.9 Consensus size: 97
54289361 GCTGTGGAAC
* * * *
54289371 AGATTAATGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGTGGGACAGATTAAAGTTGAA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCATCGCAGTGGAACAGATTAAAGTTGAA
*
54289436 GGCAGCGAATCT-TTTTCCCTGGCGTTGCAGT
66 GGCAGCGAATCTAATTTCCCTGGCGTTGCAGT
* * *
54289467 AGATTAAAGTTGAAGGCAGCGAATCTTACTTT-CTTAGCATCGCTGTGGAACAGATTAAAGTTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTA-TTTCCCTAGCATCGCAGTGGAACAGATTAAAGTTGA
54289531 AGGCAGCGAATCTAATTTCCCT
65 AGGCAGCGAATCTAATTTCCCT
54289553 AGTGTTGTAG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
96 66 0.87
97 10 0.13
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (97 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCATCGCAGTGGAACAGATTAAAGTTGAA
GGCAGCGAATCTAATTTCCCTGGCGTTGCAGT
Found at i:54290362 original size:14 final size:15
Alignment explanation
Indices: 54290338--54290374 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54290328 GTGCCGTTTT
54290338 TATTT-TTTATTT-C
1 TATTTATTTATTTAC
54290351 TATTTATTTATTTAC
1 TATTTATTTATTTAC
54290366 -ATTTATTTA
1 TATTTATTTA
54290375 AAAAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 16 0.73
15 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTATTTATTTAC
Found at i:54294704 original size:47 final size:47
Alignment explanation
Indices: 54294632--54294723 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
54294622 CACAAAAGAC
* *
54294632 AAAAAAAAGGAAGTAATGTGAAAGCAACCACAACCAAGAAAAGATTA
1 AAAAAAAAGGAAGCAACGTGAAAGCAACCACAACCAAGAAAAGATTA
* * *
54294679 AAAAAAAAGGAAGCAACGTGGAAGCAACCACAATCAAGACAAGAT
1 AAAAAAAAGGAAGCAACGTGAAAGCAACCACAACCAAGAAAAGAT
54294724 GTCATCATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.58, C:0.15, G:0.18, T:0.09
Consensus pattern (47 bp):
AAAAAAAAGGAAGCAACGTGAAAGCAACCACAACCAAGAAAAGATTA
Found at i:54296131 original size:71 final size:71
Alignment explanation
Indices: 54296014--54296157 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
54296004 GGTGAATGTT
** * *
54296014 TAACCATGGCGAATAGCATTTCTAAGTGGACTTTAACATCGAACGCATGCCTTCTTCCTTAACCT
1 TAACCATGGCGAATAGCATTTCTAAGCAGACTCTAACATCGAACGCATACCTTCTTCCTTAACCT
54296079 CGGGTG
66 CGGGTG
* * * *
54296085 TAACCATGGCGGATAGCATTTTTAGGCAGACTCTAACATCGGACGCATACCTTCTTCCTTAACCT
1 TAACCATGGCGAATAGCATTTCTAAGCAGACTCTAACATCGAACGCATACCTTCTTCCTTAACCT
*
54296150 TGGGTG
66 CGGGTG
54296156 TA
1 TA
54296158 TACTTCCATC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (71 bp):
TAACCATGGCGAATAGCATTTCTAAGCAGACTCTAACATCGAACGCATACCTTCTTCCTTAACCT
CGGGTG
Found at i:54296467 original size:48 final size:48
Alignment explanation
Indices: 54296393--54296531 Score: 208
Period size: 48 Copynumber: 2.9 Consensus size: 48
54296383 ATCAGCAATT
* *
54296393 ATACATAACATATAACACATATAGAGTTCTACTAACTTACTCTTTTTG
1 ATACATATCATATATCACATATAGAGTTCTACTAACTTACTCTTTTTG
* * *
54296441 ATACATATCATATATCACATACAGAGTCCTATTAACTTACTCTTTTTG
1 ATACATATCATATATCACATATAGAGTTCTACTAACTTACTCTTTTTG
*
54296489 ATACATATCATATATCACATATAGAG-TCATACTAACTTGCTCT
1 ATACATATCATATATCACATATAGAGTTC-TACTAACTTACTCT
54296532 ATTCAAATTC
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 1 0.01
48 80 0.99
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.37
Consensus pattern (48 bp):
ATACATATCATATATCACATATAGAGTTCTACTAACTTACTCTTTTTG
Found at i:54296863 original size:49 final size:48
Alignment explanation
Indices: 54296783--54296906 Score: 126
Period size: 49 Copynumber: 2.5 Consensus size: 48
54296773 GGCTATCAAC
* * * * *
54296783 CTAGTTAACAACTAACATATCC-TACTAGTGGCCCAAT-AGACATGCCAAT
1 CTAGTTAGCAACTAACAT-GCCTTACCAGTGGCCC-ATCACAC-TACCAAT
* *
54296832 CTGGTTAGCAACTAACATGCCTTACCAGTGGCCCATCACATCTACCATT
1 CTAGTTAGCAACTAACATGCCTTACCAGTGGCCCATCACA-CTACCAAT
*
54296881 CTAGTTTGCAACTAACATGCCTTACC
1 CTAGTTAGCAACTAACATGCCTTACC
54296907 GGTGACTCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
48 4 0.06
49 58 0.92
50 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.27
Consensus pattern (48 bp):
CTAGTTAGCAACTAACATGCCTTACCAGTGGCCCATCACACTACCAAT
Found at i:54310609 original size:30 final size:33
Alignment explanation
Indices: 54310573--54310647 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 33
54310563 AACAATAGGC
*
54310573 TTTTTATATATTTT-TAATTGTATATA-TAT-A-
1 TTTTTATATATTTTATAATT-TATAAATTATAAT
54310603 TTTTTATAT-TTTTATAATTTATAAATTATAAT
1 TTTTTATATATTTTATAATTTATAAATTATAAT
54310635 TTTTTATATATTT
1 TTTTTATATATTT
54310648 AAAATAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 9 0.23
30 17 0.44
31 1 0.03
32 9 0.23
33 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (33 bp):
TTTTTATATATTTTATAATTTATAAATTATAAT
Found at i:54310618 original size:20 final size:19
Alignment explanation
Indices: 54310573--54310618 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
54310563 AACAATAGGC
54310573 TTTT-TATATATTTTTAAT
1 TTTTATATATATTTTTAAT
*
54310591 TGTATATATATATTTTTATAT
1 T-TTTATATATATTTTTA-AT
54310612 TTTTATA
1 TTTTATA
54310619 ATTTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.04
19 2 0.09
20 17 0.74
21 3 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATATATATTTTTAAT
Found at i:54310652 original size:24 final size:24
Alignment explanation
Indices: 54310611--54310657 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54310601 TATTTTTATA
*
54310611 TTTTTATAATTTATAAATTATAAT
1 TTTTTATAATTTATAAATAATAAT
54310635 TTTTTATATATTTA-AAATAATAA
1 TTTTTATA-ATTTATAAATAATAA
54310658 CCTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTATAATTTATAAATAATAAT
Found at i:54314516 original size:22 final size:19
Alignment explanation
Indices: 54314476--54314516 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
54314466 TTAATTAAGA
54314476 AATTAATTAAATTTATTTT
1 AATTAATTAAATTTATTTT
54314495 AATTAATATATAATATTATTTT
1 AATTAAT-TA-AAT-TTATTTT
54314517 TGGGAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 3 0.16
22 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTAATTAAATTTATTTT
Found at i:54330973 original size:18 final size:18
Alignment explanation
Indices: 54330950--54330984 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54330940 TCAATTTTTA
54330950 AGTAAAGTATTATATTTG
1 AGTAAAGTATTATATTTG
* *
54330968 AGTAAATTATTCTATTT
1 AGTAAAGTATTATATTT
54330985 CTATTTACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
AGTAAAGTATTATATTTG
Found at i:54344317 original size:14 final size:14
Alignment explanation
Indices: 54344298--54344337 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54344288 TTGTTTGCCA
54344298 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
54344312 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
54344326 GGAAAATGTTTT
1 GTAAAATGTTTT
54344338 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:54344346 original size:20 final size:20
Alignment explanation
Indices: 54344321--54344360 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54344311 CGTAAAATGA
*
54344321 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
54344341 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
54344361 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:54344350 original size:34 final size:35
Alignment explanation
Indices: 54344306--54344372 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
54344296 CAGTAAAATG
*
54344306 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
54344340 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
54344373 CTGGTGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:54344376 original size:14 final size:15
Alignment explanation
Indices: 54344300--54344376 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
54344290 GTTTGCCAGT
* *
54344300 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
54344314 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
54344328 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
54344348 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
54344363 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
54344377 TGTTTAGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:54344437 original size:32 final size:32
Alignment explanation
Indices: 54344351--54344437 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
54344341 TTTCTGTAAA
* *
54344351 ATGATTTACTGGAAAATATTTTCTGGTGTTTAG
1 ATGATTT-CTTGAAAATATTTTCTGCTGTTTAG
* *
54344384 ATGA-ATCTGTGTAAAATATTTTCTGCTGTTTGG
1 ATGATTTCT-TG-AAAATATTTTCTGCTGTTTAG
54344417 CA-GATTTCTTGAAAATATTTT
1 -ATGATTTCTTGAAAATATTTT
54344438 TCGGAAAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
31 2 0.04
32 12 0.27
33 27 0.60
34 4 0.09
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (32 bp):
ATGATTTCTTGAAAATATTTTCTGCTGTTTAG
Found at i:54346565 original size:25 final size:25
Alignment explanation
Indices: 54346525--54346575 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54346515 GTTTTCGATT
*
54346525 TTGTATTTCATTTATTATTGGTGTA
1 TTGTATTTCATATATTATTGGTGTA
* *
54346550 TTGTATTTGATATATTTTTGGTGTA
1 TTGTATTTCATATATTATTGGTGTA
54346575 T
1 T
54346576 AAAGTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.02, G:0.18, T:0.61
Consensus pattern (25 bp):
TTGTATTTCATATATTATTGGTGTA
Found at i:54359405 original size:71 final size:72
Alignment explanation
Indices: 54359253--54359476 Score: 292
Period size: 72 Copynumber: 3.1 Consensus size: 72
54359243 AACTCTTCTC
* * * *
54359253 CCAAAAATACTAAACTGTTTTATTCACACACAAAA-AATATTATAAAAATAAAAATGTTATTTTA
1 CCAAAAATACTAAATTGTTTTATTCACA-A-AAAATATTATTATAAAAATAAAATTATTATTTTA
54359317 TTATACATA
64 TTATACATA
* * *
54359326 CCAAAAATAATAAATTGCTTTATTCACAAAAAATATTATTATAAAAATAAAATTATT-TTTTGTT
1 CCAAAAATACTAAATTGTTTTATTCACAAAAAATATTATTATAAAAATAAAATTATTATTTTATT
54359390 ATACATA
66 ATACATA
* *
54359397 CCACAAATACTAAATTGTTTTATT-AAAAAAACATTATTATTATAAAAATAAAATTATTATTTTA
1 CCAAAAATACTAAATTGTTTTATTCACAAAAA-A-TATTATTATAAAAATAAAATTATTATTTTA
*
54359461 CTATACATA
64 TTATACATA
*
54359470 CAAAAAA
1 CCAAAAA
54359477 ATCAACATAT
Statistics
Matches: 132, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
70 6 0.05
71 39 0.30
72 45 0.34
73 42 0.32
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (72 bp):
CCAAAAATACTAAATTGTTTTATTCACAAAAAATATTATTATAAAAATAAAATTATTATTTTATT
ATACATA
Found at i:54359444 original size:20 final size:20
Alignment explanation
Indices: 54359420--54359457 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54359410 ATTGTTTTAT
*
54359420 TAAAAA-AACATTATTATTA
1 TAAAAATAAAATTATTATTA
54359439 TAAAAATAAAATTATTATT
1 TAAAAATAAAATTATTATT
54359458 TTACTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAATAAAATTATTATTA
Found at i:54360395 original size:21 final size:22
Alignment explanation
Indices: 54360351--54360409 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
54360341 TTTTATTTGA
*
54360351 AAATAA-AAAGTACATTTGAATT
1 AAATAATAAAGT-TATTTGAATT
54360373 AAATAATAAAGTTATTT-AATT
1 AAATAATAAAGTTATTTGAATT
*
54360394 AAA-AATTAAAGCTATT
1 AAATAA-TAAAGTTATT
54360410 CTGTATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 10 0.30
23 5 0.15
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATAATAAAGTTATTTGAATT
Found at i:54362961 original size:18 final size:17
Alignment explanation
Indices: 54362940--54362992 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
54362930 TGAATCACTG
54362940 AATTTTTAAAATATATCA
1 AATTTTTAAAATATAT-A
*
54362958 AATTTTTGAAGAATACATA
1 AATTTTT-AA-AATATATA
* *
54362977 AATTTATAATATATAT
1 AATTTTTAAAATATAT
54362993 TTTCATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 9 0.31
20 6 0.21
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (17 bp):
AATTTTTAAAATATATA
Found at i:54362979 original size:19 final size:18
Alignment explanation
Indices: 54362940--54362981 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
54362930 TGAATCACTG
*
54362940 AATTTTTAAAATATATCA
1 AATTTTTAAAATACATCA
54362958 AATTTTTGAAGAATACAT-A
1 AATTTTT-AA-AATACATCA
54362977 AATTT
1 AATTT
54362982 ATAATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AATTTTTAAAATACATCA
Found at i:54367489 original size:12 final size:12
Alignment explanation
Indices: 54367474--54367507 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54367464 TTGATAAAAA
*
54367474 AATAATACTACT
1 AATAATAATACT
*
54367486 AATAATAATAGT
1 AATAATAATACT
54367498 AATAATAATA
1 AATAATAATA
54367508 ATATTAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAATAATACT
Found at i:54367494 original size:15 final size:15
Alignment explanation
Indices: 54367474--54367510 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
54367464 TTGATAAAAA
*
54367474 AATAATACTACTAAT
1 AATAATACTAATAAT
*
54367489 AATAATAGTAATAAT
1 AATAATACTAATAAT
54367504 AATAATA
1 AATAATA
54367511 TTAAACTGAA
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:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (15 bp):
AATAATACTAATAAT
Found at i:54368214 original size:78 final size:78
Alignment explanation
Indices: 54368085--54368241 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
54368075 AAAAAGAAAC
54368085 GAAAAGAGAGAAAGAACTAAAAAAGAACACCTTCTTTCAGAAATTTTTTGATTTTTTGTCTATTG
1 GAAAAGAGAGAAAGAACTAAAAAAGAACACCTTCTTTCAGAAATTTTTTGATTTTTTGTCTATTG
54368150 ATTCTGCTTCAGT
66 ATTCTGCTTCAGT
54368163 GAAAAGAGAGAAAGAACTAAAAAAGAACACCTTCTTTCAGAAATTTTTTGATTTTTTGTCTATTG
1 GAAAAGAGAGAAAGAACTAAAAAAGAACACCTTCTTTCAGAAATTTTTTGATTTTTTGTCTATTG
54368228 ATTCTGCTTCAGT
66 ATTCTGCTTCAGT
54368241 G
1 G
54368242 TTTTTACATT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (78 bp):
GAAAAGAGAGAAAGAACTAAAAAAGAACACCTTCTTTCAGAAATTTTTTGATTTTTTGTCTATTG
ATTCTGCTTCAGT
Found at i:54368560 original size:25 final size:27
Alignment explanation
Indices: 54368529--54368581 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
54368519 TGGGGAACAC
* *
54368529 TTTGGGCT-GTGTT-GGGTTTGGGTAT
1 TTTGGGCTAGAGTTCGGGTTTAGGTAT
54368554 TTTGGGCTAGAGTTCGGGTTTAGGTAT
1 TTTGGGCTAGAGTTCGGGTTTAGGTAT
54368581 T
1 T
54368582 GTATTGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 4 0.17
27 12 0.50
ACGTcount: A:0.09, C:0.06, G:0.40, T:0.45
Consensus pattern (27 bp):
TTTGGGCTAGAGTTCGGGTTTAGGTAT
Found at i:54369508 original size:40 final size:40
Alignment explanation
Indices: 54369464--54369543 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
54369454 AAGTAAGCTA
54369464 GTCGACAACTTTAATTCATATATATAATTCAAACTTAAAT
1 GTCGACAACTTTAATTCATATATATAATTCAAACTTAAAT
54369504 GTCGACAACTTTAATTCATATATATAATTCAAACTTAAAT
1 GTCGACAACTTTAATTCATATATATAATTCAAACTTAAAT
54369544 AACATTTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (40 bp):
GTCGACAACTTTAATTCATATATATAATTCAAACTTAAAT
Found at i:54373492 original size:30 final size:30
Alignment explanation
Indices: 54373456--54373517 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
54373446 AAAAAAAAAA
54373456 AGACAAAGCATTCAATTAAGAAATCTAACC
1 AGACAAAGCATTCAATTAAGAAATCTAACC
54373486 AGACAAAGCATTCAATTAAGAAATCTAACC
1 AGACAAAGCATTCAATTAAGAAATCTAACC
54373516 AG
1 AG
54373518 CAGTGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.19
Consensus pattern (30 bp):
AGACAAAGCATTCAATTAAGAAATCTAACC
Found at i:54379156 original size:30 final size:31
Alignment explanation
Indices: 54379121--54379179 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
54379111 AAAACTTCAA
* *
54379121 AATTTGAAAACTACAGGTACT-AAATTGACC
1 AATTTGAAAACTAAAGGGACTAAAATTGACC
*
54379151 AATTTGAAAAGTAAAGGGACTAAAATTGA
1 AATTTGAAAACTAAAGGGACTAAAATTGA
54379180 GCAAATTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.25
Consensus pattern (31 bp):
AATTTGAAAACTAAAGGGACTAAAATTGACC
Found at i:54385548 original size:41 final size:38
Alignment explanation
Indices: 54385497--54385583 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 38
54385487 TATAGTTTAG
* * *
54385497 ATTAGAATTTTGTATGAATATTTTAACTTTTTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAA---TGTTGTATGAAT
*
54385538 ATTATAATTTTTTATGAATATTGTAATGTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
*
54385576 ATTGTAAT
1 ATTATAAT
54385584 ATTAAATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 18 0.44
41 23 0.56
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (38 bp):
ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
Found at i:54385553 original size:19 final size:19
Alignment explanation
Indices: 54385497--54385583 Score: 93
Period size: 19 Copynumber: 4.4 Consensus size: 19
54385487 TATAGTTTAG
*
54385497 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTGTATGAAT
*
54385516 ATTTTAACTTTTTTGTATGAAT
1 ATTATAA---TTTTGTATGAAT
*
54385538 ATTATAATTTTTTATGAAT
1 ATTATAATTTTGTATGAAT
* *
54385557 ATTGTAATGTTGTATGAAT
1 ATTATAATTTTGTATGAAT
*
54385576 ATTGTAAT
1 ATTATAAT
54385584 ATTAAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 40 0.69
22 18 0.31
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (19 bp):
ATTATAATTTTGTATGAAT
Found at i:54385774 original size:28 final size:27
Alignment explanation
Indices: 54385691--54385787 Score: 83
Period size: 27 Copynumber: 3.5 Consensus size: 27
54385681 AATTTTATTA
*
54385691 TTGTAATGAATATTG-AATATTTATAATT
1 TTGT-ATGAATATTGTAATA-TTATAGTT
* * *
54385719 TTGTATGATTATATT-T-TTATAATTGTTT
1 TTGTATGA--ATATTGTAATATTATAG-TT
54385747 TTGTATGAATATTGTAATATTATAGTT
1 TTGTATGAATATTGTAATATTATAGTT
*
54385774 TTGTATGAACATTG
1 TTGTATGAATATTG
54385788 CAATTTTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
26 5 0.09
27 23 0.42
28 22 0.40
29 5 0.09
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (27 bp):
TTGTATGAATATTGTAATATTATAGTT
Found at i:54385796 original size:21 final size:19
Alignment explanation
Indices: 54385772--54385822 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
54385762 AATATTATAG
54385772 TTTTGTATGAACATTGCAA
1 TTTTGTATGAACATTGCAA
* *
54385791 TTTTTTGTATGAATATTGTAA
1 --TTTTGTATGAACATTGCAA
54385812 TTTTGTATGAA
1 TTTTGTATGAA
54385823 TATATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.39
21 17 0.61
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTTGTATGAACATTGCAA
Found at i:54385796 original size:48 final size:47
Alignment explanation
Indices: 54385744--54385920 Score: 180
Period size: 48 Copynumber: 3.9 Consensus size: 47
54385734 TTTATAATTG
*
54385744 TTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAACATTGCAAT
1 TTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGC-AT
* *
54385792 TTTTTGTATGAATATTGTAAT-TT-T-G-TATGAAT-ATATATT---T
1 TTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA-ATATTGCAT
*
54385832 TTTTTGT-TGAAT-TTGTAATATTATAATTTTGTATGAATA-TGCAGTT
1 TTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCA--T
* *
54385878 TTTTTGTATGAATATTGTAATATTGTA-ATTTGTATGAATATTG
1 TTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
54385921 TAAGGTGGGG
Statistics
Matches: 107, Mismatches: 8, Indels: 28
0.75 0.06 0.20
Matches are distributed among these distances:
38 7 0.07
39 7 0.07
40 9 0.08
41 1 0.01
42 8 0.07
43 2 0.02
44 9 0.08
45 1 0.01
46 9 0.08
47 19 0.18
48 35 0.33
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.54
Consensus pattern (47 bp):
TTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCAT
Found at i:54385817 original size:19 final size:19
Alignment explanation
Indices: 54385762--54385825 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
54385752 TGAATATTGT
* *
54385762 AATATTATAGTTTTGTATG
1 AATATTGTAATTTTGTATG
* *
54385781 AACATTGCAATTTTTTGTATG
1 AATATTGTAA--TTTTGTATG
54385802 AATATTGTAATTTTGTATG
1 AATATTGTAATTTTGTATG
54385821 AATAT
1 AATAT
54385826 ATATTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 20 0.54
21 17 0.46
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Found at i:54385834 original size:19 final size:18
Alignment explanation
Indices: 54385762--54385834 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 18
54385752 TGAATATTGT
*
54385762 AATATTATAGTTTTGTATG
1 AATATTAT-TTTTTGTATG
*
54385781 AACATTGCAATTTTTTGTATG
1 AATATT---ATTTTTTGTATG
* *
54385802 AATATTGTAATTTTGTATG
1 AATATTAT-TTTTTGTATG
54385821 AATATATATTTTTT
1 AATAT-TATTTTTT
54385835 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.02
19 23 0.55
20 2 0.05
21 14 0.33
22 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
AATATTATTTTTTGTATG
Found at i:54385836 original size:21 final size:21
Alignment explanation
Indices: 54385791--54385892 Score: 68
Period size: 21 Copynumber: 4.8 Consensus size: 21
54385781 AACATTGCAA
54385791 TTTTTTGTATGAATAT-T-GT
1 TTTTTTGTATGAATATATAGT
** *
54385810 AATTTTGTATGAATATATATT
1 TTTTTTGTATGAATATATAGT
*
54385831 TTTTTTGT-TGAATTTGTAATA-T
1 TTTTTTGTATGAA--TAT-ATAGT
**
54385853 TATAATTTTGTATGAATATGCAGT
1 T-T--TTTTGTATGAATATATAGT
54385877 TTTTTTGTATGAATAT
1 TTTTTTGTATGAATAT
54385893 TGTAATATTG
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
19 14 0.22
20 5 0.08
21 21 0.33
22 4 0.06
23 6 0.09
24 4 0.06
25 6 0.09
26 4 0.06
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTTTTGTATGAATATATAGT
Found at i:54385853 original size:86 final size:87
Alignment explanation
Indices: 54385736--54385904 Score: 254
Period size: 86 Copynumber: 2.0 Consensus size: 87
54385726 ATTATATTTT
*
54385736 TATAATTGTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAACATTGCA-ATTTTTTGTA
1 TATAATTGTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAACA-TGCAGATTTTTTGTA
*
54385800 TGAATATTGTAATTTTGTATGAA
65 TGAATATTGTAATATTGTATGAA
* * *
54385823 TATATATTTTTTTTGT-TGAAT-TTGTAATATTATAATTTTGTATGAATATGCAGTTTTTTTGTA
1 TATA-ATTGTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAACATGCAGATTTTTTGTA
54385886 TGAATATTGTAATATTGTA
65 TGAATATTGTAATATTGTA
54385905 ATTTGTATGA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
85 4 0.05
86 52 0.69
87 9 0.12
88 10 0.13
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (87 bp):
TATAATTGTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAACATGCAGATTTTTTGTAT
GAATATTGTAATATTGTATGAA
Found at i:54385864 original size:46 final size:48
Alignment explanation
Indices: 54385802--54385918 Score: 177
Period size: 46 Copynumber: 2.5 Consensus size: 48
54385792 TTTTTGTATG
* *
54385802 AATATTGTAATTTTGTATGAATATATATTTTTTTTGT-TGAAT-TTGT
1 AATATTGTAATTTTGTATGAATATACAGTTTTTTTGTATGAATATTGT
* *
54385848 AATATTATAATTTTGTATGAATATGCAGTTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATACAGTTTTTTTGTATGAATATTGT
54385896 AATATTGTAA-TTTGTATGAATAT
1 AATATTGTAATTTTGTATGAATAT
54385919 TGTAAGGTGG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
46 33 0.52
47 18 0.28
48 13 0.20
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (48 bp):
AATATTGTAATTTTGTATGAATATACAGTTTTTTTGTATGAATATTGT
Found at i:54385868 original size:26 final size:25
Alignment explanation
Indices: 54385802--54385923 Score: 84
Period size: 26 Copynumber: 5.1 Consensus size: 25
54385792 TTTTTGTATG
*
54385802 AATATTGTAATTTTGTATGAA--TAT
1 AATATT-TAATTTTGTATGAATTTGT
*
54385826 -ATATTT-TTTTTGT-TGAATTTGT
1 AATATTTAATTTTGTATGAATTTGT
*
54385848 AATATTATAATTTTGTATGAATATG-
1 AATATT-TAATTTTGTATGAATTTGT
* *
54385873 CA-GTTT--TTTTGTATGAATATTGT
1 AATATTTAATTTTGTATGAAT-TTGT
54385896 AATATTGTAA-TTTGTATGAATATTGT
1 AATATT-TAATTTTGTATGAAT-TTGT
54385922 AA
1 AA
54385924 GGTGGGGATA
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
20 4 0.05
21 18 0.23
22 5 0.06
23 12 0.16
24 5 0.06
25 8 0.10
26 25 0.32
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (25 bp):
AATATTTAATTTTGTATGAATTTGT
Found at i:54386070 original size:60 final size:59
Alignment explanation
Indices: 54385962--54386082 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 59
54385952 TGTATGAATA
* * * * * *
54385962 TTGTAATTATTTTATAATTAATTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
54386021 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAA-TTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
54386081 TT
1 TT
54386083 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 6 0.11
59 13 0.25
60 34 0.64
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.54
Consensus pattern (59 bp):
TTGTAATTATTTTAAAATTAATTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:54386160 original size:37 final size:38
Alignment explanation
Indices: 54386116--54386196 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
54386106 CATATAAAGT
54386116 TTATAAAAAAATTAAAAATC-TTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
54386153 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
54386191 TTATAA
1 TTATAA
54386197 CTGACTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 20 0.48
38 22 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:54386274 original size:15 final size:15
Alignment explanation
Indices: 54386233--54386274 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
54386223 GTTAACTCAT
*
54386233 TTAAGTTTTATATAA
1 TTAAATTTTATATAA
*
54386248 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
54386264 TTAAATTTTAT
1 TTAAATTTTAT
54386275 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:54389425 original size:22 final size:21
Alignment explanation
Indices: 54389379--54389426 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
54389369 TACCTAATTT
* *
54389379 TTCTTCTTTTCCTTCCTTCTT
1 TTCTTCTCTTCCTTCCTTCTA
54389400 TTCTTCTGCTTCCTTCCTTCTA
1 TTCTTCT-CTTCCTTCCTTCTA
54389422 TTCTT
1 TTCTT
54389427 TCGTTTCTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.62
Consensus pattern (21 bp):
TTCTTCTCTTCCTTCCTTCTA
Found at i:54389509 original size:27 final size:26
Alignment explanation
Indices: 54389478--54389542 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
54389468 AAAATAACAG
* *
54389478 CATTGGCGCCTCTCAAAATGGCACTAC
1 CATTGGCGCCTCCCAAAA-GGCACCAC
**
54389505 CATTGGCGCCTCCCAGTAGGCACCAC
1 CATTGGCGCCTCCCAAAAGGCACCAC
54389531 CATT-GCGCCTCC
1 CATTGGCGCCTCC
54389543 TAGGTAGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 8 0.24
26 11 0.32
27 15 0.44
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (26 bp):
CATTGGCGCCTCCCAAAAGGCACCAC
Found at i:54389533 original size:26 final size:26
Alignment explanation
Indices: 54389478--54389551 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
54389468 AAAATAACAG
* ** *
54389478 CATTGGCGCCTCTCAAAATGGCACTAC
1 CATTGGCGCCTCCCAGTA-GGCACCAC
54389505 CATTGGCGCCTCCCAGTAGGCACCAC
1 CATTGGCGCCTCCCAGTAGGCACCAC
*
54389531 CATT-GCGCCTCCTAGGTAGGC
1 CATTGGCGCCTCCCA-GTAGGC
54389552 CCAATACTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.22
26 17 0.41
27 15 0.37
ACGTcount: A:0.20, C:0.36, G:0.23, T:0.20
Consensus pattern (26 bp):
CATTGGCGCCTCCCAGTAGGCACCAC
Found at i:54390452 original size:12 final size:12
Alignment explanation
Indices: 54390437--54390462 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54390427 TATATTTGTT
54390437 AATATGAATATA
1 AATATGAATATA
54390449 AATATGAATATA
1 AATATGAATATA
54390461 AA
1 AA
54390463 ATTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AATATGAATATA
Found at i:54390977 original size:48 final size:48
Alignment explanation
Indices: 54390924--54391021 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
54390914 AAAAATATTT
*
54390924 TTTCAATTAAAATTATTCATTTGTTTTTGTCAAAAACTAAAATACCCA
1 TTTCAATTAAAATTATTCATTTGTTTTTGTAAAAAACTAAAATACCCA
* * *
54390972 TTTCAATTAAAATTATTTATTTGTTTTTGTAAAAAAGTAAATTACCCA
1 TTTCAATTAAAATTATTCATTTGTTTTTGTAAAAAACTAAAATACCCA
54391020 TT
1 TT
54391022 ATTATTCATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (48 bp):
TTTCAATTAAAATTATTCATTTGTTTTTGTAAAAAACTAAAATACCCA
Found at i:54391710 original size:16 final size:16
Alignment explanation
Indices: 54391689--54391748 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
54391679 TTTTCTACTT
*
54391689 TATAATATATATTTTA
1 TATAATATATAATTTA
*
54391705 TATAATATCTAATTTA
1 TATAATATATAATTTA
* *
54391721 TATAAAAT-TAA-ATA
1 TATAATATATAATTTA
54391735 TATAATAATATAAT
1 TATAAT-ATATAAT
54391749 GCAAACATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 24 0.67
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATATATAATTTA
Found at i:54393065 original size:41 final size:39
Alignment explanation
Indices: 54393020--54393189 Score: 112
Period size: 41 Copynumber: 4.2 Consensus size: 39
54393010 TTTAATCAAC
54393020 CGCCGCTAAAGTTAAGGTATTTAGCGGCGATTTCTTTGAAG
1 CGCCGCTAAAGTTAAGGT-TTTAGCGGCG-TTTCTTTGAAG
* * *
54393061 CGCCGCGAATA-TT-TGGTCTTCTAGCGGCGTTT-TTATATAAG
1 CGCCGCTAA-AGTTAAGGT-TT-TAGCGGCGTTTCTT-T-GAAG
* * * *
54393102 CGACGCTAAAGTTAAGATTTTTAGCGGCGATTCTATGATAAG
1 CGCCGCTAAAGTTAAG-GTTTTAGCGGCGTTTCTTTG--AAG
* * * *
54393144 CGCCGCTAATGTTAGGGTTTTAGTGGCGTTTTTGTTGAAG
1 CGCCGCTAAAGTTAAGGTTTTAGCGGCGTTTCT-TTGAAG
*
54393184 TGCCGC
1 CGCCGC
54393190 AAAAAAAAAC
Statistics
Matches: 98, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
39 2 0.02
40 18 0.18
41 54 0.55
42 23 0.23
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (39 bp):
CGCCGCTAAAGTTAAGGTTTTAGCGGCGTTTCTTTGAAG
Found at i:54393151 original size:42 final size:42
Alignment explanation
Indices: 54393020--54393164 Score: 129
Period size: 41 Copynumber: 3.5 Consensus size: 42
54393010 TTTAATCAAC
* *
54393020 CGCCGCTAAAGTTAAGGTATTTAGCGGCGATTTCTTTG--AAG
1 CGCCGCTAAAGTTAAGGTTTTTAGCGGCGA-TTCTATGATAAG
* * * * *
54393061 CGCCGCGAATA-TT-TGGTCTTCTAGCGGCGTTTTTAT-ATAAG
1 CGCCGCTAA-AGTTAAGGT-TTTTAGCGGCGATTCTATGATAAG
* *
54393102 CGACGCTAAAGTTAAGATTTTTAGCGGCGATTCTATGATAAG
1 CGCCGCTAAAGTTAAGGTTTTTAGCGGCGATTCTATGATAAG
* *
54393144 CGCCGCTAATGTTAGGGTTTT
1 CGCCGCTAAAGTTAAGGTTTT
54393165 AGTGGCGTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
40 8 0.10
41 46 0.58
42 25 0.32
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGTTAAGGTTTTTAGCGGCGATTCTATGATAAG
Found at i:54393172 original size:82 final size:80
Alignment explanation
Indices: 54392994--54393176 Score: 217
Period size: 82 Copynumber: 2.2 Consensus size: 80
54392984 TAATGGTCGG
* * *
54392994 GGGTTTTAGTGGCGTTTTTAATCAACCGCCGCTAAAGTTAAGGTATTTAGCGGCGATTTCTTTGA
1 GGGTTTTAGTGGCGTTTTTAATCAACCGACGCTAAAGTTAAGATATTTAGCGGCGATTTCTATGA
54393059 AGCGCCGCGAATATT
66 AGCGCCGCGAATATT
* * * *
54393074 TGGTCTTCTAGCGGCGTTTTTATAT-AAGCGACGCTAAAGTTAAGATTTTTAGCGGCGA-TTCTA
1 GGGT-TT-TAGTGGCGTTTTTA-ATCAACCGACGCTAAAGTTAAGATATTTAGCGGCGATTTCTA
* *
54393137 TGATAAGCGCCGCTAATGTT
63 TG--AAGCGCCGCGAATATT
54393157 AGGGTTTTAGTGGCGTTTTT
1 -GGGTTTTAGTGGCGTTTTT
54393177 GTTGAAGTGC
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
80 3 0.03
81 8 0.09
82 54 0.63
83 18 0.21
84 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (80 bp):
GGGTTTTAGTGGCGTTTTTAATCAACCGACGCTAAAGTTAAGATATTTAGCGGCGATTTCTATGA
AGCGCCGCGAATATT
Found at i:54394204 original size:7 final size:7
Alignment explanation
Indices: 54394192--54394293 Score: 69
Period size: 7 Copynumber: 13.9 Consensus size: 7
54394182 AATATAAGGT
54394192 TTAGGGG
1 TTAGGGG
54394199 TTAGGGG
1 TTAGGGG
*
54394206 TTAGGGAT
1 TTAGGG-G
54394214 TTAGGGG
1 TTAGGGG
*
54394221 TTAGGAG
1 TTAGGGG
*
54394228 TTAAGGG
1 TTAGGGG
**
54394235 TTAGGAAT
1 TTAGG-GG
54394243 TTAGGGG
1 TTAGGGG
* *
54394250 CTAGGAGAT
1 TTAGG-G-G
54394259 TTAGGGG
1 TTAGGGG
*
54394266 TTAGGAG
1 TTAGGGG
*
54394273 TTAGGGAT
1 TTAGGG-G
*
54394281 TTAGGGT
1 TTAGGGG
54394288 TTAGGG
1 TTAGGG
54394294 TTCAATTAAG
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
7 50 0.68
8 19 0.26
9 4 0.05
ACGTcount: A:0.23, C:0.01, G:0.45, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:54394217 original size:15 final size:15
Alignment explanation
Indices: 54394199--54394293 Score: 97
Period size: 15 Copynumber: 6.4 Consensus size: 15
54394189 GGTTTAGGGG
54394199 TTAGGGGTTAGGGAT
1 TTAGGGGTTAGGGAT
*
54394214 TTAGGGGTTA-GGAG
1 TTAGGGGTTAGGGAT
* *
54394228 TTAAGGGTTAGGAAT
1 TTAGGGGTTAGGGAT
*
54394243 TTAGGGGCTAGGAGAT
1 TTAGGGGTTAGG-GAT
*
54394259 TTAGGGGTTA-GGAG
1 TTAGGGGTTAGGGAT
*
54394273 TTAGGGATTTAGGG-T
1 TTAGGG-GTTAGGGAT
54394288 TTAGGG
1 TTAGGG
54394294 TTCAATTAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
14 20 0.31
15 32 0.49
16 13 0.20
ACGTcount: A:0.23, C:0.01, G:0.44, T:0.32
Consensus pattern (15 bp):
TTAGGGGTTAGGGAT
Found at i:54394224 original size:29 final size:29
Alignment explanation
Indices: 54394192--54394293 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
54394182 AATATAAGGT
54394192 TTAGGGGTTAGGGGTTAGGGATTTAGGGG
1 TTAGGGGTTAGGGGTTAGGGATTTAGGGG
* * *
54394221 TTAGGAGTTAAGGGTTAGGAATTTAGGGG
1 TTAGGGGTTAGGGGTTAGGGATTTAGGGG
* * * *
54394250 CTAGGAGATTTAGGGGTTA-GGAGTTAGGGAT
1 TTAGG-G-GTTAGGGGTTAGGGATTTAGGG-G
*
54394281 TTAGGGTTTAGGG
1 TTAGGGGTTAGGG
54394294 TTCAATTAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 37 0.63
30 9 0.15
31 13 0.22
ACGTcount: A:0.23, C:0.01, G:0.45, T:0.31
Consensus pattern (29 bp):
TTAGGGGTTAGGGGTTAGGGATTTAGGGG
Found at i:54398046 original size:11 final size:11
Alignment explanation
Indices: 54398026--54398058 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
54398016 ATTGATTGAC
*
54398026 TGTCAGTGAAT
1 TGTCAATGAAT
54398037 TGTCAATGAA-
1 TGTCAATGAAT
54398047 TGTCAATGAAT
1 TGTCAATGAAT
54398058 T
1 T
54398059 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (11 bp):
TGTCAATGAAT
Found at i:54398139 original size:13 final size:13
Alignment explanation
Indices: 54398093--54398184 Score: 91
Period size: 13 Copynumber: 6.9 Consensus size: 13
54398083 TTTAACTTAC
54398093 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
54398106 ATTAATTACTAAAAT
1 ATTACTTA--AATAT
54398121 -TTACTTAAATAT
1 ATTACTTAAATAT
*
54398133 ATTACTTAAATAC
1 ATTACTTAAATAT
54398146 ATTACTTACTAGA-AT
1 ATTACTTA--A-ATAT
54398161 -TTACTTAAATAT
1 ATTACTTAAATAT
54398173 ATTACTTAAATA
1 ATTACTTAAATA
54398185 CATGACTTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
11 1 0.02
12 7 0.11
13 37 0.57
14 13 0.20
15 6 0.09
16 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:54398155 original size:40 final size:38
Alignment explanation
Indices: 54398093--54398328 Score: 230
Period size: 40 Copynumber: 6.1 Consensus size: 38
54398083 TTTAACTTAC
* *
54398093 ATTACTTAAATATATTAATTACTAAAATTTACTTAAATAT
1 ATTACTTAAATACATTACTTACTAAAATTTA--TAAATAT
*
54398133 ATTACTTAAATACATTACTTACTAGAATTTACTTAAATAT
1 ATTACTTAAATACATTACTTACTAAAATTTA--TAAATAT
*
54398173 ATTACTTAAATACATGACTTACTAAAA-TTA-AAGTATAT
1 ATTACTTAAATACATTACTTACTAAAATTTATAA--ATAT
** * *
54398211 ATTACATTACTTACATTACTTACTAAAA--TAT-ATTAC
1 ATTAC-TTAAATACATTACTTACTAAAATTTATAAATAT
* * * *
54398247 ATTACTTAAATATATTACTTACAAAAATTTATAACTTAC
1 ATTACTTAAATACATTACTTACTAAAATTTATAA-ATAT
* *
54398286 ATTACTTAAATAAATTACATTACTAAAATTTATATATAT
1 ATTACTTAAATACATTAC-TTACTAAAATTTATAAATAT
54398325 ATTA
1 ATTA
54398329 AAATTTATAT
Statistics
Matches: 168, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
35 18 0.11
36 9 0.05
37 3 0.02
38 13 0.08
39 49 0.29
40 76 0.45
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (38 bp):
ATTACTTAAATACATTACTTACTAAAATTTATAAATAT
Found at i:54398192 original size:13 final size:13
Alignment explanation
Indices: 54398090--54398193 Score: 79
Period size: 13 Copynumber: 7.8 Consensus size: 13
54398080 ATTTTTAACT
54398090 TACATTACTTAAA
1 TACATTACTTAAA
* *
54398103 TATATTAATTACTAA
1 TACATTACTTA--AA
54398118 -A-ATTTACTTAAA
1 TACA-TTACTTAAA
*
54398130 TATATTACTTAAA
1 TACATTACTTAAA
*
54398143 TACATTACTT-AC
1 TACATTACTTAAA
*
54398155 TAGAATTTACTTAAA
1 TA-CA-TTACTTAAA
*
54398170 TATATTACTTAAA
1 TACATTACTTAAA
*
54398183 TACATGACTTA
1 TACATTACTTA
54398194 CTAAAATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
12 5 0.07
13 48 0.66
14 15 0.21
15 5 0.07
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (13 bp):
TACATTACTTAAA
Found at i:54398251 original size:18 final size:18
Alignment explanation
Indices: 54398225--54398314 Score: 94
Period size: 18 Copynumber: 4.9 Consensus size: 18
54398215 CATTACTTAC
54398225 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
54398242 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
*
54398260 ATTAC-TTACAAAAATTTAT
1 ATTACATTACTAAAA--TAT
* *
54398279 AACTTACATTACTTAAATAA
1 -A-TTACATTACTAAAATAT
54398299 ATTACATTACTAAAAT
1 ATTACATTACTAAAAT
54398315 TTATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 12 0.20
18 30 0.50
19 4 0.07
20 3 0.05
21 4 0.07
22 7 0.12
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:54398265 original size:31 final size:31
Alignment explanation
Indices: 54398207--54398265 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
54398197 AAATTAAAGT
*
54398207 ATATATTACATTACTTACATTACTTACTAAA
1 ATATATTACATTACTTAAATTACTTACTAAA
54398238 ATATATTACATTACTTAAATATA-TTACT
1 ATATATTACATTACTTAAAT-TACTTACT
54398266 TACAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATATTACATTACTTAAATTACTTACTAAA
Found at i:54398274 original size:17 final size:17
Alignment explanation
Indices: 54398225--54398286 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
54398215 CATTACTTAC
*
54398225 ATTACTTACTAAAATAT
1 ATTACTTACAAAAATAT
**
54398242 ATTACATTACTTAAATAT
1 ATTAC-TTACAAAAATAT
*
54398260 ATTACTTACAAAAATTT
1 ATTACTTACAAAAATAT
*
54398277 ATAACTTACA
1 ATTACTTACA
54398287 TTACTTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 23 0.59
18 16 0.41
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTACTTACAAAAATAT
Found at i:54398524 original size:120 final size:119
Alignment explanation
Indices: 54398337--54398650 Score: 558
Period size: 120 Copynumber: 2.6 Consensus size: 119
54398327 TAAAATTTAT
**
54398337 ATATATGGTATGGA-ATATAACCTATATTTCAATTTTATTGTAATATTTTTTATAATTTTAAAAA
1 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTAATAAATTTTATAATTTTAAAAA
54398401 TAATTGTAAATGTTATTTTTAAATATTAAAACCTATATTTTAATATATCACCCC
66 TAATTGTAAATGTTATTTTTAAATATTAAAACCTATATTTTAATATATCACCCC
54398455 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTCAATAAATTTTATAATTTTAAAA
1 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGT-AATAAATTTTATAATTTTAAAA
54398520 ATAATTGTAAATGTTATTTTTAAATATTAAAACCTATATTTTAATATATCACCCC
65 ATAATTGTAAATGTTATTTTTAAATATTAAAACCTATATTTTAATATATCACCCC
* * *
54398575 ATATATGGTATGGATATATAACCTACATTTCAATTTTATTGAAATGAATTTTATAATTTTAAAAA
1 ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTAATAAATTTTATAATTTTAAAAA
*
54398640 TAATTATAAAT
66 TAATTGTAAAT
54398651 AAGATATAAA
Statistics
Matches: 188, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
118 14 0.07
119 59 0.31
120 115 0.61
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (119 bp):
ATATATGGTATGGATATATAACCTATATTTCAATTTTATTGTAATAAATTTTATAATTTTAAAAA
TAATTGTAAATGTTATTTTTAAATATTAAAACCTATATTTTAATATATCACCCC
Found at i:54398711 original size:9 final size:9
Alignment explanation
Indices: 54398693--54399052 Score: 181
Period size: 9 Copynumber: 42.8 Consensus size: 9
54398683 CTTATATATA
*
54398693 AACTTGCAT
1 AACTTACAT
54398702 AACTTACAT
1 AACTTACAT
*
54398711 AA-TAACAT
1 AACTTACAT
*
54398719 AATATTACAT
1 AA-CTTACAT
54398729 AA--TA-AT
1 AACTTACAT
54398735 AGAC-T-CAT
1 A-ACTTACAT
54398743 AACTTACAT
1 AACTTACAT
*
54398752 AA--TACAA
1 AACTTACAT
54398759 AACTTACAT
1 AACTTACAT
*
54398768 AACTTAAAT
1 AACTTACAT
54398777 AA-TTACAT
1 AACTTACAT
54398785 AA---ACAT
1 AACTTACAT
*
54398791 AACTTATAACT
1 AACTTA-CA-T
* *
54398802 AATTATACAC
1 AACT-TACAT
54398812 AACTTACAT
1 AACTTACAT
54398821 AA--TACAT
1 AACTTACAT
*
54398828 TACTTA-ACT
1 AACTTACA-T
* *
54398837 TACATACAT
1 AACTTACAT
* *
54398846 AGCCTACAT
1 AACTTACAT
54398855 AACTTACAT
1 AACTTACAT
*
54398864 AA--TACAC
1 AACTTACAT
54398871 AACTTACAT
1 AACTTACAT
*
54398880 AACTTAAAT
1 AACTTACAT
54398889 AACTTACAT
1 AACTTACAT
54398898 AA--TACAT
1 AACTTACAT
**
54398905 AACTTTGAT
1 AACTTACAT
*
54398914 AACTAACAT
1 AACTTACAT
* *
54398923 TA--TACAC
1 AACTTACAT
54398930 AACTTACAT
1 AACTTACAT
*
54398939 AA--TACAC
1 AACTTACAT
54398946 AACTTACAT
1 AACTTACAT
*
54398955 AACTTAAAT
1 AACTTACAT
54398964 AACTTACAT
1 AACTTACAT
54398973 AA--TACAT
1 AACTTACAT
**
54398980 AACTTTGAT
1 AACTTACAT
*
54398989 AACTAACAT
1 AACTTACAT
* *
54398998 TA--TACAC
1 AACTTACAT
54399005 AACTTACAT
1 AACTTACAT
*
54399014 AA--TACAC
1 AACTTACAT
54399021 AACTTACAT
1 AACTTACAT
54399030 AGA-TTACAT
1 A-ACTTACAT
54399039 AA--TACAT
1 AACTTACAT
54399046 AACTTAC
1 AACTTAC
54399053 CCGTGCAATT
Statistics
Matches: 265, Mismatches: 50, Indels: 72
0.68 0.13 0.19
Matches are distributed among these distances:
6 9 0.03
7 64 0.24
8 21 0.08
9 151 0.57
10 13 0.05
11 5 0.02
12 2 0.01
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:54398860 original size:22 final size:21
Alignment explanation
Indices: 54398807--54398870 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
54398797 TAACTAATTA
* *
54398807 TACACAACTTACATAATACAT
1 TACATAACTTACATAATACAC
*
54398828 TACTTAACTTACATACATAGC-C
1 TACATAACTTACATA-ATA-CAC
54398850 TACATAACTTACATAATACAC
1 TACATAACTTACATAATACAC
54398871 AACTTACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.03
21 17 0.47
22 17 0.47
23 1 0.03
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.30
Consensus pattern (21 bp):
TACATAACTTACATAATACAC
Found at i:54398868 original size:25 final size:23
Alignment explanation
Indices: 54398740--54399046 Score: 136
Period size: 25 Copynumber: 12.9 Consensus size: 23
54398730 ATAATAGACT
*
54398740 CATAACTTACATAATACAAAACTTA
1 CATAACTTACATAATAC-ATA-TTA
* *
54398765 CATAACTTAAATAATTACATA-AA
1 CATAACTTACATAA-TACATATTA
54398788 CATAACTT--ATAACTA-AT-TATA
1 CATAACTTACATAA-TACATAT-TA
*
54398809 CACAACTTACATAATAC--ATTA
1 CATAACTTACATAATACATATTA
* *
54398830 CTTAACTTAC---ATACATAGCCTA
1 CATAACTTACATAATACATA--TTA
*
54398852 CATAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TA-TTA
* *
54398877 CATAACTTAAATAACTTACATAATA
1 CATAACTTACATAA--TACATATTA
**
54398902 CATAACTTTGATAACTAACAT-TATA
1 CATAACTTACATAA-T-ACATAT-TA
* *
54398927 CACAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TA-TTA
* *
54398952 CATAACTTAAATAACTTACATAATA
1 CATAACTTACATAA--TACATATTA
**
54398977 CATAACTTTGATAACTAACAT-TATA
1 CATAACTTACATAA-T-ACATAT-TA
* *
54399002 CACAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TA-TTA
54399027 CATAGA-TTACATAATACATA
1 CATA-ACTTACATAATACATA
54399047 ACTTACCCGT
Statistics
Matches: 215, Mismatches: 37, Indels: 61
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.02
20 3 0.01
21 24 0.11
22 14 0.07
23 19 0.09
24 5 0.02
25 129 0.60
26 9 0.04
27 8 0.04
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (23 bp):
CATAACTTACATAATACATATTA
Found at i:54398879 original size:34 final size:34
Alignment explanation
Indices: 54398741--54399030 Score: 163
Period size: 34 Copynumber: 7.8 Consensus size: 34
54398731 TAATAGACTC
* *
54398741 ATAACTTACATAATACAAAACTTACATAACTTAA
1 ATAACTTACATAATACACAACTTACATAACCTAA
* * *
54398775 ATAA-TTACATAA-ACATAACTTATAACTAA-TTATA
1 ATAACTTACATAATACACAACTTA-CA-TAACCTA-A
* *
54398809 CACAACTTACATAATACATTACTTAACTTACATACATAGCCTAC
1 -ATAACTTACATAATAC---AC--AACTTACAT--A-A-CCTAA
*
54398853 ATAACTTACATAATACACAACTTACATAACTTAA
1 ATAACTTACATAATACACAACTTACATAACCTAA
* * *
54398887 ATAACTTACATAATACATAACTTTGATAACTAACATTATA
1 ATAACTTACATAATACACAAC-TT-A-CA-TAAC-CTA-A
* *
54398927 CACAACTTACATAATACACAACTTACATAACTTAA
1 -ATAACTTACATAATACACAACTTACATAACCTAA
* * *
54398962 ATAACTTACATAATACATAACTTTGATAACTAACATTATA
1 ATAACTTACATAATACACAAC-TT-A-CA-TAAC-CTA-A
*
54399002 CACAACTTACATAATACACAACTTACATA
1 -ATAACTTACATAATACACAACTTACATA
54399031 GATTACATAA
Statistics
Matches: 205, Mismatches: 21, Indels: 57
0.72 0.07 0.20
Matches are distributed among these distances:
32 9 0.04
33 12 0.06
34 50 0.24
35 9 0.04
36 14 0.07
37 10 0.05
38 19 0.09
39 8 0.04
40 10 0.05
41 39 0.19
42 7 0.03
43 16 0.08
45 2 0.01
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (34 bp):
ATAACTTACATAATACACAACTTACATAACCTAA
Found at i:54398945 original size:75 final size:75
Alignment explanation
Indices: 54398850--54399030 Score: 353
Period size: 75 Copynumber: 2.4 Consensus size: 75
54398840 ATACATAGCC
*
54398850 TACATAACTTACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
1 TACACAACTTACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
54398915 ACTAACATTA
66 ACTAACATTA
54398925 TACACAACTTACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
1 TACACAACTTACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
54398990 ACTAACATTA
66 ACTAACATTA
54399000 TACACAACTTACATAATACACAACTTACATA
1 TACACAACTTACATAATACACAACTTACATA
54399031 GATTACATAA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 105 1.00
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.30
Consensus pattern (75 bp):
TACACAACTTACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
ACTAACATTA
Found at i:54398966 original size:59 final size:56
Alignment explanation
Indices: 54398702--54398968 Score: 203
Period size: 59 Copynumber: 4.7 Consensus size: 56
54398692 AAACTTGCAT
* * * *
54398702 AACTTACATAATAACATAATATTACATAA-TA-ATAGAC-TCATAACTTACATAATACAA
1 AACTTACATAAT-ACATAA-CTTACATAACTACATA-ACTTTATAAC-TACATTATACAC
*
54398759 AACTTACATAACTTAAATAA-TTACATAA--ACATAAC-TTATAACTA-ATTATACAC
1 AACTTACATAA--TACATAACTTACATAACTACATAACTTTATAACTACATTATACAC
* * * ** *
54398812 AACTTACATAATACATTACTTA-ACTTACATACATAGCCTACATAACTTACATAATACAC
1 AACTTACATAATACATAACTTACA-TAAC-TACATA-ACTTTATAAC-TACATTATACAC
*
54398871 AACTTACATAACTTAAATAACTTACATAA-TACATAACTTTGATAACTAACATTATACAC
1 AACTTACATAA--TACATAACTTACATAACTACATAACTTT-ATAACT-ACATTATACAC
* *
54398930 AACTTACATAATACACAACTTACATAACTTAAATAACTT
1 AACTTACATAATACATAACTTACATAAC-TACATAACTT
54398969 ACATAATACA
Statistics
Matches: 170, Mismatches: 21, Indels: 36
0.75 0.09 0.16
Matches are distributed among these distances:
51 6 0.04
52 5 0.03
53 18 0.11
54 2 0.01
55 14 0.08
56 12 0.07
57 30 0.18
58 10 0.06
59 61 0.36
61 11 0.06
62 1 0.01
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (56 bp):
AACTTACATAATACATAACTTACATAACTACATAACTTTATAACTACATTATACAC
Found at i:54399008 original size:16 final size:16
Alignment explanation
Indices: 54398989--54399030 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
54398979 TAACTTTGAT
* *
54398989 AACTAACATTATACAC
1 AACTTACATAATACAC
54399005 AACTTACATAATACAC
1 AACTTACATAATACAC
54399021 AACTTACATA
1 AACTTACATA
54399031 GATTACATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (16 bp):
AACTTACATAATACAC
Found at i:54399029 original size:50 final size:51
Alignment explanation
Indices: 54398850--54399030 Score: 153
Period size: 50 Copynumber: 3.6 Consensus size: 51
54398840 ATACATAGCC
* *
54398850 TACATAACTTACATAA-TACACAACTTACATAACTTAAATAACTTACATAA
1 TACATAACTTACATAACTACACAACTTACATAACTTAAATAACTAACATTA
** * * * *
54398900 TACATAACTTTGATAACTA-AC-ATTATACACAACTTACATAA-TACACAACT-
1 TACATAACTTACATAACTACACAACT-TACATAACTTAAATAACTA-AC-ATTA
* * **
54398950 TACATAACTTAAATAACTTACATAA--TACATAACTTTGATAACTAACATTA
1 TACATAACTTACATAAC-TACACAACTTACATAACTTAAATAACTAACATTA
*
54399000 TACACAACTTACATAA-TACACAACTTACATA
1 TACATAACTTACATAACTACACAACTTACATA
54399031 GATTACATAA
Statistics
Matches: 102, Mismatches: 18, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
48 6 0.06
49 5 0.05
50 82 0.80
51 7 0.07
52 1 0.01
53 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.30
Consensus pattern (51 bp):
TACATAACTTACATAACTACACAACTTACATAACTTAAATAACTAACATTA
Found at i:54399044 original size:41 final size:41
Alignment explanation
Indices: 54398964--54399052 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
54398954 TAACTTAAAT
* ** *
54398964 AACTTACATAATACATAACTTTGATAACTAACATTATACAC
1 AACTTACATAATACACAACTTACATAACTAACATAATACAC
* *
54399005 AACTTACATAATACACAACTTACATAGA-TTACATAATACAT
1 AACTTACATAATACACAACTTACATA-ACTAACATAATACAC
54399046 AACTTAC
1 AACTTAC
54399053 CCGTGCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 40 0.98
42 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.30
Consensus pattern (41 bp):
AACTTACATAATACACAACTTACATAACTAACATAATACAC
Found at i:54404539 original size:66 final size:65
Alignment explanation
Indices: 54404432--54404602 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
54404422 GAGCAAATTA
* * * *
54404432 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
54404496 G
65 G
*
54404497 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
54404562 G
65 G
* * * * * *
54404563 CAGTAGCTTAAAGCAGATGCGGCAGCAAAAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
54404603 CTGCAGCGAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:54404616 original size:21 final size:21
Alignment explanation
Indices: 54404593--54404685 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
54404583 GGCAGCAAAA
*
54404593 GAAGCAGAGGCTGCAGCGAGA
1 GAAGCAGAGGCTGCAGCGAGG
* *
54404614 GAAGTACAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
**
54404635 GAAGCAGAGGCTATAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
*
54404656 GAAGTAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
54404677 GAAGCAGAG
1 GAAGCAGAG
54404686 CAGCGTCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.32, C:0.16, G:0.44, T:0.08
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGCGAGG
Found at i:54404643 original size:42 final size:42
Alignment explanation
Indices: 54404593--54404685 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
54404583 GGCAGCAAAA
*
54404593 GAAGCAGAGGCTGCAGCGAGAGAAGTACAGGCTGCAGCGAGG
1 GAAGCAGAGGCTACAGCGAGAGAAGTACAGGCTGCAGCGAGG
* * *
54404635 GAAGCAGAGGCTATAGCGAGGGAAGTAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTACAGCGAGAGAAGTACAGGCTGCAGCGAGG
54404677 GAAGCAGAG
1 GAAGCAGAG
54404686 CAGCGTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.44, T:0.08
Consensus pattern (42 bp):
GAAGCAGAGGCTACAGCGAGAGAAGTACAGGCTGCAGCGAGG
Found at i:54405258 original size:42 final size:43
Alignment explanation
Indices: 54405141--54405287 Score: 147
Period size: 43 Copynumber: 3.4 Consensus size: 43
54405131 CGTTTGTGGG
* * *
54405141 AAAAGCGCTGCTAAAGACCCTAATCTTTAGCGGCGCTTCTCGC
1 AAAAGCGCCGCTAAAGACCCTAGTCTTTAGCGGCGCTTCTCAC
*
54405184 AAAAACGCCGCTAAAGACCCT-GATCTTTAGCGGCGCTTC-CAC
1 AAAAGCGCCGCTAAAGACCCTAG-TCTTTAGCGGCGCTTCTCAC
* * * * * *
54405226 TAAAGCGCCGCTAAAGATCTTAGTCTTCAGCGGCGTTTGTGC-C
1 AAAAGCGCCGCTAAAGACCCTAGTCTTTAGCGGCGCTTCT-CAC
* *
54405269 AGAAGCGCCGCTATAGACC
1 AAAAGCGCCGCTAAAGACC
54405288 AACACCTTTA
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 32 0.38
43 52 0.61
44 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGACCCTAGTCTTTAGCGGCGCTTCTCAC
Found at i:54406459 original size:39 final size:39
Alignment explanation
Indices: 54406324--54406459 Score: 193
Period size: 39 Copynumber: 3.5 Consensus size: 39
54406314 ATCCACTTTT
* *
54406324 AAGCATATATCACATTACACATATAATCACATAACA-TC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * *
54406362 TAAGCATATATCACAATAATCATATAATTACATAACGTTC
1 -AAGCATATATCACAATACTCATATAATCACATAACATTC
54406402 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
54406441 AAGCATATGTCGCAATACT
1 AAGCATATATCACAATACT
54406460 AAAAAACATG
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 84 0.98
40 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:54412737 original size:21 final size:21
Alignment explanation
Indices: 54412713--54412752 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54412703 TATCGAATAA
*
54412713 CAGATCATACTTATCATATTT
1 CAGATCATACTGATCATATTT
54412734 CAGATCATACTGATCATAT
1 CAGATCATACTGATCATAT
54412753 AACATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
CAGATCATACTGATCATATTT
Found at i:54413617 original size:20 final size:20
Alignment explanation
Indices: 54413581--54413618 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54413571 GGAAAGGGGA
*
54413581 ATGAGGAGAACGTGAGATAC
1 ATGAGGAGAAAGTGAGATAC
54413601 ATGAGAGAGAAAG-GAGAT
1 ATGAG-GAGAAAGTGAGAT
54413619 TTTTGGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.45, C:0.05, G:0.37, T:0.13
Consensus pattern (20 bp):
ATGAGGAGAAAGTGAGATAC
Done.