Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 57 of 109
Found at i:18624760 original size:2 final size:2
Alignment explanation
Indices: 18624702--18624747 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
18624692 TTTAGATGCC
*
18624702 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18624742 TA TA TA
1 TA TA TA
18624748 ACTTTATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18624760 original size:17 final size:19
Alignment explanation
Indices: 18624702--18624747 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
18624692 TTTAGATGCC
*
18624702 TATACATAT-TATA-TATA
1 TATATATATATATATTATA
18624719 TATATATATATATATTATA
1 TATATATATATATATTATA
18624738 TATATATATA
1 TATATATATA
18624748 ACTTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 14 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATATATATATTATA
Found at i:18624760 original size:21 final size:23
Alignment explanation
Indices: 18624702--18624747 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18624692 TTTAGATGCC
*
18624702 TATACATATTATATATATATATA
1 TATATATATTATATATATATATA
18624725 TATATATATTATATATATATATA
1 TATATATATTATATATATATATA
18624748 ACTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATATATTATATATATATATA
Found at i:18628972 original size:51 final size:51
Alignment explanation
Indices: 18628912--18629068 Score: 314
Period size: 51 Copynumber: 3.1 Consensus size: 51
18628902 GGAATCACAA
18628912 GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
1 GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
18628963 GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
1 GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
18629014 GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
1 GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
18629065 GGAA
1 GGAA
18629069 AGAACTCTGT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 106 1.00
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.19
Consensus pattern (51 bp):
GGAAGTATGATGACAAACTTAACGCGATTGTTGACCGAAGGGAAAGATAAG
Found at i:18636002 original size:5 final size:5
Alignment explanation
Indices: 18635984--18636087 Score: 94
Period size: 5 Copynumber: 20.8 Consensus size: 5
18635974 TATTTTTCTT
*
18635984 AAAA- AAAAG AAAAAG AAAAG AAAAG AAAAG AAAAG AAAAA AGAAAG -AAAG
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG
*
18636034 -AAAG AAAAG AAAA- ATAAAA AAAAG AAGAA- AGAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AAAAG AA-AAG A-AAAG AAAAG AAAAG
18636078 AAAAGG AAAA
1 AAAA-G AAAA
18636088 TGAGAGGCCA
Statistics
Matches: 86, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
4 17 0.20
5 52 0.60
6 17 0.20
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:18636031 original size:4 final size:4
Alignment explanation
Indices: 18635995--18636080 Score: 72
Period size: 4 Copynumber: 20.8 Consensus size: 4
18635985 AAAAAAAGAA
18635995 AAAG AAAAG AAAAG AAAAG AAAAG AAA- AAAG AAAG AAAG AAAG AAAAG
1 AAAG -AAAG -AAAG -AAAG -AAAG AAAG AAAG AAAG AAAG AAAG -AAAG
*
18636043 AAA- AATA- AAAA AAAG -AAG AAAG AAAG AAAG AAAAG AAA
1 AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAA
18636081 AGGAAAATGA
Statistics
Matches: 74, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
3 9 0.12
4 38 0.51
5 27 0.36
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:18636034 original size:35 final size:34
Alignment explanation
Indices: 18635984--18636087 Score: 142
Period size: 35 Copynumber: 3.1 Consensus size: 34
18635974 TATTTTTCTT
18635984 AAAAAAAAG-AA-AAAGAAAAGAAAAGAAAAGAAA
1 AAAAAAAAGAAAGAAAG-AAAGAAAAGAAAAGAAA
*
18636017 AGAAAAAAGAAAGAAAGAAAGAAAAGAAAA-ATAA
1 AAAAAAAAGAAAGAAAGAAAGAAAAGAAAAGA-AA
*
18636051 AAAAAAGAAGAAAGAAAGAAAGAAAAGAAAAGGAA
1 AAAAAA-AAGAAAGAAAGAAAGAAAAGAAAAGAAA
18636086 AA
1 AA
18636088 TGAGAGGCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
33 9 0.14
34 22 0.35
35 32 0.51
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (34 bp):
AAAAAAAAGAAAGAAAGAAAGAAAAGAAAAGAAA
Found at i:18637329 original size:44 final size:44
Alignment explanation
Indices: 18637262--18637420 Score: 255
Period size: 44 Copynumber: 3.6 Consensus size: 44
18637252 GAAACTTCAG
18637262 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATCAA
* * *
18637306 TCTTACCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAATCAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATCAA
* *
18637350 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATCAA
* *
18637394 TCCTATCTCCCTGAAGTTACAGCGGAG
1 TCTTATCTCCCTGAAGTTACAGTGGAG
18637421 TGGATTAACA
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 105 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATCAA
Found at i:18637483 original size:40 final size:40
Alignment explanation
Indices: 18637429--18637748 Score: 144
Period size: 40 Copynumber: 7.6 Consensus size: 40
18637419 AGTGGATTAA
* *
18637429 CATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCG
1 CATCCAG-TCTTATCTTCCTGAAGTTGCAGAGAGCAGATCG
* *
18637470 CATCCAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAG-GCAG
1 CATCCAGTCTTATCTTCCTGAAGTTGCAGA-GAGCAGATC-G
* * * * * ** **
18637511 AATAAATCAATCCTATC-TCCTTGAAGTTGCAGCGGAGTGGATTAA
1 CAT---CCAGTCTTATCTTCC-TGAAGTTGCAG-AGAGCAGA-TCG
* * *
18637556 CATCCAGATTTTATCTTTCTGAGGTTGCAGAGAGCAGATCG
1 CATCCAG-TCTTATCTTCCTGAAGTTGCAGAGAGCAGATCG
* *
18637597 CATCCAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACAGA-AG
1 CATCCAGTCTTATCTTCCTGAAGTTGC-A--GAG-AG-CAGATCG
* * * ** * * **
18637641 AAAT-CAATCCTATCCCCCTGAAGTTGCAGTGGAGCGGATTAA
1 -CATCCAGTCTTATCTTCCTGAAGTTGCAG-AGAGCAGA-TCG
* * * *
18637683 CATCCAGATCTTATTTTTCTGAGGTTGTAGAGAGCAGATCG
1 CATCCAG-TCTTATCTTCCTGAAGTTGCAGAGAGCAGATCG
* *
18637724 CATCCAGTCTTATCTCCCTAAAGTT
1 CATCCAGTCTTATCTTCCTGAAGTT
18637749 ACAGTGGAGC
Statistics
Matches: 200, Mismatches: 57, Indels: 45
0.66 0.19 0.15
Matches are distributed among these distances:
40 53 0.26
41 38 0.19
42 17 0.09
43 36 0.18
44 48 0.24
45 8 0.04
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (40 bp):
CATCCAGTCTTATCTTCCTGAAGTTGCAGAGAGCAGATCG
Found at i:18637496 original size:127 final size:127
Alignment explanation
Indices: 18637350--18637762 Score: 691
Period size: 127 Copynumber: 3.3 Consensus size: 127
18637340 AAGAAATCAA
* *
18637350 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
18637415 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
66 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
* * * *
18637477 TCTTATCTCCCTGAAGTTGCAGAGGAGCAGGCAGAATAAATCAATCCTATCTCCTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
*
18637542 GCGGAGTGGATTAACATCCAGATTTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
66 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
* *
18637604 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACAGAAGAAATCAATCCTATCCCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* * * *
18637669 GTGGAGCGGATTAACATCCAGATCTTATTTTTCTGAGGTTGTAGAGAGCAGATCGCATCCAG
66 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
* *
18637731 TCTTATCTCCCTAAAGTTACAGTGGAGCAGAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
18637763 TAATGATAGC
Statistics
Matches: 265, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 265 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (127 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAG
Found at i:18639149 original size:2 final size:2
Alignment explanation
Indices: 18639108--18639136 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18639098 ATACATATTT
18639108 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18639137 ACTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18650453 original size:34 final size:34
Alignment explanation
Indices: 18650415--18650484 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
18650405 AAATAAGCAG
*
18650415 AAACAAAATTAAATTGAACAAACTTATGTGATAA
1 AAACAAAATTAAATTGAACAAACTGATGTGATAA
18650449 AAACAAAATTAAATTGAACAAACTGATGTGATAA
1 AAACAAAATTAAATTGAACAAACTGATGTGATAA
18650483 AA
1 AA
18650485 TTCTAGCTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (34 bp):
AAACAAAATTAAATTGAACAAACTGATGTGATAA
Found at i:18652155 original size:23 final size:21
Alignment explanation
Indices: 18652129--18652171 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18652119 GGGTTTTGAG
18652129 GTTTTTTCATTATATTTTTTTAA
1 GTTTTTTCA-TA-ATTTTTTTAA
*
18652152 GTTTTTTTATAATTTTTTTA
1 GTTTTTTCATAATTTTTTTA
18652172 TATGTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (21 bp):
GTTTTTTCATAATTTTTTTAA
Found at i:18652545 original size:18 final size:18
Alignment explanation
Indices: 18652519--18652554 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18652509 ATTTTAAAAA
18652519 AAAAGTTGAGAGAGAAAT
1 AAAAGTTGAGAGAGAAAT
* *
18652537 AAAATTTGAGTGAGAAAT
1 AAAAGTTGAGAGAGAAAT
18652555 TAGAAGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (18 bp):
AAAAGTTGAGAGAGAAAT
Found at i:18656060 original size:6 final size:6
Alignment explanation
Indices: 18656049--18656080 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
18656039 TATTTTTGGG
18656049 TAAATA TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TA
18656081 TAATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATA
Found at i:18656747 original size:24 final size:24
Alignment explanation
Indices: 18656720--18656768 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
18656710 AAGTATAAGG
18656720 GATTATAGTTTAGGGTTTAGGGGT
1 GATTATAGTTTAGGGTTTAGGGGT
18656744 GATTATAGTTTAGGGTTTAGGGGT
1 GATTATAGTTTAGGGTTTAGGGGT
18656768 G
1 G
18656769 TTCATGGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (24 bp):
GATTATAGTTTAGGGTTTAGGGGT
Found at i:18657482 original size:46 final size:44
Alignment explanation
Indices: 18657381--18657655 Score: 278
Period size: 36 Copynumber: 6.7 Consensus size: 44
18657371 TACGTATAAT
*
18657381 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTA
18657423 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTA
1 -CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTA
*
18657469 CCACTTATCACTTTCTCACTTGATCAGATAA--GTA--TA-G---
1 -CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTA
*
18657506 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TA----A
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTA
*
18657542 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCT-A
18657588 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--TA-G---
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTA
*
18657624 CACTTATCACTTTTTCACTTGATCAGATAAGT
1 CACTTATCACTTTGTCACTTGATCAGATAAGT
18657656 ATANNNNNNN
Statistics
Matches: 211, Mismatches: 5, Indels: 37
0.83 0.02 0.15
Matches are distributed among these distances:
36 93 0.44
38 3 0.01
40 3 0.01
41 3 0.01
42 2 0.01
43 10 0.05
44 11 0.05
45 20 0.09
46 66 0.31
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTA
Found at i:18657592 original size:82 final size:81
Alignment explanation
Indices: 18657374--18657655 Score: 318
Period size: 82 Copynumber: 3.5 Consensus size: 81
18657364 ATGGTCTTAC
* * *
18657374 GTATAATCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTT
1 GTATAACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTA-CACTTATCACTTT
18657437 GTCACTTGATCAGATAA
65 GTCACTTGATCAGATAA
*
18657454 GTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTGATCAGATAA--GTA--TA-G---CACTT
1 --GTA--T-A----ACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTACACTT
*
18657511 ATCACTTTTTCACTTGATCAGATAA
57 ATCACTTTGTCACTTGATCAGATAA
18657536 GTATAA-CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTT
1 GTATAACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AGGCT-ACACTTATCACTT
18657600 TGTCACTTGATCAGATAA
64 TGTCACTTGATCAGATAA
*
18657618 GTAT-AGCACTTATCACTTTTTCACTTGATCAGATAAGT
1 GTATAACCACTTATCACTTTTTCACTTGATCAGATAAGT
18657656 ATANNNNNNN
Statistics
Matches: 174, Mismatches: 6, Indels: 40
0.79 0.03 0.18
Matches are distributed among these distances:
72 29 0.17
73 1 0.01
74 3 0.02
76 1 0.01
77 2 0.01
78 2 0.01
80 3 0.02
81 1 0.01
82 97 0.56
84 1 0.01
85 1 0.01
86 1 0.01
87 2 0.01
89 14 0.08
90 4 0.02
91 12 0.07
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (81 bp):
GTATAACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTACACTTATCACTTTG
TCACTTGATCAGATAA
Found at i:18657596 original size:118 final size:118
Alignment explanation
Indices: 18657424--18657658 Score: 443
Period size: 118 Copynumber: 2.0 Consensus size: 118
18657414 GCTAGGCTAC
*
18657424 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTCACT
18657489 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
* *
18657542 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTCACT
18657607 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATA
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATA
18657659 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (118 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTCACT
TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
Found at i:18660207 original size:11 final size:11
Alignment explanation
Indices: 18660193--18660279 Score: 60
Period size: 11 Copynumber: 8.3 Consensus size: 11
18660183 GAGAAATTTA
18660193 AGAGGAAATTG
1 AGAGGAAATTG
*
18660204 AGAGCAAATTG
1 AGAGGAAATTG
**
18660215 AGATTAAA-T-
1 AGAGGAAATTG
* *
18660224 A-TGG-ATTTG
1 AGAGGAAATTG
18660233 AGA-GAAACTT-
1 AGAGGAAA-TTG
18660243 AGAAGGAAATTG
1 AG-AGGAAATTG
*
18660255 AGAGGAGATTG
1 AGAGGAAATTG
18660266 AGAGGAAATTG
1 AGAGGAAATTG
18660277 AGA
1 AGA
18660280 AAATAATTGA
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.07
11 42 0.74
12 6 0.11
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:18660237 original size:51 final size:51
Alignment explanation
Indices: 18660169--18660268 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
18660159 AAATAATTAA
*
18660169 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAACTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
18660220 AAATATGGATTTGAGAGAAACTTAGAAGGAAATTGAGAGGAGATTGAGA
1 AAATAGGGATTTAAGAGAAACTTAGAAGGAAATTGAGAGCAAATTGAGA
18660269 GGAAATTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAACTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:18680717 original size:21 final size:21
Alignment explanation
Indices: 18680691--18680731 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18680681 GTAAAAAATT
18680691 TTCTTGTTGTATCGAGACATG
1 TTCTTGTTGTATCGAGACATG
* *
18680712 TTCTTGTTGTTTTGAGACAT
1 TTCTTGTTGTATCGAGACAT
18680732 TAAGGTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (21 bp):
TTCTTGTTGTATCGAGACATG
Found at i:18681563 original size:28 final size:28
Alignment explanation
Indices: 18681518--18681622 Score: 135
Period size: 28 Copynumber: 3.9 Consensus size: 28
18681508 GTAACAGTAT
*
18681518 AGTGT-GGCCTT--CCCAATATAGAAAC
1 AGTGTGGGCCTTAGCCCAATACAGAAAC
*
18681543 AGTGTGGGCCTTAGCCCAATACAGAAAT
1 AGTGTGGGCCTTAGCCCAATACAGAAAC
*
18681571 AGTGTGGGCCTTAGACCAATACAGAAAC
1 AGTGTGGGCCTTAGCCCAATACAGAAAC
* * *
18681599 AGTGTGGACCTAAGCCCGATACAG
1 AGTGTGGGCCTTAGCCCAATACAG
18681623 TATCAGTATG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
25 5 0.07
26 6 0.09
28 58 0.84
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGAAAC
Found at i:18681902 original size:32 final size:32
Alignment explanation
Indices: 18681839--18682169 Score: 312
Period size: 32 Copynumber: 10.4 Consensus size: 32
18681829 GAATGACTAC
* * *
18681839 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* **
18681870 AAGCCATCAGTAGCAGTGTTATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
18681902 AAACCATCAGTAACAGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
18681934 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
18681966 CAGCCATCAGTAATAGTGAA-ATGATCGGCACA
1 AAGCCATCAGTAACAGT-AATATGATCGGCACA
* * *
18681998 CA-CTCATCAGTAACTGTAATATGATCAGCACA
1 AAGC-CATCAGTAACAGTAATATGATCGGCACA
* * * *
18682030 AAACTATCAGTAAC-GATACTATGATCGACACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
** * *
18682062 AAGCCATCAGTAATGGTACTATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * * * *
18682094 AAACCATCAATAACGGTACTATGATAGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
18682126 AAGCCATCAATAAC-GATACTATGATCGGCACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
18682158 AAGCCATCAGTA
1 AAGCCATCAGTA
18682170 GCATCGCAGC
Statistics
Matches: 250, Mismatches: 42, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
31 15 0.06
32 232 0.93
33 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:18682011 original size:96 final size:96
Alignment explanation
Indices: 18681859--18682169 Score: 353
Period size: 96 Copynumber: 3.2 Consensus size: 96
18681849 TACAGTAATG
* ** *
18681859 TGATTGGCACAAAGCCATCAGTAGCAGTGTTATGATCGGCACAAAACCATCAGTAACAGTAACAT
1 TGATCGGCACAAAGCCATCAGTAATAGTGATATGATCGGCACAAAACCATCAGTAACAGTAACAT
*
18681924 GATCGGCACAAAGCCATCAGTAGC-AGTGA-TA
66 GATCGGCACAAAGCCATCAGTAACGA-T-ACTA
* * * * *
18681955 TGATCGGCACACAGCCATCAGTAATAGTGAAATGATCGGCAC-ACACTCATCAGTAACTGTAATA
1 TGATCGGCACAAAGCCATCAGTAATAGTGATATGATCGGCACAAAAC-CATCAGTAACAGTAACA
* * *
18682019 TGATCAGCACAAAACTATCAGTAACGATACTA
65 TGATCGGCACAAAGCCATCAGTAACGATACTA
* * * * *
18682051 TGATCGACACAAAGCCATCAGTAATGGT-ACTATGATCGGTACAAAACCATCAATAACGGT-ACT
1 TGATCGGCACAAAGCCATCAGTAATAGTGA-TATGATCGGCACAAAACCATCAGTAACAGTAAC-
* * *
18682114 ATGATAGACACAAAGCCATCAATAACGATACTA
64 ATGATCGGCACAAAGCCATCAGTAACGATACTA
18682147 TGATCGGCACAAAGCCATCAGTA
1 TGATCGGCACAAAGCCATCAGTA
18682170 GCATCGCAGC
Statistics
Matches: 180, Mismatches: 29, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
95 6 0.03
96 170 0.94
97 4 0.02
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (96 bp):
TGATCGGCACAAAGCCATCAGTAATAGTGATATGATCGGCACAAAACCATCAGTAACAGTAACAT
GATCGGCACAAAGCCATCAGTAACGATACTA
Found at i:18682201 original size:26 final size:26
Alignment explanation
Indices: 18682172--18682223 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
18682162 CATCAGTAGC
*
18682172 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGCTACCAGCAACAGT
* *
18682198 ATCGTAGCAAAGCTACCAGTAACAGT
1 ATCGCAGCAAAGCTACCAGCAACAGT
18682224 GATTGTGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (26 bp):
ATCGCAGCAAAGCTACCAGCAACAGT
Found at i:18682346 original size:24 final size:24
Alignment explanation
Indices: 18682314--18682447 Score: 153
Period size: 24 Copynumber: 5.6 Consensus size: 24
18682304 CCATGCACGG
** *
18682314 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATTTAAATCACAGACA
*
18682338 AATCAGTCATTTAAATCACAGAGA
1 AATCAGTCATTTAAATCACAGACA
*
18682362 AATCAGTCATTTAAATCATAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
18682386 AATCAGTCATTTACATCTC-GAACA
1 AATCAGTCATTTAAATCACAG-ACA
* * *
18682410 AATCATTCATTTACATCACAGGCA
1 AATCAGTCATTTAAATCACAGACA
*
18682434 AATCAATCATTTAA
1 AATCAGTCATTTAA
18682448 CCCTGAGGGG
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 92 0.98
25 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:18682522 original size:27 final size:26
Alignment explanation
Indices: 18682465--18682526 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
18682455 GGGTAAAATA
* * *
18682465 GTCATTTTATCCTATAGGGAATTACG
1 GTCATTTTAGCCTAAAGGGAATTAAG
* *
18682491 ATCATTTTAGCCTACAAGGGAGTTAAG
1 GTCATTTTAGCCTA-AAGGGAATTAAG
18682518 GTCATTTTA
1 GTCATTTTA
18682527 CCCTTTTAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (26 bp):
GTCATTTTAGCCTAAAGGGAATTAAG
Found at i:18685859 original size:27 final size:27
Alignment explanation
Indices: 18685828--18685889 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
18685818 AATGTTCTAT
18685828 TTAATTCATTACTAAATAATTTTATTTC
1 TTAATTCATTA-TAAATAATTTTATTTC
* * *
18685856 -TAATTTAATTATCAATATTTTTATTTC
1 TTAA-TTCATTATAAATAATTTTATTTC
18685883 TTAATTC
1 TTAATTC
18685890 CATAATTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAATTCATTATAAATAATTTTATTTC
Found at i:18688188 original size:9 final size:9
Alignment explanation
Indices: 18688174--18688210 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18688164 TATAGTTTGA
18688174 TATTCAAAT
1 TATTCAAAT
18688183 TATTCAAAT
1 TATTCAAAT
* *
18688192 TATTCGAGT
1 TATTCAAAT
18688201 TATTCAAAT
1 TATTCAAAT
18688210 T
1 T
18688211 TGAAAACTCA
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:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (9 bp):
TATTCAAAT
Found at i:18688290 original size:8 final size:9
Alignment explanation
Indices: 18688263--18688294 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
18688253 TCAAGTTGAT
18688263 TCGATTAAC
1 TCGATTAAC
18688272 TCGATTAAC
1 TCGATTAAC
18688281 TCGA-TAAC
1 TCGATTAAC
18688289 TCGATT
1 TCGATT
18688295 CATTTAACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (9 bp):
TCGATTAAC
Found at i:18693721 original size:4 final size:4
Alignment explanation
Indices: 18693712--18693740 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
18693702 AAAATAAGGA
18693712 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
18693741 TTAAAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:18693776 original size:18 final size:16
Alignment explanation
Indices: 18693696--18693777 Score: 51
Period size: 16 Copynumber: 4.8 Consensus size: 16
18693686 ATTTACTTCT
* *
18693696 AAAACAAAAATAA-GG
1 AAAATAAAAATAATAG
*
18693711 AAAATAAATAAATAAATAA
1 AAAAT-AA-AAAT-AATAG
*
18693730 ATAAATAAATATTAA-AG
1 A-AAATAAA-AATAATAG
18693747 AAAATAAAAATAATAG
1 AAAATAAAAATAATAG
18693763 AATAATAAAGAATAA
1 AA-AATAAA-AATAA
18693778 AATAATAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
15 8 0.15
16 13 0.25
17 12 0.23
18 10 0.19
19 5 0.10
20 4 0.08
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAATAAAAATAATAG
Found at i:18693781 original size:15 final size:15
Alignment explanation
Indices: 18693747--18693784 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18693737 AATATTAAAG
*
18693747 AAAATAA-AAATAAT
1 AAAATAATAAAGAAT
*
18693761 AGAATAATAAAGAAT
1 AAAATAATAAAGAAT
18693776 AAAATAATA
1 AAAATAATA
18693785 GTAAAAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATAATAAAGAAT
Found at i:18693784 original size:18 final size:17
Alignment explanation
Indices: 18693720--18693790 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 17
18693710 GAAAATAAAT
18693720 AAATAAATA-AATAAATAA
1 AAATAAA-AGAAT-AATAA
* *
18693738 ATATTAAAGAA-AATAA
1 AAATAAAAGAATAATAA
*
18693754 AAATAATAGAATAATAA
1 AAATAAAAGAATAATAA
* *
18693771 AGAATAAAATAATAGTAA
1 A-AATAAAAGAATAATAA
18693789 AA
1 AA
18693791 GAAGGTAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
16 13 0.31
17 8 0.19
18 21 0.50
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.23
Consensus pattern (17 bp):
AAATAAAAGAATAATAA
Found at i:18700928 original size:20 final size:20
Alignment explanation
Indices: 18700903--18700945 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18700893 AGGAACTATC
18700903 CTAGAATTAGGAGATTACAA
1 CTAGAATTAGGAGATTACAA
* *
18700923 CTAGAATTAGGGGGTTACAA
1 CTAGAATTAGGAGATTACAA
18700943 CTA
1 CTA
18700946 ATTACTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.26
Consensus pattern (20 bp):
CTAGAATTAGGAGATTACAA
Found at i:18703481 original size:20 final size:21
Alignment explanation
Indices: 18703430--18703485 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
18703420 AATTAATTAC
*
18703430 TTAAATTAA-TATTTTTTAAT
1 TTAAATTAATTATTATTTAAT
18703450 TTGAAATTAATTATTATTT-AT
1 TT-AAATTAATTATTATTTAAT
*
18703471 TTAAATAAATTATTA
1 TTAAATTAATTATTA
18703486 CAAATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
21 11 0.34
22 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAAATTAATTATTATTTAAT
Found at i:18711471 original size:30 final size:31
Alignment explanation
Indices: 18711431--18711488 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
18711421 AAAAATCACA
* *
18711431 TTTTAGAAAAATTA-CATTTTTCCCCTAAAG
1 TTTTACAAAAATTATCATTTTGCCCCTAAAG
*
18711461 TTTTACAAAAATTATGATTTTGCCCCTA
1 TTTTACAAAAATTATCATTTTGCCCCTA
18711489 GGCTCAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (31 bp):
TTTTACAAAAATTATCATTTTGCCCCTAAAG
Found at i:18714025 original size:13 final size:13
Alignment explanation
Indices: 18714007--18714031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18713997 ATAATAGGCA
18714007 AGAAAATAAAAGC
1 AGAAAATAAAAGC
18714020 AGAAAATAAAAG
1 AGAAAATAAAAG
18714032 TGTTTTCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.16, T:0.08
Consensus pattern (13 bp):
AGAAAATAAAAGC
Found at i:18720161 original size:18 final size:18
Alignment explanation
Indices: 18720110--18720161 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
18720100 AAAAAAATTT
*
18720110 TATTTTATAATAACATAATT
1 TATTTT-TAATAA-ATAATA
*
18720130 TACTTTGTAA-AAATAATA
1 TA-TTTTTAATAAATAATA
18720148 TATTTTTAATAAAT
1 TATTTTTAATAAAT
18720162 TTTCAGCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.22
18 11 0.41
19 2 0.07
20 5 0.19
21 3 0.11
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTTTAATAAATAATA
Found at i:18723732 original size:31 final size:31
Alignment explanation
Indices: 18723674--18723748 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
18723664 ATTTAATAGA
* * *
18723674 GAGTGACCAAAATATAAACGATCTAAAACGT
1 GAGTGACCAAAATAAAAACAATCTAAAACAT
* *
18723705 GAGTGACCAAAATAAAAATAATGTAAAACAT
1 GAGTGACCAAAATAAAAACAATCTAAAACAT
* *
18723736 TAGTAACCAAAAT
1 GAGTGACCAAAAT
18723749 TGAAAACTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (31 bp):
GAGTGACCAAAATAAAAACAATCTAAAACAT
Found at i:18737521 original size:23 final size:23
Alignment explanation
Indices: 18737495--18737564 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
18737485 ATTTGATAAA
18737495 AAATCGACCTTAAAACTTGAATT
1 AAATCGACCTTAAAACTTGAATT
18737518 AAATCGACCTTAAAACTTGAATT
1 AAATCGACCTTAAAACTTGAATT
18737541 AAATCGACCTTAAAACTTGAATT
1 AAATCGACCTTAAAACTTGAATT
18737564 A
1 A
18737565 TACTTATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
AAATCGACCTTAAAACTTGAATT
Found at i:18741759 original size:38 final size:38
Alignment explanation
Indices: 18741717--18741793 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
18741707 GATAACTCCA
* *
18741717 CAATCCCATATTTTTCTCCTAAAATCACTCCAACACTC
1 CAATCCCATATTTTCCTCATAAAATCACTCCAACACTC
18741755 CAATCCCATATTTTCCTCATAAAATCACTCCAACACTC
1 CAATCCCATATTTTCCTCATAAAATCACTCCAACACTC
18741793 C
1 C
18741794 CCCACCACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.38, G:0.00, T:0.30
Consensus pattern (38 bp):
CAATCCCATATTTTCCTCATAAAATCACTCCAACACTC
Found at i:18752482 original size:29 final size:27
Alignment explanation
Indices: 18752450--18752510 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
18752440 TTTTTGTATT
*
18752450 AACTTCAATTATTTATATATATTTGCATG
1 AACTT-AATT-TTCATATATATTTGCATG
* *
18752479 AACTTGATTTTCATGTATATTTGCATG
1 AACTTAATTTTCATATATATTTGCATG
18752506 AACTT
1 AACTT
18752511 GATGGGCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.72
28 3 0.10
29 5 0.17
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (27 bp):
AACTTAATTTTCATATATATTTGCATG
Found at i:18752524 original size:27 final size:27
Alignment explanation
Indices: 18752466--18752527 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
18752456 AATTATTTAT
*** *
18752466 ATATATTTGCATGAACTTGATTTTCAT
1 ATATATTTGCATGAACTTGATGGGCAC
*
18752493 GTATATTTGCATGAACTTGATGGGCAC
1 ATATATTTGCATGAACTTGATGGGCAC
18752520 ATATATTT
1 ATATATTT
18752528 AAAAATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (27 bp):
ATATATTTGCATGAACTTGATGGGCAC
Found at i:18753856 original size:21 final size:21
Alignment explanation
Indices: 18753818--18753857 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18753808 GTTTAATCTG
*
18753818 TTCAAAACACGATCAAACATA
1 TTCAAAACACGATAAAACATA
* *
18753839 TTCAAAACATGCTAAAACA
1 TTCAAAACACGATAAAACA
18753858 ATCATCCTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
TTCAAAACACGATAAAACATA
Found at i:18755873 original size:4 final size:4
Alignment explanation
Indices: 18755856--18755905 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
18755846 CATGCGTCTC
**
18755856 TTCT TTCT CCCT TTCT TTCT TTCT ATT-T TTCT TTC- TT-T TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT
18755902 TTCT
1 TTCT
18755906 AATTTCTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.16
4 30 0.79
5 2 0.05
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:18755994 original size:15 final size:16
Alignment explanation
Indices: 18755947--18756014 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 16
18755937 TTCATTTTTT
*
18755947 TTATTATACTAACTTTTA
1 TTATTATATTAA--TTTA
18755965 TTATTATATTTTAATTTA
1 TTATTATA--TTAATTTA
18755983 TTATTATA-TAATTTA
1 TTATTATATTAATTTA
18755998 -TATT-TACTTAA-TTA
1 TTATTATA-TTAATTTA
18756012 TTA
1 TTA
18756015 AGATAACATA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 2 0.05
14 7 0.16
15 12 0.27
18 20 0.45
20 3 0.07
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATATTAATTTA
Found at i:18756020 original size:27 final size:27
Alignment explanation
Indices: 18755968--18756020 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
18755958 ACTTTTATTA
* *
18755968 TTATATTTTAATTTATTATTATATAAT
1 TTATATTTTAATTAATTATTAGATAAT
*
18755995 TTATA-TTTACTTAATTATTAAGATAA
1 TTATATTTTAATTAATTATT-AGATAA
18756021 CATATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TTATATTTTAATTAATTATTAGATAAT
Found at i:18771765 original size:21 final size:21
Alignment explanation
Indices: 18771741--18771789 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
18771731 ATGTTCACTT
*
18771741 TTATATCA-TAAAATAAACAAA
1 TTATAT-ATTAAAATAAAAAAA
18771762 TTAT-TATTAAAATAAAAAAA
1 TTATATATTAAAATAAAAAAA
18771782 TATATATA
1 T-TATATA
18771790 CTAGTCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 7 0.29
22 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
TTATATATTAAAATAAAAAAA
Found at i:18772725 original size:13 final size:13
Alignment explanation
Indices: 18772709--18772735 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18772699 AATTTTTGGT
18772709 GGCAAGAGAGGGA
1 GGCAAGAGAGGGA
18772722 GGCAAGAGAGGGA
1 GGCAAGAGAGGGA
18772735 G
1 G
18772736 TATCCTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.56, T:0.00
Consensus pattern (13 bp):
GGCAAGAGAGGGA
Found at i:18782350 original size:38 final size:38
Alignment explanation
Indices: 18782290--18782364 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
18782280 GAATTTCATA
*
18782290 TTTTATCTTTAAGATAAATTTT-ATTAAAAAATCACATT
1 TTTTATATTTAAGATAAATTTTAATTAAAAAAT-ACATT
* ** *
18782328 TTTTATATTTAATATATTTTTTAATTTAAAAATACAT
1 TTTTATATTTAAGATAAATTTTAATTAAAAAATACAT
18782365 AATGACAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 22 0.71
39 9 0.29
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.52
Consensus pattern (38 bp):
TTTTATATTTAAGATAAATTTTAATTAAAAAATACATT
Found at i:18783166 original size:24 final size:22
Alignment explanation
Indices: 18783110--18783167 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
18783100 AAAAGAGATT
*
18783110 AATAATAAAAATTAAATAACTA
1 AATAATAAAAATAAAATAACTA
18783132 AACTAAATAAACAATAAAATAGAC-A
1 AA-T-AATAAA-AATAAAATA-ACTA
18783157 AATAACTAAAA
1 AATAA-TAAAA
18783168 TAGATAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
22 2 0.07
23 4 0.13
24 11 0.37
25 11 0.37
26 2 0.07
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.21
Consensus pattern (22 bp):
AATAATAAAAATAAAATAACTA
Found at i:18783168 original size:17 final size:17
Alignment explanation
Indices: 18783123--18783171 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
18783113 AATAAAAATT
* * *
18783123 AAATAACTAAACTAAAT
1 AAATAACTAAAATAGAC
*
18783140 AAACAA-TAAAATAGAC
1 AAATAACTAAAATAGAC
18783156 AAATAACTAAAATAGA
1 AAATAACTAAAATAGA
18783172 TAAAACCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.18
Consensus pattern (17 bp):
AAATAACTAAAATAGAC
Found at i:18784585 original size:32 final size:32
Alignment explanation
Indices: 18784544--18784609 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
18784534 TCGAGTTGCA
18784544 TATTGAAACCAAAGAAATTAAAATAAACTTAG
1 TATTGAAACCAAAGAAATTAAAATAAACTTAG
18784576 TATTGAAACCAAAGAAATTAAAATAAACTTAG
1 TATTGAAACCAAAGAAATTAAAATAAACTTAG
18784608 TA
1 TA
18784610 ACTTGAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (32 bp):
TATTGAAACCAAAGAAATTAAAATAAACTTAG
Found at i:18784632 original size:34 final size:32
Alignment explanation
Indices: 18784544--18784637 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 32
18784534 TCGAGTTGCA
* *
18784544 TATTGAAACCAAAGAAATTAAAATAAACTTAG
1 TATTGAAACAAAAGAAACTAAAATAAACTTAG
* *
18784576 TATTGAAACCAAAGAAATTAAAATAAACTTAG
1 TATTGAAACAAAAGAAACTAAAATAAACTTAG
* **
18784608 TAACTTGAAATAAAATTAACTAAAACTAAA
1 T-A-TTGAAACAAAAGAAACTAAAA-TAAA
18784638 ATTTGTATCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
32 33 0.61
33 1 0.02
34 16 0.30
35 4 0.07
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (32 bp):
TATTGAAACAAAAGAAACTAAAATAAACTTAG
Found at i:18784987 original size:136 final size:136
Alignment explanation
Indices: 18784829--18785136 Score: 555
Period size: 136 Copynumber: 2.3 Consensus size: 136
18784819 AAGTATACGA
18784829 GTCAAATTGTAATATAGTAAAGTGTTACAATGAAACACTTCAGGAAATACTGACTGCTTATAAAC
1 GTCAAATTGTAATATAGTAAAGTGTTACAATGAAACACTTCAGGAAATACTGACTGCTTATAAAC
18784894 ATGTTATCGTTTATAGTAAAAATACACCAACAATATATTAAATAATACCAAAGGTGTCCGCAAGT
66 ATGTTATCGTTTATAGTAAAAATACACCAACAATATATTAAATAATACCAAAGGTGTCCGCAAGT
18784959 GCGCGG
131 GCGCGG
18784965 GTCAAATTGTAATATAGTAAAGTGTTACAATGAAACACTTCAGGAAATACTGACTGCTTATAAAC
1 GTCAAATTGTAATATAGTAAAGTGTTACAATGAAACACTTCAGGAAATACTGACTGCTTATAAAC
* * **
18785030 ATGTTATCGTTTATAGTAAAAATACACCAACAATATATTAAATTATATCAGTGGTGTCCGCAAGT
66 ATGTTATCGTTTATAGTAAAAATACACCAACAATATATTAAATAATACCAAAGGTGTCCGCAAGT
*
18785095 GTGCGG
131 GCGCGG
*
18785101 GTCAAATTGTAATATAGTAAAGTG-TACAACGAAACA
1 GTCAAATTGTAATATAGTAAAGTGTTACAATGAAACA
18785137 TTGGTAAGTA
Statistics
Matches: 166, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
135 11 0.07
136 155 0.93
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (136 bp):
GTCAAATTGTAATATAGTAAAGTGTTACAATGAAACACTTCAGGAAATACTGACTGCTTATAAAC
ATGTTATCGTTTATAGTAAAAATACACCAACAATATATTAAATAATACCAAAGGTGTCCGCAAGT
GCGCGG
Found at i:18793726 original size:27 final size:27
Alignment explanation
Indices: 18793690--18794049 Score: 408
Period size: 27 Copynumber: 13.4 Consensus size: 27
18793680 ACCCTAAAAT
18793690 AGGTAAAATGACCGAAATACCCCCATA
1 AGGTAAAATGACCGAAATACCCCCATA
* * * *
18793717 AGATAGAATGACCAAAATACCCTCATA
1 AGGTAAAATGACCGAAATACCCCCATA
*
18793744 GGGTAAAATGACCGAAATACCCCCATA
1 AGGTAAAATGACCGAAATACCCCCATA
18793771 AGGTAAAAT-AGCCGAAATACCCCCATA
1 AGGTAAAATGA-CCGAAATACCCCCATA
* * * *
18793798 GGGTAAAATAACTGAAATACCCCTATA
1 AGGTAAAATGACCGAAATACCCCCATA
* * *
18793825 GGGTACAATGACTGAAATACCCCCAT-
1 AGGTAAAATGACCGAAATACCCCCATA
*
18793851 AGGATAAAATGACTGAAATACCCCCATA
1 AGG-TAAAATGACCGAAATACCCCCATA
* *
18793879 AGGTAGAATGACCGAAATACCCTCATA
1 AGGTAAAATGACCGAAATACCCCCATA
* * *
18793906 TGGTAAACTAACCGAAATACCCCTC-TA
1 AGGTAAAATGACCGAAATACCCC-CATA
* *
18793933 TGGTAGAATGACCGAAATA-CCCCATA
1 AGGTAAAATGACCGAAATACCCCCATA
* *
18793959 AGGTAGAATGACCGAAATA-CCCCACA
1 AGGTAAAATGACCGAAATACCCCCATA
* *
18793985 AGGTAAAATGACCAAAATA-CCCTATA
1 AGGTAAAATGACCGAAATACCCCCATA
* *
18794011 AGGTAGAATGACCGAAATACCCCTATA
1 AGGTAAAATGACCGAAATACCCCCATA
*
18794038 GGGTAAAATGAC
1 AGGTAAAATGAC
18794050 TATTATACCC
Statistics
Matches: 287, Mismatches: 39, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
25 1 0.00
26 71 0.25
27 210 0.73
28 5 0.02
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
AGGTAAAATGACCGAAATACCCCCATA
Found at i:18796610 original size:33 final size:33
Alignment explanation
Indices: 18796573--18796640 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
18796563 GAATGTCTTA
18796573 AAACATGTGCGAATGAGAAGAATAACATGTGAC
1 AAACATGTGCGAATGAGAAGAATAACATGTGAC
*
18796606 AAACATGTGCGAATGCGAAGAATAACATGTGAC
1 AAACATGTGCGAATGAGAAGAATAACATGTGAC
18796639 AA
1 AA
18796641 CTTTAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.18
Consensus pattern (33 bp):
AAACATGTGCGAATGAGAAGAATAACATGTGAC
Found at i:18799299 original size:2 final size:2
Alignment explanation
Indices: 18799292--18799326 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18799282 ATTTGTTTCT
18799292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18799327 GTATGTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18802037 original size:15 final size:16
Alignment explanation
Indices: 18802003--18802045 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
18801993 ACTCATTTAA
*
18802003 TTATATATATTAGCTTC
1 TTATTTATATTA-CTTC
18802020 TTATTTATATTA-TTC
1 TTATTTATATTACTTC
*
18802035 TTAGTTATATT
1 TTATTTATATT
18802046 TATGCATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
17 11 0.46
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (16 bp):
TTATTTATATTACTTC
Found at i:18808350 original size:24 final size:24
Alignment explanation
Indices: 18808318--18808369 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
18808308 CGTTCATGAA
18808318 GGCATTATAAGTAACGGCATCAGG
1 GGCATTATAAGTAACGGCATCAGG
18808342 GGCATTATAAGTAACGGCATCAGG
1 GGCATTATAAGTAACGGCATCAGG
18808366 GGCA
1 GGCA
18808370 ATTCCAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (24 bp):
GGCATTATAAGTAACGGCATCAGG
Found at i:18820106 original size:89 final size:90
Alignment explanation
Indices: 18819913--18820129 Score: 242
Period size: 89 Copynumber: 2.4 Consensus size: 90
18819903 CTTTGAAGAT
* * * * *
18819913 TCTGGCGTGTTATCAGTTGGAAAGCTTTTATGAGCAAACTAACGTGTTACCGTGGGAGAATGTTT
1 TCTGGCATGTTATC-GTTGGAAAGCTCTTATGAGCAAACTAACATGTTACCGAGGGAAAATGTTT
* *
18819978 GGCCTACAGGCTTTGCACTATGTGCA
65 AGCATACAGGCTTTGCACTATGTGCA
** * * *
18820004 TCTGGTTTATTATCTGTTGGAAAGCTCTTATGAG-AAACTAGCATGTTATC-AGGGAAAATGTTT
1 TCTGGCATGTTATC-GTTGGAAAGCTCTTATGAGCAAACTAACATGTTACCGAGGGAAAATGTTT
** *
18820067 AGCATACGAGTTTTTTC-CTATGTGCA
65 AGCATAC-AGGCTTTGCACTATGTGCA
18820093 TCTGGCATGTTATCGATTGGAAAGCTCTTATGAGCAA
1 TCTGGCATGTTATCG-TTGGAAAGCTCTTATGAGCAA
18820130 TCCGATATGT
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
88 1 0.01
89 54 0.51
90 21 0.20
91 29 0.28
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (90 bp):
TCTGGCATGTTATCGTTGGAAAGCTCTTATGAGCAAACTAACATGTTACCGAGGGAAAATGTTTA
GCATACAGGCTTTGCACTATGTGCA
Found at i:18823296 original size:76 final size:76
Alignment explanation
Indices: 18823178--18823322 Score: 227
Period size: 76 Copynumber: 1.9 Consensus size: 76
18823168 TCATTAGCCA
*
18823178 TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATGTAATGCAA
1 TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATATAATGCAA
18823243 GATATTAGTTG
66 GATATTAGTTG
* * * * * *
18823254 TTTGGGGTGTATTTAGACACTTATTGTTTAGGGATTTTTATGTAAAGATATTGTATATAATGTAA
1 TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATATAATGCAA
18823319 GATA
66 GATA
18823323 GGGGAGAGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (76 bp):
TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATATAATGCAA
GATATTAGTTG
Found at i:18824334 original size:3 final size:3
Alignment explanation
Indices: 18824328--18824391 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
18824318 GTAGTAGTAG
*
18824328 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA -AA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
18824376 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
18824392 CTTAAGTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 53 0.93
4 2 0.04
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18830665 original size:211 final size:211
Alignment explanation
Indices: 18830111--18830739 Score: 994
Period size: 211 Copynumber: 3.0 Consensus size: 211
18830101 GAATGAGAAG
* * *
18830111 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGGATGATATTCAATCC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
* *
18830176 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTGCATCATTCGGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
* * *
18830241 TGAGCTATGTTACCCAGGCTC-AGTGGATCTTGGTTGCTGACATTTGTCTAACACTGATATGGTA
131 TGAGCTATGTTACCCAGGCTCAAGT-GATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
*
18830305 AACCTTTCGAAGTGAAT
195 AACCTTTCTAAGTGAAT
* *
18830322 C-TTTATTTGTTTGCGTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAGTTC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
* * *
18830386 TCTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTCATTTGGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
* * * *
18830451 TGAGCTATGTTAGCCACGCTCAAGTGACTCTTGGATGCTGACTTTTGTCCAACACTGGTATGCTA
131 TGAGCTATGTTACCCAGGCTCAAGTGA-TCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
18830516 AACCTTTCTAAGTGAAT
195 AACCTTTCTAAGTGAAT
*
18830533 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAAGGTTGCAAAAAGAATGATCTTCAATTC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
* * *
18830598 TTTCATGTACTTTATTTCCCATTGAATGTGG-TTTTTCAATTTTTTTTCTTTACTTCATTCAGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
* *
18830662 TGAGGTATGTTACCCAGGCTCAAGTCAATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
131 TGAGCTATGTTACCCAGGCTCAAGT-GATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
18830727 AACCTTTCTAAGT
195 AACCTTTCTAAGT
18830740 TTTTCATATA
Statistics
Matches: 382, Mismatches: 32, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
210 139 0.36
211 152 0.40
212 91 0.24
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (211 bp):
CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
TGAGCTATGTTACCCAGGCTCAAGTGATCTTGGATGCTGACATTTGTCCAACACTGATATGCTAA
ACCTTTCTAAGTGAAT
Found at i:18842505 original size:49 final size:49
Alignment explanation
Indices: 18842411--18842513 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
18842401 CTAGGCTCTT
*
18842411 GAGTTATACTCCAACCTGTTAACACATAACCACCGTCAATGGGGAGCCC
1 GAGTTATACTCCAACCTGTTAACACATAACCACCATCAATGGGGAGCCC
* * * * *
18842460 TAGTTATACTTCAACCT-TTGACCATATAACCACCATGAACT-GGGAGCCC
1 GAGTTATACTCCAACCTGTT-AACACATAACCACCATCAA-TGGGGAGCCC
18842509 GAGTT
1 GAGTT
18842514 GTAATTCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
48 2 0.04
49 42 0.93
50 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
GAGTTATACTCCAACCTGTTAACACATAACCACCATCAATGGGGAGCCC
Found at i:18857633 original size:7 final size:7
Alignment explanation
Indices: 18857621--18857653 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
18857611 TCAACCTATA
18857621 CCTAAAC
1 CCTAAAC
*
18857628 CCTAAAT
1 CCTAAAC
18857635 CCTAAAC
1 CCTAAAC
18857642 CCTAAAC
1 CCTAAAC
18857649 CCTAA
1 CCTAA
18857654 TAATTTCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (7 bp):
CCTAAAC
Found at i:18859237 original size:28 final size:28
Alignment explanation
Indices: 18859202--18859263 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
18859192 AAAATAACCC
**
18859202 AAATATTATAACTTTTTTTTATTTACCA
1 AAATATTATAAAATTTTTTTATTTACCA
*
18859230 AAATATTATAAAATTTTTTTATTTATCA
1 AAATATTATAAAATTTTTTTATTTACCA
18859258 AAATAT
1 AAATAT
18859264 ACCAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATATTATAAAATTTTTTTATTTACCA
Found at i:18859969 original size:19 final size:19
Alignment explanation
Indices: 18859947--18860011 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
18859937 TGAAATATAA
18859947 TAAATTAAAATAGAGTTAT
1 TAAATTAAAATAGAGTTAT
* * *
18859966 TAAATGAGAATAG-TTTAT
1 TAAATTAAAATAGAGTTAT
*
18859984 TACATTAAAATAGAGTTAT
1 TAAATTAAAATAGAGTTAT
18860003 TAAATTAAA
1 TAAATTAAA
18860012 CTATTTTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.38
19 23 0.62
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (19 bp):
TAAATTAAAATAGAGTTAT
Found at i:18860405 original size:27 final size:27
Alignment explanation
Indices: 18860322--18860397 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
18860312 TTTTAGTCCT
18860322 TTGGCA-CATTGGTGCCGCCAATCACA
1 TTGGCACCATTGGTGCCGCCAATCACA
18860348 TTGGCACCATTGGTGCCGCCAATCACA
1 TTGGCACCATTGGTGCCGCCAATCACA
* *
18860375 TTGGCACCTTTGGTGCTGCCAAT
1 TTGGCACCATTGGTGCCGCCAAT
18860398 GTGATTGGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 6 0.13
27 41 0.87
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCACA
Found at i:18860513 original size:26 final size:28
Alignment explanation
Indices: 18860460--18860520 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
18860450 TTTTGGTATC
* *
18860460 TTTTAGTAAATAAAAAAAAGTTATAATA
1 TTTTGGTAAATAAAAAAAAGTTAAAATA
18860488 TTTTGGTAAAT-AAAAAAA-TTAAAATA
1 TTTTGGTAAATAAAAAAAAGTTAAAATA
18860514 TTTTGGT
1 TTTTGGT
18860521 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 14 0.45
27 7 0.23
28 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (28 bp):
TTTTGGTAAATAAAAAAAAGTTAAAATA
Found at i:18861290 original size:27 final size:27
Alignment explanation
Indices: 18861260--18861327 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
18861250 CCTATCTAGA
18861260 AGGCGCCAATGGTGGTGCCTACTTGGG
1 AGGCGCCAATGGTGGTGCCTACTTGGG
*
18861287 AGGCGCCAATGGTGGTGCCTATTTGGG
1 AGGCGCCAATGGTGGTGCCTACTTGGG
18861314 AGGCGCCAATGGTG
1 AGGCGCCAATGGTG
18861328 AACAAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.16, C:0.21, G:0.41, T:0.22
Consensus pattern (27 bp):
AGGCGCCAATGGTGGTGCCTACTTGGG
Found at i:18861634 original size:19 final size:19
Alignment explanation
Indices: 18861610--18861722 Score: 82
Period size: 20 Copynumber: 5.3 Consensus size: 19
18861600 NNNNNNNNNN
18861610 AAAATTACAATATTCATAC
1 AAAATTACAATATTCATAC
*
18861629 AAAATTATAATATTACAATATTC
1 AAAATTACAATATT-C-ATA--C
*
18861652 ATACAACATTACAATATTCATAAA
1 --A-AA-ATTACAATATTCAT-AC
*
18861676 AAAATTATAATATTCATAC
1 AAAATTACAATATTCATAC
*
18861695 AAAAAATTTAAAATATTCATAC
1 --AAAA-TTACAATATTCATAC
18861717 AAAATT
1 AAAATT
18861723 CTAATCTAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
19 16 0.21
20 18 0.24
21 9 0.12
22 15 0.20
23 1 0.01
25 3 0.04
26 4 0.05
27 10 0.13
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTACAATATTCATAC
Found at i:18861651 original size:27 final size:27
Alignment explanation
Indices: 18861613--18861669 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
18861603 NNNNNNNAAA
*
18861613 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
*
18861640 ATTACAATATTCATACAACATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
18861667 ATT
1 ATT
18861670 CATAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:18861687 original size:20 final size:21
Alignment explanation
Indices: 18861610--18861720 Score: 102
Period size: 22 Copynumber: 5.1 Consensus size: 21
18861600 NNNNNNNNNN
18861610 AAAATTACAATATTCATAC--
1 AAAATTACAATATTCATACAA
*
18861629 AAAATTATAATATTACAATATTCATA
1 AAAATTACAATATT-C-ATA--CA-A
*
18861655 CAACATTACAATATTCATA-AA
1 -AAAATTACAATATTCATACAA
*
18861676 AAAATTATAATATTCATACAA
1 AAAATTACAATATTCATACAA
*
18861697 AAAATTTAAAATATTCATACAA
1 AAAA-TTACAATATTCATACAA
18861719 AA
1 AA
18861721 TTCTAATCTA
Statistics
Matches: 76, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
19 13 0.17
20 17 0.22
21 10 0.13
22 19 0.25
23 1 0.01
25 3 0.04
26 1 0.01
27 12 0.16
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTACAATATTCATACAA
Found at i:18861722 original size:20 final size:20
Alignment explanation
Indices: 18861645--18861722 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
18861635 ATAATATTAC
* *
18861645 AATATTCATACAACA-TTAC
1 AATATTCATACAAAATTTAA
* * *
18861664 AATATTCATAAAAAAATTAT
1 AATATTCATACAAAATTTAA
18861684 AATATTCATACAAAAAATTTAA
1 AATATTCATAC--AAAATTTAA
18861706 AATATTCATACAAAATT
1 AATATTCATACAAAATT
18861723 CTAATCTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.26
20 19 0.38
22 18 0.36
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATTCATACAAAATTTAA
Found at i:18870788 original size:27 final size:27
Alignment explanation
Indices: 18870732--18870800 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
18870722 AATATTGGAA
*
18870732 TTTTTTTATATTTTTAAAATCATTCTTT
1 TTTTTTTA-ATTTTTAAAATAATTCTTT
*
18870760 TTTTTTTAAATTTTAAAA-AATT-TTAT
1 TTTTTTTAATTTTTAAAATAATTCTT-T
18870786 TTTTTCTTAATTTTT
1 TTTTT-TTAATTTTT
18870801 TATTTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.25
27 17 0.47
28 8 0.22
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTTTTAATTTTTAAAATAATTCTTT
Found at i:18873810 original size:16 final size:16
Alignment explanation
Indices: 18873789--18873819 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18873779 TTCACTATTA
*
18873789 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
18873805 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
18873820 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:18874206 original size:571 final size:567
Alignment explanation
Indices: 18873128--18874252 Score: 1456
Period size: 571 Copynumber: 2.0 Consensus size: 567
18873118 TGACATGTTG
* * ** *
18873128 GGAAATGTGTCCATATTGTAGTAAACATTTAACTGTTTTCCATGTATTTGAACGATGAATAAATA
1 GGAAATGAGCCCATATTGTAGTAAACATGCAACTGTTTTCCATGTATTTAAACGATGAATAAATA
* * *
18873193 AATAAAGTTAATTTCACATTTCACTGTTATATCTTTTATGTTTCTATCTTTCATGTTTTGCATAC
66 AATAAAGTTAAATTCACATTTCACTATTATATCTTTTATGTTTCTATCTTTCATATTTTGCATAC
* * *
18873258 ATAGAAAAATTATGACAAGAAAATATTAGCTCATTGATTGTTTAAGTTCAAACTGATGATAAGTG
131 ATAGAAAAATTATGACAAGAAAATATTAGCTCATTAATTGTTAAAGTTCAAACTGAAGATAAGTG
* * * * *
18873323 GAACTGTAAGAACATTTACATTACGAGAAGACAACTTAGTTCAGTAGATAATCTAAACAAGTCCT
196 GAACTGTAACAACATTTACATTACAAAAAGACAACTTACTTCAGTAGATAATCTAAACAAGTCCG
* * * * * *
18873388 TAATCCTGTAAAAGAATCAAATTTAGCGTTTGATTTAAATACTTAGAAAGATTAGTATGTCGTCT
261 TAATCCTATAAAAGAATCAAAGTGAGCGTTTGATTCAAACACTGAGAAAGATTAGTATGTCGTCT
* * *
18873453 ACAATTCCAATCGGGGAGATGACTAGTCTTGACTACCGAAGTAGTTGAATCCACGGGTAGAAACA
326 ACAATTCCAATCGGGGAGATGACTAGTCTTGACTACAGAAGCAGTTGAATCCACGAGTAGAAACA
* **
18873518 TAGATGTATTCATTGAAAGAATGATACATTGGACTGAAACCAAGATGAATTAATTCTGAATCCGT
391 TAGATGTATTCATTGAAAGAATGATACATTGCACTGAAACCAAGATGAATTAATTCTGAATCCAC
* *
18873583 TTGTGAATTAATACACTTGTGAAGTTCATTGTGTGATTTTCCTAAATCCTGAGTTAGCCACTGAC
456 TTGTGAATTAATACACTTGTGAAGTTCATGGTGTGATTTTCCTAAATCCTGAGTTAACCACTGAC
*
18873648 CATGCGTATGTAACTCATATGCTTTAATATAAGTGGAGGCTTTTTAA
521 CATGCGTATGCAACTCATATGCTTTAATATAAGTGGAGGCTTTTTAA
* * *
18873695 GGAAATGAGCCCATATTGTAGTAAACATGCAACTGTTTTCTATTTATTTAAATGATGAATAAATA
1 GGAAATGAGCCCATATTGTAGTAAACATGCAACTGTTTTCCATGTATTTAAACGATGAATAAATA
* * * *
18873760 AATAAAGTTAAATTCACATTTCACTATTATGTCTTTTGTAT-TTTTTGTCTTTTATATTTTGCAT
66 AATAAAGTTAAATTCACATTTCACTATTATATC-TTT-TATGTTTCTATCTTTCATATTTTGCAT
* ** *
18873824 GCATAGCGAAATTATGACAATAAAATATTAGCTCATTAATTGTCTAAAGTTCAAACTGAAGATAA
129 ACATAGAAAAATTATGACAAGAAAATATTAGCTCATTAATTGT-TAAAGTTCAAACTGAAGATAA
* * * * * * *
18873889 GTGGCATTGTAAACAACGTTTACATTGCAAAAAATACAACTTACTTCGGTAGATAATCTAAATAA
193 GTGGAACTGT-AACAACATTTACATTAC-AAAAAGACAACTTACTTCAGTAGATAATCTAAACAA
* *
18873954 GTTCGTAATACC-ATAAAAGAATCAAAGTGAG-GATTTGATTCAAACACTGA-AAAGGATTATTA
256 GTCCGTAAT-CCTATAAAAGAATCAAAGTGAGCG-TTTGATTCAAACACTGAGAAA-GATTAGTA
* * ** * * * *
18874016 TGTCGTCTACAATTTCAATTGGGGAGATGGTTAGTCTTGGCTATCAG-AGCAGTTGACTGCATGA
318 TGTCGTCTACAATTCCAATCGGGGAGATGACTAGTCTTGACTA-CAGAAGCAGTTGAATCCACGA
* * * ** *
18874080 GTGGAGACATAGATGTATTGATTGGTAGAATGATACATTGCTCT-AAACCCAAGATGAATTAATT
382 GTAGAAACATAGATGTATTCATTGAAAGAATGATACATTGCACTGAAA-CCAAGATGAATTAATT
*
18874144 CTGAATCCACTTGTGAATTAATTCACTTGTGACA-TTCATGGTGTGATTTAT-CTAAATCCTGAG
446 CTGAATCCACTTGTGAATTAATACACTTGTGA-AGTTCATGGTGTGATTT-TCCTAAATCCTGAG
* * * *
18874207 TTAATCACTGACCATGCGTATGCAATTCATGTGCTTTGATATAAGT
509 TTAACCACTGACCATGCGTATGCAACTCATATGCTTTAATATAAGT
18874253 CAATGATTAT
Statistics
Matches: 476, Mismatches: 70, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
567 87 0.18
568 60 0.13
569 30 0.06
570 21 0.04
571 272 0.57
572 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (567 bp):
GGAAATGAGCCCATATTGTAGTAAACATGCAACTGTTTTCCATGTATTTAAACGATGAATAAATA
AATAAAGTTAAATTCACATTTCACTATTATATCTTTTATGTTTCTATCTTTCATATTTTGCATAC
ATAGAAAAATTATGACAAGAAAATATTAGCTCATTAATTGTTAAAGTTCAAACTGAAGATAAGTG
GAACTGTAACAACATTTACATTACAAAAAGACAACTTACTTCAGTAGATAATCTAAACAAGTCCG
TAATCCTATAAAAGAATCAAAGTGAGCGTTTGATTCAAACACTGAGAAAGATTAGTATGTCGTCT
ACAATTCCAATCGGGGAGATGACTAGTCTTGACTACAGAAGCAGTTGAATCCACGAGTAGAAACA
TAGATGTATTCATTGAAAGAATGATACATTGCACTGAAACCAAGATGAATTAATTCTGAATCCAC
TTGTGAATTAATACACTTGTGAAGTTCATGGTGTGATTTTCCTAAATCCTGAGTTAACCACTGAC
CATGCGTATGCAACTCATATGCTTTAATATAAGTGGAGGCTTTTTAA
Found at i:18875493 original size:36 final size:35
Alignment explanation
Indices: 18875431--18875537 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 35
18875421 ATTCCAAAAG
*
18875431 TAATATTATTTTAATAGTTTAATATTAATTTTAAT-T
1 TAATATTATCTTAATAGTTT-ATATTAA-TTTAATAT
18875467 TAATACTTATCTTAATAGTATT-TATTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTATATTAATTTAATAT
*
18875503 TAAAGTGATTATCTTAATA--TTAAATTTAATTTAAT
1 T-AA-T-ATTATCTTAATAGTTTATA-TTAATTTAAT
18875538 GTTTATATAA
Statistics
Matches: 61, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
35 8 0.13
36 14 0.23
37 24 0.39
38 14 0.23
39 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTATATTAATTTAATAT
Found at i:18876651 original size:28 final size:28
Alignment explanation
Indices: 18876612--18876670 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
18876602 ACCATTACTT
18876612 AAAACCTCTTTAACCTCTAATTCTTTCA
1 AAAACCTCTTTAACCTCTAATTCTTTCA
* *
18876640 AAAACCTTTTTAACCTCTAATTCTTTTA
1 AAAACCTCTTTAACCTCTAATTCTTTCA
18876668 AAA
1 AAA
18876671 TCCCCTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAACCTCTTTAACCTCTAATTCTTTCA
Found at i:18891571 original size:16 final size:16
Alignment explanation
Indices: 18891549--18891582 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18891539 TACATTTTAA
*
18891549 GGGTTTTT-TGTTTTC
1 GGGTTTTTGAGTTTTC
18891564 GGGTTTTTGAGTTTTC
1 GGGTTTTTGAGTTTTC
18891580 GGG
1 GGG
18891583 GTTTAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.03, C:0.06, G:0.35, T:0.56
Consensus pattern (16 bp):
GGGTTTTTGAGTTTTC
Found at i:18892246 original size:14 final size:14
Alignment explanation
Indices: 18892227--18892265 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
18892217 TTATAACTTT
*
18892227 TATTATTTATTGTA
1 TATTATTTATAGTA
*
18892241 TATTATTTGTAGTA
1 TATTATTTATAGTA
18892255 TA-TATTTATAG
1 TATTATTTATAG
18892266 GATAGGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (14 bp):
TATTATTTATAGTA
Found at i:18899007 original size:25 final size:25
Alignment explanation
Indices: 18898978--18899027 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
18898968 AATTACAGTT
*
18898978 TTAAAAATTTATAAATTAT-AAAAAA
1 TTAAAAA-TAATAAATTATCAAAAAA
*
18899003 TTAAAAATAATAAATTTTCAAAAAA
1 TTAAAAATAATAAATTATCAAAAAA
18899028 AAAATACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TTAAAAATAATAAATTATCAAAAAA
Found at i:18903782 original size:23 final size:22
Alignment explanation
Indices: 18903755--18903814 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
18903745 CTACAATTTT
*
18903755 TTAAATA-GTTAGTAAGATTTTAA
1 TTAAATAGGTTAG--AGATTTAAA
18903778 TTAAATTAGGTTAGAGATTTAAA
1 TTAAA-TAGGTTAGAGATTTAAA
18903801 TTAAAATAGGTTAG
1 TT-AAATAGGTTAG
18903815 GGTTAGGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 23 0.70
24 5 0.15
25 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (22 bp):
TTAAATAGGTTAGAGATTTAAA
Found at i:18903888 original size:23 final size:23
Alignment explanation
Indices: 18903862--18904071 Score: 116
Period size: 28 Copynumber: 8.1 Consensus size: 23
18903852 TTTTTAATTA
18903862 AATTAAGTTAGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTTTT
*
18903885 AATTAAGTTAGGTTAGGGATTTT
1 AATTAAGTTAGGTTAGGGTTTTT
*
18903908 AATTAAAATATGTTAGGGTTAGTG-TTTT
1 AATT---A-A-GTTA-GGTTAGGGTTTTT
* **
18903936 CATGTAAAATAGGTTAGGGTTAGTGTTTTT
1 AAT-TAAGTTAGGTTA--G---G-GTTTTT
* *
18903966 AATTAAATTAAGTTAGGTTAGGGTTTTT
1 AATTAAGTTAGGTTA-----GGGTTTTT
*
18903994 AATTAAGTTAAGTTAGGGTTTTGTTTTT
1 AATTAAGTTAGGTTA-GG----GTTTTT
*
18904022 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTTTT
18904045 AATTAAGTTAAGGTTAGGGTTTTT
1 AATTAAGTT-AGGTTAGGGTTTTT
18904069 AAT
1 AAT
18904072 CAAATAATGT
Statistics
Matches: 149, Mismatches: 16, Indels: 43
0.72 0.08 0.21
Matches are distributed among these distances:
23 45 0.30
24 21 0.14
25 2 0.01
26 2 0.01
27 3 0.02
28 49 0.33
29 20 0.13
30 6 0.04
32 1 0.01
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (23 bp):
AATTAAGTTAGGTTAGGGTTTTT
Found at i:18903991 original size:28 final size:28
Alignment explanation
Indices: 18903776--18904076 Score: 222
Period size: 29 Copynumber: 11.1 Consensus size: 28
18903766 GTAAGATTTT
* * * *
18903776 AATTAAATTAGGTTAGAGATTTAAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
* * *
18903804 AAATAGGTTAGGGTTAGGG-TTTTCATGTA
1 AATTAAGTTA-GGTTAGGGTTTTTAAT-TA
* *
18903833 AAATAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAAGTTA-GGTTAGGGTTTTTAATTA
18903862 AATTAAGTTAGGTTAGGG--TTT--TT-
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
18903885 AATTAAGTTAGGTTAGGGATTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
* * * *
18903913 AAATATGTTAGGGTTAGTG-TTTTCATGTA
1 AATTAAGTTA-GGTTAGGGTTTTTAAT-TA
* * *
18903942 AAATAGGTTAGGGTTAGTGTTTTTAATTA
1 AATTAAGTTA-GGTTAGGGTTTTTAATTA
18903971 AATTAAGTTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
* **
18903999 AGTTAAGTTAGGGTT-TTGTTTTTAATT-
1 AATTAAGTTA-GGTTAGGGTTTTTAATTA
18904026 -A--AA-TTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
* *
18904050 AGTT-A---AGGTTAGGGTTTTTAATCA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
18904074 AAT
1 AAT
18904077 AATGTCAAAA
Statistics
Matches: 229, Mismatches: 27, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
22 4 0.02
23 31 0.14
24 24 0.10
25 3 0.01
26 4 0.02
27 2 0.01
28 70 0.31
29 79 0.34
30 12 0.05
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (28 bp):
AATTAAGTTAGGTTAGGGTTTTTAATTA
Found at i:18904010 original size:109 final size:109
Alignment explanation
Indices: 18903772--18904015 Score: 418
Period size: 109 Copynumber: 2.2 Consensus size: 109
18903762 GTTAGTAAGA
* * *
18903772 TTTTAATTAAATTAGGTTAGAGATTTAAATTAAAATAGGTTAGGGTTAGGGTTTTCATGTAAAAT
1 TTTTAATTAAGTTAGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTTCATGTAAAAT
18903837 AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
66 AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
* *
18903881 TTTTAATTAAGTTAGGTTAGGGATTTTAATTAAAATATGTTAGGGTTAGTGTTTTCATGTAAAAT
1 TTTTAATTAAGTTAGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTTCATGTAAAAT
*
18903946 AGGTTAGGGTTAGTGTTTTTAATTAAATTAAGTTAGGTTAGGGT
66 AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
*
18903990 TTTTAATTAAGTTAAGTTAGGG-TTTT
1 TTTTAATTAAGTTAGGTTAGGGATTTT
18904016 GTTTTTAATT
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 4 0.03
109 124 0.97
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (109 bp):
TTTTAATTAAGTTAGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTTCATGTAAAAT
AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
Found at i:18904033 original size:109 final size:109
Alignment explanation
Indices: 18903772--18904043 Score: 386
Period size: 109 Copynumber: 2.5 Consensus size: 109
18903762 GTTAGTAAGA
* * * * **
18903772 TTTTAATTAAATTAGGTTAGAGATTTAAATTAAAATAGGTTAGGGTTAGGGTTTTCATGTAAAAT
1 TTTTAATTAAGTTAAGTTAGGGATTTTAATTAAAATAAATTAGGGTTAGGGTTTTCATGTAAAAT
18903837 AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
66 AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
* ** *
18903881 TTTTAATTAAGTTAGGTTAGGGATTTTAATTAAAATATGTTAGGGTTAGTGTTTTCATGTAAAAT
1 TTTTAATTAAGTTAAGTTAGGGATTTTAATTAAAATAAATTAGGGTTAGGGTTTTCATGTAAAAT
*
18903946 AGGTTAGGGTTAGTGTTTTTAATTAAATTAAGTTAGGTTAGGGT
66 AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
** * *
18903990 TTTTAATTAAGTTAAGTTAGGG-TTTTGTTTTTAATTAAATTA-GGTTAGGGTTTT
1 TTTTAATTAAGTTAAGTTAGGGATTTT-AATTAAAATAAATTAGGGTTAGGGTTTT
18904044 TAATTAAGTT
Statistics
Matches: 148, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
108 15 0.10
109 133 0.90
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.45
Consensus pattern (109 bp):
TTTTAATTAAGTTAAGTTAGGGATTTTAATTAAAATAAATTAGGGTTAGGGTTTTCATGTAAAAT
AGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
Found at i:18914232 original size:10 final size:10
Alignment explanation
Indices: 18914202--18914255 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
18914192 ATTGTTAAGA
*
18914202 AATTATGATT
1 AATTAAGATT
18914212 AATTAAG-TT
1 AATTAAGATT
*
18914221 AATTAGGATT
1 AATTAAGATT
18914231 AATTAAG-TT
1 AATTAAGATT
*
18914240 AATTAGGATT
1 AATTAAGATT
18914250 AATTAA
1 AATTAA
18914256 TTAATAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (10 bp):
AATTAAGATT
Found at i:18914235 original size:4 final size:4
Alignment explanation
Indices: 18914209--18914260 Score: 50
Period size: 4 Copynumber: 11.5 Consensus size: 4
18914199 AGAAATTATG
18914209 ATTA ATTA AGTTA ATTA GGATTA ATTA AGTTA ATTA GGATTA ATTA ATTA
1 ATTA ATTA A-TTA ATTA --ATTA ATTA A-TTA ATTA --ATTA ATTA ATTA
18914259 AT
1 AT
18914261 AAACTATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 26 0.62
5 8 0.19
6 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (4 bp):
ATTA
Found at i:18914235 original size:23 final size:19
Alignment explanation
Indices: 18914202--18914260 Score: 102
Period size: 19 Copynumber: 3.2 Consensus size: 19
18914192 ATTGTTAAGA
*
18914202 AATTATGATTAATTAAGTT
1 AATTAGGATTAATTAAGTT
18914221 AATTAGGATTAATTAAGTT
1 AATTAGGATTAATTAAGTT
18914240 AATTAGGATTAATTAA-TT
1 AATTAGGATTAATTAAGTT
18914258 AAT
1 AAT
18914261 AAACTATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 5 0.13
19 34 0.87
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (19 bp):
AATTAGGATTAATTAAGTT
Found at i:18918137 original size:10 final size:10
Alignment explanation
Indices: 18918107--18918160 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
18918097 ATTGTTAAGA
*
18918107 AATTATGATT
1 AATTAAGATT
18918117 AATTAAG-TT
1 AATTAAGATT
*
18918126 AATTAGGATT
1 AATTAAGATT
18918136 AATTAAG-TT
1 AATTAAGATT
*
18918145 AATTAGGATT
1 AATTAAGATT
18918155 AATTAA
1 AATTAA
18918161 TTAATAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (10 bp):
AATTAAGATT
Found at i:18918140 original size:4 final size:4
Alignment explanation
Indices: 18918114--18918165 Score: 50
Period size: 4 Copynumber: 11.5 Consensus size: 4
18918104 AGAAATTATG
18918114 ATTA ATTA AGTTA ATTA GGATTA ATTA AGTTA ATTA GGATTA ATTA ATTA
1 ATTA ATTA A-TTA ATTA --ATTA ATTA A-TTA ATTA --ATTA ATTA ATTA
18918164 AT
1 AT
18918166 AAACTATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 26 0.62
5 8 0.19
6 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (4 bp):
ATTA
Found at i:18918140 original size:23 final size:19
Alignment explanation
Indices: 18918107--18918165 Score: 102
Period size: 19 Copynumber: 3.2 Consensus size: 19
18918097 ATTGTTAAGA
*
18918107 AATTATGATTAATTAAGTT
1 AATTAGGATTAATTAAGTT
18918126 AATTAGGATTAATTAAGTT
1 AATTAGGATTAATTAAGTT
18918145 AATTAGGATTAATTAA-TT
1 AATTAGGATTAATTAAGTT
18918163 AAT
1 AAT
18918166 AAACTATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 5 0.13
19 34 0.87
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (19 bp):
AATTAGGATTAATTAAGTT
Found at i:18919719 original size:61 final size:57
Alignment explanation
Indices: 18919597--18919738 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 57
18919587 AAACTTAATC
* * * *
18919597 AATTTAATATTAAATAATATTAAATTATATAATACTTATCGAGATAAATATTAGATTA
1 AATTTAATATTAAAT-CTATTAAATTATAGAATACTTATCAAGATAAATATTAAATTA
*
18919655 AATTTAATATTAAATCTATTAAATTAATAGAATATTTATCTATAAGATAAATATTAAATTA
1 AATTTAATATTAAATCTATTAAATT-ATAGAATACTTATC---AAGATAAATATTAAATTA
* *
18919716 AATTAAATATTAAAACTATTAAA
1 AATTTAATATTAAATCTATTAAA
18919739 ACAATATTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 9 0.12
58 27 0.37
61 37 0.51
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (57 bp):
AATTTAATATTAAATCTATTAAATTATAGAATACTTATCAAGATAAATATTAAATTA
Found at i:18920085 original size:19 final size:19
Alignment explanation
Indices: 18920061--18920098 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18920051 GTTTTTGGGT
18920061 TCTCAGGTCCAATTTTCAA
1 TCTCAGGTCCAATTTTCAA
18920080 TCTCAGGTCCAATTTTCAA
1 TCTCAGGTCCAATTTTCAA
18920099 GTTCAATTAC
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:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTCAGGTCCAATTTTCAA
Found at i:18925442 original size:41 final size:42
Alignment explanation
Indices: 18925380--18925487 Score: 150
Period size: 41 Copynumber: 2.6 Consensus size: 42
18925370 ATTGTTAGTG
*
18925380 ACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGA-
1 ACAT-ATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
18925422 A-ATTATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
1 ACA-TATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
* *
18925464 ACAT-TTCGGACTATAAGTCTAGCA
1 ACATATTCAGACTATACGTCTAGCA
18925488 AGCTCAAGAG
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
41 55 0.92
42 4 0.07
43 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
ACATATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
Found at i:18925816 original size:37 final size:37
Alignment explanation
Indices: 18925709--18925823 Score: 169
Period size: 37 Copynumber: 3.1 Consensus size: 37
18925699 ATAGATAAAA
* *
18925709 ATATATGTATGCATTCGGCATAGGTGACTATAAGGGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
*
18925746 ATATATGTATGCATTCGGCATAGGTGAAAATAAGTGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
* *
18925783 ATATATGTATGCATTCGGCATAAGT-AGGTATAAGTGT
1 ATATATGTATGCATTCGGCATAGGTGA-ATATAAGTGT
18925820 ATAT
1 ATAT
18925824 GTGCATTCTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
36 1 0.01
37 70 0.99
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (37 bp):
ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
Found at i:18927800 original size:5 final size:5
Alignment explanation
Indices: 18927790--18927819 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
18927780 ATATCAAACT
18927790 TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA
18927820 ACATTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:18928750 original size:20 final size:20
Alignment explanation
Indices: 18928725--18928806 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
18928715 TTAACTTTAC
18928725 TATTAAATCTATTAAATTAA
1 TATTAAATCTATTAAATTAA
* *
18928745 TATTAAA-ATATGAAGA-TAA
1 TATTAAATCTATTAA-ATTAA
*
18928764 GTATTAAAT-TA--AATTTAA
1 -TATTAAATCTATTAAATTAA
* *
18928782 TATTAAAGCTATTAAAATAA
1 TATTAAATCTATTAAATTAA
18928802 TATTA
1 TATTA
18928807 TTTTTGGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 7 0.14
18 7 0.14
19 8 0.16
20 27 0.55
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (20 bp):
TATTAAATCTATTAAATTAA
Found at i:18928806 original size:37 final size:36
Alignment explanation
Indices: 18928735--18928806 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
18928725 TATTAAATCT
*
18928735 ATTAAATTAATATTAAAATATGAAGATAAGTATTAA
1 ATTAAATTAATATTAAAATATGAAAATAAGTATTAA
* *
18928771 ATTAAATTTAATATTAAAGCTATTAAAATAA-TATTA
1 ATTAAA-TTAATATTAAA-ATATGAAAATAAGTATTA
18928807 TTTTTGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 16 0.52
38 9 0.29
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (36 bp):
ATTAAATTAATATTAAAATATGAAAATAAGTATTAA
Found at i:18929791 original size:16 final size:15
Alignment explanation
Indices: 18929770--18929838 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 15
18929760 TCAAGAAATA
18929770 ATTAATTCACAAAGTG
1 ATTAATTCAC-AAGTG
**
18929786 ATTAATTCACTTGT-
1 ATTAATTCACAAGTG
*
18929800 A-T-ATTTATCAA-TG
1 ATTAATTCA-CAAGTG
18929813 ATTAATTCACAAAGTG
1 ATTAATTCAC-AAGTG
18929829 ATTAATTCAC
1 ATTAATTCAC
18929839 TTATATGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
12 5 0.12
13 3 0.07
14 3 0.07
15 8 0.20
16 22 0.54
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (15 bp):
ATTAATTCACAAGTG
Found at i:18938062 original size:15 final size:15
Alignment explanation
Indices: 18938042--18938071 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18938032 TAATTTTAAA
*
18938042 TTTTGATTTATAATG
1 TTTTGATTCATAATG
18938057 TTTTGATTCATAATG
1 TTTTGATTCATAATG
18938072 AAATGATATA
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:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTTGATTCATAATG
Found at i:18938998 original size:21 final size:21
Alignment explanation
Indices: 18938974--18939015 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18938964 ATGGTCAGGA
*
18938974 TATTCATTGTCTCAGGTGTGG
1 TATTCATTGTCTCAAGTGTGG
18938995 TATTCATTGTCTCAAGTGTGG
1 TATTCATTGTCTCAAGTGTGG
18939016 CTTAGGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (21 bp):
TATTCATTGTCTCAAGTGTGG
Found at i:18940347 original size:102 final size:103
Alignment explanation
Indices: 18940171--18940375 Score: 403
Period size: 102 Copynumber: 2.0 Consensus size: 103
18940161 ACTTTTTCTT
18940171 TTTGACATATATGATTAATTTATCCTATAAAACGCTATGGATTTTAAAATCTTTCATTATTTGAA
1 TTTGACATATATGATTAATTTATCCTATAAAACGCTATGGATTTTAAAATCTTTCATTATTTGAA
18940236 GCTACTAAGTATAAATATGTTCGAGGC-CGTATGTTTA
66 GCTACTAAGTATAAATATGTTCGAGGCACGTATGTTTA
18940273 TTTGACATATATGATTAATTTATCCTATAAAACGCTATGGATTTTAAAATCTTTCATTATTTGAA
1 TTTGACATATATGATTAATTTATCCTATAAAACGCTATGGATTTTAAAATCTTTCATTATTTGAA
18940338 GCTACTAAGTATAAATATGTTCGAGGCACGTATGTTTA
66 GCTACTAAGTATAAATATGTTCGAGGCACGTATGTTTA
18940376 ACTTTTCTAT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 92 0.90
103 10 0.10
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (103 bp):
TTTGACATATATGATTAATTTATCCTATAAAACGCTATGGATTTTAAAATCTTTCATTATTTGAA
GCTACTAAGTATAAATATGTTCGAGGCACGTATGTTTA
Found at i:18948006 original size:33 final size:33
Alignment explanation
Indices: 18947958--18948057 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 33
18947948 AGATCGATCA
* * *
18947958 GAATTTGAG-AAGGAGACAGATGTACAGTCGGT
1 GAATTTGGGAAAGGAGACAAATGTACAGCCGGT
* *
18947990 GAATTTGGGAAAGGAGACAAATGTACAACCAGT
1 GAATTTGGGAAAGGAGACAAATGTACAGCCGGT
*
18948023 GAATTTGGGACAGGAGACAAATGTACAGCCGGT
1 GAATTTGGGAAAGGAGACAAATGTACAGCCGGT
18948056 GA
1 GA
18948058 CAGAACATTC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
32 8 0.14
33 51 0.86
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.19
Consensus pattern (33 bp):
GAATTTGGGAAAGGAGACAAATGTACAGCCGGT
Found at i:18953334 original size:25 final size:25
Alignment explanation
Indices: 18953306--18953387 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
18953296 TATTATTTAT
18953306 TTATCTTATTATTTTTCACATGCAA
1 TTATCTTATTATTTTTCACATGCAA
**
18953331 TTATCTTATT-TGGTT---AT-CTAA
1 TTATCTTATTATTTTTCACATGC-AA
*
18953352 GTATCTTATTATTTTTCACATGCAA
1 TTATCTTATTATTTTTCACATGCAA
18953377 TTATCTTATTA
1 TTATCTTATTA
18953388 GGTTATCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.02
21 13 0.29
22 3 0.07
24 3 0.07
25 24 0.53
26 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.06, T:0.54
Consensus pattern (25 bp):
TTATCTTATTATTTTTCACATGCAA
Found at i:18953374 original size:46 final size:46
Alignment explanation
Indices: 18953307--18953400 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
18953297 ATTATTTATT
*
18953307 TATCTTATTATTTTTCACATGCAATTATCTTATTTGGTTATCTAAG
1 TATCTTATTATTTTTCACATGCAATTATCTTATTAGGTTATCTAAG
18953353 TATCTTATTATTTTTCACATGCAATTATCTTATTAGGTTATCTAAG
1 TATCTTATTATTTTTCACATGCAATTATCTTATTAGGTTATCTAAG
18953399 TA
1 TA
18953401 ATAAATTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (46 bp):
TATCTTATTATTTTTCACATGCAATTATCTTATTAGGTTATCTAAG
Found at i:18959020 original size:9 final size:9
Alignment explanation
Indices: 18959003--18959047 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
18958993 TTTTTTCTCC
18959003 AAAACCCTA
1 AAAACCCTA
*
18959012 AAAATCCTA
1 AAAACCCTA
*
18959021 AAAA-CCTT
1 AAAACCCTA
18959029 AAAACCCT-
1 AAAACCCTA
18959037 -AAACCCTA
1 AAAACCCTA
18959045 AAA
1 AAA
18959048 TCCAAAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 7 0.23
8 7 0.23
9 17 0.55
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAACCCTA
Found at i:18960878 original size:28 final size:29
Alignment explanation
Indices: 18960845--18960945 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
18960835 GCTATCTCTG
*
18960845 AAAGGACGCCTTT-AGACAATCTCTATTA
1 AAAGGAAGCCTTTGAGACAATCTCTATTA
* *
18960873 AAAGGAAGCCTTTGTGGCAATCTCTATTA
1 AAAGGAAGCCTTTGAGACAATCTCTATTA
*
18960902 AAAGGAAGCCTTTTGTGGA-AATCTCTATTA
1 AAAGGAAGCC-TTTG-AGACAATCTCTATTA
*
18960932 AAAGAAAGCCTTTG
1 AAAGGAAGCCTTTG
18960946 TGGTTATCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 12 0.19
29 27 0.42
30 24 0.38
31 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (29 bp):
AAAGGAAGCCTTTGAGACAATCTCTATTA
Found at i:18960919 original size:30 final size:29
Alignment explanation
Indices: 18960861--18960993 Score: 169
Period size: 29 Copynumber: 4.6 Consensus size: 29
18960851 CGCCTTTAGA
18960861 CAATCTCTATTAAAAGGAAGCCTTTGTGG
1 CAATCTCTATTAAAAGGAAGCCTTTGTGG
18960890 CAATCTCTATTAAAAGGAAGCCTTTTGTGG
1 CAATCTCTATTAAAAGGAAGCC-TTTGTGG
* *
18960920 AAATCTCTATTAAAAGAAAGCCTTTGTGG
1 CAATCTCTATTAAAAGGAAGCCTTTGTGG
** * * *
18960949 TTATCTTTGTT-AAAGGAAGCCCTTGTGG
1 CAATCTCTATTAAAAGGAAGCCTTTGTGG
* *
18960977 CGATCTCTGTTAAAAGG
1 CAATCTCTATTAAAAGG
18960994 GTGTCTTTGT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 23 0.25
29 41 0.45
30 27 0.30
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (29 bp):
CAATCTCTATTAAAAGGAAGCCTTTGTGG
Found at i:18960941 original size:59 final size:57
Alignment explanation
Indices: 18960825--18960992 Score: 164
Period size: 59 Copynumber: 3.0 Consensus size: 57
18960815 CATAAAAATG
* * * * *
18960825 AGCCTTTGTGGCTATCTC--TGAAAGGACG-CCTT-TAGACAATCTCTATTAAAAGGA
1 AGCCTTTGTGGCAATCTCTATTAAAGGAAGCCCTTGTGGA-AATCTCTATTAAAAGAA
*
18960879 AGCCTTTGTGGCAATCTCTATTAAAAGGAAGCCTTTTGTGGAAATCTCTATTAAAAGAA
1 AGCCTTTGTGGCAATCTCTATT-AAAGGAAGCC-CTTGTGGAAATCTCTATTAAAAGAA
** * * ** *
18960938 AGCCTTTGTGGTTATCTTTGTTAAAGGAAGCCCTTGTGGCGATCTCTGTTAAAAG
1 AGCCTTTGTGGCAATCTCTATTAAAGGAAGCCCTTGTGGAAATCTCTATTAAAAG
18960993 GGTGTCTTTG
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
54 17 0.18
56 1 0.01
57 26 0.28
58 11 0.12
59 36 0.38
60 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (57 bp):
AGCCTTTGTGGCAATCTCTATTAAAGGAAGCCCTTGTGGAAATCTCTATTAAAAGAA
Found at i:18975243 original size:75 final size:75
Alignment explanation
Indices: 18975120--18975270 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
18975110 TACAATTTAT
*
18975120 AGGGATGCTGACAATAAATAAATAAAAAGAATAATTTATATTAGAATATATAAAAAAATAGTGTT
1 AGGGATGCTGACAATAAATAAATAAAAAGAATAATTTATATTAGAATATATAAAAAAATAGTGTG
18975185 ACGTTATTAA
66 ACGTTATTAA
*
18975195 AGGGATGCTGACAATAAATAAATAAAAAGAATAATTTATATTAGAATATATTAAAAAATAGTGTG
1 AGGGATGCTGACAATAAATAAATAAAAAGAATAATTTATATTAGAATATATAAAAAAATAGTGTG
18975260 ACGTTATTAA
66 ACGTTATTAA
18975270 A
1 A
18975271 TTTTAAAGAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (75 bp):
AGGGATGCTGACAATAAATAAATAAAAAGAATAATTTATATTAGAATATATAAAAAAATAGTGTG
ACGTTATTAA
Found at i:18979632 original size:159 final size:159
Alignment explanation
Indices: 18979358--18979675 Score: 636
Period size: 159 Copynumber: 2.0 Consensus size: 159
18979348 TTATTACACA
18979358 ACGTGATATTTTTGTAAACTCAATTGATTTTTTTCTATTTTTTTGATTTGTTTTTTCAAAAAGTC
1 ACGTGATATTTTTGTAAACTCAATTGATTTTTTTCTATTTTTTTGATTTGTTTTTTCAAAAAGTC
18979423 TTTCTTTATTACATATCGAAAATAATCATGACATCTGTTAGGATCGCCCCGATTAAGTAACAAAC
66 TTTCTTTATTACATATCGAAAATAATCATGACATCTGTTAGGATCGCCCCGATTAAGTAACAAAC
18979488 AAGTAAAATAGCAGAAGAAATTGAGAAGG
131 AAGTAAAATAGCAGAAGAAATTGAGAAGG
18979517 ACGTGATATTTTTGTAAACTCAATTGATTTTTTTCTATTTTTTTGATTTGTTTTTTCAAAAAGTC
1 ACGTGATATTTTTGTAAACTCAATTGATTTTTTTCTATTTTTTTGATTTGTTTTTTCAAAAAGTC
18979582 TTTCTTTATTACATATCGAAAATAATCATGACATCTGTTAGGATCGCCCCGATTAAGTAACAAAC
66 TTTCTTTATTACATATCGAAAATAATCATGACATCTGTTAGGATCGCCCCGATTAAGTAACAAAC
18979647 AAGTAAAATAGCAGAAGAAATTGAGAAGG
131 AAGTAAAATAGCAGAAGAAATTGAGAAGG
18979676 TGAACACACA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (159 bp):
ACGTGATATTTTTGTAAACTCAATTGATTTTTTTCTATTTTTTTGATTTGTTTTTTCAAAAAGTC
TTTCTTTATTACATATCGAAAATAATCATGACATCTGTTAGGATCGCCCCGATTAAGTAACAAAC
AAGTAAAATAGCAGAAGAAATTGAGAAGG
Found at i:18982464 original size:79 final size:79
Alignment explanation
Indices: 18982368--18982522 Score: 247
Period size: 79 Copynumber: 2.0 Consensus size: 79
18982358 AGGCATGCTT
*
18982368 ATATACAGATAAAACATATCAGAACATACTAGTTGCACACATAATTAACAAATCAAAACATGCTA
1 ATATACAGATAAAACATATCAGAACATACTAATTGCACACATAATTAACAAATCAAAACATGCTA
18982433 TTGGCATATTCCCC
66 TTGGCATATTCCCC
* * * * *
18982447 ATATGCAGATAAAACATATCAGAACATACTAATTGTACATATAGTTAACAGATCAAAACATGCTA
1 ATATACAGATAAAACATATCAGAACATACTAATTGCACACATAATTAACAAATCAAAACATGCTA
*
18982512 TTGGTATATTC
66 TTGGCATATTC
18982523 GACCATCACA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (79 bp):
ATATACAGATAAAACATATCAGAACATACTAATTGCACACATAATTAACAAATCAAAACATGCTA
TTGGCATATTCCCC
Found at i:18987827 original size:32 final size:32
Alignment explanation
Indices: 18987791--18987854 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
18987781 TCCATACTTG
18987791 AATTC-ATTTCAATGTTCACATCTCAT-TTCATC
1 AATTCAATTTC-AT-TTCACATCTCATATTCATC
*
18987823 AATTCATATTTCATTTCCCATCTCATATTCAT
1 AATTCA-ATTTCATTTCACATCTCATATTCAT
18987855 TTTTCATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 16 0.57
33 7 0.25
34 5 0.18
ACGTcount: A:0.28, C:0.25, G:0.02, T:0.45
Consensus pattern (32 bp):
AATTCAATTTCATTTCACATCTCATATTCATC
Found at i:18989108 original size:35 final size:34
Alignment explanation
Indices: 18989052--18989117 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
18989042 TTTTAATTTC
*
18989052 ATTCATTATTATTATATTATAATATATACATTAG
1 ATTCATTATTATTATATTATAACATATACATTAG
18989086 ATTCATT-TTATTTATTATTATAACATATACAT
1 ATTCATTATTA-TTA-TATTATAACATATACAT
18989118 ATCTATACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.10
34 10 0.34
35 16 0.55
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (34 bp):
ATTCATTATTATTATATTATAACATATACATTAG
Found at i:18997385 original size:2 final size:2
Alignment explanation
Indices: 18997378--18997424 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
18997368 CAAATTGTTT
18997378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18997420 TA TA T
1 TA TA T
18997425 CCAACAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.