Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 157 of 173
Found at i:47176832 original size:37 final size:35
Alignment explanation
Indices: 47176746--47176862 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 35
47176736 CAACAACTTT
* * *
47176746 TTTTTAAACACGAA-TTTTT-AAAATACA--AGAA
1 TTTTGAAACACGAATTTTTTAAAAAAACACGAAAA
47176777 TTTTAGAAACACGAATTTTTTAAAAAAAACACGAAAA
1 TTTT-GAAACACGAATTTTTT-AAAAAAACACGAAAA
****
47176814 TTTTGAAACACGAGATTTTTTTTTGAAACACGAAAA
1 TTTTGAAACACGA-ATTTTTTAAAAAAACACGAAAA
47176850 TTTATGAAACACG
1 TTT-TGAAACACG
47176863 GTTTTCTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.06
32 9 0.13
33 5 0.07
35 7 0.10
36 23 0.32
37 23 0.32
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (35 bp):
TTTTGAAACACGAATTTTTTAAAAAAACACGAAAA
Found at i:47177163 original size:16 final size:16
Alignment explanation
Indices: 47177142--47177187 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
47177132 TATTAAAATT
47177142 AATTAAAATAAAATAA
1 AATTAAAATAAAATAA
** *
47177158 AATTAAAATGGAATTA
1 AATTAAAATAAAATAA
47177174 AATTAAAGATAAAA
1 AATTAAA-ATAAAA
47177188 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (16 bp):
AATTAAAATAAAATAA
Found at i:47177341 original size:7 final size:7
Alignment explanation
Indices: 47177329--47177366 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
47177319 GAATTGAACC
47177329 TCTTTTT
1 TCTTTTT
47177336 TCTTTTT
1 TCTTTTT
47177343 TCTTTTT
1 TCTTTTT
47177350 CTCTTTTT
1 -TCTTTTT
47177358 TCTTTTT
1 TCTTTTT
47177365 TC
1 TC
47177367 CTCCTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TCTTTTT
Found at i:47177354 original size:15 final size:15
Alignment explanation
Indices: 47177329--47177405 Score: 79
Period size: 15 Copynumber: 5.1 Consensus size: 15
47177319 GAATTGAACC
47177329 TCTTTTT-TCTTTTT
1 TCTTTTTCTCTTTTT
47177343 TCTTTTTCTCTTTTT
1 TCTTTTTCTCTTTTT
47177358 TCTTTTTTCCTCCTTTTT
1 TC-TTTTT-CT-CTTTTT
* *
47177376 TCCTTCTCT-TTTTCT
1 TCTTTTTCTCTTTT-T
47177391 TCTTTTTCT-TTTTT
1 TCTTTTTCTCTTTTT
47177405 T
1 T
47177406 TTTCTACTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 13 0.24
15 21 0.39
16 7 0.13
17 5 0.09
18 8 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TCTTTTTCTCTTTTT
Found at i:47177357 original size:9 final size:8
Alignment explanation
Indices: 47177331--47177405 Score: 55
Period size: 8 Copynumber: 8.8 Consensus size: 8
47177321 ATTGAACCTC
47177331 TTTTTTC-
1 TTTTTTCT
47177338 TTTTTTCT
1 TTTTTTCT
*
47177346 TTTTCTC-
1 TTTTTTCT
47177353 TTTTTTCT
1 TTTTTTCT
47177361 TTTTTCCTCCTT
1 TTTTT--T-C-T
47177373 TTTTCCTTCT
1 TTTT--TTCT
*
47177383 CTTTTTCT
1 TTTTTTCT
47177391 TCTTTTTCT
1 T-TTTTTCT
47177400 TTTTTT
1 TTTTTT
47177406 TTTCTACTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
7 13 0.24
8 20 0.36
9 8 0.15
10 5 0.09
11 2 0.04
12 6 0.11
14 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:47177549 original size:5 final size:5
Alignment explanation
Indices: 47177537--47177580 Score: 72
Period size: 5 Copynumber: 8.8 Consensus size: 5
47177527 TTCTTTTCTC
47177537 TTTT- TTTTG TTTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG -TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
47177581 TGGGCTGCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.11
5 29 0.76
6 5 0.13
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:47177656 original size:9 final size:9
Alignment explanation
Indices: 47177642--47177689 Score: 69
Period size: 9 Copynumber: 5.1 Consensus size: 9
47177632 ACTGTTATAA
47177642 TATTTTTTT
1 TATTTTTTT
47177651 TATTTTTTT
1 TATTTTTTT
47177660 TATTTTTCTT
1 TATTTTT-TT
*
47177670 TTTTCTTTTT
1 TATT-TTTTT
47177680 TATTTTTTT
1 TATTTTTTT
47177689 T
1 T
47177690 CTTTCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 22 0.63
10 10 0.29
11 3 0.09
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:47177671 original size:23 final size:23
Alignment explanation
Indices: 47177647--47177700 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
47177637 TATAATATTT
* *
47177647 TTTTTATTTTTT-TTATTTTTCT
1 TTTTTCTTTTTTATTTTTTTTCT
47177669 TTTTTCTTTTTTATTTTTTTTCT
1 TTTTTCTTTTTTATTTTTTTTCT
47177692 TTCTTTCTT
1 TT-TTTCTT
47177701 CTTCTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 11 0.39
23 11 0.39
24 6 0.21
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (23 bp):
TTTTTCTTTTTTATTTTTTTTCT
Found at i:47177678 original size:20 final size:19
Alignment explanation
Indices: 47177642--47177697 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
47177632 ACTGTTATAA
*
47177642 TATTTTTTTTATT-TTTTT
1 TATTTTTTTTTTTCTTTTT
47177660 TATTTTTCTTTTTTCTTTTT
1 TATTTTT-TTTTTTCTTTTT
47177680 TATTTTTTTTCTTTCTTT
1 TATTTTTTTT-TTTCTTT
47177698 CTTCTTCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 19 0.56
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (19 bp):
TATTTTTTTTTTTCTTTTT
Found at i:47177698 original size:8 final size:7
Alignment explanation
Indices: 47177646--47177703 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
47177636 TTATAATATT
*
47177646 TTTTTTA
1 TTTTTTC
*
47177653 TTTTTTT
1 TTTTTTC
47177660 TATTTTTC
1 T-TTTTTC
47177668 TTTTTTC
1 TTTTTTC
*
47177675 TTTTTTA
1 TTTTTTC
47177682 TTTTTT-
1 TTTTTTC
*
47177688 TTCTTTC
1 TTTTTTC
*
47177695 TTTCTTC
1 TTTTTTC
47177702 TT
1 TT
47177704 CTTCTTCTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
6 5 0.12
7 32 0.74
8 6 0.14
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:47177702 original size:3 final size:3
Alignment explanation
Indices: 47177696--47177752 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
47177686 TTTTCTTTCT
47177696 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
47177744 TTC TTC TTC
1 TTC TTC TTC
47177753 AAAACCCTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:47178169 original size:29 final size:29
Alignment explanation
Indices: 47178132--47178231 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
47178122 AGAAAATTTA
* *
47178132 GGGTAAAAATGTATTTTCAAAAAGGTTGT
1 GGGTCAAAATGTAATTTCAAAAAGGTTGT
47178161 GGGTCAAAATGTAATTTC-AAAAGGTT-T
1 GGGTCAAAATGTAATTTCAAAAAGGTTGT
*
47178188 AGGGGTCAAAATATAATTTCAAAAA-GTTCAG-
1 --GGGTCAAAATGTAATTTCAAAAAGGTT--GT
47178219 GGGTCAAAATGTA
1 GGGTCAAAATGTA
47178232 TTTTTTGATT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.02
28 8 0.13
29 48 0.79
30 4 0.07
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTCAAAAAGGTTGT
Found at i:47178706 original size:81 final size:81
Alignment explanation
Indices: 47178409--47179490 Score: 1668
Period size: 81 Copynumber: 13.3 Consensus size: 81
47178399 AAAATTTTCT
* * * * *
47178409 TTTTATTTGAAAAACAGAAA-TT--GA-AAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCT
1 TTTT-TTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTT
**
47178470 CTAACAATATGAGTTGA
65 CTCGCAATATGAGTTGA
47178487 --TTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47178550 TCGCAATATGAGTTGA
66 TCGCAATATGAGTTGA
* * * *
47178566 TTTTTTTTTTGAAAAGACAAAAATTTAAAAGAAATACCTCAACGTGAGACCCGACGCTCAACTCA
1 ---TTTTTTTGAAAA-ACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCA
47178631 CTTCTCGCAATATGAGTTGA
62 CTTCTCGCAATATGAGTTGA
47178651 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47178716 TCGCAATATGAGTTGA
66 TCGCAATATGAGTTGA
* *
47178732 TTTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCA--GTGTGACCCGAGGCTCAACTCA-T
1 -TTTTTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACT
*
47178794 CTCTCGCATTATGAGTTGA
64 -TCTCGCAATATGAGTTGA
47178813 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47178878 TCGCAATATGAGTTGA
66 TCGCAATATGAGTTGA
* *
47178894 TTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTTATTT
1 -TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTT
*
47178959 CTCGTAATATGAGTTGA
65 CTCGCAATATGAGTTGA
*
47178976 TTTTTTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCATGCGACCCGAGGCTCAACTC
1 -----TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTC
47179041 ACTTCTCGCAATATGAGTTGA
61 ACTTCTCGCAATATGAGTTGA
* *
47179062 TTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCATTT
1 TTTTTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTT
*
47179125 CTCGCATTATGAGTTGA
65 CTCGCAATATGAGTTGA
47179142 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47179207 TCGCAATATGAGTTGA
66 TCGCAATATGAGTTGA
* * * *
47179223 TTTTCTTGAAAAACAGAAATTTAAAAGAAATACCTCAGTGTGCGACCCGAGACTCATCTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47179288 TCGCAATATGAGTTGA
66 TCGCAATATGAGTTGA
47179304 -TTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47179368 TCGCAATATGAGTTGA
66 TCGCAATATGAGTTGA
*
47179384 TTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTGAACTCACTT
1 -TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTT
47179449 CTCGCAATATGAGTTGA
65 CTCGCAATATGAGTTGA
* * *
47179466 -TTTATTGAAAAATAGAAATTGAAAA
1 TTTTTTTGAAAAACAGAAATTTAAAA
47179491 ATATTTCTTA
Statistics
Matches: 931, Mismatches: 47, Indels: 50
0.91 0.05 0.05
Matches are distributed among these distances:
75 15 0.02
76 4 0.00
78 1 0.00
79 110 0.12
80 149 0.16
81 261 0.28
82 209 0.22
83 29 0.03
84 10 0.01
85 65 0.07
86 78 0.08
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (81 bp):
TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
TCGCAATATGAGTTGA
Found at i:47179191 original size:410 final size:406
Alignment explanation
Indices: 47178409--47179490 Score: 1720
Period size: 410 Copynumber: 2.7 Consensus size: 406
47178399 AAAATTTTCT
* * * * *
47178409 TTTTATTTGAAAAACAGAAA-TT--GA-AAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCT
1 TTTT-TTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTT
**
47178470 CTAACAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCG
65 CTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCG
*
47178534 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAGACAAAAATTTAAAAGAA
130 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAA-ACAGAAATTTAAAAGAA
* * *
47178599 ATACCTCAACGTGAGACCCGACGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAA
194 ATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAA
47178664 CAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGT
259 CAGAAATTTAAAAGAAATACCTCAGCGT-CGACCCGAGGCTCAACTCACTTCTCGCAATATGAGT
* *
47178729 TGATTTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGTGTGACCCGAGGCTCAACTCA-
323 TGATTTTTTTTCGAAAAACAGAAATTTAAAAGAAATACCTCAGTGCGACCCGAGGCTCAACTCAC
*
47178793 TCTCTCGCATTATGAGTTGA
388 T-TCTCGCAATATGAGTTGA
47178813 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47178878 TCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCC
66 TCGCAATATGAGTTGA--TTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCC
* * *
47178943 GAGGCTCAACTTATTTCTCGTAATATGAGTTGATTTTTTTTTTTTGAAAAACAGAAATTTAAAAG
129 GAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTTTTTGAAAAACAGAAATTTAAAAG
*
47179008 AAATACCTCAGCATGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTCGAA
192 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT-GAA
* * *
47179073 AAACAGAGATTTAAAAGAAATACCTCAGCGT-GACCCGAGGCTCAACTCATTTCTCGCATTATGA
256 AAACAGAAATTTAAAAGAAATACCTCAGCGTCGACCCGAGGCTCAACTCACTTCTCGCAATATGA
47179137 GTTGA-TTTTTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAAC
321 GTTGATTTTTTTTCGAAAAACAGAAATTTAAAAGAAATACCTCA--GTGCGACCCGAGGCTCAAC
47179200 TCACTTCTCGCAATATGAGTTGA
384 TCACTTCTCGCAATATGAGTTGA
* * * *
47179223 TTTTCTTGAAAAACAGAAATTTAAAAGAAATACCTCAGTGTGCGACCCGAGACTCATCTCACTTC
1 TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
47179288 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGA
66 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGA
47179353 GGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTTTGAAAAACAGAAATTTAAAAGAAAT
131 GGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTTAAAAGAAAT
* * *
47179416 ACCTCAGCGTGCGACCCGAGGCTGAACTCACTTCTCGCAATATGAGTTGA-TTTATTGAAAAATA
196 ACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACA
*
47179480 GAAATTGAAAA
261 GAAATTTAAAA
47179491 ATATTTCTTA
Statistics
Matches: 631, Mismatches: 34, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
402 16 0.03
403 20 0.03
404 86 0.14
406 1 0.00
407 48 0.08
408 106 0.17
409 7 0.01
410 227 0.36
411 72 0.11
412 48 0.08
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (406 bp):
TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTC
TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGA
GGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTTAAAAGAAAT
ACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACA
GAAATTTAAAAGAAATACCTCAGCGTCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA
TTTTTTTTCGAAAAACAGAAATTTAAAAGAAATACCTCAGTGCGACCCGAGGCTCAACTCACTTC
TCGCAATATGAGTTGA
Found at i:47186584 original size:36 final size:37
Alignment explanation
Indices: 47186516--47186586 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
47186506 ACGAATTTTT
47186516 AAAATATAAGAATTTTAGAAACACGAATTTTTTTAAA
1 AAAATATAAGAATTTTAGAAACACGAATTTTTTTAAA
47186553 AAAATATGAA-AATTTT-GAAACACGAGATTTTTTT
1 AAAATAT-AAGAATTTTAGAAACACGA-ATTTTTTT
47186587 TGAAACACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 9 0.28
37 21 0.66
38 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (37 bp):
AAAATATAAGAATTTTAGAAACACGAATTTTTTTAAA
Found at i:47186609 original size:17 final size:16
Alignment explanation
Indices: 47186560--47186611 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 16
47186550 AAAAAAATAT
47186560 GAAAATTTTGAAACAC
1 GAAAATTTTGAAACAC
**
47186576 GAGATTTTTTTTGAAACAC
1 GA-A--AATTTTGAAACAC
47186595 GAAAATTTATGAAACAC
1 GAAAATTT-TGAAACAC
47186612 TGTTTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 1 0.04
19 13 0.46
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (16 bp):
GAAAATTTTGAAACAC
Found at i:47187285 original size:16 final size:15
Alignment explanation
Indices: 47187266--47187309 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 15
47187256 GGCTTGCTTC
47187266 TTTTCTGTTTTTTTTG
1 TTTT-TGTTTTTTTTG
47187282 TTTTTGTTTTGTTTTG
1 TTTTTGTTTT-TTTTG
47187298 TTTTTGTTTTTT
1 TTTTTGTTTTTT
47187310 GGGCTGCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (15 bp):
TTTTTGTTTTTTTTG
Found at i:47187287 original size:6 final size:6
Alignment explanation
Indices: 47187276--47187308 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
47187266 TTTTCTGTTT
47187276 TTTTTG TTTTTG -TTTTG -TTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
47187309 TGGGCTGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:47187400 original size:23 final size:23
Alignment explanation
Indices: 47187372--47187416 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47187362 TATTATAATA
*
47187372 TTTTTTATTATTTCTTTTTCTTT
1 TTTTTTATTATTTCTTCTTCTTT
* *
47187395 TTTTTTCTTTTTTCTTCTTCTT
1 TTTTTTATTATTTCTTCTTCTT
47187417 CTTCTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTATTATTTCTTCTTCTTT
Found at i:47187412 original size:3 final size:3
Alignment explanation
Indices: 47187406--47187438 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
47187396 TTTTTCTTTT
47187406 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
47187439 AAAACCCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:47187842 original size:29 final size:28
Alignment explanation
Indices: 47187797--47187904 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 28
47187787 TAATTTTGAG
*
47187797 AAAA-TTTAGGGTAAAAATGTAATTTCA
1 AAAAGTTTAGGGTCAAAATGTAATTTCA
47187824 AAAAGGTTGTA-GGTCAAAATGTAATTTC-
1 AAAA-GTT-TAGGGTCAAAATGTAATTTCA
*
47187852 AAAAGTTTTAGGGGTCAAAATATAATTTCA
1 AAAAG-TTTA-GGGTCAAAATGTAATTTCA
47187882 AAAAGTTTAGGGGTCAAAATGTA
1 AAAAGTTTA-GGGTCAAAATGTA
47187905 TTTTTTGATT
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.10
28 6 0.08
29 51 0.72
30 7 0.10
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (28 bp):
AAAAGTTTAGGGTCAAAATGTAATTTCA
Found at i:47192723 original size:20 final size:19
Alignment explanation
Indices: 47192681--47192720 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
47192671 TTATTAAAAT
47192681 ATAAATTATATAAATTATTA
1 ATAAATTATAT-AATTATTA
47192701 ATAAATTATCAT-ATTATTA
1 ATAAATTAT-ATAATTATTA
47192720 A
1 A
47192721 ATATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATTATATAATTATTA
Found at i:47192736 original size:22 final size:22
Alignment explanation
Indices: 47192671--47192736 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
47192661 GCTAAATAAC
*
47192671 TTATTAAAATATAAATTATATAAA
1 TTATT-AAATATAAATTAT-TATA
*
47192695 TTATT--A-ATAAATTATCATA
1 TTATTAAATATAAATTATTATA
*
47192714 TTATTAAATATAAATAATTATA
1 TTATTAAATATAAATTATTATA
47192736 T
1 T
47192737 AAGTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 2 0.06
22 12 0.34
24 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATTAAATATAAATTATTATA
Found at i:47203786 original size:10 final size:10
Alignment explanation
Indices: 47203771--47203803 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
47203761 AAAATAGAAT
47203771 AATTCTAAAA
1 AATTCTAAAA
47203781 AATTCTAAAA
1 AATTCTAAAA
47203791 AATT-TATAAA
1 AATTCTA-AAA
47203801 AAT
1 AAT
47203804 GTATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 20 0.91
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (10 bp):
AATTCTAAAA
Found at i:47204323 original size:20 final size:19
Alignment explanation
Indices: 47204298--47204368 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
47204288 CGAGTTCAAG
47204298 TTTTTATGATTTATTTATAA
1 TTTTTAT-ATTTATTTATAA
*
47204318 TTTTTATAAATTTATAT-TAA
1 TTTTTAT--ATTTATTTATAA
* *
47204338 TTTTAATATTTA-TTACAA
1 TTTTTATATTTATTTATAA
47204356 TTTTT-TA-TTATTT
1 TTTTTATATTTATTT
47204369 TTTAAAGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 3 0.07
17 5 0.12
18 11 0.26
20 16 0.38
21 7 0.17
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTATTTATAA
Found at i:47210611 original size:29 final size:29
Alignment explanation
Indices: 47210578--47210634 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
47210568 AAATAAATAA
* *
47210578 ATAAA-AAGAAAGAAAGATAGAAATGAAAC
1 ATAAAGAA-AAAGAAAGAAAGAAAAGAAAC
47210607 ATAAAGAAAAAGAAAGAAAGAAAAGAAA
1 ATAAAGAAAAAGAAAGAAAGAAAAGAAA
47210635 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.07
Consensus pattern (29 bp):
ATAAAGAAAAAGAAAGAAAGAAAAGAAAC
Found at i:47210641 original size:29 final size:29
Alignment explanation
Indices: 47210586--47210644 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
47210576 AAATAAAAAG
* * *
47210586 AAAGAAAGATAGAAATGAAACATAAAGAA
1 AAAGAAAGAAAGAAAAGAAACAAAAAGAA
47210615 AAAGAAAGAAAGAAAAGAAA-AGAAAAGAA
1 AAAGAAAGAAAGAAAAGAAACA-AAAAGAA
47210644 A
1 A
47210645 GGAAGGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.05
Consensus pattern (29 bp):
AAAGAAAGAAAGAAAAGAAACAAAAAGAA
Found at i:47211105 original size:5 final size:5
Alignment explanation
Indices: 47211095--47211133 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
47211085 GCAATATAAA
*
47211095 ATTGT ATTGT ATTGT ATTGT ATTGT ATTTT ATTGT ATTG
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTG
47211134 ATGAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (5 bp):
ATTGT
Found at i:47211366 original size:24 final size:24
Alignment explanation
Indices: 47211339--47211385 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
47211329 ATTGAAATGG
47211339 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
47211363 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
47211386 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:47213591 original size:7 final size:7
Alignment explanation
Indices: 47213581--47213607 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
47213571 ATAAAGTTTA
47213581 AAAATTC
1 AAAATTC
47213588 AAAATTC
1 AAAATTC
47213595 AAAATTC
1 AAAATTC
47213602 AAAATT
1 AAAATT
47213608 AATATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTC
Found at i:47217988 original size:22 final size:22
Alignment explanation
Indices: 47217942--47217988 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
47217932 CCATTGGGCA
* *
47217942 AAAAATAATTAAATAAGCAATT
1 AAAAATAATTAAAAAAGCAAGT
47217964 AAAAA-AATTAAAAAAGCCAAGT
1 AAAAATAATTAAAAAAG-CAAGT
47217986 AAA
1 AAA
47217989 CTTGGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAAATAATTAAAAAAGCAAGT
Found at i:47219694 original size:72 final size:72
Alignment explanation
Indices: 47219577--47219710 Score: 205
Period size: 72 Copynumber: 1.9 Consensus size: 72
47219567 CGTTGAATAT
*
47219577 TTCCAGAAATGTAAGATTTGTGAATTCTGGACATAGTTCACCAAAGAGCTTGTCATGGGAGACAT
1 TTCCAGAAATGTAAGATTTGTGAATTCTGGACACAGTTCACCAAAGAGCTTGTCATGGGAGACAT
47219642 CCAACAC
66 CCAACAC
** * * * *
47219649 TTCCAGATCTGTAAGTTTTGTTAATTCTGGAGACAGTTCACCAAAGAGCTTGTTATGGGAGA
1 TTCCAGAAATGTAAGATTTGTGAATTCTGGACACAGTTCACCAAAGAGCTTGTCATGGGAGA
47219711 GATTCAACGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (72 bp):
TTCCAGAAATGTAAGATTTGTGAATTCTGGACACAGTTCACCAAAGAGCTTGTCATGGGAGACAT
CCAACAC
Found at i:47236164 original size:3 final size:3
Alignment explanation
Indices: 47236156--47236184 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
47236146 TCCCACTCCC
47236156 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
47236185 CTGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:47237740 original size:23 final size:23
Alignment explanation
Indices: 47237714--47237767 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
47237704 TAATTTTTAA
*
47237714 ATTTTAAATTATTTAGTGATAAT
1 ATTTTAAATTATTTAATGATAAT
*
47237737 A-TTTAGGATTATTTAATGATAAT
1 ATTTTA-AATTATTTAATGATAAT
47237760 ATTTTAAA
1 ATTTTAAA
47237768 AAAATCTAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 18 0.69
24 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
ATTTTAAATTATTTAATGATAAT
Found at i:47237741 original size:13 final size:13
Alignment explanation
Indices: 47237723--47237763 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
47237713 AATTTTAAAT
47237723 TATTTAGTGATAA
1 TATTTAGTGATAA
47237736 TATTTAG-GAT--
1 TATTTAGTGATAA
*
47237746 TATTTAATGATAA
1 TATTTAGTGATAA
47237759 TATTT
1 TATTT
47237764 TAAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:47259973 original size:21 final size:21
Alignment explanation
Indices: 47259949--47259990 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47259939 TCATACTCAA
*
47259949 ATTTATTTATTC-TCTTCTCTT
1 ATTT-TTTATTCTTCCTCTCTT
*
47259970 ATTTTTTCTTCTTCCTCTCTT
1 ATTTTTTATTCTTCCTCTCTT
47259991 TGTTAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTTTATTCTTCCTCTCTT
Found at i:47261111 original size:22 final size:24
Alignment explanation
Indices: 47261085--47261128 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
47261075 GAAAAATATT
47261085 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
47261107 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
47261129 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:47261239 original size:9 final size:9
Alignment explanation
Indices: 47261225--47261261 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
47261215 TTTTGTTACA
47261225 ACAATTAAT
1 ACAATTAAT
47261234 ACAATTAAT
1 ACAATTAAT
47261243 ACAATTAAT
1 ACAATTAAT
47261252 ACAATTAAT
1 ACAATTAAT
47261261 A
1 A
47261262 ATTTGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:47261355 original size:16 final size:16
Alignment explanation
Indices: 47261334--47261375 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
47261324 AATAATTTGA
*
47261334 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
47261350 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
47261366 TAGTTTTAAT
1 TAATTTTAAT
47261376 TTTATTAAAA
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:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:47261364 original size:59 final size:65
Alignment explanation
Indices: 47261229--47261367 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 65
47261219 GTTACAACAA
47261229 TTAAT-ACAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGAT
1 TTAATAACAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAA-GTTAGAT
47261293 T
65 T
* *
47261294 TTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGATAATTTTACTAA-C-AA-TTA-A
1 TTA--ATAACAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAAGTTAGA
47261353 TT
64 TT
47261355 TTAATAACAATTA
1 TTAATAACAATTA
47261368 GTTTTAATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
59 9 0.13
61 6 0.09
62 3 0.04
64 2 0.03
65 4 0.06
66 27 0.40
67 2 0.03
68 15 0.22
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (65 bp):
TTAATAACAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAAGTTAGATT
Found at i:47264018 original size:13 final size:13
Alignment explanation
Indices: 47264000--47264151 Score: 67
Period size: 13 Copynumber: 11.2 Consensus size: 13
47263990 ATTTTGAATA
47264000 TAATATACTGTTT
1 TAATATACTGTTT
47264013 TAATATACTGATTACT
1 TAATATACTG-TT--T
* * * *
47264029 GTTATAAAAT-TTG
1 -TAATATACTGTTT
*
47264042 TAATATATTGTTT
1 TAATATACTGTTT
*
47264055 TAACTTTTAACT-TTT
1 TAA--TAT-ACTGTTT
*
47264070 -AATATACTATTAT
1 TAATATACTGTT-T
* *
47264083 AAATATACTTTTT
1 TAATATACTGTTT
* *
47264096 TAATATATTATTT
1 TAATATACTGTTT
*
47264109 TAATATATTGTTAT
1 TAATATACTGTT-T
* *
47264123 AAATATATTGTTT
1 TAATATACTGTTT
*
47264136 TAATATAATGTTT
1 TAATATACTGTTT
47264149 TAA
1 TAA
47264152 CTTTTAATAT
Statistics
Matches: 108, Mismatches: 19, Indels: 24
0.72 0.13 0.16
Matches are distributed among these distances:
11 3 0.03
12 10 0.09
13 53 0.49
14 26 0.24
15 7 0.06
16 3 0.03
17 6 0.06
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:47264109 original size:15 final size:13
Alignment explanation
Indices: 47264066--47264142 Score: 75
Period size: 13 Copynumber: 5.8 Consensus size: 13
47264056 AACTTTTAAC
*
47264066 TTTTAATATACTA
1 TTTTAATATATTA
*
47264079 TTATAAATATACTT-
1 TT-TTAATATA-TTA
47264093 TTTTAATATATTA
1 TTTTAATATATTA
*
47264106 TTTTAATATATTG
1 TTTTAATATATTA
* *
47264119 TTATAAATATATTG
1 TT-TTAATATATTA
47264133 TTTTAATATA
1 TTTTAATATA
47264143 ATGTTTTAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.04
13 30 0.56
14 21 0.39
15 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTTAATATATTA
Found at i:47264123 original size:40 final size:40
Alignment explanation
Indices: 47264043--47264151 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 40
47264033 TAAAATTTGT
* *
47264043 AATATATTGTTTTAACTTTTAA-CTTTTAATATACTATTATA
1 AATATATTGTTTTAA--TATAATATTTTAATATACTATTATA
* * *
47264084 AATATACTT-TTTTAATATATTATTTTAATATATTGTTATA
1 AATATA-TTGTTTTAATATAATATTTTAATATACTATTATA
*
47264124 AATATATTGTTTTAATATAATGTTTTAA
1 AATATATTGTTTTAATATAATATTTTAA
47264152 CTTTTAATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 5 0.09
40 39 0.67
41 12 0.21
42 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (40 bp):
AATATATTGTTTTAATATAATATTTTAATATACTATTATA
Found at i:47264176 original size:14 final size:13
Alignment explanation
Indices: 47264070--47264177 Score: 57
Period size: 13 Copynumber: 8.5 Consensus size: 13
47264060 TTTAACTTTT
*
47264070 AATATACTATTATA
1 AATATACTGTT-TA
* *
47264084 AATATACTTTTTT
1 AATATACTGTTTA
* * *
47264097 AATATATTATTTT
1 AATATACTGTTTA
*
47264110 AATATATTGTTATA
1 AATATACTGTT-TA
* *
47264124 AATATATTGTTTT
1 AATATACTGTTTA
*
47264137 AATATAATGTTT-
1 AATATACTGTTTA
47264149 --TA-ACT-TTT-
1 AATATACTGTTTA
47264157 AATATACTGTTATA
1 AATATACTGTT-TA
47264171 AATATAC
1 AATATAC
47264178 ATTTAATTTG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
8 3 0.04
9 2 0.03
10 4 0.05
11 3 0.04
12 2 0.03
13 35 0.45
14 29 0.37
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.52
Consensus pattern (13 bp):
AATATACTGTTTA
Found at i:47266828 original size:30 final size:30
Alignment explanation
Indices: 47266792--47266883 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
47266782 AAAGATAGTT
*
47266792 TGAAGCAAAATTAGAGATTGGGATTTTCAA
1 TGAAGCAAAATTACAGATTGGGATTTTCAA
*
47266822 TGAAGCAAAATTACAGATTGGGATTTTCAG
1 TGAAGCAAAATTACAGATTGGGATTTTCAA
*
47266852 TGAAGCAAAATTATAGATTGGGATTTTCAA
1 TGAAGCAAAATTACAGATTGGGATTTTCAA
47266882 TG
1 TG
47266884 CTTGATTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (30 bp):
TGAAGCAAAATTACAGATTGGGATTTTCAA
Found at i:47272501 original size:5 final size:5
Alignment explanation
Indices: 47272491--47272534 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
47272481 GATTATGTTT
47272491 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -TATA T
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T
47272535 AACAAAAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 22 0.63
6 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:47272516 original size:19 final size:19
Alignment explanation
Indices: 47272492--47272534 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
47272482 ATTATGTTTT
47272492 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
47272511 TATATTATATTATATTATA
1 TATATTATATTATATTATA
47272530 TATAT
1 TATAT
47272535 AACAAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:47273020 original size:34 final size:34
Alignment explanation
Indices: 47272977--47273042 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
47272967 AGTAAAATAT
47272977 TTTTCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
47273010 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
47273043 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:47273984 original size:41 final size:37
Alignment explanation
Indices: 47273936--47274035 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 37
47273926 TCGACCTTGA
47273936 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
47273976 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
47274014 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
47274036 CTTTATTGCT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 16 0.35
38 11 0.24
40 2 0.04
41 17 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:47276942 original size:32 final size:32
Alignment explanation
Indices: 47276906--47276972 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
47276896 TATATAGCCT
*
47276906 CTTATTCAAGCAGAACTTATCTCTCCTTGATC
1 CTTATTCAAGCAAAACTTATCTCTCCTTGATC
*
47276938 CTTATTCAAGCAAAACTTATCTCTCTTTGATC
1 CTTATTCAAGCAAAACTTATCTCTCCTTGATC
47276970 CTT
1 CTT
47276973 CCTCTATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.40
Consensus pattern (32 bp):
CTTATTCAAGCAAAACTTATCTCTCCTTGATC
Found at i:47277368 original size:21 final size:21
Alignment explanation
Indices: 47277342--47277400 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
47277332 AATTATTCTT
47277342 TAAATTTTATTTGCATGCAAC
1 TAAATTTTATTTGCATGCAAC
* ** * *
47277363 TAAA-TTTCTTCCCTTTACAAC
1 TAAATTTTATTTGC-ATGCAAC
47277384 TAAATTTTATTTGCATG
1 TAAATTTTATTTGCATG
47277401 AGGAGAAAGA
Statistics
Matches: 26, Mismatches: 10, Indels: 4
0.65 0.25 0.10
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.46
Consensus pattern (21 bp):
TAAATTTTATTTGCATGCAAC
Found at i:47283223 original size:8 final size:7
Alignment explanation
Indices: 47283203--47283235 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
47283193 TTAACAAGTC
47283203 TTAAAAA
1 TTAAAAA
47283210 TTAAAAA
1 TTAAAAA
47283217 TTAAAAA
1 TTAAAAA
47283224 TTACAAAA
1 TTA-AAAA
47283232 TTAA
1 TTAA
47283236 TTAGCCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:47288713 original size:30 final size:30
Alignment explanation
Indices: 47288677--47288735 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
47288667 TTGGGTATTT
*
47288677 CCACACGGGCTGGCCACACG-CTCGTGTGCG
1 CCACACGAGCTGGCCACACGCCTC-TGTGCG
47288707 CCACACGAGCTGGCCACACGCCTCTGTGC
1 CCACACGAGCTGGCCACACGCCTCTGTGC
47288736 CAGCCCGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.15, C:0.42, G:0.29, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACACGCCTCTGTGCG
Found at i:47295276 original size:14 final size:15
Alignment explanation
Indices: 47295257--47295290 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47295247 TCAACATGTC
47295257 TAAAAAAT-TATAAA
1 TAAAAAATATATAAA
*
47295271 TAAAAAATATTTAAA
1 TAAAAAATATATAAA
47295286 TAAAA
1 TAAAA
47295291 GTACGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAAATATATAAA
Found at i:47306900 original size:27 final size:27
Alignment explanation
Indices: 47306870--47307391 Score: 410
Period size: 27 Copynumber: 19.3 Consensus size: 27
47306860 TCATCTCCTA
** *
47306870 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
* * *
47306897 GGGGTATTT-TGATCATTTTACCCTATA
1 GGGGTATTTCAG-TCATTTTACCTTATG
*
47306924 GGGGTATTTCAGTCATTTTACCTTATA
1 GGGGTATTTCAGTCATTTTACCTTATG
* * * *
47306951 GGGGTATTTCGGCCAGTCTACCTTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
* * *
47306978 GCGGTATTTCAGTCATTCTACCTTATA
1 GGGGTATTTCAGTCATTTTACCTTATG
*
47307005 GGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCTTATG
* ** * * ** *
47307032 AGATTAATTCGGTCAACTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
*
47307059 GGGGTATTTCAGTTATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
** * * *
47307086 GGGGTATTTTGGTCATTATACCCTATA
1 GGGGTATTTCAGTCATTTTACCTTATG
* * * * * *
47307113 GGTGTACTTCGGTCATTCTACTTTATA
1 GGGGTATTTCAGTCATTTTACCTTATG
** * *
47307140 GGGGTATTTTGGTCATTTTACCCTAGAG
1 GGGGTATTTCAGTCATTTTACCTTA-TG
* * *
47307168 GGGGTAATTCTA-ACATTTTACGTTATG
1 GGGGTATTTC-AGTCATTTTACCTTATG
* * *
47307195 GGGATATTTC-GATCATTCTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCTTATG
*
47307222 GGGGTATTTC-GATCA-TTTACCTTATA
1 GGGGTATTTCAG-TCATTTTACCTTATG
*
47307248 GGGGTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
* ** * *
47307275 TGGGTATTTTGGTTATTTTAGCTTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
**
47307302 GGGGTATTTTGGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
*
47307329 AGGGTATTTCAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCTTATG
* * *
47307356 GGGGTATTTC-GATCAATCTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCTTATG
47307383 GGGGTATTT
1 GGGGTATTT
47307392 TGGTCATAAC
Statistics
Matches: 394, Mismatches: 90, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
26 24 0.06
27 350 0.89
28 20 0.05
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCTTATG
Found at i:47307392 original size:81 final size:81
Alignment explanation
Indices: 47306881--47307398 Score: 515
Period size: 81 Copynumber: 6.4 Consensus size: 81
47306871 GGGTATAACA
* * *
47306881 GTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCAGTCATTTTACC
1 GTCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTACC
* *
47306946 TTATAGGGGTATTTCG
66 CTATGGGGGTATTTCG
* * * * ** *
47306962 GCCAGTCTACCTTATGGCGGTATTTCAGTCATTCTACCTTATAGGGGTATTTC-GATCATTTTAC
1 GTCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATAGGGGTATTTCAG-TCATTTTAC
* ** *
47307026 CCTATGAGATTAATTCG
65 CCTATGGGGGTATTTCG
* ** * * ** *
47307043 GTCA-ACTTACCCTATGGGGGTATTTCAGTTATTTTACCTTATGGGGGTATTTTGGTCATTATAC
1 GTCATTC-TACCCTATGGGGGTATTTTGGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTAC
* * *
47307107 CCTATAGGTGTACTTCG
65 CCTATGGGGGTATTTCG
** * * * * *
47307124 GTCATTCTACTTTATAGGGGTATTTTGGTCATTTTACCCTAGAGGGGGTAATTCTA-ACATTTTA
1 GTCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATA-GGGGTATTTC-AGTCATTTTA
** *
47307188 CGTTATGGGGATATTTCG
64 CCCTATGGGGGTATTTCG
* * *
47307206 ATCATTCTACCCTATGGGGGTATTTCGATCA-TTTACCTTATAGGGGTATTTCAGTCATTTTACC
1 GTCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTACC
* *
47307270 CTATGTGGGTATTTTG
66 CTATGGGGGTATTTCG
* * * *
47307286 GTTATTTTAGCTTATGGGGGTATTTTGGTCATTTTACCTTAT-GAGGGTATTTCAGTCATTTTAC
1 GTCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATAG-GGGTATTTCAGTCATTTTAC
*
47307350 CTTATGGGGGTATTTCG
65 CCTATGGGGGTATTTCG
* *
47307367 ATCAATCTACCCTATGGGGGTATTTTGGTCAT
1 GTCATTCTACCCTATGGGGGTATTTTGGTCAT
47307399 AACAGTGTAG
Statistics
Matches: 346, Mismatches: 82, Indels: 18
0.78 0.18 0.04
Matches are distributed among these distances:
79 1 0.00
80 56 0.16
81 236 0.68
82 53 0.15
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (81 bp):
GTCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTACC
CTATGGGGGTATTTCG
Found at i:47320561 original size:2 final size:2
Alignment explanation
Indices: 47320556--47320595 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
47320546 TTTAGAGGGG
*
47320556 GA GA GA GA GA GA TA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
47320596 TTTTTTTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:47327824 original size:27 final size:27
Alignment explanation
Indices: 47327796--47328286 Score: 581
Period size: 27 Copynumber: 18.2 Consensus size: 27
47327786 GGATATAACA
*
47327796 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
47327823 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
47327849 ATCATTCTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
47327876 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
47327903 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
47327930 ATCAATTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
47327957 ATCAATTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
47327984 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
47328011 GTCATTATACCCTATGGGGGTACTTT-G
1 GTCATTTTACCCTATGGGGGTA-TTTCG
* * *
47328038 GTCATTCTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
47328065 GTCATTTTACCCTATGGGGGCTATTTCG
1 GTCATTTTACCCTATGGGGG-TATTTCG
* * *
47328093 ATCATTTTACCCTATAGGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * **
47328120 GTCATTCTATCTTATAAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
47328147 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
47328174 GTTATTTTACCTTATGGGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
47328201 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** *
47328228 GTTATTTTACCCTATAAGGGTATTTCT
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
47328255 ATCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
47328282 GTCAT
1 GTCAT
47328287 AACAATGTAA
Statistics
Matches: 401, Mismatches: 59, Indels: 8
0.86 0.13 0.02
Matches are distributed among these distances:
26 26 0.06
27 349 0.87
28 26 0.06
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:47345682 original size:41 final size:41
Alignment explanation
Indices: 47345574--47345717 Score: 229
Period size: 41 Copynumber: 3.5 Consensus size: 41
47345564 AACTTTATGT
47345574 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
47345615 CAAGCAGGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
47345655 CTAGTAGGCTAAGTGCCGGTGATCTGAATTA-GTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
47345696 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
47345718 ATATGTTAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 40 0.42
41 55 0.58
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:47347005 original size:197 final size:196
Alignment explanation
Indices: 47346668--47347067 Score: 746
Period size: 197 Copynumber: 2.0 Consensus size: 196
47346658 ATTATGATCT
*
47346668 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCGAAAGA
1 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAGA
47346733 AAAAAAGATAGATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATGA
66 AAAAAAGATAGATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATGA
47346798 GATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATTA
131 GATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATTA
47346863 G
196 G
47346864 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAGA
1 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAG-
* *
47346929 AAAAAAAGATATATATTGATTATTTAGTTCTATGATTGAGCTTGAATAGTTAAATTAATATTATG
65 AAAAAAAGATAGATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATG
* *
47346994 AGATTAAGCTCGTTTTTATTCTTGATTAGTTTTAGATTGATGTAATTTTTTTAAAATTCAGCATT
130 AGATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATT
47347059 AG
195 AG
47347061 TTTATTT
1 TTTATTT
47347068 TTCTAGTTTG
Statistics
Matches: 198, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
196 63 0.32
197 135 0.68
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (196 bp):
TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAGA
AAAAAAGATAGATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATGA
GATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATTA
G
Found at i:47350657 original size:13 final size:13
Alignment explanation
Indices: 47350639--47350664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47350629 AATGAAATTA
47350639 AAAAAGAATTTTC
1 AAAAAGAATTTTC
47350652 AAAAAGAATTTTC
1 AAAAAGAATTTTC
47350665 TTGAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAAAGAATTTTC
Found at i:47352360 original size:2 final size:2
Alignment explanation
Indices: 47352353--47352381 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47352343 TTTTTCAGAT
47352353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
47352382 ACGATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47352889 original size:16 final size:17
Alignment explanation
Indices: 47352868--47352900 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47352858 GATGTAGTTG
47352868 CCTTTATAT-TGTTTTT
1 CCTTTATATGTGTTTTT
*
47352884 CCTTTATGTGTGTTTTT
1 CCTTTATATGTGTTTTT
47352901 TAGTCAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.67
Consensus pattern (17 bp):
CCTTTATATGTGTTTTT
Found at i:47353923 original size:30 final size:29
Alignment explanation
Indices: 47353889--47353945 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
47353879 ATGTGAATTA
* *
47353889 TAAAATATACATAATATATATAATATATTT
1 TAAAATATAAAGAATATATA-AATATATTT
47353919 TAAAATATAAAGAATATATAAATATAT
1 TAAAATATAAAGAATATATAAATATAT
47353946 ATAAATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAATATAAAGAATATATAAATATATTT
Found at i:47353994 original size:16 final size:16
Alignment explanation
Indices: 47353970--47354004 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
47353960 ATACATAGGT
*
47353970 ATATAAAAATTATGAA
1 ATATAAAAATAATGAA
*
47353986 ATATGAAAATAATGAA
1 ATATAAAAATAATGAA
47354002 ATA
1 ATA
47354005 CATGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
ATATAAAAATAATGAA
Found at i:47356014 original size:50 final size:50
Alignment explanation
Indices: 47355954--47356497 Score: 382
Period size: 50 Copynumber: 10.9 Consensus size: 50
47355944 CACCGCCTAA
* *
47355954 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCATTGTC-GG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * * * ** * ** * *
47356003 AGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGG
1 -GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * * *
47356054 GAAGTAAGATTCGTCGTTTTGGCATCAATC-TTTTAATTGCAATGTCAGG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * ** * * *
47356103 GAAGTGAGATTCACCGTTGTAGCTTCAAT-TTGTTCCACTGC-ATCGCCAGA
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTT-TTTAATTGCAAT-GTCAGG
* * * * *
47356153 TAAGTAAGATTCTCCGTTTTGGCTTCAATCTTTTAAATTGCAATGTCAGG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * * * ** * ** *
47356203 GAAGCGAGATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* *
47356253 GAAGT-ACGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGG
1 GAAGTGA-GATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * * ** * * ** * *
47356303 GAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCTGG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * * * *
47356353 GAAGTAAGATTCGCCGTTATGGCTTTAATC-TTTTAATTGTAATGTCGGG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
* * * * * * * * * * *
47356402 GAAGCGAGATTCACCGTCGTAGCTTTAATC-TTCTCACTGTACTGCCAGG
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
*
47356451 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATGTC
1 GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC
47356498 GAGGAACAAG
Statistics
Matches: 363, Mismatches: 122, Indels: 18
0.72 0.24 0.04
Matches are distributed among these distances:
49 109 0.30
50 247 0.68
51 7 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
GAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
Found at i:47356027 original size:100 final size:100
Alignment explanation
Indices: 47355847--47356553 Score: 913
Period size: 100 Copynumber: 7.1 Consensus size: 100
47355837 TCAATCTGTT
* * * ** *
47355847 CGCCAGGGAAGTAAGATTTGTCGTTGCGGCTTTGATCTTTTTAATTGCAATGTCGGGGAAACGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* * * *
47355912 ATTCACCATCGTAGCTTTAATTTGTTCCACTGCAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* * *
47355947 CGCCTA-AGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCATTGTCGGAGAAGCGA
1 CGCC-AGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGA
47356011 GATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
65 GATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* * * * * *
47356047 CGCCTGGGAAGTAAGATTCGTCGTTTTGGCATCAATC-TTTTAATTGCAATGTCAGGGAAGTGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* *
47356111 ATTCACCGTTGTAGCTTCAATTTGTTCCACTGCAT
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
** * * * *
47356146 CGCCAGATAAGTAAGATTCTCCGTTTTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
*
47356211 ATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* *
47356246 CGCCAGGGAAGTACGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* *
47356311 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTACAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* * * *
47356346 CGCCTGGGAAGTAAGATTCGCCGTTATGGCTTTAATC-TTTTAATTGTAATGTCGGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* * *
47356410 ATTCACCGTCGTAGCTTTAATC--TTCTCACTGTAC
66 ATTCACCGTTGTAGCTTCAATCTGTTC-CACTGCAC
* * * * *
47356444 TGCCAGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATGTCGAGGAA-CAAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* * * *
47356508 ATTCACCGTCGTAGCTTTAATCTGCTCCATTGCAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
*
47356543 TGCCAGGGAAG
1 CGCCAGGGAAG
47356554 GTAACTTCAT
Statistics
Matches: 534, Mismatches: 66, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
97 3 0.01
98 63 0.12
99 169 0.32
100 298 0.56
101 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
Found at i:47356385 original size:299 final size:296
Alignment explanation
Indices: 47355848--47356553 Score: 950
Period size: 299 Copynumber: 2.4 Consensus size: 296
47355838 CAATCTGTTC
* * * * **
47355848 GCCAGGGAAGTAAGATTTGTCGTTGCGGCTTTGATCTTTTTAATTGCAATGTCGGGGAAACGAGA
1 GCCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGG-AACGAGA
* * *
47355913 TTCACCATCGTAGCTTTAATTTGTTCCACTGCACCGCCTA-AGAAGTAAGATTCGCCGTTGTGGC
64 TTCACCGTCGTAGCTTTAATCTGTTCCACTGCACCGCC-AGGGAAGTAAGATTCGCCGTTGTGGC
*
47355977 TTCAATCTTTTTAATTGCATTGTCGGAGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
128 TTCAATCTTTTTAATTGCAATGTCGGAGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* * *
47356042 TGCACCGCCTGGGAAGTAAGATTCGTCGTTTTGGCATCAATCTTTTAATTGCAATGTCAGGGAAG
193 TACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCATCAATCTTTTAATTGCAATGTCAGGGAAG
* * *
47356107 TGAGATTCACCGTTGTAGCTTCAAT-TTGTTCCACTGCA-T
258 CGAGATTCACCGTCGTAGCTTCAATCTT-CT-CACTGCACT
* * * *
47356146 CGCCAGATAAGTAAGATTCTCCGTTTTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCGAG
1 -GCCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGGAA-CGAG
* * * *
47356211 ATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTACGATTCGCCGTTGTGGC
63 ATTCACCGTCGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGGC
* * *
47356276 TTCAATCTTTTTAATTGTAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
128 TTCAATCTTTTTAATTGCAATGTCGGAGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* * * *
47356341 TACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCTTTAATCTTTTAATTGTAATGTCGGGGAAG
193 TACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCATCAATCTTTTAATTGCAATGTCAGGGAAG
* *
47356406 CGAGATTCACCGTCGTAGCTTTAATCTTCTCACTGTACT
258 CGAGATTCACCGTCGTAGCTTCAATCTTCTCACTGCACT
* * * *
47356445 GCCAGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATGTCGAGGAACAAGAT
1 GCCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG-GGAACGAGAT
* * *
47356510 TCACCGTCGTAGCTTTAATCTGCTCCATTGCACTGCCAGGGAAG
65 TCACCGTCGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAG
47356554 GTAACTTCAT
Statistics
Matches: 354, Mismatches: 48, Indels: 12
0.86 0.12 0.03
Matches are distributed among these distances:
297 44 0.12
298 59 0.17
299 249 0.70
300 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (296 bp):
GCCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGAACGAGATT
CACCGTCGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
AATCTTTTTAATTGCAATGTCGGAGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTAC
ACCGCCTGGGAAGTAAGATTCGCCGTTATGGCATCAATCTTTTAATTGCAATGTCAGGGAAGCGA
GATTCACCGTCGTAGCTTCAATCTTCTCACTGCACT
Found at i:47357830 original size:15 final size:15
Alignment explanation
Indices: 47357803--47357847 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 15
47357793 TTAGCCTCTC
*
47357803 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
47357817 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
47357832 CATTTTTTTCATTTTT
1 CA-TTTTTTCATTTTT
47357848 TTGTTTCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:47357849 original size:9 final size:8
Alignment explanation
Indices: 47357812--47357848 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
47357802 CCATTTTTAC
47357812 TTTTTCAT
1 TTTTTCAT
47357820 TTTTTCA-
1 TTTTTCAT
47357827 TTTTTCATT
1 TTTTTCA-T
47357836 TTTTTCAT
1 TTTTTCAT
47357844 TTTTT
1 TTTTT
47357849 TGTTTCACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.26
8 13 0.48
9 7 0.26
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:47362728 original size:23 final size:22
Alignment explanation
Indices: 47362679--47362729 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
47362669 ACATTCATTC
47362679 AAAAT-AATAATGAAAATAAAA
1 AAAATAAATAATGAAAATAAAA
* *
47362700 ATAAATAAATAATGAATATAATTA
1 A-AAATAAATAATGAAAATAA-AA
47362724 AAAATA
1 AAAATA
47362730 TAAAGAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 4 0.16
23 18 0.72
24 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAATAAATAATGAAAATAAAA
Found at i:47362870 original size:27 final size:27
Alignment explanation
Indices: 47362813--47362887 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
47362803 TATTTTAAAA
* * *
47362813 TATAAAGAATATATAAATATATATATC
1 TATAAAAAATATATAAATATACATAGC
* * *
47362840 TATAAAAAATATGTACATATACATAGG
1 TATAAAAAATATATAAATATACATAGC
47362867 TATATAAAAAT-TATGAAATAT
1 TATA-AAAAATATAT-AAATAT
47362888 GAAAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
27 27 0.71
28 11 0.29
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.35
Consensus pattern (27 bp):
TATAAAAAATATATAAATATACATAGC
Found at i:47362892 original size:16 final size:16
Alignment explanation
Indices: 47362868--47362902 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
47362858 ATACATAGGT
*
47362868 ATATAAAAATTATGAA
1 ATATAAAAATAATGAA
*
47362884 ATATGAAAATAATGAA
1 ATATAAAAATAATGAA
47362900 ATA
1 ATA
47362903 CATGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
ATATAAAAATAATGAA
Found at i:47374719 original size:17 final size:18
Alignment explanation
Indices: 47374687--47374721 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
47374677 CAATGATGTT
*
47374687 CGCCCGTTTGGGCCCACA
1 CGCCCGTGTGGGCCCACA
47374705 CGCCCGTGT-GGCCCACA
1 CGCCCGTGTGGGCCCACA
47374722 TGGCCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.46, G:0.29, T:0.14
Consensus pattern (18 bp):
CGCCCGTGTGGGCCCACA
Found at i:47377362 original size:24 final size:25
Alignment explanation
Indices: 47377315--47377362 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
47377305 TTGGCTCTCA
*
47377315 CGAGCTTCCCGTTATATAGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
*
47377340 CGAGCTTCTCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
47377363 CAGATTATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:47389343 original size:18 final size:17
Alignment explanation
Indices: 47389313--47389346 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47389303 ATTTTGATCT
*
47389313 AATTTTTACTTTTTTAG
1 AATTTTTAATTTTTTAG
47389330 AATTTTCTAATTTTTTA
1 AATTTT-TAATTTTTTA
47389347 AAAAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (17 bp):
AATTTTTAATTTTTTAG
Found at i:47390656 original size:145 final size:143
Alignment explanation
Indices: 47390416--47390702 Score: 495
Period size: 142 Copynumber: 2.0 Consensus size: 143
47390406 TCAGCCATGC
47390416 AGGAGCATCAAATCTTGAGTTTATTTACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTG
1 AGGAGCATCAAATCTTGAGTTTATTTACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTG
* * *
47390481 GTAGACCTAAACCAGACTTTCTAATTAAAAAAAGGCAATTCCACTAATCACAACATTCATTACCA
66 GTAGACCTAAACCAGACTTTATAA--AAAAAAAAGCAATTCCACTAATCACAACATTCATCACCA
47390546 ACTCAAGTGTCACAT
129 ACTCAAGTGTCACAT
* * *
47390561 AGGAGCATCAATTCTTGATTTTATTTCCTTACTTTAATATCTCAATTTGG-TCTTCTATCACTTG
1 AGGAGCATCAAATCTTGAGTTTATTTACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTG
47390625 GTAGACCTAAACCAGACTTTATAAAAAAAAAAGCAATTCCACTAATCACAACATTCATCACCAAC
66 GTAGACCTAAACCAGACTTTATAAAAAAAAAAGCAATTCCACTAATCACAACATTCATCACCAAC
47390690 TCAAGTGTCACAT
131 TCAAGTGTCACAT
47390703 TAAAAATTCG
Statistics
Matches: 136, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
142 52 0.38
144 37 0.27
145 47 0.35
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (143 bp):
AGGAGCATCAAATCTTGAGTTTATTTACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTG
GTAGACCTAAACCAGACTTTATAAAAAAAAAAGCAATTCCACTAATCACAACATTCATCACCAAC
TCAAGTGTCACAT
Found at i:47391296 original size:34 final size:35
Alignment explanation
Indices: 47391253--47391325 Score: 139
Period size: 34 Copynumber: 2.1 Consensus size: 35
47391243 ATTCTCTCCC
47391253 TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
1 TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
47391288 TCTT-CCATTGTAAGTTATGCTGCCTCTCTTTGTT
1 TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
47391322 TCTT
1 TCTT
47391326 TCTCTCATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.11, C:0.23, G:0.15, T:0.51
Consensus pattern (35 bp):
TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
Found at i:47395222 original size:23 final size:23
Alignment explanation
Indices: 47395189--47395232 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47395179 TGGGTAGGAA
*
47395189 GTTTTCTAAAAATTCTGCATTAT
1 GTTTTCCAAAAATTCTGCATTAT
*
47395212 GTTTTCCAAAAATTTTGCATT
1 GTTTTCCAAAAATTCTGCATT
47395233 TACATAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (23 bp):
GTTTTCCAAAAATTCTGCATTAT
Found at i:47398981 original size:21 final size:22
Alignment explanation
Indices: 47398955--47399003 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
47398945 TTGAGGAGAG
47398955 AAAAATAAAATAAA-TAAAAAT
1 AAAAATAAAATAAACTAAAAAT
* * *
47398976 AAAAATAAACTAAACTCAAACT
1 AAAAATAAAATAAACTAAAAAT
47398998 AAAAAT
1 AAAAAT
47399004 CCCATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAAATAAAATAAACTAAAAAT
Found at i:47413875 original size:44 final size:44
Alignment explanation
Indices: 47413812--47414216 Score: 260
Period size: 44 Copynumber: 9.2 Consensus size: 44
47413802 TATCTCCATG
* * * *
47413812 AAAGTTGCAGTGGAGCAGATTAAAGCCAAAAATCTTGTCT-TCCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCT-CT
* * *
47413856 AAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCTCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTA-CAAATCTTATCTCTCT
** * *
47413901 AAAGTTATAGTAGAGCAAATTAAAGCTACAAACCTTATCTCTCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT
* ** * *
47413945 AAAGTTGCAATAGAGCAGATTAAAAATAGTAAATCTTATCTCCCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTA-CAAATCTTATCTCTCT
* * * * * * *
47413990 GAAGTT-CTAGTGGAGTAGATTGAAGTTACAAAACTTATCTCCCT
1 AAAGTTGC-AGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT
* * * * * * *
47414034 GAAGTTACAGTGGAGCGGATTGAAGTTACAAATCTCATCTC-CAT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTC-T
* * * * * * * * *
47414078 GAAGTTGCAATAGAGTAGATTGAAGATACGAGTCTCATCTCCCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT
* * * * *
47414122 AAAGTTGTAGTGGAGCAGATTAAAGCTACAAGTCTAATCTCCCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT
* ** * * * * *
47414166 GAAGTTATAGTGGAGTAGATTGAAGCAACAAATCCTATAC-CTCT
1 AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTAT-CTCTCT
47414210 AAAGTTG
1 AAAGTTG
47414217 TAGTGGGTTA
Statistics
Matches: 291, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
43 1 0.00
44 220 0.76
45 69 0.24
46 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (44 bp):
AAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT
Found at i:47413947 original size:89 final size:88
Alignment explanation
Indices: 47413853--47414222 Score: 348
Period size: 88 Copynumber: 4.2 Consensus size: 88
47413843 ATCTTGTCTT
* * * *
47413853 CCTAAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCTCTAAAGTTATAGTAGAGCA
1 CCTAAAGTTGCAGTGGAGCAGATTAAAGATA-CAAATCTTATCTCCCTGAAGTTATAGTAGAGTA
* *
47413918 AATTAAAGCTACAAACCTTATCTC
65 GATTGAAGCTACAAACCTTATCTC
* * * * * * *
47413942 TCTAAAGTTGCAATAGAGCAGATTAAAAATAGTAAATCTTATCTCCCTGAAGTTCTAGTGGAGTA
1 CCTAAAGTTGCAGTGGAGCAGATTAAAGATA-CAAATCTTATCTCCCTGAAGTTATAGTAGAGTA
* *
47414007 GATTGAAGTTACAAAACTTATCTC
65 GATTGAAGCTACAAACCTTATCTC
* * * * * * * ** *
47414031 CCTGAAGTTACAGTGGAGCGGATTGAAGTTACAAATCTCATCTCCATGAAGTTGCAATAGAGTAG
1 CCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAGTTATAGTAGAGTAG
* * ** *
47414096 ATTGAAGATACGAGTCTCATCTC
66 ATTGAAGCTACAAACCTTATCTC
* * * * *
47414119 CCTAAAGTTGTAGTGGAGCAGATTAAAGCTACAAGTCTAATCTCCCTGAAGTTATAGTGGAGTAG
1 CCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAGTTATAGTAGAGTAG
*
47414184 ATTGAAGCAACAAATCC-TATAC-C
66 ATTGAAGCTACAAA-CCTTAT-CTC
* *
47414207 TCTAAAGTTGTAGTGG
1 CCTAAAGTTGCAGTGG
47414223 GTTAGAATGA
Statistics
Matches: 223, Mismatches: 56, Indels: 5
0.79 0.20 0.02
Matches are distributed among these distances:
88 125 0.56
89 98 0.44
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (88 bp):
CCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAGTTATAGTAGAGTAG
ATTGAAGCTACAAACCTTATCTC
Found at i:47414234 original size:132 final size:132
Alignment explanation
Indices: 47413853--47414199 Score: 322
Period size: 132 Copynumber: 2.6 Consensus size: 132
47413843 ATCTTGTCTT
* * * * * * * *
47413853 CCTAAAGTTGC-AGTGGAGCAGATTGAAGATAGCAAATCTTATCTCTCTAAAGTTATAGTAGAGC
1 CCTAAAGTT-CTAGTGGAGCAGATTAAAGCTA-CAAAACTAATCTCCCTGAAGTTACAGTGGAGC
* * * * * * * * * *
47413917 AAATTAAAGCTACAAACCTTATCTCTC-TAAAGTTGCAATAGAGCAGATTAAAAATA-GTAAATC
64 AGATTGAAGCAACAAATCTCATCTC-CATAAAGTTGCAATAGAGTAGAATGAAGATACG--AGTC
*
47413980 TTATCTC
126 TCATCTC
* * * * * *
47413987 CCTGAAGTTCTAGTGGAGTAGATTGAAGTTACAAAACTTATCTCCCTGAAGTTACAGTGGAGCGG
1 CCTAAAGTTCTAGTGGAGCAGATTAAAGCTACAAAACTAATCTCCCTGAAGTTACAGTGGAGCAG
** * *
47414052 ATTGAAGTTACAAATCTCATCTCCATGAAGTTGCAATAGAGTAGATTGAAGATACGAGTCTCATC
66 ATTGAAGCAACAAATCTCATCTCCATAAAGTTGCAATAGAGTAGAATGAAGATACGAGTCTCATC
47414117 TC
131 TC
* ** * *
47414119 CCTAAAGTTGTAGTGGAGCAGATTAAAGCTACAAGTCTAATCTCCCTGAAGTTATAGTGGAGTAG
1 CCTAAAGTTCTAGTGGAGCAGATTAAAGCTACAAAACTAATCTCCCTGAAGTTACAGTGGAGCAG
47414184 ATTGAAGCAACAAATC
66 ATTGAAGCAACAAATC
47414200 CTATACCTCT
Statistics
Matches: 177, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
132 78 0.44
133 72 0.41
134 27 0.15
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (132 bp):
CCTAAAGTTCTAGTGGAGCAGATTAAAGCTACAAAACTAATCTCCCTGAAGTTACAGTGGAGCAG
ATTGAAGCAACAAATCTCATCTCCATAAAGTTGCAATAGAGTAGAATGAAGATACGAGTCTCATC
TC
Found at i:47415788 original size:12 final size:12
Alignment explanation
Indices: 47415771--47415795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47415761 GTTCCTTTAT
47415771 TTTATTTTATTA
1 TTTATTTTATTA
47415783 TTTATTTTATTA
1 TTTATTTTATTA
47415795 T
1 T
47415796 GATTTATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:47416014 original size:28 final size:28
Alignment explanation
Indices: 47415982--47416039 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
47415972 ATTTATGTTG
47415982 TTCATATTTGTACATTTTTCGCTCATTA
1 TTCATATTTGTACATTTTTCGCTCATTA
*
47416010 TTCATATTTGTACATTTTTTGCTCATTA
1 TTCATATTTGTACATTTTTCGCTCATTA
47416038 TT
1 TT
47416040 TATTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (28 bp):
TTCATATTTGTACATTTTTCGCTCATTA
Found at i:47418405 original size:17 final size:17
Alignment explanation
Indices: 47418382--47418415 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
47418372 AGTTCAATTG
*
47418382 ATTTTTAAT-ATTTTTT
1 ATTTTTTATAATTTTTT
47418398 ATTTTTTATAATTTTTT
1 ATTTTTTATAATTTTTT
47418415 A
1 A
47418416 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTTATAATTTTTT
Found at i:47421467 original size:46 final size:47
Alignment explanation
Indices: 47421355--47421469 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 47
47421345 CTGCACTATC
* * * *
47421355 TAGTGGTTTAACCACAT-T-TCTGTTCTGGCAGCTTGACTACATTTA
1 TAGTGGCTTCACCACATATATCTGTTATGGCAGCTTGACTACATATA
* * *
47421400 TGGTGGC-TCGACCACAGATATCTGTTATGGCAGCTT-AGCTGCA-ATA
1 TAGTGGCTTC-ACCACATATATCTGTTATGGCAGCTTGA-CTACATATA
47421446 TAGTGGCTTCACCACATATATCTG
1 TAGTGGCTTCACCACATATATCTG
47421470 ATCTAGCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
44 1 0.02
45 11 0.20
46 23 0.41
47 21 0.38
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (47 bp):
TAGTGGCTTCACCACATATATCTGTTATGGCAGCTTGACTACATATA
Found at i:47421613 original size:23 final size:23
Alignment explanation
Indices: 47421583--47421626 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
47421573 TGGGTAGGAA
47421583 GTTTTCTGAAAA-ATCTGCATTTT
1 GTTTTCTGAAAATAT-TGCATTTT
47421606 GTTTTCTGAAAATATTGCATT
1 GTTTTCTGAAAATATTGCATT
47421627 CACGTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (23 bp):
GTTTTCTGAAAATATTGCATTTT
Found at i:47424081 original size:13 final size:13
Alignment explanation
Indices: 47424063--47424088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47424053 TACCTTTAGG
47424063 TTCAAAAGCACTT
1 TTCAAAAGCACTT
47424076 TTCAAAAGCACTT
1 TTCAAAAGCACTT
47424089 CTGACTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TTCAAAAGCACTT
Found at i:47425720 original size:14 final size:14
Alignment explanation
Indices: 47425699--47425740 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
47425689 GTTTGATTGC
47425699 CAGTAAAATATTTT
1 CAGTAAAATATTTT
*
47425713 CCGTAAAAT-TATTT
1 CAGTAAAATAT-TTT
*
47425727 CAGGAAAATATTTT
1 CAGTAAAATATTTT
47425741 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (14 bp):
CAGTAAAATATTTT
Found at i:47425753 original size:34 final size:35
Alignment explanation
Indices: 47425709--47425775 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
47425699 CAGTAAAATA
*
47425709 TTTTCCGTAAAATTATTT-CAGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
* *
47425743 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTT
47425776 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
Found at i:47430250 original size:60 final size:59
Alignment explanation
Indices: 47430176--47430307 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 59
47430166 CAATCTCAAT
* * * * *
47430176 TAGTTGAGTGACCAAATTTAATAAATTGATAGTTAGGTGACCAAAAGAGAAAAGGGGCAA
1 TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAA-GGACAA
* *
47430236 TAGTTGGGTGACCAAATTAAAAAAATTGGTAGTTGGGTGACCAAAAAAGAAAAGGACAA
1 TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAAGGACAA
*
47430295 TAGTTGGCTGACC
1 TAGTTGGGTGACC
47430308 TATGTTGTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 17 0.27
60 47 0.73
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (59 bp):
TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAAGGACAA
Found at i:47437208 original size:17 final size:17
Alignment explanation
Indices: 47437188--47437234 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
47437178 CACATTTTAT
47437188 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
47437205 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
47437223 A-TATTTATATTA
1 ATTATTTATATTA
47437235 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:47437848 original size:60 final size:61
Alignment explanation
Indices: 47437724--47437856 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 61
47437714 GTCACTCTTA
* ** * *
47437724 TTTTTTGGTCATCCAACTATGAAAAGTTACAAAATGGTCACTTAATTATGTTTTTTTTTTC
1 TTTTTTGGTCATCCAACCATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
47437785 TTTTTTGGTCA-CCAAACCATGAAAAGTTACAAAATAATCACTCAACTATG-TTTTTTTTTC
1 TTTTTTGGTCATCC-AACCATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
*
47437845 TTTTTTGATCAT
1 TTTTTTGGTCAT
47437857 GAGTAGACCT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
60 22 0.34
61 42 0.66
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (61 bp):
TTTTTTGGTCATCCAACCATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
Found at i:47438212 original size:16 final size:16
Alignment explanation
Indices: 47438191--47438232 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
47438181 AATAATTTGA
*
47438191 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
47438207 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
47438223 TAGTTTTAAT
1 TAATTTTAAT
47438233 TTTATTAAAA
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:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:47438216 original size:22 final size:23
Alignment explanation
Indices: 47438206--47438268 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
47438196 TTACTAACAA
* * *
47438206 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
47438228 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
47438251 TTAATTTTAATTAAAAAA
1 TTAATTTTAATAAAAAAA
47438269 GGCCGGGCCG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 10 0.29
23 24 0.71
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:47439012 original size:22 final size:22
Alignment explanation
Indices: 47438984--47439036 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
47438974 GGCCTATTTT
47438984 TATTTTAAAAAAT-TTTAAAAAG
1 TATTTTAAAAAATATTT-AAAAG
*
47439006 TATTTT-AAAAATATTTAAAAT
1 TATTTTAAAAAATATTTAAAAG
47439027 TATTTTAAAA
1 TATTTTAAAA
47439037 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTTAAAAAATATTTAAAAG
Found at i:47439037 original size:11 final size:11
Alignment explanation
Indices: 47438983--47439039 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
47438973 CGGCCTATTT
47438983 TTATTTTAAAA
1 TTATTTTAAAA
*
47438994 -AATTTTAAAAA
1 TTATTTT-AAAA
*
47439005 GTATTTTAAAA
1 TTATTTTAAAA
*
47439016 ATA-TTTAAAA
1 TTATTTTAAAA
47439026 TTATTTTAAAA
1 TTATTTTAAAA
47439037 TTA
1 TTA
47439040 AAAAAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 14 0.36
11 20 0.51
12 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:47439077 original size:42 final size:40
Alignment explanation
Indices: 47439012--47439127 Score: 173
Period size: 42 Copynumber: 2.9 Consensus size: 40
47439002 AAAGTATTTT
*
47439012 AAAAA-TATTTAAAATTATTTTAAAATTAAAAAAATTTAAA
1 AAAAAGTATTTAAAAATATTTTAAAATTAAAAAAATTT-AA
47439052 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA-TTAA
1 AAAAAGTA-TTTAAAAATATTTTAAAATTAAAAAAATTTAA
* *
47439092 AAAAAGTATGTAAAAATATTTTAAAGTTAAAAAAAT
1 AAAAAGTATTTAAAAATATTTTAAAATTAAAAAAAT
47439128 AAATATATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
39 25 0.36
40 15 0.21
41 4 0.06
42 26 0.37
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
AAAAAGTATTTAAAAATATTTTAAAATTAAAAAAATTTAA
Found at i:47439571 original size:22 final size:22
Alignment explanation
Indices: 47439530--47439572 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47439520 TATTCAAACA
*
47439530 ATAAAAATAAAATAATATCAAT
1 ATAAAAATAAAATAACATCAAT
* *
47439552 ATAATAATAAAATGACATCAA
1 ATAAAAATAAAATAACATCAA
47439573 AATGGCAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAAAAATAAAATAACATCAAT
Found at i:47440827 original size:23 final size:22
Alignment explanation
Indices: 47440796--47440843 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
47440786 TTTTTTTTCA
47440796 TTTCTCTTCTACTTCTCCATCTAT
1 TTTCTCTTCT--TTCTCCATCTAT
*
47440820 TTTC-CTTCTTTCTCCATCTCT
1 TTTCTCTTCTTTCTCCATCTAT
47440841 TTT
1 TTT
47440844 AACATAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
23 5 0.22
24 4 0.17
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTCTCTTCTTTCTCCATCTAT
Found at i:47445412 original size:14 final size:15
Alignment explanation
Indices: 47445393--47445425 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
47445383 ATATAATTAC
*
47445393 TTAATT-AATTTATT
1 TTAATTAAACTTATT
47445407 TTAATTAAACTTATT
1 TTAATTAAACTTATT
47445422 TTAA
1 TTAA
47445426 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAAACTTATT
Found at i:47451502 original size:14 final size:14
Alignment explanation
Indices: 47451480--47451513 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
47451470 CAATCAATTC
*
47451480 TTTTGAGTTTAATA
1 TTTTTAGTTTAATA
47451494 TTTTTAGTTTAATA
1 TTTTTAGTTTAATA
*
47451508 TATTTA
1 TTTTTA
47451514 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (14 bp):
TTTTTAGTTTAATA
Found at i:47458215 original size:31 final size:31
Alignment explanation
Indices: 47458177--47458239 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
47458167 CCTATAATTT
* *
47458177 ATTCATTATATCTGCTAGAAAAAGCAGATTG
1 ATTCATTACATCTGCTAGAAAAACCAGATTG
* *
47458208 ATTCATTACATCTGTTGGAAAAACCAGATTG
1 ATTCATTACATCTGCTAGAAAAACCAGATTG
47458239 A
1 A
47458240 AAAAAGGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (31 bp):
ATTCATTACATCTGCTAGAAAAACCAGATTG
Found at i:47458498 original size:20 final size:21
Alignment explanation
Indices: 47458470--47458510 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
47458460 TTCTAATTAG
* *
47458470 AAAATTCTAA-TAATTAAAAT
1 AAAAATCTAAGTAAATAAAAT
47458490 AAAAATCTAAGTAAATAAAAT
1 AAAAATCTAAGTAAATAAAAT
47458511 TTTCTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATCTAAGTAAATAAAAT
Found at i:47465953 original size:31 final size:31
Alignment explanation
Indices: 47465893--47465953 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
47465883 TTTTTTGGTC
* * *
47465893 CACATTTGTTTTGAAATTTGACAATTTTTCT
1 CACATTTGTCTTGAAACTTGACAAGTTTTCT
*
47465924 CACATTTGTCTTGAAACTTGACGAGTTTTC
1 CACATTTGTCTTGAAACTTGACAAGTTTTC
47465954 CTATGGTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (31 bp):
CACATTTGTCTTGAAACTTGACAAGTTTTCT
Found at i:47473286 original size:25 final size:26
Alignment explanation
Indices: 47473238--47473286 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
47473228 TATATTAATA
* **
47473238 ATTAATAATTTCATATATTTTTATTT
1 ATTAAAAATTTCATATATAATTATTT
47473264 ATTAAAAATTT-ATATATAATTAT
1 ATTAAAAATTTCATATATAATTAT
47473287 CTTAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTAAAAATTTCATATATAATTATTT
Found at i:47473338 original size:22 final size:23
Alignment explanation
Indices: 47473303--47473346 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
47473293 ATTTTTTAAT
47473303 ATTTAAATTATTATATACTATAG
1 ATTTAAATTATTATATACTATAG
* *
47473326 ATTT-AATTTTTATATATTATA
1 ATTTAAATTATTATATACTATA
47473347 AATTACGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATTATTATATACTATAG
Found at i:47474267 original size:25 final size:25
Alignment explanation
Indices: 47474217--47474267 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
47474207 AAACCGAGCC
* *
47474217 AAGCTCAAGCTCAACTCAAAATTCG
1 AAGCTCAAACTCAACTCAAAACTCG
*
47474242 AAGCTCAATACTCAACTC-GAACTCG
1 AAGCTCAA-ACTCAACTCAAAACTCG
47474267 A
1 A
47474268 TCGAATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (25 bp):
AAGCTCAAACTCAACTCAAAACTCG
Found at i:47477002 original size:24 final size:22
Alignment explanation
Indices: 47476966--47477011 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
47476956 TATTCCTCAA
47476966 AATACCATCATATATAAAAACT
1 AATACCATCATATATAAAAACT
47476988 AATACCATCATATATAAAAACT
1 AATACCATCATATATAAAAACT
47477010 AA
1 AA
47477012 GCTAAGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (22 bp):
AATACCATCATATATAAAAACT
Found at i:47477219 original size:18 final size:18
Alignment explanation
Indices: 47477196--47477230 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47477186 GAAACTTGTC
* *
47477196 CAACAGGGTTAGAGTTTT
1 CAACAGAGTCAGAGTTTT
47477214 CAACAGAGTCAGAGTTT
1 CAACAGAGTCAGAGTTT
47477231 CGAATGGAAT
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:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (18 bp):
CAACAGAGTCAGAGTTTT
Found at i:47479336 original size:3 final size:3
Alignment explanation
Indices: 47479328--47479354 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
47479318 CAGTACCATT
47479328 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
47479355 CAAATTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:47483658 original size:28 final size:31
Alignment explanation
Indices: 47483626--47483688 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
47483616 TATATAAAAA
*
47483626 ATAATT-T-TTTTATAAAATTAAAA-AATAT
1 ATAATTATATTTTATAAAATCAAAATAATAT
*
47483654 ATAATTATATTTTTTAAAATCAAAATAATAT
1 ATAATTATATTTTATAAAATCAAAATAATAT
47483685 ATAA
1 ATAA
47483689 AAATTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 1 0.03
30 14 0.47
31 9 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATTATATTTTATAAAATCAAAATAATAT
Found at i:47483721 original size:22 final size:24
Alignment explanation
Indices: 47483686--47483733 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
47483676 AAATAATATA
*
47483686 TAAAAATTTATTTTTA-AACTTTT
1 TAAAAATATATTTTTACAACTTTT
47483709 TAAAAATAT-TTTTTACAACTTTT
1 TAAAAATATATTTTTACAACTTTT
47483732 TA
1 TA
47483734 CATTTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAAAATATATTTTTACAACTTTT
Found at i:47484309 original size:29 final size:29
Alignment explanation
Indices: 47484251--47484309 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
47484241 GAATTTGATC
*
47484251 AAATCAAAATTTCATGCATAAAATTACACA
1 AAATCAAAATTTCAT-CATAAAAGTACACA
* *
47484281 AAATCAAAATTCTTAT-ATAAAAGTGCACA
1 AAATCAAAATT-TCATCATAAAAGTACACA
47484310 TTAAACTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 11 0.44
30 11 0.44
31 3 0.12
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATCAAAATTTCATCATAAAAGTACACA
Found at i:47499295 original size:30 final size:30
Alignment explanation
Indices: 47499256--47499312 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
47499246 TTTTATAAAT
47499256 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
47499286 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
47499313 AATAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:47499520 original size:26 final size:26
Alignment explanation
Indices: 47499490--47499539 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
47499480 CTTAAACCAA
*
47499490 ACTTTTTAAAAATATTTCTCAAAATC
1 ACTTTTCAAAAATATTTCTCAAAATC
* *
47499516 ACTTTTCCAAACTATTTCTCAAAA
1 ACTTTTCAAAAATATTTCTCAAAA
47499540 GAAATGCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (26 bp):
ACTTTTCAAAAATATTTCTCAAAATC
Found at i:47502723 original size:31 final size:29
Alignment explanation
Indices: 47502688--47502750 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
47502678 GTAAATTTAA
*
47502688 AAAATATATATATATACAGGGGTGAAGCCAG
1 AAAATAT-T-TATATACAGGGGCGAAGCCAG
47502719 -AAA-ATTTATATACAGGGGCGAAGCCAG
1 AAAATATTTATATACAGGGGCGAAGCCAG
47502746 AAAAT
1 AAAAT
47502751 TTTTCTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 20 0.69
28 4 0.14
29 2 0.07
30 3 0.10
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (29 bp):
AAAATATTTATATACAGGGGCGAAGCCAG
Found at i:47502764 original size:27 final size:27
Alignment explanation
Indices: 47502698--47502752 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
47502688 AAAATATATA
*
47502698 TATATACAGGGGTGAAGCCAGAAAATT
1 TATATACAGGGGCGAAGCCAGAAAATT
47502725 TATATACAGGGGCGAAGCCAGAAAATT
1 TATATACAGGGGCGAAGCCAGAAAATT
47502752 T
1 T
47502753 TTCTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (27 bp):
TATATACAGGGGCGAAGCCAGAAAATT
Found at i:47503958 original size:106 final size:106
Alignment explanation
Indices: 47503773--47503976 Score: 327
Period size: 106 Copynumber: 1.9 Consensus size: 106
47503763 TGGGTTGAGA
* * *
47503773 TTTAAGAGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACGTTAGGACACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGACACGTTT
** *
47503838 TCTTGAATTTCCAAACGTAAAATATTACCTTATTTTGAAAT
66 TCTCAAATTTCCAAACGCAAAATATTACCTTATTTTGAAAT
* *
47503879 TTTAAAAGGATATTTGGCTGTTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGACACGTTT
*
47503944 TCTCAAATTTCCAAACGCAAAATATTGCCTTAT
66 TCTCAAATTTCCAAACGCAAAATATTACCTTAT
47503977 CTTAAAACAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGACACGTTT
TCTCAAATTTCCAAACGCAAAATATTACCTTATTTTGAAAT
Done.