Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 33 of 117
Found at i:5284017 original size:16 final size:16
Alignment explanation
Indices: 5283998--5284032 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5283988 ATTAAAATTT
*
5283998 TAATTGAAATATAAAA
1 TAATTCAAATATAAAA
5284014 TAATTCAAATATAAAA
1 TAATTCAAATATAAAA
5284030 TAA
1 TAA
5284033 AAAATACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (16 bp):
TAATTCAAATATAAAA
Found at i:5284177 original size:27 final size:27
Alignment explanation
Indices: 5284127--5284192 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
5284117 AATTTTATTT
5284127 AATTT-ATTTAATATATAAAAATTTAA
1 AATTTAATTTAATATATAAAAATTTAA
* *
5284153 AATTTAATTTAATTTA-AAAATATTTAT
1 AATTTAATTTAATATATAAAA-ATTTAA
*
5284180 TATTTAA-TTAATA
1 AATTTAATTTAATA
5284193 AAAATTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 14 0.41
27 20 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTTAATTTAATATATAAAAATTTAA
Found at i:5284296 original size:15 final size:15
Alignment explanation
Indices: 5284274--5284309 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5284264 AAAAATAAAA
5284274 TAAAATAATTTAATT
1 TAAAATAATTTAATT
*
5284289 TCAAATAATTTAATT
1 TAAAATAATTTAATT
5284304 TAAAAT
1 TAAAAT
5284310 TAATAGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATAATTTAATT
Found at i:5287116 original size:13 final size:13
Alignment explanation
Indices: 5287079--5287120 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5287069 CATTAAAAAA
*
5287079 TTTTTAGAG-AAT
1 TTTTTGGAGAAAT
5287091 TTTTCTGGGAGAAAT
1 TTTT-T-GGAGAAAT
5287106 TTTTTGGAGAAAT
1 TTTTTGGAGAAAT
5287119 TT
1 TT
5287121 GGAAATCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.15
13 11 0.42
14 4 0.15
15 7 0.27
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (13 bp):
TTTTTGGAGAAAT
Found at i:5287760 original size:7 final size:7
Alignment explanation
Indices: 5287750--5287782 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
5287740 TTTCAATTGA
5287750 TTATTTT
1 TTATTTT
5287757 TTATTTT
1 TTATTTT
5287764 TTA--TT
1 TTATTTT
5287769 TTATTTT
1 TTATTTT
5287776 TTATTTT
1 TTATTTT
5287783 ACTTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.21
7 19 0.79
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTATTTT
Found at i:5287772 original size:12 final size:12
Alignment explanation
Indices: 5287755--5287797 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
5287745 ATTGATTATT
5287755 TTTTATTTTTTA
1 TTTTATTTTTTA
5287767 TTTTATTTTTTA
1 TTTTATTTTTTA
5287779 TTTTACTTATATTTA
1 TTTTA-TT-T-TTTA
5287794 TTTT
1 TTTT
5287798 TTTAATCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.61
13 2 0.07
14 1 0.04
15 8 0.29
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:5287772 original size:19 final size:21
Alignment explanation
Indices: 5287756--5287799 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
5287746 TTGATTATTT
5287756 TTTATTTT-TTAT-TTTATTT
1 TTTATTTTATTATATTTATTT
5287775 TTTATTTTACTTATATTTATTT
1 TTTATTTTA-TTATATTTATTT
5287797 TTT
1 TTT
5287800 TAATCCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTATTTTATTATATTTATTT
Found at i:5289180 original size:6 final size:6
Alignment explanation
Indices: 5289169--5289195 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5289159 TGTTCAGCAA
5289169 TCTTTC TCTTTC TCTTTC TCTTTC TCT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCT
5289196 CGTATATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTTTC
Found at i:5308158 original size:5 final size:5
Alignment explanation
Indices: 5308143--5308172 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5308133 AAAATGAAGC
5308143 AAAATT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAA
5308173 ACAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:5320837 original size:26 final size:26
Alignment explanation
Indices: 5320804--5320867 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
5320794 TATTTGATTA
* **
5320804 TAATTTATTTATTATTATGTATATAT
1 TAATTTATATATTATTATAAATATAT
*
5320830 TAATTTATATATTTTTATAAATATAT
1 TAATTTATATATTATTATAAATATAT
*
5320856 TTATTTA-ATATT
1 TAATTTATATATT
5320868 CACAACGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TAATTTATATATTATTATAAATATAT
Found at i:5320846 original size:10 final size:11
Alignment explanation
Indices: 5320808--5320859 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 11
5320798 TGATTATAAT
5320808 TTATTTAT-TA
1 TTATTTATATA
*
5320818 TTATGTATATA
1 TTATTTATATA
5320829 TTAATTTATATA
1 TT-ATTTATATA
*
5320841 TT-TTTATAAA
1 TTATTTATATA
5320851 TATATTTAT
1 T-TATTTAT
5320860 TTAATATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 15 0.43
11 5 0.14
12 15 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TTATTTATATA
Found at i:5323720 original size:24 final size:26
Alignment explanation
Indices: 5323679--5323729 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
5323669 TAAATTATTA
* *
5323679 TTTTTTATATGTAAAATTGTTTAAAT
1 TTTTTTATATGTAAAATTATTGAAAT
*
5323705 TTTTTTATAT-T-TAATTATTGAAAT
1 TTTTTTATATGTAAAATTATTGAAAT
5323729 T
1 T
5323730 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTTTATATGTAAAATTATTGAAAT
Found at i:5324172 original size:2 final size:2
Alignment explanation
Indices: 5324165--5324207 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5324155 ACTTGCTATA
5324165 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5324207 T
1 T
5324208 ATTATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5324371 original size:7 final size:7
Alignment explanation
Indices: 5324361--5324385 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5324351 AACTTTAGAC
5324361 TTTGGAT
1 TTTGGAT
5324368 TTTGGAT
1 TTTGGAT
5324375 TTTGGAT
1 TTTGGAT
5324382 TTTG
1 TTTG
5324386 TCGCACCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TTTGGAT
Found at i:5328185 original size:18 final size:18
Alignment explanation
Indices: 5328140--5328188 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5328130 AATTATTCAA
5328140 TTAAATATAATTATATTTAT
1 TTAAATA-AATT-TATTTAT
* *
5328160 TT-ATTAAATTTATTTTT
1 TTAAATAAATTTATTTAT
5328177 TTAAATAAATTT
1 TTAAATAAATTT
5328189 TAAAAACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 8 0.32
18 12 0.48
19 3 0.12
20 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATAAATTTATTTAT
Found at i:5329614 original size:26 final size:26
Alignment explanation
Indices: 5329585--5329641 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
5329575 GTCAACTTTT
* *
5329585 TTTATTTGTAATAATATTTAATAATA
1 TTTATTTGCAATAATATTCAATAATA
5329611 TTTATTTGCAATAATATTCAATAATA
1 TTTATTTGCAATAATATTCAATAATA
5329637 TTTAT
1 TTTAT
5329642 AAATTGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTATTTGCAATAATATTCAATAATA
Found at i:5329798 original size:27 final size:27
Alignment explanation
Indices: 5329768--5329823 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
5329758 CACATGCTAT
*
5329768 TACACCAACAAGTGCTAACAAATTTTA
1 TACACCAACAAGGGCTAACAAATTTTA
*
5329795 TACACCAAGAAGGGCTAACAAATTTTA
1 TACACCAACAAGGGCTAACAAATTTTA
5329822 TA
1 TA
5329824 TAGTGTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.25
Consensus pattern (27 bp):
TACACCAACAAGGGCTAACAAATTTTA
Found at i:5330171 original size:32 final size:32
Alignment explanation
Indices: 5330130--5330196 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
5330120 TTTGTTTACC
5330130 AAAAATATTTT-TAAAAACAAAAAATAAAAAAT
1 AAAAATATTTTCTAAAAA-AAAAAATAAAAAAT
* *
5330162 AAAATTATTTTCTAAAAATAAAAATAAAAAAT
1 AAAAATATTTTCTAAAAAAAAAAATAAAAAAT
5330194 AAA
1 AAA
5330197 TTTTCAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (32 bp):
AAAAATATTTTCTAAAAAAAAAAATAAAAAAT
Found at i:5332465 original size:29 final size:29
Alignment explanation
Indices: 5332432--5332493 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
5332422 TTTTCTTAAG
*
5332432 TAAGCCCCTATACTTTTATTATACCCAAA
1 TAAGCCCCTATACTTTGATTATACCCAAA
** * * *
5332461 TAAGCCTTTATCCTTTGATTCTATCCAAA
1 TAAGCCCCTATACTTTGATTATACCCAAA
5332490 TAAG
1 TAAG
5332494 ACCTTAATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.37
Consensus pattern (29 bp):
TAAGCCCCTATACTTTGATTATACCCAAA
Found at i:5332622 original size:59 final size:60
Alignment explanation
Indices: 5332523--5332658 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 60
5332513 AGTGATTTAT
* * * * *
5332523 GTTAGGGGCTTCTTTAGGT-ACTAATTAAAAGTTAAGGGCTTATTTGGATACAAATTAAAG
1 GTTAAGGGCTTATTT-GGTAACAAATTAAAAGTTAAGGGCTTATCTGGATACAAATTAAAA
* * * * *
5332583 GTT-ATGGCTTATTTGGTAACAAATTAAAGGTTGAGGGCTTATCTGGGTGCAAATTAAAA
1 GTTAAGGGCTTATTTGGTAACAAATTAAAAGTTAAGGGCTTATCTGGATACAAATTAAAA
5332642 GTTAAGGGCTTATTTGG
1 GTTAAGGGCTTATTTGG
5332659 GTGTAATAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 3 0.05
59 45 0.71
60 15 0.24
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (60 bp):
GTTAAGGGCTTATTTGGTAACAAATTAAAAGTTAAGGGCTTATCTGGATACAAATTAAAA
Found at i:5332661 original size:30 final size:30
Alignment explanation
Indices: 5332523--5332660 Score: 154
Period size: 30 Copynumber: 4.6 Consensus size: 30
5332513 AGTGATTTAT
* * * *
5332523 GTTAGGGGCTTCTTTAGGTACTAATTAAAA
1 GTTAAGGGCTTATTTGGGTACAAATTAAAA
* *
5332553 GTTAAGGGCTTATTTGGATACAAATTAAAG
1 GTTAAGGGCTTATTTGGGTACAAATTAAAA
* *
5332583 GTT-ATGGCTTATTT-GGTAACAAATTAAAG
1 GTTAAGGGCTTATTTGGGT-ACAAATTAAAA
* * *
5332612 GTTGAGGGCTTATCTGGGTGCAAATTAAAA
1 GTTAAGGGCTTATTTGGGTACAAATTAAAA
5332642 GTTAAGGGCTTATTTGGGT
1 GTTAAGGGCTTATTTGGGT
5332661 GTAATAAAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.02
29 24 0.26
30 62 0.68
31 3 0.03
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (30 bp):
GTTAAGGGCTTATTTGGGTACAAATTAAAA
Found at i:5346606 original size:22 final size:22
Alignment explanation
Indices: 5346565--5346608 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5346555 ATTTTCTATC
** *
5346565 CTTAATTCTAGGGATGCAAATA
1 CTTAATTCTAGAAATACAAATA
5346587 CTTAATTCTAGAAATACAAATA
1 CTTAATTCTAGAAATACAAATA
5346609 TAAATATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAAATACAAATA
Found at i:5348517 original size:14 final size:14
Alignment explanation
Indices: 5348498--5348524 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5348488 TTAGTTAAAG
5348498 AAAAATCAAAATAA
1 AAAAATCAAAATAA
5348512 AAAAATCAAAATA
1 AAAAATCAAAATA
5348525 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATCAAAATAA
Found at i:5348657 original size:59 final size:58
Alignment explanation
Indices: 5348561--5348898 Score: 405
Period size: 59 Copynumber: 5.7 Consensus size: 58
5348551 TTGTGTAAAA
*
5348561 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTCGA-TTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTT--ATTTTTCAAGG
* * *
5348620 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGAAAATTTATTTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTGAAAATTTATTTTTCAAGG
* *
5348679 AAAATTGATACTTTCAACTTTTTCC-CAGAAATATTTTTTGGAAATTTATTTTTCTTTTAAGG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTGAAAATTTATTTTTC----AAGG
* * *
5348741 AAAATTGATACTTTCCACTTTTCCTTAAAAATATTTTTTGAAAATTTCGATATTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTT--ATTTTTCAAGG
* * * * *
5348801 AAAATGGATACTTTCAACTTTTACTCAAAAATTTTTTTTTTGAAAATTTACTTTT-AAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAATTTATTTTTCAAGG
5348860 AAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTT
5348899 TTGGAATTTT
Statistics
Matches: 241, Mismatches: 25, Indels: 28
0.82 0.09 0.10
Matches are distributed among these distances:
57 7 0.03
58 22 0.09
59 91 0.38
60 55 0.23
61 6 0.02
62 54 0.22
64 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTATTTTTCAAGG
Found at i:5348864 original size:181 final size:180
Alignment explanation
Indices: 5348561--5348898 Score: 572
Period size: 181 Copynumber: 1.9 Consensus size: 180
5348551 TTGTGTAAAA
* *
5348561 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTCGATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTCGATTTTCAAGGAAAATG
* *
5348626 GATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGAAAATTTATTTTTTAAGAAAAATTGATACT
66 GATACTTTCAACTTTTACTCAAAAATTTTTTTTTGAAAATTTATCTTTTAAGAAAAATTGATACT
*
5348691 TTCAACTTTTTCCC-AGAAATATTTTTTGGAAATTTATTTTTCTTTTAAGG
131 TTCAAC-TTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTCTTTTAAGG
* *
5348741 AAAATTGATACTTTCCACTTTTCCTTAAAAATATTTTTTGAAAATTTCGATATTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTCGAT-TTTCAAGGAAAAT
5348806 GGATACTTTCAACTTTTACTCAAAAATTTTTTTTTTGAAAATTTA-CTTTTAAGAAAAATTGATA
65 GGATACTTTCAACTTTTACTCAAAAA-TTTTTTTTTGAAAATTTATCTTTTAAGAAAAATTGATA
5348870 CTTTCAACTTTTCCCTAAAAATATTTTTT
129 CTTTCAACTTTTCCCTAAAAATATTTTTT
5348899 TTGGAATTTT
Statistics
Matches: 148, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
180 55 0.37
181 75 0.51
182 18 0.12
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (180 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTCGATTTTCAAGGAAAATG
GATACTTTCAACTTTTACTCAAAAATTTTTTTTTGAAAATTTATCTTTTAAGAAAAATTGATACT
TTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTCTTTTAAGG
Found at i:5348959 original size:11 final size:10
Alignment explanation
Indices: 5348932--5349031 Score: 58
Period size: 10 Copynumber: 9.0 Consensus size: 10
5348922 AAAAAAATAG
*
5348932 AATAATAAAA
1 AATAAAAAAA
5348942 AATAAAAAAA
1 AATAAAAAAA
5348952 AATAAAAAAA
1 AATAAAAAAA
*
5348962 AAGAATATTAAATA
1 AATAA-A--AAA-A
*
5348976 AACCTAATATAATA
1 AA--TAA-A-AAAA
5348990 AATAAAAAATA
1 AATAAAAAA-A
*
5349001 AA-AAAAACA
1 AATAAAAAAA
5349010 AATAAACAAAGA
1 AATAAA-AAA-A
5349022 AATAAAAAAA
1 AATAAAAAAA
5349032 TTCAAAGAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
9 3 0.04
10 34 0.47
11 10 0.14
12 10 0.14
13 3 0.04
14 6 0.08
15 3 0.04
16 4 0.05
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:5348968 original size:23 final size:25
Alignment explanation
Indices: 5348922--5349031 Score: 75
Period size: 25 Copynumber: 4.2 Consensus size: 25
5348912 TTTTTATTTT
*
5348922 AAAAAAATAGAATAATAAAAAATAA
1 AAAAAAATAGAATAAAAAAAAATAA
5348947 AAAAAAATA-AA-AAAAAAGAATATTAA
1 AAAAAAATAGAATAAAAAA-AA-A-TAA
* *
5348973 ATAAACCTAATATAATAAATAAAAAAT-A
1 A-AAA--AAATAGAATAAA-AAAAAATAA
*
5349001 AAAAAAACA-AATAAACAAAGAAATAA
1 AAAAAAATAGAATAAA-AAA-AAATAA
5349027 AAAAA
1 AAAAA
5349032 TTCAAAGAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
23 5 0.07
24 13 0.19
25 17 0.25
26 10 0.14
27 6 0.09
28 2 0.03
29 5 0.07
30 3 0.04
31 5 0.07
32 3 0.04
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.15
Consensus pattern (25 bp):
AAAAAAATAGAATAAAAAAAAATAA
Found at i:5349028 original size:24 final size:24
Alignment explanation
Indices: 5348986--5349057 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
5348976 AACCTAATAT
*
5348986 AATAAATAAAAAATAAAAAAAACA
1 AATAAACAAAAAATAAAAAAAACA
*
5349010 AATAAACAAAGAAATAAAAAAATTCA
1 AATAAACAAA-AAATAAAAAAA-ACA
* * *
5349036 AAGAAAGAAAAAAAAAAAAAAA
1 AATAAACAAAAAATAAAAAAAA
5349058 ACCTGGAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 9 0.22
25 21 0.52
26 10 0.25
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.10
Consensus pattern (24 bp):
AATAAACAAAAAATAAAAAAAACA
Found at i:5350325 original size:1 final size:1
Alignment explanation
Indices: 5350314--5350395 Score: 65
Period size: 1 Copynumber: 82.0 Consensus size: 1
5350304 AACATTGTCA
* * * * * * * * *
5350314 TTTTTTGTTTTTTTGTGTTTTTTGTTTTGTTTTTTTGTTCTTTTTTTTGTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
5350379 TGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTT
5350396 ACCAAAGCTT
Statistics
Matches: 59, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.87
Consensus pattern (1 bp):
T
Found at i:5350334 original size:9 final size:8
Alignment explanation
Indices: 5350314--5350395 Score: 78
Period size: 9 Copynumber: 9.6 Consensus size: 8
5350304 AACATTGTCA
5350314 TTTTTTGT
1 TTTTTTGT
5350322 TTTTTTGT
1 TTTTTTGT
5350330 GTTTTTTGT
1 -TTTTTTGT
5350339 TTTGTTT-T
1 TTT-TTTGT
5350347 TTTGTTCT-T
1 TTT-TT-TGT
5350356 TTTTTTGTT
1 TTTTTTG-T
*
5350365 TTTTTATTT
1 TTTTT-TGT
5350374 TTTTTTGTT
1 TTTTTTG-T
5350383 TTTTTTGT
1 TTTTTTGT
5350391 TTTTT
1 TTTTT
5350396 ACCAAAGCTT
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
7 1 0.02
8 27 0.42
9 36 0.55
10 1 0.02
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.87
Consensus pattern (8 bp):
TTTTTTGT
Found at i:5350537 original size:41 final size:41
Alignment explanation
Indices: 5350406--5350615 Score: 339
Period size: 41 Copynumber: 5.0 Consensus size: 41
5350396 ACCAAAGCTT
* * *
5350406 CTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATTGCTC
*
5350449 CTCTAAACAGAGGCAGCACGACTTTGGAAAAGTAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTC
*
5350491 CTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
*
5350532 TTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
5350573 CTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
1 CTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
5350614 CT
1 CT
5350616 TTGAAAAGTA
Statistics
Matches: 157, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
41 97 0.62
42 33 0.21
43 25 0.16
44 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
CTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
Found at i:5350619 original size:20 final size:20
Alignment explanation
Indices: 5350594--5350637 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
5350584 GGCACCACGA
5350594 CTTTGAAAAGTAAATTGCTC
1 CTTTGAAAAGTAAATTGCTC
5350614 CTTTGAAAAGTAAATTGCTC
1 CTTTGAAAAGTAAATTGCTC
5350634 CTTT
1 CTTT
5350638 AAACAGAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CTTTGAAAAGTAAATTGCTC
Found at i:5350648 original size:61 final size:60
Alignment explanation
Indices: 5350553--5350675 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 60
5350543 GGCACCACGA
5350553 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
1 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC-ACTTTGAAAAGTAAATTGCTC
*
5350614 CTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACACTTTGAAAAGTAAATTGCTC
1 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACACTTTGAAAAGTAAATTGCTC
5350674 CT
1 CT
5350676 CTAAACAGAG
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 23 0.38
61 38 0.62
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (60 bp):
CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACACTTTGAAAAGTAAATTGCTC
Found at i:5350669 original size:40 final size:41
Alignment explanation
Indices: 5350614--5350717 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 41
5350604 TAAATTGCTC
5350614 CTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCAC-A
1 CTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACGA
*
5350654 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
1 CTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACGA
*
5350695 CTTTGGAAAGTAAATTGCTCCTT
1 CTTTGAAAAGTAAATTGCTCCTT
5350718 GACAATCATG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 38 0.63
41 22 0.37
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (41 bp):
CTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACGA
Found at i:5350688 original size:101 final size:102
Alignment explanation
Indices: 5350512--5350717 Score: 380
Period size: 101 Copynumber: 2.0 Consensus size: 102
5350502 GGTACCACGA
5350512 CTTTGAAAAGTAAATTGCTCTTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCT
1 CTTTGAAAAGTAAATTGCTCTTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCT
5350577 AAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
66 AAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
5350614 CTTTGAAAAGTAAATTGCTCCTT-TAAACAGAGGCACCAC-ACTTTGAAAAGTAAATTGCTCCTC
1 CTTTGAAAAGTAAATTGCT-CTTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTC
*
5350677 TAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
65 TAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
5350715 CTT
1 CTT
5350718 GACAATCATG
Statistics
Matches: 102, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
101 64 0.63
102 35 0.34
103 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (102 bp):
CTTTGAAAAGTAAATTGCTCTTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCT
AAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
Found at i:5351909 original size:8 final size:7
Alignment explanation
Indices: 5351894--5351948 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
5351884 AATTTGAATC
5351894 TCTTTTT
1 TCTTTTT
5351901 TCATTTTT
1 TC-TTTTT
5351909 TCTTTTT
1 TCTTTTT
*
5351916 TTTTTCTT
1 TCTTT-TT
5351924 TC-TTTT
1 TCTTTTT
*
5351930 T-TTTTC
1 TCTTTTT
5351936 TCTTTTT
1 TCTTTTT
5351943 T-TTTTT
1 TCTTTTT
5351949 CATCATCTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
6 12 0.30
7 18 0.45
8 10 0.25
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (7 bp):
TCTTTTT
Found at i:5351929 original size:14 final size:14
Alignment explanation
Indices: 5351894--5351949 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
5351884 AATTTGAATC
5351894 TCTTTTTTCATTT-TT
1 TCTTTTTT--TTTCTT
5351909 TCTTTTTTTTTTCTT
1 TC-TTTTTTTTTCTT
5351924 TCTTTTTTTTTCTCT
1 TCTTTTTTTTTCT-T
5351939 T-TTTTTTTTTC
1 TCTTTTTTTTTC
5351950 ATCATCTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 24 0.63
15 8 0.21
16 6 0.16
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (14 bp):
TCTTTTTTTTTCTT
Found at i:5351933 original size:16 final size:16
Alignment explanation
Indices: 5351894--5351948 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
5351884 AATTTGAATC
**
5351894 TCTTTTTTCATTT-TT
1 TCTTTTTTTTTTTCTT
5351909 TC-TTTTTTTTTTCTT
1 TCTTTTTTTTTTTCTT
*
5351924 TCTTTTTTTTTCTCTT
1 TCTTTTTTTTTTTCTT
5351940 T-TTTTTTTT
1 TCTTTTTTTT
5351949 CATCATCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.23
15 14 0.40
16 13 0.37
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (16 bp):
TCTTTTTTTTTTTCTT
Found at i:5351974 original size:17 final size:17
Alignment explanation
Indices: 5351923--5351975 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
5351913 TTTTTTTTCT
*
5351923 TTCTT-TTTTTTTCTC-
1 TTCTTCTTTTTTCCTCA
* *
5351938 TT-TTTTTTTTTCATCA
1 TTCTTCTTTTTTCCTCA
5351954 -TCTTCTTTTTTCCTCA
1 TTCTTCTTTTTTCCTCA
5351970 TTCTTC
1 TTCTTC
5351976 ACCTATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 11 0.37
16 12 0.40
17 5 0.17
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.72
Consensus pattern (17 bp):
TTCTTCTTTTTTCCTCA
Found at i:5354415 original size:9 final size:9
Alignment explanation
Indices: 5354401--5354432 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
5354391 GGCTTGTACT
5354401 TCCTTCAAC
1 TCCTTCAAC
5354410 TCCTTCAAC
1 TCCTTCAAC
5354419 TCCTTCAAC
1 TCCTTCAAC
5354428 TCCTT
1 TCCTT
5354433 TTCCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.38
Consensus pattern (9 bp):
TCCTTCAAC
Found at i:5355889 original size:59 final size:58
Alignment explanation
Indices: 5355822--5356162 Score: 427
Period size: 59 Copynumber: 5.7 Consensus size: 58
5355812 TTTTGTGTAG
5355822 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTCGA-TTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTT--ATTTTTCAA
* *
5355881 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTATTTTT-AA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT--ATTTTTTGAAAATTTATTTTTCAA
* *
5355940 GGAAAATTGATACTTTCAACTTTTCCCCAGAAATATTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTTTC----AA
* *
5356003 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCGATTTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTT--ATTTTTCAA
* * * *
5356063 GGAAAATGGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTACTTTT-AA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT--ATTTTTTGAAAATTTATTTTTCAA
* * *
5356122 GAAAAATTGATACTTTTAACTTTTCCCTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
5356163 TTGGAATTTT
Statistics
Matches: 249, Mismatches: 20, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
57 6 0.02
58 19 0.08
59 99 0.40
60 42 0.17
61 14 0.06
62 27 0.11
63 35 0.14
64 7 0.03
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTCAA
Found at i:5356039 original size:181 final size:183
Alignment explanation
Indices: 5355822--5356168 Score: 608
Period size: 182 Copynumber: 1.9 Consensus size: 183
5355812 TTTTGTGTAG
5355822 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTCGA-TTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTCGATTTTTCAAGGAAA
* * *
5355886 ATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTATTTTTAAGGAAAATTGAT
66 ATGGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTACTTTTAAGAAAAATTGAT
*
5355951 ACTTTCAACTTTTCCCCAGAAATA-TTTTTTTGGAAATTTATTTTTCTTTTAA
131 ACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTTTCTTTTAA
* *
5356003 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCGATTTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTCGATTTTTCAAGGAAA
5356068 ATGGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTACTTTTAAGAAAAATTGAT
66 ATGGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTACTTTTAAGAAAAATTGAT
* *
5356133 ACTTTTAACTTTTCCCTAAAAATATTTTTTTTGGAA
131 ACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAA
5356169 TTTTTGATTT
Statistics
Matches: 156, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
181 50 0.32
182 95 0.61
183 11 0.07
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (183 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTCGATTTTTCAAGGAAA
ATGGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTACTTTTAAGAAAAATTGAT
ACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTTTCTTTTAA
Found at i:5356210 original size:16 final size:16
Alignment explanation
Indices: 5356184--5356236 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5356174 GATTTTTATT
5356184 TAAAGAAAATAGAAT-AA
1 TAAA-AAAATA-AATAAA
5356201 TAAAAAAATAAATAAA
1 TAAAAAAATAAATAAA
*
5356217 TAAAAAGAAT-ATTAAA
1 TAAAAA-AATAAATAAA
5356233 TAAA
1 TAAA
5356237 TCTAATCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 3 0.09
16 23 0.70
17 7 0.21
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
TAAAAAAATAAATAAA
Found at i:5356272 original size:24 final size:23
Alignment explanation
Indices: 5356245--5356314 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
5356235 AATCTAATCT
*
5356245 AATAAATAATAATAAAAAAAAACA
1 AATAAACAA-AATAAAAAAAAACA
**
5356269 AATAAACAAAAATAAAAAAATTCA
1 AATAAAC-AAAATAAAAAAAAACA
* * *
5356293 AAGAAAGAAAAAAAAAAAAAAC
1 AATAAACAAAATAAAAAAAAAC
5356315 CTGGAGCGGC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 12 0.32
24 23 0.62
25 2 0.05
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (23 bp):
AATAAACAAAATAAAAAAAAACA
Found at i:5357293 original size:17 final size:17
Alignment explanation
Indices: 5357267--5357310 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
5357257 AAAAAAAATG
* *
5357267 ATAATGATAATAATAAT
1 ATAATAATAATAATAAC
*
5357284 ATAATAATAATGATAAC
1 ATAATAATAATAATAAC
5357301 ATAATAATAA
1 ATAATAATAA
5357311 CAAATATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAATAATAATAATAAC
Found at i:5357327 original size:20 final size:19
Alignment explanation
Indices: 5357282--5357333 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
5357272 GATAATAATA
*
5357282 ATATAATAATAATGATAAC
1 ATATAATAAAAATGATAAC
5357301 ATAATAATAACAAAT-ATAAC
1 AT-ATAATAA-AAATGATAAC
5357321 TATATAAATAAAA
1 -ATAT-AATAAAA
5357334 TACATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.07
20 16 0.57
21 10 0.36
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (19 bp):
ATATAATAAAAATGATAAC
Found at i:5368205 original size:11 final size:11
Alignment explanation
Indices: 5368162--5368206 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5368152 ATTTAGTTTG
5368162 AATTAAATTTAA
1 AATTAAATTT-A
*
5368174 ATATTAAATATA
1 A-ATTAAATTTA
*
5368186 TATTAAATTTA
1 AATTAAATTTA
5368197 AATTAAATTT
1 AATTAAATTT
5368207 TAGATCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 18 0.64
12 2 0.07
13 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:5368338 original size:21 final size:21
Alignment explanation
Indices: 5368308--5368347 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5368298 TAATATTTTG
5368308 TATTAAATTTTAT-TTAAATA
1 TATTAAATTTTATATTAAATA
5368328 TATTAAAATTTTATATTAAA
1 TATT-AAATTTTATATTAAA
5368348 ATAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAAATTTTATATTAAATA
Found at i:5368344 original size:13 final size:13
Alignment explanation
Indices: 5368325--5368364 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5368315 TTTTATTTAA
5368325 ATATATTAAAATT
1 ATATATTAAAATT
* *
5368338 TTATATTAAAATA
1 ATATATTAAAATT
*
5368351 ATATATAAAAATT
1 ATATATTAAAATT
5368364 A
1 A
5368365 AAAATCGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:5368429 original size:29 final size:27
Alignment explanation
Indices: 5368384--5368438 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 27
5368374 AAATGAATTC
5368384 AATTAAATTTGATTCAAATCAAATTTA
1 AATTAAATTTGATTCAAATCAAATTTA
5368411 AATTAAAATTTAGATTCAAATCAAATTT
1 AATT-AAATTT-GATTCAAATCAAATTT
5368439 TAAAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 4 0.15
28 6 0.23
29 16 0.62
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (27 bp):
AATTAAATTTGATTCAAATCAAATTTA
Found at i:5368471 original size:27 final size:26
Alignment explanation
Indices: 5368439--5368492 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
5368429 AATCAAATTT
*
5368439 TAAAATATT-ATATAATATTTTAAAAAA
1 TAAAAT-TTAATATAAT-TTTAAAAAAA
*
5368466 TAAAATTTAATTTAATTTTAAAAAAA
1 TAAAATTTAATATAATTTTAAAAAAA
5368492 T
1 T
5368493 CGTTATTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAATTTAATATAATTTTAAAAAAA
Found at i:5369943 original size:9 final size:9
Alignment explanation
Indices: 5369931--5369976 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
5369921 CCCAAAACAA
5369931 AAAAAAATT
1 AAAAAAATT
*
5369940 -AAAAAA-C
1 AAAAAAATT
**
5369947 AAAAAAACA
1 AAAAAAATT
5369956 AAAAAAATT
1 AAAAAAATT
5369965 AAAAAAATT
1 AAAAAAATT
5369974 AAA
1 AAA
5369977 GTATATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 12 0.39
9 19 0.61
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAATT
Found at i:5377443 original size:14 final size:15
Alignment explanation
Indices: 5377418--5377446 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5377408 GAAGAGCGGC
5377418 GAGTAGGGAGGGAGA
1 GAGTAGGGAGGGAGA
5377433 GAGTA-GGAGGGAGA
1 GAGTAGGGAGGGAGA
5377447 CGGTGGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.59, T:0.07
Consensus pattern (15 bp):
GAGTAGGGAGGGAGA
Found at i:5378642 original size:13 final size:13
Alignment explanation
Indices: 5378624--5378689 Score: 82
Period size: 13 Copynumber: 5.2 Consensus size: 13
5378614 GTAATATTTT
5378624 TATTAAATTAATA
1 TATTAAATTAATA
*
5378637 TATTAAATTAAGA
1 TATTAAATTAATA
5378650 TATTAAA-TAATA
1 TATTAAATTAATA
**
5378662 T-TTTTATTAATA
1 TATTAAATTAATA
5378674 TATATAAATTAATA
1 TAT-TAAATTAATA
5378688 TA
1 TA
5378690 AAATTAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
11 3 0.07
12 11 0.25
13 20 0.45
14 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:5378653 original size:26 final size:26
Alignment explanation
Indices: 5378624--5378696 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 26
5378614 GTAATATTTT
5378624 TATTAAATTAATATATTAAATTAAGA
1 TATTAAATTAATATATTAAATTAAGA
** *
5378650 TATTAAA-TAATAT-TTTTATTAATA
1 TATTAAATTAATATATTAAATTAAGA
5378674 TATATAAATTAATATA--AAATTAA
1 TAT-TAAATTAATATATTAAATTAA
5378697 ATAAATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 11 0.28
25 15 0.38
26 13 0.33
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
TATTAAATTAATATATTAAATTAAGA
Found at i:5378665 original size:42 final size:39
Alignment explanation
Indices: 5378606--5378692 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 39
5378596 CATCTTAATT
5378606 ATATAAAAGTAATATTTTTATTAAATTAATATATTAAATTAAG
1 ATATAAAAGTAATATTTTTATT-AA-T-ATATA-TAAATTAAG
*
5378649 ATATTAAA-TAATATTTTTATTAATATATATAAATT-A-
1 ATATAAAAGTAATATTTTTATTAATATATATAAATTAAG
5378685 ATATAAAA
1 ATATAAAA
5378693 TTAAATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 6 0.14
39 5 0.12
40 1 0.02
41 2 0.05
42 13 0.31
43 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (39 bp):
ATATAAAAGTAATATTTTTATTAATATATATAAATTAAG
Found at i:5378979 original size:27 final size:27
Alignment explanation
Indices: 5378949--5379006 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5378939 TATATCGATA
5378949 TAAAAATAAAAAAAATTTTTATT-TTGT
1 TAAAAATAAAAAAAATTTTTATTATT-T
** * *
5378976 TAAATCTAAATATAATTTTTATTATTT
1 TAAAAATAAAAAAAATTTTTATTATTT
5379003 TAAA
1 TAAA
5379007 TTATATTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TAAAAATAAAAAAAATTTTTATTATTT
Found at i:5379047 original size:24 final size:24
Alignment explanation
Indices: 5378993--5379067 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
5378983 AAATATAATT
* *
5378993 TTTATTATTTTA-AATTATATTAC-
1 TTTA-TATTTTATATTTATATCACA
5379016 TTTCATATTTTATATTTATATCACA
1 TTT-ATATTTTATATTTATATCACA
* *
5379041 TTTATATTATAT-TATTATATCATA
1 TTTATATTTTATAT-TTATATCACA
5379065 TTT
1 TTT
5379068 TAGATTACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 11 0.25
24 30 0.68
25 3 0.07
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATATTTTATATTTATATCACA
Found at i:5380143 original size:12 final size:12
Alignment explanation
Indices: 5380126--5380163 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5380116 GTTTTTCTCA
5380126 TTTTCTTTTCAT
1 TTTTCTTTTCAT
*
5380138 TTTTCTTAT--T
1 TTTTCTTTTCAT
5380148 TTTTCTTTTCAT
1 TTTTCTTTTCAT
5380160 TTTT
1 TTTT
5380164 TTATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTCAT
Found at i:5380150 original size:21 final size:21
Alignment explanation
Indices: 5380117--5380167 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
5380107 AAGGCCTTTG
*
5380117 TTTTTCTCA-TTTTCTTTTCA
1 TTTTTCTTATTTTTCTTTTCA
5380137 TTTTTCTTATTTTTTCTTTTCA
1 TTTTTCTTA-TTTTTCTTTTCA
5380159 TTTTT-TTAT
1 TTTTTCTTAT
5380168 ATTTAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 16 0.57
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCTTATTTTTCTTTTCA
Found at i:5380154 original size:22 final size:21
Alignment explanation
Indices: 5380126--5380167 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
5380116 GTTTTTCTCA
5380126 TTTTCTTTTCATTTTTCTTATT
1 TTTTCTTTTCATTTTT-TTATT
5380148 TTTTCTTTTCATTTTTTTAT
1 TTTTCTTTTCATTTTTTTAT
5380168 ATTTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTCATTTTTTTATT
Found at i:5382453 original size:18 final size:18
Alignment explanation
Indices: 5382407--5382441 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5382397 ATTAAAATTA
5382407 AATAAAAAC--AAATTTT
1 AATAAAAACAAAAATTTT
5382423 AATAAAAACAAAAATTTT
1 AATAAAAACAAAAATTTT
5382441 A
1 A
5382442 GTCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAAACAAAAATTTT
Found at i:5388731 original size:14 final size:14
Alignment explanation
Indices: 5388692--5388731 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5388682 ATTTTATCTG
*
5388692 ATAATTTAAAAATA
1 ATAATTTAAAATTA
5388706 ATAATTTAAAATT-
1 ATAATTTAAAATTA
5388719 ATATATTTAAAAT
1 ATA-ATTTAAAAT
5388732 GATTTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATTTAAAATTA
Found at i:5391844 original size:22 final size:22
Alignment explanation
Indices: 5391816--5391857 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5391806 TCACTAACAC
*
5391816 CAACAACATC-ATCACCTTTCAG
1 CAACAAC-TCAATAACCTTTCAG
5391838 CAACAACTCAATAACCTTTC
1 CAACAACTCAATAACCTTTC
5391858 TTCTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (22 bp):
CAACAACTCAATAACCTTTCAG
Found at i:5393220 original size:17 final size:17
Alignment explanation
Indices: 5393188--5393237 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5393178 TTGCCTACTT
5393188 AAAATCAAAGATGAAATG
1 AAAATCAAA-ATGAAATG
*
5393206 AAAATGAAAATGAAATG
1 AAAATCAAAATGAAATG
*
5393223 CAAATTC-AAATGAAA
1 -AAAATCAAAATGAAA
5393238 CATTCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.62, C:0.06, G:0.14, T:0.18
Consensus pattern (17 bp):
AAAATCAAAATGAAATG
Found at i:5396359 original size:26 final size:26
Alignment explanation
Indices: 5396329--5396396 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
5396319 AAGTACTTTA
5396329 ATTATATAATCAACTAAATAATCAA-T
1 ATTATATAATCAACTAAATAA-CAATT
* * *
5396355 ATTATATTAT-AATTAAATTACAATT
1 ATTATATAATCAACTAAATAACAATT
5396380 ATTGA-ATAATCAACTAA
1 ATT-ATATAATCAACTAA
5396397 CAAATTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 3 0.09
25 16 0.47
26 15 0.44
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.38
Consensus pattern (26 bp):
ATTATATAATCAACTAAATAACAATT
Found at i:5399165 original size:3 final size:3
Alignment explanation
Indices: 5399159--5399198 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5399149 TATTATTATC
5399159 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5399199 TATCAAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5400634 original size:2 final size:2
Alignment explanation
Indices: 5400610--5400651 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
5400600 ATTAGAAGGA
* * *
5400610 AT AT AT AA AT AA AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5400651 A
1 A
5400652 GATGATGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:5402387 original size:25 final size:25
Alignment explanation
Indices: 5402334--5402393 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5402324 ATCCAATGAT
5402334 AAAATTTTTA-AAAATTTTAAATAG
1 AAAATTTTTATAAAATTTTAAATAG
* **
5402358 TAAATTTTTATAAAATTCTTAGGT-G
1 AAAATTTTTATAAAATT-TTAAATAG
5402383 AAAATTTTTAT
1 AAAATTTTTAT
5402394 TTAAATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.30
25 17 0.57
26 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (25 bp):
AAAATTTTTATAAAATTTTAAATAG
Found at i:5403044 original size:48 final size:48
Alignment explanation
Indices: 5402870--5403077 Score: 207
Period size: 49 Copynumber: 4.3 Consensus size: 48
5402860 AAATTGGCCA
* * *
5402870 AAATGGTAAAAAATTTAGAAATTAAAAAA-AAA--TCTAAATTGAC-C
1 AAATAGTAAAAATTTTAGAAATTAAAAAAGAAATTTCTAAATTAACTC
*
5402914 AAA-ATGATGAAAAATTTTCGAAATTAAAAAAAGAAATTTCTAAATTAACTC
1 AAATA-G-T-AAAAATTTTAGAAATT-AAAAAAGAAATTTCTAAATTAACTC
*
5402965 AAATGACG-AAAAA-TTTAGATATTTAAAAAAGAAATTTCTAAATTGAAC-C
1 AAAT-A-GTAAAAATTTTAGA-AATTAAAAAAGAAATTTCTAAATT-AACTC
* *
5403014 AAATAGTAAAAATTTTAGAGATTAAAAAAGAAATTTCTAAACTAACTC
1 AAATAGTAAAAATTTTAGAAATTAAAAAAGAAATTTCTAAATTAACTC
*
5403062 AAATTGTGAAAAATTT
1 AAATAGT-AAAAATTT
5403078 AAAAATTTTA
Statistics
Matches: 137, Mismatches: 11, Indels: 27
0.78 0.06 0.15
Matches are distributed among these distances:
44 4 0.03
45 1 0.01
46 14 0.10
47 10 0.07
48 37 0.27
49 44 0.32
50 21 0.15
51 4 0.03
53 2 0.01
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (48 bp):
AAATAGTAAAAATTTTAGAAATTAAAAAAGAAATTTCTAAATTAACTC
Found at i:5403114 original size:97 final size:98
Alignment explanation
Indices: 5402878--5403092 Score: 266
Period size: 97 Copynumber: 2.2 Consensus size: 98
5402868 CAAAATGGTA
* *
5402878 AAAAATTTAGAAA-TTAAAAAA-AAA--TCTAAATTG-ACCAAA-ATGATGAAAAATTTTCGAAA
1 AAAAATTTAAAAATTTAAAAAAGAAATTTCTAAATTGAACCAAATA-G-T-AAAAATTTTAGAAA
*
5402937 TTAAAAAAAGAAATTTCTAAATTAACTCAAATGACG
63 TTAAAAAAAGAAATTTCTAAACTAACTCAAATGACG
* * *
5402973 AAAAATTTAGATATTTAAAAAAGAAATTTCTAAATTGAACCAAATAGTAAAAATTTTAGAGATT-
1 AAAAATTTAAAAATTTAAAAAAGAAATTTCTAAATTGAACCAAATAGTAAAAATTTTAGAAATTA
*
5403037 AAAAAAGAAATTTCTAAACTAACTCAAATTG-TG
66 AAAAAAGAAATTTCTAAACTAACTCAAA-TGACG
5403070 AAAAATTTAAAAATTTTAAAAAA
1 AAAAATTTAAAAA-TTTAAAAAA
5403093 ATATTTTTAA
Statistics
Matches: 105, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
95 12 0.11
96 8 0.08
97 42 0.40
98 25 0.24
99 10 0.10
100 7 0.07
101 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (98 bp):
AAAAATTTAAAAATTTAAAAAAGAAATTTCTAAATTGAACCAAATAGTAAAAATTTTAGAAATTA
AAAAAAGAAATTTCTAAACTAACTCAAATGACG
Found at i:5405613 original size:17 final size:17
Alignment explanation
Indices: 5405588--5405641 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
5405578 TAAAAGAGAA
5405588 TGAAAGGTCACTTGTTT
1 TGAAAGGTCACTTGTTT
*
5405605 TGGAAGGTCACTTGTTT
1 TGAAAGGTCACTTGTTT
5405622 TGAAAGGTCACTTGTTT
1 TGAAAGGTCACTTGTTT
5405639 TGA
1 TGA
5405642 GATATCAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (17 bp):
TGAAAGGTCACTTGTTT
Found at i:5406761 original size:30 final size:30
Alignment explanation
Indices: 5406725--5406814 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
5406715 GGCTCTCAAC
*
5406725 CTTTAATTTATACTTAAATATATCCTTAAT
1 CTTTAATTTATACTTAAATAAATCCTTAAT
**
5406755 CTTTAATTTGTATAC--AAATAAATTTTTAA-
1 CTTTAA-TT-TATACTTAAATAAATCCTTAAT
* *
5406784 CTTTTAATTTATATTTAAATAAACCCTTAAT
1 C-TTTAATTTATACTTAAATAAATCCTTAAT
5406815 ATAATACATA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
28 4 0.09
29 3 0.06
30 33 0.70
31 2 0.04
32 5 0.11
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (30 bp):
CTTTAATTTATACTTAAATAAATCCTTAAT
Found at i:5411891 original size:27 final size:27
Alignment explanation
Indices: 5411861--5411912 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5411851 CAATTTACAT
5411861 TTTGCTGATTATATGATTTCAATAAAA
1 TTTGCTGATTATATGATTTCAATAAAA
*
5411888 TTTGCTGATTTTATGATTTCAATAA
1 TTTGCTGATTATATGATTTCAATAA
5411913 TATAATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (27 bp):
TTTGCTGATTATATGATTTCAATAAAA
Found at i:5412243 original size:27 final size:27
Alignment explanation
Indices: 5412213--5412269 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
5412203 GATAGTCGAA
5412213 TAATCT-ATTAATAGATCATTGAATTTT
1 TAATCTCATTAAT-GATCATTGAATTTT
* * * *
5412240 TAATTTCATTGATGATGATTTAATTTT
1 TAATCTCATTAATGATCATTGAATTTT
5412267 TAA
1 TAA
5412270 CGAGCTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (27 bp):
TAATCTCATTAATGATCATTGAATTTT
Found at i:5414081 original size:2 final size:2
Alignment explanation
Indices: 5414076--5414101 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5414066 ACACACACAC
5414076 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5414102 GAACGAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5417361 original size:18 final size:18
Alignment explanation
Indices: 5417338--5417382 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5417328 TTGACTTGTG
*
5417338 CTACAATATTGCCACCTA
1 CTACAATACTGCCACCTA
5417356 CTACAATACTGCCACCTA
1 CTACAATACTGCCACCTA
*
5417374 CTATAATAC
1 CTACAATAC
5417383 CGTCGAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.27
Consensus pattern (18 bp):
CTACAATACTGCCACCTA
Found at i:5418205 original size:21 final size:23
Alignment explanation
Indices: 5418161--5418210 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
5418151 AATATAACTC
5418161 TTATCATATAATATTTAATAATTT
1 TTATCATATAATATTT-ATAATTT
*
5418185 TTATGATATAATA-TT-TAATTT
1 TTATCATATAATATTTATAATTT
5418206 TTATC
1 TTATC
5418211 TACAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
23 2 0.08
24 12 0.50
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATCATATAATATTTATAATTT
Found at i:5419227 original size:16 final size:15
Alignment explanation
Indices: 5419202--5419248 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
5419192 GAGGCTTAAT
*
5419202 TTATTTAATTTAAAA
1 TTATTAAATTTAAAA
5419217 TTATTAAAATTT-AAA
1 TTATT-AAATTTAAAA
5419232 TTATTAAATCTTAAAA
1 TTATTAAAT-TTAAAA
5419248 T
1 T
5419249 CAAATCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.14
15 15 0.54
16 9 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATTAAATTTAAAA
Found at i:5431024 original size:11 final size:11
Alignment explanation
Indices: 5431008--5431052 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5430998 TGATAATTTA
5431008 AAATATAATAT
1 AAATATAATAT
*
5431019 AAATATAATAC
1 AAATATAATAT
5431030 AAATATAAAATAT
1 AAATAT--AATAT
*
5431043 AAAAATAATA
1 AAATATAATA
5431053 CAATTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 20 0.69
13 9 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATATAATAT
Found at i:5431075 original size:24 final size:24
Alignment explanation
Indices: 5431014--5431063 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5431004 TTTAAAATAT
*
5431014 AATATAAATATAATACAAATATAA
1 AATATAAAAATAATACAAATATAA
*
5431038 AATATAAAAATAATAC-AATTTAA
1 AATATAAAAATAATACAAATATAA
5431061 AAT
1 AAT
5431064 TTTAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AATATAAAAATAATACAAATATAA
Found at i:5435540 original size:52 final size:52
Alignment explanation
Indices: 5435406--5435524 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 52
5435396 ATCGGGTCGA
5435406 ATATTAT-TAAAAAAAATTAGATTTGAATTTTAAGCAAACCCAACTTGATCTG
1 ATATTATAT-AAAAAAATTAGATTTGAATTTTAAGCAAACCCAACTTGATCTG
*
5435458 ATATTATATAAAAAAATTAGATTTGAATTTTAAGCAAATCCAA-TCTGATCTG
1 ATATTATATAAAAAAATTAGATTTGAATTTTAAGCAAACCCAACT-TGATCTG
5435510 ATATTATATAAAAAA
1 ATATTATATAAAAAA
5435525 TTATTTTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
51 1 0.02
52 62 0.97
53 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (52 bp):
ATATTATATAAAAAAATTAGATTTGAATTTTAAGCAAACCCAACTTGATCTG
Found at i:5437817 original size:12 final size:12
Alignment explanation
Indices: 5437800--5437825 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5437790 ATATAAATGA
5437800 TTTAATTAAAAT
1 TTTAATTAAAAT
5437812 TTTAATTAAAAT
1 TTTAATTAAAAT
5437824 TT
1 TT
5437826 AAATCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAATTAAAAT
Found at i:5450891 original size:25 final size:25
Alignment explanation
Indices: 5450862--5450909 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5450852 TATATTTTAA
**
5450862 AAAATATTCAAAATTAAACTCAAAT
1 AAAATATAAAAAATTAAACTCAAAT
5450887 AAAATATAAAAAATTAAACTCAA
1 AAAATATAAAAAATTAAACTCAA
5450910 CAAAATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAATATAAAAAATTAAACTCAAAT
Found at i:5450914 original size:24 final size:25
Alignment explanation
Indices: 5450862--5450915 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
5450852 TATATTTTAA
** *
5450862 AAAATATTCAAAATTAAACTCAAAT
1 AAAATATAAAAAATTAAACTCAAAC
5450887 AAAATATAAAAAATTAAACTC-AAC
1 AAAATATAAAAAATTAAACTCAAAC
5450911 AAAAT
1 AAAAT
5450916 TTGAGATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAATATAAAAAATTAAACTCAAAC
Found at i:5455465 original size:20 final size:20
Alignment explanation
Indices: 5455440--5455479 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5455430 TGAGAAAACT
*
5455440 AGTTACCTCCTTGGTGTAGA
1 AGTTACCGCCTTGGTGTAGA
5455460 AGTTACCGCCTTGGTGTAGA
1 AGTTACCGCCTTGGTGTAGA
5455480 CACCTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (20 bp):
AGTTACCGCCTTGGTGTAGA
Found at i:5456528 original size:26 final size:25
Alignment explanation
Indices: 5456466--5456537 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
5456456 TAATAATAAT
*
5456466 CTAATGATGAAATTTTTA-AAAATTT
1 CTAATGA-GAAATTTTTATAAAATTC
*
5456491 CAAAT-AGTAAATTTTTATAAAATTC
1 CTAATGAG-AAATTTTTATAAAATTC
*
5456516 CTAAGTGAGAAATTTTTTTAAA
1 CTAA-TGAGAAATTTTTATAAA
5456538 TTTACCCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.03
24 10 0.26
25 13 0.33
26 13 0.33
27 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (25 bp):
CTAATGAGAAATTTTTATAAAATTC
Found at i:5457034 original size:45 final size:45
Alignment explanation
Indices: 5456978--5457074 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
5456968 TTTTCAAAGA
*
5456978 TAAAAACAAAAAAAAATTCTAAATAGAG-CTAAATGGTGAAAAATT
1 TAAAAATAAAAAAAAATTCTAAATAG-GTCTAAATGGTGAAAAATT
* **** * *
5457023 TAGAAATAAAAATTTTTTCTAAATTGGTCTAAATGGTGAAAATTT
1 TAAAAATAAAAAAAAATTCTAAATAGGTCTAAATGGTGAAAAATT
5457068 TAAAAAT
1 TAAAAAT
5457075 TAAACTTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (45 bp):
TAAAAATAAAAAAAAATTCTAAATAGGTCTAAATGGTGAAAAATT
Found at i:5460473 original size:3 final size:3
Alignment explanation
Indices: 5460465--5460493 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5460455 TGACCCATTA
5460465 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5460494 AACCCCATGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5477224 original size:59 final size:59
Alignment explanation
Indices: 5477157--5477452 Score: 310
Period size: 58 Copynumber: 4.8 Consensus size: 59
5477147 GCTTAAAGTT
* *
5477157 CTTTCTAAAAAAATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTTTTTAAAATAAA
1 CTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTTAAAATAAA
* * *
5477216 CTTTCT-AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA
1 CTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTTAAAATAAA
*
5477274 CTTTCTAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTAGTATCAATTTTCCTTACA
1 CTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAA-TTT--T-TC-----T--TTA-A
5477339 AATAAA
54 AATAAA
* * * * *
5477345 TTTTCAAAAAAAATATTTTT-AGAAAAAAGTTGAAAGTTTCAATTTTTCTTAAAAATAAG
1 CTTTCTAAAAAAATATTTTTAAG-AAAAAGTTGAAAGTATCAATTTTTCTTTAAAATAAA
* *** *
5477404 TTTTC-AAAAATGGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 CTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT
5477453 ACACAAAAGC
Statistics
Matches: 203, Mismatches: 19, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
58 90 0.44
59 51 0.25
60 5 0.02
62 2 0.01
63 2 0.01
67 2 0.01
68 2 0.01
70 6 0.03
71 43 0.21
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (59 bp):
CTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTTAAAATAAA
Found at i:5477330 original size:71 final size:71
Alignment explanation
Indices: 5477249--5477390 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 71
5477239 AAAAGTTGAA
* * *
5477249 AGTATCAATTTTTCTTGA-AAATAAACTTTCTAAAAAAATATTTTTAGGAAAAAGTTGAAAGTAT
1 AGTATCAATTTTCCTT-ACAAATAAACTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTAT
5477313 CAATTTT
65 CAATTTT
* *
5477320 AGTATCAATTTTCCTTACAAATAAATTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTTTC
1 AGTATCAATTTTCCTTACAAATAAACTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTATC
5477385 AATTTT
66 AATTTT
5477391 TCTTAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 1 0.02
71 64 0.98
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (71 bp):
AGTATCAATTTTCCTTACAAATAAACTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTATC
AATTTT
Found at i:5477330 original size:129 final size:129
Alignment explanation
Indices: 5477191--5477448 Score: 344
Period size: 129 Copynumber: 2.0 Consensus size: 129
5477181 AAAAATTGAA
** * *
5477191 AGTATCAATTTTTTTTTA-AAATAAACTTTC-TAAAAAATATTTTT-GAGGAAAAGTTGAAAGTA
1 AGTATCAA-TTTTCCTTACAAATAAACTTTCAAAAAAAATATTTTTAGA-AAAAAGTTGAAAGTA
* *
5477253 TCAATTTTTCTTGAAAATAAACTTTCTAAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAAT
64 TCAATTTTTCTTAAAAATAAACTTTC-AAAAAAAGATTTTTGA-GAAAAAGTTGAAAGTATCAAT
5477317 TTT
127 TTT
* *
5477320 AGTATCAATTTTCCTTACAAATAAATTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTTTC
1 AGTATCAATTTTCCTTACAAATAAACTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTATC
** **
5477385 AATTTTTCTTAAAAATAAGTTTTCAAAAATGGATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
66 AATTTTTCTTAAAAATAAACTTTCAAAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
5477449 TCTTACACAA
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
128 7 0.06
129 54 0.48
130 50 0.44
131 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (129 bp):
AGTATCAATTTTCCTTACAAATAAACTTTCAAAAAAAATATTTTTAGAAAAAAGTTGAAAGTATC
AATTTTTCTTAAAAATAAACTTTCAAAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
Found at i:5484826 original size:41 final size:41
Alignment explanation
Indices: 5484769--5484851 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5484759 GGCAATAAAT
5484769 ATGTTATTTACTTTTTCAAAATTTCCTTGATTATGAACAGG
1 ATGTTATTTACTTTTTCAAAATTTCCTTGATTATGAACAGG
5484810 ATGTTATTTACTTTTTCAAAATTTCCTTGATTATGAACAGG
1 ATGTTATTTACTTTTTCAAAATTTCCTTGATTATGAACAGG
5484851 A
1 A
5484852 CTGCTGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (41 bp):
ATGTTATTTACTTTTTCAAAATTTCCTTGATTATGAACAGG
Found at i:5487917 original size:16 final size:15
Alignment explanation
Indices: 5487896--5487925 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5487886 TTTATGTAGA
5487896 AAAATATCTCCGAAAG
1 AAAATATCT-CGAAAG
5487912 AAAATATCTCGAAA
1 AAAATATCTCGAAA
5487926 AAGTGCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (15 bp):
AAAATATCTCGAAAG
Found at i:5488217 original size:27 final size:26
Alignment explanation
Indices: 5488174--5488233 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 26
5488164 TATTATAATA
5488174 TATAAATAAAAGTTTATAAAATATTTTT
1 TATAAATAAAAG-TTATAAAAT-TTTTT
5488202 TATAATATAAAA-TTATAAAATTTTTT
1 TATAA-ATAAAAGTTATAAAATTTTTT
*
5488228 GATAAA
1 TATAAA
5488234 ATCGGATAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 9 0.30
27 9 0.30
28 5 0.17
29 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
TATAAATAAAAGTTATAAAATTTTTT
Found at i:5510367 original size:15 final size:16
Alignment explanation
Indices: 5510332--5510367 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
5510322 ATTAAGTGTC
5510332 AAATATGGATATGTATT
1 AAATATGGATATG-ATT
5510349 AAATATGGATATG-TT
1 AAATATGGATATGATT
5510364 AAAT
1 AAAT
5510368 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
17 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (16 bp):
AAATATGGATATGATT
Found at i:5514342 original size:2 final size:2
Alignment explanation
Indices: 5514335--5514366 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5514325 TTGAATGACA
*
5514335 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5514367 GTGTGTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5515698 original size:16 final size:17
Alignment explanation
Indices: 5515677--5515708 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5515667 TTATTATTAT
5515677 TATTATTTG-AATATAC
1 TATTATTTGCAATATAC
5515693 TATTATTTGCAATATA
1 TATTATTTGCAATATA
5515709 AAATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
TATTATTTGCAATATAC
Found at i:5520682 original size:149 final size:149
Alignment explanation
Indices: 5520370--5520671 Score: 523
Period size: 149 Copynumber: 2.0 Consensus size: 149
5520360 TTATTATTTA
* * *
5520370 ATTTATCCCATTAATAAGATAGTATTATCTAATTCATTAACTGTATATAAAATTTATACACTAAT
1 ATTTATCTCATTAATAAAATAGTATTATCTAATTCATTAACAGTATATAAAATTTATACACTAAT
*
5520435 AAAATATTAAATATAAACTTATTTAGTAATATAAATTAATACGTTACGTAATATTAAAATGATTC
66 AAAATATTAAATATAAACTTATTTAGTAATATAAATTAATACATTACGTAATATTAAAATGATTC
**
5520500 AATGAGTTAAGTAATAAGG
131 AACAAGTTAAGTAATAAGG
* *
5520519 ATTTATCTCATTAATAAAATAGTATTATCTTATTCATTAACAGTATATAAAATTTATACACTATT
1 ATTTATCTCATTAATAAAATAGTATTATCTAATTCATTAACAGTATATAAAATTTATACACTAAT
5520584 AAAATATTAAATATAAACTTATTTAGTAATATAAATTAATACATTACGTAATATTAAAATGATTC
66 AAAATATTAAATATAAACTTATTTAGTAATATAAATTAATACATTACGTAATATTAAAATGATTC
*
5520649 CACAAGTTAAGTAATAAGG
131 AACAAGTTAAGTAATAAGG
5520668 ATTT
1 ATTT
5520672 TTTACATTAA
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
149 144 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (149 bp):
ATTTATCTCATTAATAAAATAGTATTATCTAATTCATTAACAGTATATAAAATTTATACACTAAT
AAAATATTAAATATAAACTTATTTAGTAATATAAATTAATACATTACGTAATATTAAAATGATTC
AACAAGTTAAGTAATAAGG
Found at i:5521526 original size:54 final size:54
Alignment explanation
Indices: 5521425--5521527 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 54
5521415 TTGGGCTTCC
* * * * ** *
5521425 ATTACTAAGGAATAGAAACTTTACAAATAAAACTCAAGGATTGGCATTCATTCG
1 ATTACCAAGCAATAGAAACTCTACAAATAAAACTAAAAAATTAGCATTCATTCG
* *
5521479 ATTACCAAGCAATAGAGACTCTACAAATAAAGCTAAAAAATTAGCATTC
1 ATTACCAAGCAATAGAAACTCTACAAATAAAACTAAAAAATTAGCATTC
5521528 CATTGCTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 40 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.25
Consensus pattern (54 bp):
ATTACCAAGCAATAGAAACTCTACAAATAAAACTAAAAAATTAGCATTCATTCG
Found at i:5524099 original size:27 final size:26
Alignment explanation
Indices: 5524069--5524130 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
5524059 TATAAAAATA
*
5524069 ATATAATTTAAAATTTTAATAATTATT
1 ATATAATTTAAAATTTTAAT-ATTAAT
* * *
5524096 ATATATATTTTATATTTTTATATTAAT
1 ATATA-ATTTAAAATTTTAATATTAAT
5524123 ATA-AATTT
1 ATATAATTT
5524131 TGATACATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 4 0.13
26 1 0.03
27 13 0.43
28 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATAATTTAAAATTTTAATATTAAT
Found at i:5530142 original size:21 final size:22
Alignment explanation
Indices: 5530114--5530156 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5530104 AATTCATATA
*
5530114 TATATATATATTTAATTTTTACG
1 TATATAAAT-TTTAATTTTTACG
*
5530137 TATATAAATTTTTATTTTTA
1 TATATAAATTTTAATTTTTA
5530157 ATTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TATATAAATTTTAATTTTTACG
Found at i:5533871 original size:30 final size:30
Alignment explanation
Indices: 5533824--5533926 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 30
5533814 TTTTATTAAA
* * *
5533824 AAATAATTAATGATTTAATTGAGTGAAAAT
1 AAATATTTAAAGATTTAATTGAGTAAAAAT
* * *
5533854 AAAT-TTATACAGATTTAATTAAGAAAAAAT
1 AAATATT-TAAAGATTTAATTGAGTAAAAAT
* * *
5533884 AAATATTTAAATATTTAATTGATTTAAAAT
1 AAATATTTAAAGATTTAATTGAGTAAAAAT
*
5533914 AAAAAATTTAAAG
1 -AAATATTTAAAG
5533927 TTTGATTAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
29 1 0.02
30 43 0.77
31 12 0.21
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (30 bp):
AAATATTTAAAGATTTAATTGAGTAAAAAT
Found at i:5544686 original size:11 final size:11
Alignment explanation
Indices: 5544656--5544688 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5544646 TTTTTATTAG
*
5544656 TTTTTATATAA
1 TTTTTATAAAA
5544667 TTTTT-TAAAA
1 TTTTTATAAAA
5544677 TTTTTATAAAA
1 TTTTTATAAAA
5544688 T
1 T
5544689 AAAAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTATAAAA
Found at i:5544698 original size:20 final size:19
Alignment explanation
Indices: 5544675--5544724 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
5544665 AATTTTTTAA
*
5544675 AATTTTTATAAAATAAAAAT
1 AATTATTAT-AAATAAAAAT
*
5544695 AATTATTATATATAAAAAT
1 AATTATTATAAATAAAAAT
5544714 --TTATT-TAAATA
1 AATTATTATAAATA
5544725 TATTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 9 0.33
20 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTATTATAAATAAAAAT
Found at i:5544717 original size:17 final size:17
Alignment explanation
Indices: 5544673--5544741 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 17
5544663 ATAATTTTTT
*
5544673 AAAATTT-TTATAAAATA
1 AAAATTTATTAT-ATATA
5544690 AAAATAATTATTATATATA
1 AAAAT--TTATTATATATA
5544709 AAAATTTATTTAAATATATTA
1 AAAATTTA-TT--ATATA-TA
5544730 AAAATTTTATTA
1 AAAA-TTTATTA
5544742 AAATAATACA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
17 8 0.19
18 2 0.05
19 12 0.28
20 9 0.21
21 8 0.19
22 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTATTATATATA
Found at i:5544733 original size:21 final size:23
Alignment explanation
Indices: 5544701--5544757 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
5544691 AAATAATTAT
*
5544701 TATATATAAAAA-TTTATTTAAA
1 TATATATAAAAATTTTATTAAAA
5544723 TATAT-TAAAAATTTTATTAAAA
1 TATATATAAAAATTTTATTAAAA
*
5544745 TAATACATAAAAA
1 T-ATATATAAAAA
5544758 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.20
22 15 0.50
23 3 0.10
24 6 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TATATATAAAAATTTTATTAAAA
Found at i:5564670 original size:21 final size:21
Alignment explanation
Indices: 5564646--5564698 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5564636 GTCCTCAATT
5564646 TCTGCAACTAAGCCTATAACA
1 TCTGCAACTAAGCCTATAACA
* * * *
5564667 TCTGCAGCAAAGCCTGTAATA
1 TCTGCAACTAAGCCTATAACA
5564688 TCTGCAACTAA
1 TCTGCAACTAA
5564699 ACCTGCAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (21 bp):
TCTGCAACTAAGCCTATAACA
Found at i:5564703 original size:21 final size:21
Alignment explanation
Indices: 5564646--5564708 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5564636 GTCCTCAATT
* *
5564646 TCTGCAACTAAGCCTATAACA
1 TCTGCAACTAAACCTGTAACA
* *
5564667 TCTGCAGC-AAAGCCTGTAATA
1 TCTGCAACTAAA-CCTGTAACA
*
5564688 TCTGCAACTAAACCTGCAACA
1 TCTGCAACTAAACCTGTAACA
5564709 AAACCTGGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.85
22 3 0.09
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.22
Consensus pattern (21 bp):
TCTGCAACTAAACCTGTAACA
Found at i:5573879 original size:10 final size:10
Alignment explanation
Indices: 5573861--5573895 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
5573851 CAGAATAAAT
*
5573861 TTTTTTTTGG
1 TTTTGTTTGG
5573871 TTTTGTTTGG
1 TTTTGTTTGG
5573881 TTTTGTTTGG
1 TTTTGTTTGG
5573891 TTTTG
1 TTTTG
5573896 ATATGTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (10 bp):
TTTTGTTTGG
Found at i:5584935 original size:41 final size:39
Alignment explanation
Indices: 5584880--5585011 Score: 156
Period size: 39 Copynumber: 3.3 Consensus size: 39
5584870 GCCTTTCAGA
* * *
5584880 TTTTTAAATTTAAAGTTCGTTGCCTTTGGTCAGAGGAAC
1 TTTTTAAATTTAAAGTTTGTTACCTTTGGTCAGAGGAGC
* *
5584919 TTTTTTAATATTTAAAGTTTGTTACCTCTAGTCAGAGGAGC
1 -TTTTTAA-ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGC
* * * *
5584960 ATTTTGAATTTAAAGTTTATTACCTTTGATCAGAGGAGC
1 TTTTTAAATTTAAAGTTTGTTACCTTTGGTCAGAGGAGC
*
5584999 TTTTTAATTTTAA
1 TTTTTAAATTTAA
5585012 GAGTCTCTGG
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
39 38 0.49
40 12 0.16
41 27 0.35
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (39 bp):
TTTTTAAATTTAAAGTTTGTTACCTTTGGTCAGAGGAGC
Found at i:5585291 original size:39 final size:39
Alignment explanation
Indices: 5585170--5585610 Score: 304
Period size: 39 Copynumber: 11.3 Consensus size: 39
5585160 GCCTTTTAAC
* * *
5585170 ATTTAAAGTTTGTTACCTTTGGTT-AATGAGCCTTTTGG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
* *** * *
5585208 ATTTAAAGTTCGTTGCCTCAAGTTATAA-GAGC-CTTTGAA
1 ATTTAAAGTTTGTTGCCTTTGGTTA-AAGGAGCTTTTTG-G
*
5585247 ATTTAAAGTTTGTTGCCTTTGATTAAAGGAGCTTTTTGG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
* ** * **
5585286 TTTTAAAGTTCATTGTCTTTGGTTAGAA-GAGCTTTTTACT
1 ATTTAAAGTTTGTTGCCTTTGGTTA-AAGGAGCTTTTT-GG
* ** * * * * *
5585326 ATTTAAAGTTTATTATCTCTGGTGAGAA-GAAC-CTTTGAA
1 ATTTAAAGTTTGTTGCCTTTGGTTA-AAGGAGCTTTTTG-G
* * *
5585365 ATTTAAAGTTTATTGCCTTTGGTTAAAGGAGTTTTTTAG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
** ** * * ***
5585404 ATTTAAAGTTCATTGCCACTGGTCAAAAGAGCCTTTTAAT
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTTTTTGG
* *
5585444 ATTTAAAGTTTGTTGCTTTTGGTTAAAAGAGC-TTTTGG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
* * *
5585482 AATTTAAAGTTTGTTAG-CTTTGGTTAAATGAGTTTTTTGA
1 -ATTTAAAGTTTGTT-GCCTTTGGTTAAAGGAGCTTTTTGG
*
5585522 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTCTTTGG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
* * * * * **
5585561 ATTTAAAGTTTGTTACCTCTGATGAGAGGAGCTTTTTAA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
5585600 ATTTAAAGTTT
1 ATTTAAAGTTT
5585611 TATAGCCTCT
Statistics
Matches: 316, Mismatches: 72, Indels: 29
0.76 0.17 0.07
Matches are distributed among these distances:
38 31 0.10
39 212 0.67
40 73 0.23
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (39 bp):
ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGG
Found at i:5585374 original size:118 final size:117
Alignment explanation
Indices: 5585170--5585610 Score: 420
Period size: 118 Copynumber: 3.8 Consensus size: 117
5585160 GCCTTTTAAC
** * * * ** * * ** * *
5585170 ATTTAAAGTTTGTTACCTTTGGTTAATGAGCCTTTT-GGATTTAAAGTTCGTTGCCTCAAGTTAT
1 ATTTAAAGTTCATTGCCTTTGGTTAAAGAGCTTTTTAATATTTAAAGTTTGTTACCTCTGGTGAG
* *
5585234 AAGAGCCTTTGAAATTTAAAGTTTGTTGCCTTTGATTAAAGGAGCTTTTTGG
66 AAGAGCCTTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGTTTTTTGG
* * * * *
5585286 TTTTAAAGTTCATTGTCTTTGGTTAGAAGAGCTTTTTACTATTTAAAGTTTATTATCTCTGGTGA
1 ATTTAAAGTTCATTGCCTTTGGTTA-AAGAGCTTTTTAATATTTAAAGTTTGTTACCTCTGGTGA
* * *
5585351 GAAGAACCTTTGAAATTTAAAGTTTATTGCCTTTGGTTAAAGGAGTTTTTTAG
65 GAAGAGCCTTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGTTTTTTGG
** * * * * * *
5585404 ATTTAAAGTTCATTGCCACTGGTCAAAAGAGCCTTTTAATATTTAAAGTTTGTTGCTTTTGGTTA
1 ATTTAAAGTTCATTGCCTTTGGT-TAAAGAGCTTTTTAATATTTAAAGTTTGTTACCTCTGGTGA
* * * * *
5585469 AAAGAGCTTTTGGAATTTAAAGTTTGTTAG-CTTTGGTTAAATGAGTTTTTTGA
65 GAAGAGCCTTTGAAATTTAAAGTTTGTT-GCCTTTGGTTAAAGGAGTTTTTTGG
** * ** *
5585522 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTCTTT-GGATTTAAAGTTTGTTACCTCTGATGA
1 ATTTAAAGTTCATTGCCTTTGGTTAAA-GAGCTTTTTAATATTTAAAGTTTGTTACCTCTGGTGA
* * *
5585586 GAGGAGCTTTTTAAATTTAAAGTTT
65 GAAGAGCCTTTGAAATTTAAAGTTT
5585611 TATAGCCTCT
Statistics
Matches: 259, Mismatches: 61, Indels: 9
0.79 0.19 0.03
Matches are distributed among these distances:
116 20 0.08
117 53 0.20
118 184 0.71
119 2 0.01
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (117 bp):
ATTTAAAGTTCATTGCCTTTGGTTAAAGAGCTTTTTAATATTTAAAGTTTGTTACCTCTGGTGAG
AAGAGCCTTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGTTTTTTGG
Found at i:5585573 original size:78 final size:77
Alignment explanation
Indices: 5585170--5585575 Score: 313
Period size: 79 Copynumber: 5.2 Consensus size: 77
5585160 GCCTTTTAAC
* * * ***
5585170 ATTTAAAGTTTGTTACCTTTGGTT-AATGAGCCTTTTGGATTTAAAGTTCGTTGCCTCAAGTTAT
1 ATTTAAAGTTTGTTAGCTTTGGTTAAATGAGCCTTTTGAATTTAAAGTTTGTTGCCTTTGGTTA-
*
5585234 AAGAGC-CTTTGAA
65 AAGAGCTCTTTG-G
* * * ** ** *
5585247 ATTTAAAGTTTGTT-GCCTTTGATTAAAGGAGCTTTTTGGTTTTAAAGTTCATTGTCTTTGGTTA
1 ATTTAAAGTTTGTTAG-CTTTGGTTAAATGAGCCTTTTGAATTTAAAGTTTGTTGCCTTTGGTTA
* **
5585311 GAAGAGCTTTTTACT
65 -AAGAGCTCTTT-GG
* * * * * *
5585326 ATTTAAAGTTTATTATCTCTGGTGAGAA-GAACC-TTTGAAATTTAAAGTTTATTGCCTTTGGTT
1 ATTTAAAGTTTGTTAGCTTTGGTTA-AATGAGCCTTTTG-AATTTAAAGTTTGTTGCCTTTGGTT
* * *
5585389 AAAGGAGTTTTTTAG
64 AAA-GAGCTCTTTGG
** ** * * * *
5585404 ATTTAAAGTTCATT-GCCACTGGTCAAAAGAGCCTTTTAATATTTAAAGTTTGTTGCTTTTGGTT
1 ATTTAAAGTTTGTTAG-CTTTGGTTAAATGAGCCTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
5585468 AAAAGAGCT-TTTGG
64 -AAAGAGCTCTTTGG
**
5585482 AATTTAAAGTTTGTTAGCTTTGGTTAAATGAGTTTTTTGAATTTAAAGTTTGTTGCCTTTGGTTA
1 -ATTTAAAGTTTGTTAGCTTTGGTTAAATGAGCCTTTTGAATTTAAAGTTTGTTGCCTTTGGTTA
5585547 AAGGAGCTCTTTGG
65 AA-GAGCTCTTTGG
5585561 ATTTAAAGTTTGTTA
1 ATTTAAAGTTTGTTA
5585576 CCTCTGATGA
Statistics
Matches: 264, Mismatches: 48, Indels: 33
0.77 0.14 0.10
Matches are distributed among these distances:
77 26 0.10
78 115 0.44
79 117 0.44
80 6 0.02
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (77 bp):
ATTTAAAGTTTGTTAGCTTTGGTTAAATGAGCCTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAA
AGAGCTCTTTGG
Found at i:5585642 original size:40 final size:39
Alignment explanation
Indices: 5585521--5585643 Score: 106
Period size: 39 Copynumber: 3.1 Consensus size: 39
5585511 GAGTTTTTTG
* * * * * *
5585521 AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTCTTT-G
1 AATTTAAAGTTTGTTACCTCTGATGAGAGGAGC-CTTTCA
* * *
5585560 GATTTAAAGTTTGTTACCTCTGATGAGAGGAGCTTTTTA
1 AATTTAAAGTTTGTTACCTCTGATGAGAGGAGCCTTTCA
* *
5585599 AATTTAAAGTTT-TATAGCCTCTGTTTAGAGGAGCCTTTCA
1 AATTTAAAGTTTGT-TA-CCTCTGATGAGAGGAGCCTTTCA
5585639 AATTT
1 AATTT
5585644 TCACTCAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
38 4 0.06
39 40 0.59
40 24 0.35
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.42
Consensus pattern (39 bp):
AATTTAAAGTTTGTTACCTCTGATGAGAGGAGCCTTTCA
Found at i:5585797 original size:3 final size:3
Alignment explanation
Indices: 5585791--5585816 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5585781 TCTTCTTCTT
5585791 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5585817 CTTTTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5586695 original size:11 final size:10
Alignment explanation
Indices: 5586671--5586744 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 10
5586661 ATTTCGTAGG
5586671 TTTTCTTTTT-
1 TTTT-TTTTTA
5586681 TTTTTTTTCTA
1 TTTTTTTT-TA
*
5586692 TTTTGATTTTA
1 TTTT-TTTTTA
*
5586703 TTTATTTTGTA
1 TTT-TTTTTTA
*
5586714 TTTATTTTTA
1 TTTTTTTTTA
5586724 TGTTGATTTTTTA
1 T-TT--TTTTTTA
5586737 TTTTTTTT
1 TTTTTTTT
5586745 CATGATATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
9 4 0.08
10 16 0.31
11 18 0.35
12 6 0.12
13 7 0.14
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:5586701 original size:15 final size:14
Alignment explanation
Indices: 5586683--5586740 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
5586673 TTCTTTTTTT
5586683 TTTTTTCTATTTTGA
1 TTTTTT-TATTTTGA
5586698 TTTTATTTATTTTGTA
1 TTTT-TTTATTTTG-A
*
5586714 TTTATTTTTATGTTGA
1 -TT-TTTTTATTTTGA
5586730 -TTTTTTATTTT
1 TTTTTTTATTTT
5586741 TTTTCATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 11 0.30
16 4 0.11
17 10 0.27
18 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTATTTTGA
Found at i:5586732 original size:23 final size:20
Alignment explanation
Indices: 5586676--5586744 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
5586666 GTAGGTTTTC
*
5586676 TTTTTT-TTT-TTTTCTATT
1 TTTTTTATTTATTTTGTATT
5586694 TTGATTTTATTTATTTTGTATT
1 TT--TTTTATTTATTTTGTATT
*
5586716 TATTTTTATGTTGATTTTTTATT
1 T-TTTTTAT-TT-ATTTTGTATT
5586739 TTTTTT
1 TTTTTT
5586745 CATGATATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
18 2 0.05
20 4 0.10
21 9 0.21
22 16 0.38
23 11 0.26
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (20 bp):
TTTTTTATTTATTTTGTATT
Found at i:5586969 original size:17 final size:17
Alignment explanation
Indices: 5586949--5586996 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5586939 TAATTTTTGC
5586949 TAAAAAATAATAAATTA
1 TAAAAAATAATAAATTA
*
5586966 TAAAAAATGATAAA-TA
1 TAAAAAATAATAAATTA
5586982 -AAATAAA-AATAAATT
1 TAAA-AAATAATAAATT
5586997 GTTTAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
17 13 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAAAATAATAAATTA
Done.