Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 23 of 25
Found at i:3476788 original size:16 final size:16
Alignment explanation
Indices: 3476767--3476808 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3476757 AATTTATATA
3476767 AATATTTAAAAAAAAT
1 AATATTTAAAAAAAAT
*
3476783 AATATTTAATAAATAAT
1 AATATTTAA-AAAAAAT
3476800 AAT-TTTAAA
1 AATATTTAAA
3476809 TTTTAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 14 0.58
17 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTTAAAAAAAAT
Found at i:3477227 original size:28 final size:28
Alignment explanation
Indices: 3477196--3477274 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 28
3477186 AATTTTATAT
*
3477196 TTAAATTAAATTTTTTATTTAT-TATTAA
1 TTAAATTAAATTTTTTATTTATATAAT-A
* * * *
3477224 TTAATTTTAATTATATATTTATATAATA
1 TTAAATTAAATTTTTTATTTATATAATA
3477252 TTAACATTTAAAATTTTTTATTT
1 TTAA-A-TT-AAATTTTTTATTT
3477275 TTTTATTTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
28 23 0.61
29 3 0.08
30 2 0.05
31 10 0.26
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
TTAAATTAAATTTTTTATTTATATAATA
Found at i:3477378 original size:13 final size:14
Alignment explanation
Indices: 3477360--3477388 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3477350 TTATTAAATT
3477360 TTAAATTTT-TTTA
1 TTAAATTTTGTTTA
3477373 TTAAATTTTGTTTA
1 TTAAATTTTGTTTA
3477387 TT
1 TT
3477389 TATTACTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTAAATTTTGTTTA
Found at i:3477392 original size:18 final size:19
Alignment explanation
Indices: 3477349--3477393 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3477339 TATTCTCACG
*
3477349 TTTATTAAATTTTAAATTTT
1 TTTATTAAATTTT-AATTTA
*
3477369 TTTATTAAATTTT-GTTTA
1 TTTATTAAATTTTAATTTA
3477387 TTTATTA
1 TTTATTA
3477394 CTTTCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTAAATTTTAATTTA
Found at i:3479518 original size:17 final size:17
Alignment explanation
Indices: 3479477--3479518 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3479467 TTAATTTAAA
*
3479477 TTAATTA-AAATAATAT
1 TTAATTATAAAAAATAT
* *
3479493 GTAAATATAAAAAATAT
1 TTAATTATAAAAAATAT
3479510 TTAATTATA
1 TTAATTATA
3479519 TATATTGATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAATTATAAAAAATAT
Found at i:3482278 original size:21 final size:23
Alignment explanation
Indices: 3482254--3482297 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3482244 TTGTATGTTT
*
3482254 AAAATTT-TTATT-TTATATCAA
1 AAAATTTATTATTCATATATCAA
3482275 AAAATTTATTATTCATATATCAA
1 AAAATTTATTATTCATATATCAA
3482298 TATTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATTTATTATTCATATATCAA
Found at i:3482864 original size:17 final size:19
Alignment explanation
Indices: 3482824--3482864 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
3482814 TAGATATTTT
3482824 TAATTTTTAAAATTTAAGA
1 TAATTTTTAAAATTTAAGA
*
3482843 T-ATTTTT-AAGTTT-AGA
1 TAATTTTTAAAATTTAAGA
3482859 TAATTT
1 TAATTT
3482865 CAGTTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 6 0.30
19 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TAATTTTTAAAATTTAAGA
Found at i:3483013 original size:16 final size:16
Alignment explanation
Indices: 3482992--3483033 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3482982 AATATGATCC
*
3482992 TTTTAAATTTAGAT-T
1 TTTTAAATTTAAATAT
3483007 ATTTTAAATTTAAATAT
1 -TTTTAAATTTAAATAT
3483024 TTTTAAATTT
1 TTTTAAATTT
3483034 GAATCAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTAAATTTAAATAT
Found at i:3483122 original size:20 final size:20
Alignment explanation
Indices: 3483097--3483139 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3483087 GAGCGGAGTT
3483097 GATTAGAGTTTTTGTATTCA
1 GATTAGAGTTTTTGTATTCA
3483117 GATTAGAGTTTTTGTATTCA
1 GATTAGAGTTTTTGTATTCA
3483137 GAT
1 GAT
3483140 CAAAATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (20 bp):
GATTAGAGTTTTTGTATTCA
Found at i:3487857 original size:13 final size:14
Alignment explanation
Indices: 3487841--3487881 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3487831 AAAAATTATT
3487841 TTATTAAAT-TTAA
1 TTATTAAATATTAA
*
3487854 TTATAAAATATTAA
1 TTATTAAATATTAA
3487868 TATATT-AATATTAA
1 T-TATTAAATATTAA
3487882 ATAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 13 0.54
15 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTATTAAATATTAA
Found at i:3487923 original size:12 final size:12
Alignment explanation
Indices: 3487906--3487930 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3487896 TTTTTAAAAA
3487906 ATAAATAAATTT
1 ATAAATAAATTT
3487918 ATAAATAAATTT
1 ATAAATAAATTT
3487930 A
1 A
3487931 ATTAAATTTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAATAAATTT
Found at i:3487938 original size:10 final size:10
Alignment explanation
Indices: 3487907--3487946 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
3487897 TTTTAAAAAA
3487907 TAAATAAATTT
1 TAAATAAA-TT
3487918 ATAAATAAATT
1 -TAAATAAATT
*
3487929 TAATTAAATT
1 TAAATAAATT
3487939 TAAATAAA
1 TAAATAAA
3487947 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAATAAATT
Found at i:3488075 original size:10 final size:10
Alignment explanation
Indices: 3488062--3488116 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
3488052 ATTTAAATAA
3488062 ATTTTTATAT
1 ATTTTTATAT
3488072 ATTTTTATAT
1 ATTTTTATAT
3488082 ATATATTTA-AT
1 AT-T-TTTATAT
*
3488093 -TTTTTAAAT
1 ATTTTTATAT
*
3488102 TTTTTTATAT
1 ATTTTTATAT
3488112 ATTTT
1 ATTTT
3488117 AAAAATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.10
9 3 0.08
10 25 0.64
11 3 0.08
12 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:3488075 original size:39 final size:37
Alignment explanation
Indices: 3488032--3488118 Score: 86
Period size: 40 Copynumber: 2.2 Consensus size: 37
3488022 TATATAAAAT
*
3488032 TATTTTAATGTATGATTTGAATTTAAATAAA-TTTTTATA
1 TATTTTAATATAT-ATTT-AATTT-AATAAATTTTTTATA
**
3488071 TATTTTTATATATATATTTAATTTTTTAAATTTTTTTATA
1 TA-TTTTA-ATATATATTTAATTTAATAAA-TTTTTTATA
3488111 TATTTTAA
1 TATTTTAA
3488119 AAATTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
38 5 0.12
39 12 0.29
40 19 0.46
41 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (37 bp):
TATTTTAATATATATTTAATTTAATAAATTTTTTATA
Found at i:3488115 original size:21 final size:23
Alignment explanation
Indices: 3488083--3488134 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
3488073 TTTTTATATA
*
3488083 TATATTTA-AT-TTTT-TAAATT
1 TATATTTATATATTTTAAAAATT
3488103 T-T-TTTATATATTTTAAAAATT
1 TATATTTATATATTTTAAAAATT
3488124 TATATTTATAT
1 TATATTTATAT
3488135 TTAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.15
19 3 0.12
20 5 0.19
21 6 0.23
22 1 0.04
23 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATTTATATATTTTAAAAATT
Found at i:3488124 original size:30 final size:30
Alignment explanation
Indices: 3488059--3488119 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
3488049 TGAATTTAAA
*
3488059 TAAATTTTTATATATTTTTATATATATATT
1 TAAATTTTTATAAATTTTTATATATATATT
*
3488089 T-AATTTTT-TAAATTTTTTTATATAT-TT
1 TAAATTTTTATAAATTTTTATATATATATT
3488116 TAAA
1 TAAA
3488120 AATTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 17 0.61
29 7 0.25
30 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TAAATTTTTATAAATTTTTATATATATATT
Found at i:3488135 original size:21 final size:21
Alignment explanation
Indices: 3488083--3488136 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3488073 TTTTTATATA
**
3488083 TATATTTA-ATTTTTTAAATT
1 TATATTTATATTTTAAAAATT
*
3488103 T-TTTTATATATTTTAAAAATT
1 TATATT-TATATTTTAAAAATT
3488124 TATATTTATATTT
1 TATATTTATATTT
3488137 AAATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 18 0.67
22 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATATTTATATTTTAAAAATT
Found at i:3488541 original size:23 final size:24
Alignment explanation
Indices: 3488515--3488560 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3488505 ATTATGTATG
3488515 AATTATAAA-AATAAAATATAAAA
1 AATTATAAATAATAAAATATAAAA
* *
3488538 AATTATAAATATTAAAATTTAAA
1 AATTATAAATAATAAAATATAAA
3488561 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTATAAATAATAAAATATAAAA
Found at i:3488646 original size:33 final size:33
Alignment explanation
Indices: 3488604--3488668 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3488594 TTATTAATAT
*
3488604 AATTTTTATTTAAATTAATA-AAA-TATAATTTTA
1 AATTATTATTT-AA-TAATATAAATTATAATTTTA
3488637 AATTATTATTTAATAATATAAATTATAATTTT
1 AATTATTATTTAATAATATAAATTATAATTTT
3488669 TTATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.17
32 5 0.17
33 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATTATTATTTAATAATATAAATTATAATTTTA
Found at i:3488672 original size:27 final size:28
Alignment explanation
Indices: 3488618--3488682 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
3488608 TTTATTTAAA
*
3488618 TTAATAAAATATAATTTTAAATTATTAT
1 TTAATAAAATATAATTATAAATTATTAT
* * *
3488646 TTAATAATATA-AATTATAATTTTTTAT
1 TTAATAAAATATAATTATAAATTATTAT
3488673 TTATATAAAA
1 TTA-ATAAAA
3488683 AATATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATAAAATATAATTATAAATTATTAT
Found at i:3490020 original size:7 final size:7
Alignment explanation
Indices: 3490008--3490034 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3489998 TTGAAAAGTC
3490008 ATATCCT
1 ATATCCT
3490015 ATATCCT
1 ATATCCT
3490022 ATATCCT
1 ATATCCT
3490029 ATATCC
1 ATATCC
3490035 AAATATCGTC
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:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATCCT
Found at i:3493785 original size:31 final size:32
Alignment explanation
Indices: 3493703--3493785 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 32
3493693 AATTTTTAAA
* *
3493703 AAATATT--TTTAAATTAATATTTATATATTTC
1 AAATATTAATTTAAATTAA-ATTTAAATAATTC
* *
3493734 ATAAT-TAAATTTAAA-AAAATTTAAATAATT-
1 A-AATATTAATTTAAATTAAATTTAAATAATTC
3493764 AAATATTAATTTAAATTAAATT
1 AAATATTAATTTAAATTAAATT
3493786 AATTTAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
29 3 0.07
30 10 0.24
31 17 0.41
32 5 0.12
33 6 0.15
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
AAATATTAATTTAAATTAAATTTAAATAATTC
Found at i:3493786 original size:15 final size:15
Alignment explanation
Indices: 3493768--3493803 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3493758 ATAATTAAAT
3493768 ATTAATTTAAATTAA
1 ATTAATTTAAATTAA
3493783 ATTAATTTAAATTAA
1 ATTAATTTAAATTAA
*
3493798 AATAAT
1 ATTAAT
3493804 ACGAGTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTTAAATTAA
Found at i:3494173 original size:2 final size:2
Alignment explanation
Indices: 3494166--3494196 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3494156 ATGCATGATA
3494166 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
3494197 TACGTAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3495587 original size:13 final size:13
Alignment explanation
Indices: 3495556--3495602 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
3495546 ATTAATTACG
*
3495556 AAAATAATATTTA
1 AAAATAATAATTA
**
3495569 TGAATAATAATTA
1 AAAATAATAATTA
3495582 AAAAT-AT-ATTA
1 AAAATAATAATTA
3495593 AAAATAATAA
1 AAAATAATAA
3495603 AATGAAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
11 9 0.33
12 4 0.15
13 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
AAAATAATAATTA
Found at i:3496392 original size:16 final size:16
Alignment explanation
Indices: 3496368--3496426 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
3496358 ATATTTTAAT
*
3496368 TATTAATATATATATA
1 TATTTATATATATATA
*
3496384 TATTTATATTTATATTTA
1 TATTTATA--TATATATA
3496402 TATTTATATAT-TATA
1 TATTTATATATATATA
3496417 TAATTTATAT
1 T-ATTTATAT
3496427 CATAAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.11
16 18 0.49
18 15 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATATATATATA
Found at i:3496397 original size:12 final size:12
Alignment explanation
Indices: 3496376--3496417 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
3496366 ATTATTAATA
*
3496376 TATATATATATT
1 TATATTTATATT
3496388 TATATTTATATT
1 TATATTTATATT
3496400 TATATTTATATAT
1 TATATTTATAT-T
3496413 TATAT
1 TATAT
3496418 AATTTATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTATATT
Found at i:3496424 original size:9 final size:8
Alignment explanation
Indices: 3496368--3496426 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
3496358 ATATTTTAAT
*
3496368 TATTAATA
1 TATTTATA
*
3496376 TATATATA
1 TATTTATA
3496384 TATTTATA
1 TATTTATA
3496392 T-TTATATTTA
1 TATT-TA--TA
3496402 TATTTATA
1 TATTTATA
3496410 TA-TTATA
1 TATTTATA
3496417 TAATTTATA
1 T-ATTTATA
3496426 T
1 T
3496427 CATAAAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
7 8 0.19
8 21 0.50
9 6 0.14
10 5 0.12
11 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTATA
Found at i:3496666 original size:18 final size:19
Alignment explanation
Indices: 3496628--3496686 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
3496618 TTTAAATATG
3496628 ATATAAAAATATTAT-ATAA
1 ATAT-AAAATATTATAATAA
* *
3496647 ATATAATAT-TTTTAATAA
1 ATATAAAATATTATAATAA
3496665 ATA-AAAATATTATAATAA
1 ATATAAAATATTATAATAA
3496683 ATAT
1 ATAT
3496687 GATACGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 7 0.21
18 22 0.67
19 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAAAATATTATAATAA
Found at i:3496697 original size:36 final size:35
Alignment explanation
Indices: 3496630--3496699 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
3496620 TAAATATGAT
**
3496630 ATAAAAATATTATATAAATATAATATTTTTAATAA
1 ATAAAAATATTATATAAATATAATACGTTTAATAA
*
3496665 ATAAAAATATTATAATAAATATGATACGTTTAATA
1 ATAAAAATATTAT-ATAAATATAATACGTTTAATA
3496700 TATATTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
ATAAAAATATTATATAAATATAATACGTTTAATAA
Found at i:3496980 original size:20 final size:23
Alignment explanation
Indices: 3496956--3497012 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
3496946 TGTGTTATTT
3496956 TAAAAAAA-TATTTTTT-TAA-A
1 TAAAAAAATTATTTTTTATAACA
3496976 -AAAAAAATTCATTTTTTATAACA
1 TAAAAAAATT-ATTTTTTATAACA
3496999 TAAAAAAATTATTT
1 TAAAAAAATTATTT
3497013 CAGTGCCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.22
20 1 0.03
21 7 0.22
22 3 0.09
23 5 0.16
24 9 0.28
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAAAAATTATTTTTTATAACA
Found at i:3497521 original size:2 final size:2
Alignment explanation
Indices: 3497516--3497568 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3497506 GCCAAAAAAC
3497516 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3497558 AG AG AG AG AG A
1 AG AG AG AG AG A
3497569 ACATCTGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3498093 original size:22 final size:22
Alignment explanation
Indices: 3498055--3498119 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
3498045 TTACCTATAT
*
3498055 ATATATATATATATATATTATTA
1 ATATATA-ATTTATATATTATTA
*
3498078 ATTTAT-ATTTGATATATTATTA
1 ATATATAATTT-ATATATTATTA
3498100 ATATATGAATTTATATATTA
1 ATATAT-AATTTATATATTA
3498120 ATAGTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.08
22 16 0.44
23 13 0.36
24 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
ATATATAATTTATATATTATTA
Found at i:3498197 original size:10 final size:10
Alignment explanation
Indices: 3498182--3498213 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
3498172 AATTTAAAAC
3498182 ATAATTACAA
1 ATAATTACAA
3498192 ATAATTACAA
1 ATAATTACAA
3498202 ATAATTACAA
1 ATAATTACAA
3498212 AT
1 AT
3498214 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAATTACAA
Found at i:3498694 original size:21 final size:22
Alignment explanation
Indices: 3498643--3498696 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3498633 ATTTAATTTA
*
3498643 ATTTTAATTTTAATTATAAAAT
1 ATTTTAATATTAATTATAAAAT
** * *
3498665 AGGTAAATATTAA-TATAAATT
1 ATTTTAATATTAATTATAAAAT
3498686 ATTTTAATATT
1 ATTTTAATATT
3498697 TTATTAATTT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTTAATATTAATTATAAAAT
Found at i:3502717 original size:18 final size:18
Alignment explanation
Indices: 3502676--3502717 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3502666 AATAATAAAA
3502676 TATATTTAAAAATAAATT
1 TATATTTAAAAATAAATT
*
3502694 TA-ATTTCAAAAA-ATATT
1 TATATTT-AAAAATAAATT
3502711 TATATTT
1 TATATTT
3502718 GATTAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTTAAAAATAAATT
Found at i:3502801 original size:7 final size:6
Alignment explanation
Indices: 3502765--3502800 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
3502755 TTAAACTTGA
*
3502765 AAAAAG AAAGAAG AAAAAG GAAAAG AAAAAG AAAAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAA
3502801 ATAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3503055 original size:21 final size:22
Alignment explanation
Indices: 3503025--3503067 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3503015 TAAAATATTT
* *
3503025 ATTTACATTATTCTA-AAATTA
1 ATTTAAATTATTATATAAATTA
3503046 ATTTAAATTATTATATAAATTA
1 ATTTAAATTATTATATAAATTA
3503068 TTATTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAATTATTATATAAATTA
Found at i:3503195 original size:20 final size:19
Alignment explanation
Indices: 3503144--3503198 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3503134 ATAAAAATTC
* *
3503144 ATTTAAATAAA-TATTTAT
1 ATTTTAATAAATTAATTAT
3503162 ATTTTAATAAATTAATTAT
1 ATTTTAATAAATTAATTAT
3503181 ATTTTCACA-AAATTAATT
1 ATTTT-A-ATAAATTAATT
3503199 CAAATTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 10 0.31
19 11 0.34
20 10 0.31
21 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAATAAATTAATTAT
Found at i:3503566 original size:28 final size:29
Alignment explanation
Indices: 3503525--3503581 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
3503515 TAATAATTTT
3503525 AAAAGATTATAAATTTAATATAA-ATATA
1 AAAAGATTATAAATTTAATATAATATATA
* * *
3503553 AAAATATTTTAAATTTTATATAATATATA
1 AAAAGATTATAAATTTAATATAATATATA
3503582 TTGTTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAAGATTATAAATTTAATATAATATATA
Found at i:3503609 original size:19 final size:19
Alignment explanation
Indices: 3503587--3503624 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3503577 ATATATTGTT
3503587 ATATATTAA-ATTTTAAATA
1 ATATA-TAATATTTTAAATA
3503606 ATATATAATATTTTAAATA
1 ATATATAATATTTTAAATA
3503625 TAATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATAATATTTTAAATA
Found at i:3504487 original size:2 final size:2
Alignment explanation
Indices: 3504480--3504508 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3504470 TTACATGCAC
3504480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3504509 ATTACGTAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3505465 original size:14 final size:13
Alignment explanation
Indices: 3505442--3505471 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3505432 ATTTATTTAT
3505442 TATTTTTTAAATA
1 TATTTTTTAAATA
3505455 TATTTTATTAAATA
1 TATTTT-TTAAATA
3505469 TAT
1 TAT
3505472 GTCATCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTTTTAAATA
Found at i:3507322 original size:27 final size:26
Alignment explanation
Indices: 3507239--3507322 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
3507229 ATGTGTCATT
* * *
3507239 TAAAAAAAATCATTTTTGTTTATCACA
1 TAAAAAAAATTATTTTT-TTAATTACA
* * *
3507266 TAAAAGAAATTATTTTTTAAATATATA
1 TAAAAAAAATTATTTTTTTAAT-TACA
3507293 TAAAAATAAATTATTTTTTTAATTACA
1 TAAAAA-AAATTATTTTTTTAATTACA
3507320 TAA
1 TAA
3507323 TTACACGTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.07
27 28 0.61
28 15 0.33
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAAAAAAATTATTTTTTTAATTACA
Found at i:3508431 original size:24 final size:26
Alignment explanation
Indices: 3508386--3508433 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3508376 TAAATATTTT
*
3508386 AAAATTAATATAATAATTAAAATATA
1 AAAATTAATATAATAATAAAAATATA
*
3508412 AAAATTTATAT-A-AATAAAAATA
1 AAAATTAATATAATAATAAAAATA
3508434 ACTTAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 1 0.05
26 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATTAATATAATAATAAAAATATA
Found at i:3508654 original size:2 final size:2
Alignment explanation
Indices: 3508647--3508695 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3508637 TCAGTTGAAC
3508647 GA GA GA GA GA GA GA GA 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 GA
3508689 GA GA GA G
1 GA GA GA G
3508696 CGCAAGCGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3509270 original size:17 final size:17
Alignment explanation
Indices: 3509250--3509303 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
3509240 TTTATATTTG
* *
3509250 ATATTTATATTTAAAAT
1 ATATTTAAATATAAAAT
3509267 ATATTTAAATATAAAAT
1 ATATTTAAATATAAAAT
**
3509284 ATACGTAAATATTAAAAT
1 ATATTTAAATA-TAAAAT
3509302 AT
1 AT
3509304 GATTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
ATATTTAAATATAAAAT
Found at i:3509612 original size:2 final size:2
Alignment explanation
Indices: 3509605--3509631 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3509595 AGTTAGGACC
3509605 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3509632 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3509873 original size:22 final size:22
Alignment explanation
Indices: 3509848--3509891 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3509838 ATCCGTACCA
3509848 TCTGGGGATAAAATATACGACG
1 TCTGGGGATAAAATATACGACG
*
3509870 TCTGGGGATGAAATATACGACG
1 TCTGGGGATAAAATATACGACG
3509892 GCAACGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (22 bp):
TCTGGGGATAAAATATACGACG
Found at i:3517638 original size:16 final size:18
Alignment explanation
Indices: 3517614--3517649 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3517604 GCAAGACCTC
*
3517614 TCTT-TCTCTTTCTTTTT
1 TCTTCTCTCTCTCTTTTT
3517631 TCTTCTCTCTCTCTTTTT
1 TCTTCTCTCTCTCTTTTT
3517649 T
1 T
3517650 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TCTTCTCTCTCTCTTTTT
Found at i:3517643 original size:22 final size:22
Alignment explanation
Indices: 3517612--3517653 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3517602 TGGCAAGACC
*
3517612 TCTCTTTCTCTTTCTTTTTTCT
1 TCTCTCTCTCTTTCTTTTTTCT
*
3517634 TCTCTCTCTCTTTTTTTTTT
1 TCTCTCTCTCTTTCTTTTTT
3517654 TTTTTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTCTCTCTCTTTCTTTTTTCT
Found at i:3518754 original size:16 final size:16
Alignment explanation
Indices: 3518662--3518754 Score: 66
Period size: 16 Copynumber: 5.8 Consensus size: 16
3518652 TATTTTTAAC
3518662 ATATATATTAAAAATAT
1 ATATATATTAAAAAT-T
* * *
3518679 ATTTATACTAAATCA-T
1 ATATATATTAAA-AATT
* *
3518695 AAATATATT-AATATT
1 ATATATATTAAAAATT
*
3518710 ATATATA-TAAATTATT
1 ATATATATTAAA-AATT
**
3518726 ATATATACGAAAAATT
1 ATATATATTAAAAATT
3518742 ATATATATTAAAA
1 ATATATATTAAAA
3518755 TTAGTCTGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
14 2 0.03
15 11 0.19
16 32 0.54
17 13 0.22
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (16 bp):
ATATATATTAAAAATT
Found at i:3520076 original size:26 final size:24
Alignment explanation
Indices: 3520047--3520099 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3520037 AGAAGAGATA
* *
3520047 TTAAAATTTATATTTTGATATATATT
1 TTAAAATTTAAATTAT-ATATA-ATT
*
3520073 TTAATATTTAAATTATATATAATT
1 TTAAAATTTAAATTATATATAATT
3520097 TTA
1 TTA
3520100 CAGATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTAAAATTTAAATTATATATAATT
Found at i:3521475 original size:24 final size:24
Alignment explanation
Indices: 3521448--3521498 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3521438 TATTTCAAAT
*
3521448 AAAA-ACTTATTTATATACAAATAA
1 AAAATACTTATTTAAATA-AAATAA
* *
3521472 AAAATATTTATTTAAATATAATAA
1 AAAATACTTATTTAAATAAAATAA
3521496 AAA
1 AAA
3521499 TAAATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATACTTATTTAAATAAAATAA
Found at i:3521492 original size:21 final size:21
Alignment explanation
Indices: 3521421--3521497 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
3521411 TACAAATCTC
*
3521421 AATATAAATAAATTTTTTATTTCA
1 AATATAAA-AAA-TATTTATTT-A
** *
3521445 AATA-AAAACTTATTTATATA
1 AATATAAAAAATATTTATTTA
3521465 CAA-ATAAAAAATATTTATTTA
1 -AATATAAAAAATATTTATTTA
3521486 AATATAATAAAA
1 AATATAA-AAAA
3521498 ATAAATATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 4 0.10
21 26 0.62
22 5 0.12
23 3 0.07
24 4 0.10
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATAAAAAATATTTATTTA
Found at i:3521503 original size:27 final size:28
Alignment explanation
Indices: 3521473--3521525 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3521463 TACAAATAAA
* *
3521473 AAATATTTAT-TTAAATATAATAAAAAT
1 AAATATTTATCTAAAAAATAATAAAAAT
3521500 AAATATTTATCTAAAAAATAATAAAA
1 AAATATTTATCTAAAAAATAATAAAA
3521526 TTTAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATATTTATCTAAAAAATAATAAAAAT
Found at i:3521869 original size:26 final size:25
Alignment explanation
Indices: 3521837--3521889 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
3521827 TGATATATTA
3521837 TTATATTATA-ATTATATTTAAAATAT
1 TTATATTATATA-TAT-TTTAAAATAT
3521863 TTATATTATATATATTTTAAAATAT
1 TTATATTATATATATTTTAAAATAT
3521888 TT
1 TT
3521890 TTATATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 12 0.46
26 13 0.50
27 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATATTATATATATTTTAAAATAT
Found at i:3521900 original size:24 final size:23
Alignment explanation
Indices: 3521842--3521900 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
3521832 TATTATTATA
*
3521842 TTATAATTATATTTAAAATATTT
1 TTATATTTATATTTAAAATATTT
* *
3521865 ATATTATATATATTTTAAAATATTT
1 TTA-TATTTATA-TTTAAAATATTT
3521890 TTATATTTATA
1 TTATATTTATA
3521901 ACATGTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.07
24 13 0.45
25 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATTTATATTTAAAATATTT
Found at i:3521928 original size:19 final size:19
Alignment explanation
Indices: 3521868--3521943 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
3521858 AATATTTATA
*
3521868 TTATATATATTTTAAAATATT
1 TTATAT-TATTTT-TAATATT
* * *
3521889 TT-TA-TATTTATAACATG
1 TTATATTATTTTTAATATT
3521906 TTATATTATTTTTAATATT
1 TTATATTATTTTTAATATT
*
3521925 TTATTATAATTTTT-ATATT
1 TTA-TATTATTTTTAATATT
3521944 ATTTTTAACC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
17 6 0.14
18 7 0.16
19 18 0.41
20 11 0.25
21 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
TTATATTATTTTTAATATT
Found at i:3521947 original size:11 final size:11
Alignment explanation
Indices: 3521906--3521950 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
3521896 TTATAACATG
3521906 TTATATTATTT
1 TTATATTATTT
3521917 TTA-A-TA-TT
1 TTATATTATTT
*
3521925 TTATTATAATTT
1 TTA-TATTATTT
3521937 TTATATTATTT
1 TTATATTATTT
3521948 TTA
1 TTA
3521951 ACCTTATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.18
9 2 0.07
10 2 0.07
11 14 0.50
12 5 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTATTT
Found at i:3522239 original size:14 final size:15
Alignment explanation
Indices: 3522210--3522269 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 15
3522200 AATTAATATT
*
3522210 TAATAATTTAAAATA
1 TAATTATTTAAAATA
*
3522225 TTATTATTT-AAATA
1 TAATTATTTAAAATA
*
3522239 TAATTA-TAAAAATA
1 TAATTATTTAAAATA
* *
3522253 TAAATA-TTAATATA
1 TAATTATTTAAAATA
3522267 TAA
1 TAA
3522270 ATCATTGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 1 0.03
14 29 0.78
15 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTATTTAAAATA
Found at i:3522650 original size:13 final size:14
Alignment explanation
Indices: 3522627--3522659 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3522617 GTACAAGAAT
3522627 TATTT-AATTTTTA
1 TATTTAAATTTTTA
3522640 T-TTTAAATTTTTA
1 TATTTAAATTTTTA
3522653 TATTTAA
1 TATTTAA
3522660 CGTATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 10 0.56
14 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTAAATTTTTA
Found at i:3522879 original size:19 final size:19
Alignment explanation
Indices: 3522824--3522880 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
3522814 AATTTTTTAC
*
3522824 TATTAACAAAATTTATATAT
1 TATTAAAAAAATTTA-ATAT
*
3522844 TA-TAAGTAAAAATTTTAATTT
1 TATTAA--AAAAA-TTTAATAT
3522865 TATTAAAAAAATTTAA
1 TATTAAAAAAATTTAA
3522881 ATAAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
21 9 0.29
22 7 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TATTAAAAAAATTTAATAT
Found at i:3523807 original size:26 final size:27
Alignment explanation
Indices: 3523777--3523828 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3523767 TTAAATCAAA
3523777 TATATATTTT-TATTT-AATATTAAAAT
1 TATAT-TTTTATATTTAAATATTAAAAT
*
3523803 TATATTTTTATATTTAAATTTTAAAA
1 TATATTTTTATATTTAAATATTAAAA
3523829 ATTTTAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATTTTTATATTTAAATATTAAAAT
Found at i:3524640 original size:16 final size:15
Alignment explanation
Indices: 3524619--3524668 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
3524609 TATCTCTAGT
3524619 ATATTTTAAATTATAA
1 ATATTTTAAATT-TAA
3524635 ATA-TTTAATATTTAA
1 ATATTTTAA-ATTTAA
3524650 A-ATTTTTAAATATTAA
1 ATA-TTTTAAAT-TTAA
3524666 ATA
1 ATA
3524669 AATAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 16 0.55
17 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTAAATTTAA
Found at i:3525775 original size:27 final size:27
Alignment explanation
Indices: 3525745--3525806 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3525735 TTTCAAATTG
*
3525745 AATTTATATAAATTAAAAATATTAA-AT
1 AATTAATATAAATTAAAAATA-TAATAT
* *
3525772 AATTAATTTAAATTTAAAATATAATAT
1 AATTAATATAAATTAAAAATATAATAT
3525799 AATCTAAT
1 AAT-TAAT
3525807 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.77
28 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTAATATAAATTAAAAATATAATAT
Found at i:3525812 original size:27 final size:27
Alignment explanation
Indices: 3525753--3525825 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
3525743 TGAATTTATA
*
3525753 TAAATTAAAAATATTAAATAATTAATT
1 TAAATTTAAAATATTAAATAATTAATT
3525780 TAAATTTAAAATA-TAATATAATCTAATT
1 TAAATTTAAAATATTAA-ATAAT-TAATT
*
3525808 TAATTTTTAAAAT-TTAAA
1 TAA-ATTTAAAATATTAAA
3525826 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.08
27 17 0.43
28 9 0.22
29 11 0.28
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTTAAAATATTAAATAATTAATT
Found at i:3533092 original size:28 final size:28
Alignment explanation
Indices: 3533034--3533091 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
3533024 TTTAATATTT
*
3533034 AATATTTATATAATTAAATTTAAATAAA
1 AATATTTATATAATTAAATATAAATAAA
* * *
3533062 AATATTTTTATTATTAAATAATAATTAAA
1 AATATTTATATAATTAAAT-ATAAATAAA
3533091 A
1 A
3533092 TTAAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATTTATATAATTAAATATAAATAAA
Found at i:3533326 original size:6 final size:6
Alignment explanation
Indices: 3533308--3533339 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3533298 GAAACGTCTT
*
3533308 CTCTCC CTTTCC CTCTCC CTCTCC CTCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT
3533340 GGGCTACGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CTCTCC
Found at i:3536653 original size:13 final size:13
Alignment explanation
Indices: 3536631--3536662 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3536621 TCGTATACTA
3536631 ACTT-ATGTGAAT
1 ACTTCATGTGAAT
3536643 ACTTCATGTGAAT
1 ACTTCATGTGAAT
3536656 ACTTCAT
1 ACTTCAT
3536663 TTGTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (13 bp):
ACTTCATGTGAAT
Found at i:3541897 original size:30 final size:31
Alignment explanation
Indices: 3541836--3541898 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
3541826 AATAAGATTA
* *
3541836 ATTTAATTAAATCAATTTAAATTATTAAAAT
1 ATTTAATTAAATCAATTGAAATTATGAAAAT
** *
3541867 ATTTAA-TAAATCAATTGCCATTATGCAAAT
1 ATTTAATTAAATCAATTGAAATTATGAAAAT
3541897 AT
1 AT
3541899 GATTTTCATG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (31 bp):
ATTTAATTAAATCAATTGAAATTATGAAAAT
Found at i:3543906 original size:18 final size:18
Alignment explanation
Indices: 3543864--3543906 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3543854 TTTTTATGTT
**
3543864 ATAAAAAATTAAACATTA
1 ATAAAAAATTAAACAAAA
* *
3543882 ATTAAAAATTAAATAAAA
1 ATAAAAAATTAAACAAAA
3543900 ATAAAAA
1 ATAAAAA
3543907 TAAATTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAAATTAAACAAAA
Found at i:3544609 original size:21 final size:21
Alignment explanation
Indices: 3544584--3544654 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
3544574 AAATAAAAAA
3544584 AAATTATAAATATTAAAATTT
1 AAATTATAAATATTAAAATTT
*
3544605 AAATT-TAAAAATATAAAATATT
1 AAATTATAAATAT-TAAAAT-TT
* * * *
3544627 -ATTTTTACGATATTAAATTTT
1 AAATTATA-AATATTAAAATTT
3544648 AAATTAT
1 AAATTAT
3544655 TTAAATTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 6 0.16
21 16 0.42
22 13 0.34
23 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
AAATTATAAATATTAAAATTT
Found at i:3544615 original size:14 final size:15
Alignment explanation
Indices: 3544582--3544627 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3544572 GAAAATAAAA
3544582 AAAAATTATAAATATT
1 AAAAATT-TAAATATT
3544598 -AAAATTTAAAT-TT
1 AAAAATTTAAATATT
*
3544611 AAAAATATAAAATATT
1 AAAAAT-TTAAATATT
3544627 A
1 A
3544628 TTTTTACGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.08
14 10 0.38
15 11 0.42
16 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATTTAAATATT
Found at i:3548654 original size:37 final size:37
Alignment explanation
Indices: 3548588--3548664 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
3548578 TTTGTGATTT
**
3548588 TTTTAAATATAAATATAAAAATATGATATTTAAAAA-A
1 TTTTAAATATAAATATAAAAATAAAATA-TTAAAAATA
3548625 TTTTAAA-ATAAATA-AAAAATAAAAAATATTAAAAATA
1 TTTTAAATATAAATATAAAAAT--AAAATATTAAAAATA
3548662 TTT
1 TTT
3548665 ATATTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 6 0.17
36 14 0.40
37 15 0.43
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (37 bp):
TTTTAAATATAAATATAAAAATAAAATATTAAAAATA
Found at i:3548657 original size:36 final size:38
Alignment explanation
Indices: 3548588--3548664 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 38
3548578 TTTGTGATTT
** *
3548588 TTTTAAATATAAATATAAAAATATGATATTTAAAAA-A
1 TTTTAAATATAAATATAAAAATAAAAAATTTAAAAATA
3548625 TTTTAAA-ATAAATA-AAAAATAAAAAATATTAAAAATA
1 TTTTAAATATAAATATAAAAATAAAAAAT-TTAAAAATA
3548662 TTT
1 TTT
3548665 ATATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 10 0.29
36 14 0.40
37 11 0.31
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
TTTTAAATATAAATATAAAAATAAAAAATTTAAAAATA
Found at i:3548668 original size:15 final size:17
Alignment explanation
Indices: 3548650--3548691 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
3548640 AAAATAAAAA
3548650 ATATTAAA-A-ATATTT
1 ATATTAAATACATATTT
3548665 ATATTAAATACATATTT
1 ATATTAAATACATATTT
*
3548682 ATATTTAATA
1 ATATTAAATA
3548692 TTTTCAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.33
16 1 0.04
17 15 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAAATACATATTT
Found at i:3552947 original size:22 final size:22
Alignment explanation
Indices: 3552906--3552959 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
3552896 TTTAAAATTT
*
3552906 AAAATTTATTTTATATTTTATC
1 AAAATTTATTTTATAATTTATC
*
3552928 AAAATTTATTTT-TAAATT-T-
1 AAAATTTATTTTATAATTTATC
*
3552947 AAAATTTAATTTA
1 AAAATTTATTTTA
3552960 AGATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 11 0.39
20 1 0.04
21 4 0.14
22 12 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAAATTTATTTTATAATTTATC
Found at i:3553305 original size:18 final size:18
Alignment explanation
Indices: 3553282--3553319 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3553272 TTTATATTAC
3553282 AAAAATTAAA-AAATGATT
1 AAAAATTAAATAAA-GATT
3553300 AAAAATTAAATAAAGATT
1 AAAAATTAAATAAAGATT
3553318 AA
1 AA
3553320 TTTTTGGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAATTAAATAAAGATT
Found at i:3556538 original size:12 final size:12
Alignment explanation
Indices: 3556521--3556555 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
3556511 AGCTTATTTT
3556521 CACATACAAGCA
1 CACATACAAGCA
3556533 CACATATACAAGCA
1 CAC--ATACAAGCA
3556547 CACATACAA
1 CACATACAA
3556556 AGAAGACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
14 12 0.57
ACGTcount: A:0.51, C:0.31, G:0.06, T:0.11
Consensus pattern (12 bp):
CACATACAAGCA
Found at i:3556543 original size:14 final size:14
Alignment explanation
Indices: 3556524--3556552 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3556514 TTATTTTCAC
3556524 ATACAAGCACACAT
1 ATACAAGCACACAT
3556538 ATACAAGCACACAT
1 ATACAAGCACACAT
3556552 A
1 A
3556553 CAAAGAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (14 bp):
ATACAAGCACACAT
Found at i:3558064 original size:20 final size:20
Alignment explanation
Indices: 3558041--3558079 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3558031 ATAAAAAAAA
3558041 TATTAGCACAAGCAAAAGTC
1 TATTAGCACAAGCAAAAGTC
**
3558061 TATTAGTGCAAGCAAAAGT
1 TATTAGCACAAGCAAAAGT
3558080 TAACTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (20 bp):
TATTAGCACAAGCAAAAGTC
Found at i:3561256 original size:18 final size:20
Alignment explanation
Indices: 3561235--3561273 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3561225 TTAAATTATG
3561235 TATTTAA-A-TTAAAAAATT
1 TATTTAATATTTAAAAAATT
3561253 TATTTAATATTTAAAAAATT
1 TATTTAATATTTAAAAAATT
3561273 T
1 T
3561274 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTAATATTTAAAAAATT
Found at i:3561535 original size:19 final size:20
Alignment explanation
Indices: 3561511--3561554 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3561501 TAATAATAAC
*
3561511 TTATTAAAAA-TATATTAAA
1 TTATTAAAAATTAAATTAAA
3561530 TTATTAAAAATTAAATTAAA
1 TTATTAAAAATTAAATTAAA
*
3561550 ATATT
1 TTATT
3561555 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATTAAAAATTAAATTAAA
Found at i:3561956 original size:28 final size:28
Alignment explanation
Indices: 3561877--3561958 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
3561867 TTAAAACGTG
* * * * *
3561877 ATATTAAAAATAATATGAATATATGAAT
1 ATATTAAAATTTATATAAATATATTAAC
* *
3561905 ATATCAAAATTT-TATATAACATATTAAC
1 ATATTAAAATTTATATA-AATATATTAAC
3561933 ATATTAAAATTTATATAAATATATTA
1 ATATTAAAATTTATATAAATATATTA
3561959 TAAAAAATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
27 3 0.07
28 36 0.84
29 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
ATATTAAAATTTATATAAATATATTAAC
Found at i:3564235 original size:21 final size:20
Alignment explanation
Indices: 3564210--3564253 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3564200 AAATTTGATA
3564210 AAATTATAATTTATTTTATAT
1 AAATT-TAATTTATTTTATAT
* * *
3564231 AAATTTTATTTTTTTTACAT
1 AAATTTAATTTATTTTATAT
3564251 AAA
1 AAA
3564254 AAAGATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTTAATTTATTTTATAT
Found at i:3565340 original size:12 final size:12
Alignment explanation
Indices: 3565323--3565348 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3565313 ACATATTTTT
3565323 AAAATAAATTAA
1 AAAATAAATTAA
3565335 AAAATAAATTAA
1 AAAATAAATTAA
3565347 AA
1 AA
3565349 TTAAAACATA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAAATTAA
Found at i:3566993 original size:2 final size:2
Alignment explanation
Indices: 3566952--3566979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3566942 AGATCTACTA
3566952 AT 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 AT
3566980 GTTCCCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3570237 original size:16 final size:16
Alignment explanation
Indices: 3570213--3570290 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
3570203 AAAGTTGTTC
3570213 TTATAATTTAAATATT
1 TTATAATTTAAATATT
* * *
3570229 TTATTATTTTATTATT
1 TTATAATTTAAATATT
3570245 TTATAA--T-AATATT
1 TTATAATTTAAATATT
* **
3570258 TTAAAATATTTTATATT
1 TTATAAT-TTAAATATT
3570275 TATATAATTTTAAATA
1 T-TATAA-TTTAAATA
3570291 CATTAATAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
13 10 0.22
14 1 0.02
16 19 0.41
17 6 0.13
18 9 0.20
19 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATAATTTAAATATT
Found at i:3570403 original size:31 final size:32
Alignment explanation
Indices: 3570337--3570423 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
3570327 TTAATGTGAC
*
3570337 ATTATTTTTAA-ATTATTTTATTTATATCATATA
1 ATTATATTTAATATTATTTTA--TATATCATATA
*
3570370 ATTATATTTAATATTATTTTATAT-TTATATA
1 ATTATATTTAATATTATTTTATATATCATATA
*
3570401 ATTATATCTAATA-TA-TTTATATA
1 ATTATATTTAATATTATTTTATATA
3570424 AGTAATTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.14
30 2 0.04
31 18 0.37
32 3 0.06
33 10 0.20
34 9 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTATATTTAATATTATTTTATATATCATATA
Found at i:3571479 original size:13 final size:13
Alignment explanation
Indices: 3571461--3571485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3571451 TATATAAATA
3571461 TAAAAATTATTTT
1 TAAAAATTATTTT
3571474 TAAAAATTATTT
1 TAAAAATTATTT
3571486 AAATATATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAAATTATTTT
Found at i:3574211 original size:12 final size:12
Alignment explanation
Indices: 3574194--3574218 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3574184 TTCCTGTATT
3574194 AAAAAAAAAAGA
1 AAAAAAAAAAGA
3574206 AAAAAAAAAAGA
1 AAAAAAAAAAGA
3574218 A
1 A
3574219 TTGAAAGTAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:3574742 original size:23 final size:23
Alignment explanation
Indices: 3574704--3574749 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3574694 TATTATTAAT
*
3574704 AAATTAAATAATATTATTTTTTA
1 AAATTAAATAATATTAATTTTTA
3574727 AAATTAAATACA-ATTAATTTTTA
1 AAATTAAATA-ATATTAATTTTTA
3574750 TTTTAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTAAATAATATTAATTTTTA
Found at i:3574928 original size:18 final size:18
Alignment explanation
Indices: 3574893--3574927 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3574883 TTATCATTAA
*
3574893 ATTAAATAATATAATTTT
1 ATTAAATAATAAAATTTT
3574911 ATTAAA-AATAAAATTTT
1 ATTAAATAATAAAATTTT
3574928 TTATATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAATAATAAAATTTT
Found at i:3575915 original size:21 final size:21
Alignment explanation
Indices: 3575890--3575940 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3575880 ATTAAAAAAT
3575890 TTATAT-TTTTATAAT-ATAA
1 TTATATATTTTATAATAATAA
3575909 TTATATATTTTATAATAATAA
1 TTATATATTTTATAATAATAA
*
3575930 TTA-AAATTTTA
1 TTATATATTTTA
3575941 ATTTACTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 6 0.21
20 16 0.55
21 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATATTTTATAATAATAA
Found at i:3576388 original size:17 final size:18
Alignment explanation
Indices: 3576357--3576417 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 18
3576347 GTCGTAAATA
3576357 TAAATATGATATAAATTAT
1 TAAATAT-ATATAAATTAT
*
3576376 TAAATATAT-TAAATTTT
1 TAAATATATATAAATTAT
* *
3576393 TAATTATA-ATATA-TAT
1 TAAATATATATAAATTAT
*
3576409 GAAATATAT
1 TAAATATAT
3576418 CGTATATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.24
17 17 0.50
18 2 0.06
19 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TAAATATATATAAATTAT
Found at i:3576432 original size:5 final size:5
Alignment explanation
Indices: 3576422--3576482 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
3576412 ATATATCGTA
* * *
3576422 TATAT TATAT TATTTT TATAT T-TAT TA-AA TATAT TATATT TATAT TATTT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT
*
3576472 TTTAT TATAT T
1 TATAT TATAT T
3576483 TAAAATTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
4 7 0.16
5 28 0.64
6 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATAT
Found at i:3576438 original size:45 final size:37
Alignment explanation
Indices: 3576396--3576495 Score: 100
Period size: 36 Copynumber: 2.7 Consensus size: 37
3576386 AAATTTTTAA
* *
3576396 TTATAATATATATGAAATATATCGTATATATTATATTATTT
1 TTATTATAT-TATTAAATATAT--TATAT-TTATATTATTT
3576437 TTA-TAT-TTATTAAATATATTATATTTATATTATTTT
1 TTATTATATTATTAAATATATTATATTTATATTA-TTT
*
3576473 TTATTATATT-TAAAAT-TATTATA
1 TTATTATATTATTAAATATATTATA
3576496 AAATATAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
35 8 0.15
36 18 0.34
37 8 0.15
38 13 0.25
39 1 0.02
40 2 0.04
41 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (37 bp):
TTATTATATTATTAAATATATTATATTTATATTATTT
Found at i:3576440 original size:11 final size:11
Alignment explanation
Indices: 3576426--3576484 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
3576416 ATCGTATATA
3576426 TTATATTATTT
1 TTATATTATTT
*
3576437 TTATATTTATTAA
1 TTATA-TTATT-T
* *
3576450 ATATATTATAT
1 TTATATTATTT
3576461 TTATATTATTT
1 TTATATTATTT
*
3576472 TT-TATTATAT
1 TTATATTATTT
3576482 TTA
1 TTA
3576485 AAATTATTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 9 0.24
11 16 0.42
12 9 0.24
13 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTATTT
Found at i:3576460 original size:36 final size:35
Alignment explanation
Indices: 3576372--3576495 Score: 112
Period size: 35 Copynumber: 3.5 Consensus size: 35
3576362 ATGATATAAA
* * * *
3576372 TTATTAAATATATTAAATTT-T-TAATTATAATAT
1 TTATTAAATATATTATATTTATATTATTTTTATAT
* *
3576405 ATATGAAATATATCGTATATATTATATTATTTTTATAT
1 TTATTAAATATAT--TATAT-TTATATTATTTTTATAT
3576443 TTATTAAATATATTATATTTATATTATTTTT-TAT
1 TTATTAAATATATTATATTTATATTATTTTTATAT
3576477 TATATTTAAA-ATTATTATA
1 T-TA-TTAAATA-TATTATA
3576496 AAATATAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
33 11 0.15
34 4 0.05
35 20 0.27
36 19 0.25
37 1 0.01
38 20 0.27
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (35 bp):
TTATTAAATATATTATATTTATATTATTTTTATAT
Found at i:3576469 original size:29 final size:30
Alignment explanation
Indices: 3576421--3576478 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3576411 AATATATCGT
*
3576421 ATATATTATATTATTTTTA-TATTTATTAA
1 ATATATTATATTATTATTATTATTTATTAA
*
3576450 ATATATTATATT-TATATTATTTTTTATTA
1 ATATATTATATTAT-TATTATTATTTATTA
3576479 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.64
30 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATATTATATTATTATTATTATTTATTAA
Found at i:3576867 original size:24 final size:21
Alignment explanation
Indices: 3576840--3576887 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 21
3576830 AAATAAAGAA
3576840 TTTTAATTTTAATATATATAATTT
1 TTTTAATTTTAA-AT-TAT-ATTT
*
3576864 TTTTATTTTTAAATTATATTT
1 TTTTAATTTTAAATTATATTT
3576885 TTT
1 TTT
3576888 ATTAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 3 0.13
23 2 0.09
24 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTAATTTTAAATTATATTT
Found at i:3580778 original size:21 final size:21
Alignment explanation
Indices: 3580728--3580793 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3580718 ATTAAATACG
* *
3580728 AAATAAAATATAATATATATT-
1 AAATAAATTATAA-ATTTATTA
*
3580749 -AATATATTA-AAATTTATATA
1 AAATAAATTATAAATTTAT-TA
*
3580769 AAATAAATTATTAATTTATTA
1 AAATAAATTATAAATTTATTA
3580790 AAAT
1 AAAT
3580794 TTATATAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 7 0.19
21 14 0.39
22 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATTATAAATTTATTA
Found at i:3584893 original size:2 final size:2
Alignment explanation
Indices: 3584886--3584925 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3584876 TCTGAAAAAG
3584886 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
3584926 GGGTTCTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3585664 original size:19 final size:19
Alignment explanation
Indices: 3585631--3585669 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3585621 ATTAAATCAA
3585631 ATAGATATAATAAAAATTT
1 ATAGATATAATAAAAATTT
3585650 ATAGAATATAA-AAAAATTT
1 ATAG-ATATAATAAAAATTT
3585669 A
1 A
3585670 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAGATATAATAAAAATTT
Found at i:3586051 original size:18 final size:19
Alignment explanation
Indices: 3586030--3586070 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
3586020 ATTTAAAAAA
*
3586030 ATAATTAGCAT-TAAATTT
1 ATAATTAGAATATAAATTT
3586048 ATAA-TAGAATATAAATTT
1 ATAATTAGAATATAAATTT
3586066 ATAAT
1 ATAAT
3586071 AATTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
ATAATTAGAATATAAATTT
Found at i:3587784 original size:575 final size:570
Alignment explanation
Indices: 3585596--3588340 Score: 3337
Period size: 575 Copynumber: 4.8 Consensus size: 570
3585586 TACTAGATAC
* * * * * * *
3585596 TTCGTATTATATTAATTTTTATAAAATTAAATCAAATAGATATAATAAAAAT-TTATAGAATATA
1 TTCGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTGAT-AAAGTCTTATAAAATATA
* * *
3585660 AAAAAATTTAATTAAAATATATTAAAAATAATTATAAAATT-GAAAAAA-A--TTAATAAATATT
65 AAAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATTAAAAAAAATATTTTAATAAATATT
* * * * *
3585721 ATATGTCAGATAAAGATACTTTTTTTTTATCTAAAATTGCTCTTGAATCAACTTCAAAAATC-TG
130 ATAAGTCAGGTAAAGAT--TATTTTTTTATCTAAAATTGCT-TTGAATCAACTCCAAAAATCTTA
* * ** * * *
3585785 TAAAAAATTAACT-ATCTCTCTTAAAACTCAAATTTTAAAAATATTTGTCTTATAAAATTGAATA
192 TAAAAAATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATC
* * * * * ** * * * *
3585849 GAATCAGAACTTACAGGGTTTTGATTATTTTTTTAATACTAAATACATTGTATAGTTTTAGATAA
257 GATTCAAAACTTATA-AGTTCTGATTATTTTTCCAATACTAAATACGTTGTACAATTTTAGACAA
* ** * * **
3585914 GATGGACGCAAAATGGGCCCACAATAATTCTTTCTTCTTTCCCGGTGTTGTTTGGTCTTTAATTT
321 GATGGACGCAATATAAGCCCACAATAATTCTTTTTTCTTTCTCACTGTTGTTTGGTCTTTAATTT
* * * ** *
3585979 GTTCCTTTAAAGATGTTTT-TCGAAATTACATTAT-T-TATATTATTTAAAAAAATAATTAGCAT
386 GTTCCTTTGATGATGTTTTCT-AAAATTTTATTATCTGTAT-TTTTTTAAAAAAATAATTAGCAT
* * * * *
3586041 TAAATTTATAATAGAATATAAATTTATAATAATTTTTTAAATATATTATTTTTTAAAAAATTAAA
449 TAAATTCATAATTGAGTATAAATATATAATAATTATTTAAATATATTATTTTTTAAAAAATTAAA
* * * *
3586106 TATATTTATCT-TAA-ATAT--ATA--TATATAATATTCATTGGAATCCATATAATA
514 TTTATTTATATAAAATATATAGATATTTATATAATATTCATTGAAATCCATATAATA
*
3586157 TTCGTATTATATTAATTTTTATAAAA-TAAAATTAAATACATATGATAAAGTCTTATAAAATATA
1 TTCGTATTATATTAATTTTTATAAAACT-AAATTAAATACATGTGATAAAGTCTTATAAAATATA
*
3586221 AGAAAATTTT-ATTAAAATATATTAAAAATAGTTATAAAATTAAAAAATATATTTTAATAAATAT
65 A-AAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATTAAAAAAAATATTTTAATAAATAT
* * * * * *
3586285 TATAAGTCAGGTAAAAATAATTTTTTCATCTAAAATTGCTCTGAATCAATTTCAAAAATCTTAAT
129 TATAAGTCAGGTAAAGATTATTTTTTTATCTAAAATTGCTTTGAATCAACTCCAAAAATCTT-AT
* * *
3586350 AAAAAATCAACTCGTCTTTTTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATCT
193 AAAAAATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATCG
* * *
3586415 ATTCAAAACTTATAAGTTCTGATTATTTTTTCAATACTAAATACGTTGTATAATTTTA-AGCAGG
258 ATTCAAAACTTATAAGTTCTGATTATTTTTCCAATACTAAATACGTTGTACAATTTTAGA-CAAG
* * * *
3586479 ATGGACGTAATATAAGCCCACAACAATTCTTTTTTCTTTCTCATTGTTGTTTGGTCTTTAATCTG
322 ATGGACGCAATATAAGCCCACAATAATTCTTTTTTCTTTCTCACTGTTGTTTGGTCTTTAATTTG
* * * * * * *
3586544 TTCTTTTGATGACGTTTTTTAAAATTTTATTATTTGTATTTCTTTAAAAAAAGAATAAGCATTAA
387 TTCCTTTGATGATGTTTTCTAAAATTTTATTATCTGTATTTTTTTAAAAAAATAATTAGCATTAA
*
3586609 ATTCATAATTGAGTAT-AA-ATATAATAATTTTTTAAAT-TA-TAGTTTTTTAAAAAATTAAATT
452 ATTCATAATTGAGTATAAATATATAATAATTATTTAAATATATTA-TTTTTTAAAAAATTAAATT
* * * *
3586670 TATTTATATTAAATATGTAGATATATATATATAATATTCACTGAAATCCATAAAATA
516 TATTTATATAAAATATATAGATAT-T-TATATAATATTCATTGAAATCCATATAATA
* *
3586727 TTTGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTGATAAAGTCTTATAAAACATAA
1 TTCGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTGATAAAGTCTTATAAAATATAA
* * * *
3586792 AAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATTTTAAAAAACTATTTCAATAGATATT
66 AAAATTTTAATTAAAATATATTAAAAATAGTTATAAAA-TTAAAAAAAATATTTTAATAAATATT
* * * * * *
3586857 ATAAGTCAGGCAAAGA-TAATTTTTTATCTAAAATTACTTTGAATCAACTCCATAAATAATAATA
130 ATAAGTCAGGTAAAGATTATTTTTTTATCTAAAATTGCTTTGAATCAACTCCAAAAAT-CTTATA
* * ** *
3586921 AAAAACCAACTCGTCTCTCTTAAAACTCGAATTTTAAAAATATTTATTTTTTAAATTTAAATCGA
194 AAAAATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATCGA
* *
3586986 TTCAAAACTTATAAGTTCTGATTATTTTT-CAATACTAAATACGTTGCACAATTTTAGACAGGAT
259 TTCAAAACTTATAAGTTCTGATTATTTTTCCAATACTAAATACGTTGTACAATTTTAGACAAGAT
* * * * *
3587050 AGACGCAATACAAGCACACAATAATTCTTTCTTCTTTCTCACTATTGTTTGGTCTTTAATTTGTT
324 GGACGCAATATAAGCCCACAATAATTCTTTTTTCTTTCTCACTGTTGTTTGGTCTTTAATTTGTT
* * * ** *
3587115 CCTTTGATAATGTTTTTTAAAATTTTGTTATCAATATTTTTGTAAAAAAATAATTAGCATTAAAT
389 CCTTTGATGATGTTTTCTAAAATTTTATTATCTGTATTTTTTTAAAAAAATAATTAGCATTAAAT
* * * *
3587180 TTATAATTAAGTATAAATATATAATAATTATTTAAATATATTATTTTTAAAAAAAGTTAATTTTA
454 TCATAATTGAGTATAAATATATAATAATTATTTAAATATATTATTTTTTAAAAAA-TTAAATTTA
*
3587245 TTTATATAAAATATATAGATATTTATATAATATTCATT-AGAATCCATGTAATA
518 TTTATATAAAATATATAGATATTTATATAATATTCATTGA-AATCCATATAATA
* *
3587298 TTCATATTATATTAATTTTTATAAAACTAAATTAAATACATGCGATAAAGTCTTATAAAATATAA
1 TTCGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTGATAAAGTCTTATAAAATATAA
*
3587363 GAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATTAAAAAAAAAAGTATTTTAATAAATA
66 AAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATT--AAAAAAAA-TATTTTAATAAATA
* ** *
3587428 TCATAAGTCAGACAAAGATTATTTTTTTATCTAAAATTGCTTTGAATCAACTCCAGAAATCATTA
128 TTATAAGTCAGGTAAAGATTATTTTTTTATCTAAAATTGCTTTGAATCAACTCCAAAAATC-TTA
* * * **
3587493 TAAAAAACCAACACGTCTCTCTCAAAACTTGAATTTTAAAAATATTTACCTTATAAATTTAAATC
192 TAAAAAATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATC
* * * * * *
3587558 GATTCAAAACTTATATGTTCTAATTATTTTTCCAAAACTAAATGCGTCGTAAAATTTTAGACAAG
257 GATTCAAAACTTATAAGTTCTGATTATTTTTCCAATACTAAATACGTTGTACAATTTTAGACAAG
* * *
3587623 ATGGACGCAATATAAGCCCACAACAATTCTTTTTTCTTTCTCACTCTTGTTTGGGCTTTAATTTG
322 ATGGACGCAATATAAGCCCACAATAATTCTTTTTTCTTTCTCACTGTTGTTTGGTCTTTAATTTG
* *
3587688 TTCCTTTGATGATGTTTTCTAAAATTTTGTTATCTGTATTTTTTTAAAAAAATAACTAGCATTAA
387 TTCCTTTGATGATGTTTTCTAAAATTTTATTATCTGTATTTTTTTAAAAAAATAATTAGCATTAA
* *
3587753 ATTCATAATTGAGTATAAATATATGATAATTATTTAAATATATTATTTTTTTAAAAAGTTAAATT
452 ATTCATAATTGAGTATAAATATATAATAATTATTTAAATATATTA-TTTTTTAAAAAATTAAATT
* * * **
3587818 TATTTATATAAAATATATAAATATATATATTATATTCATTGAAATTTATATAATA
516 TATTTATATAAAATATATAGATATTTATATAATATTCATTGAAATCCATATAATA
* *
3587873 TTCGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTAATAAAGTCTTATAAAACAT-A
1 TTCGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTGATAAAGTCTTATAAAATATAA
* *
3587937 AAAATTTTTATTAAAATATATTAAAAATAGTTATAAAATTAAGAAAAAAATATTTTAATAAATTT
66 AAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATT-A-AAAAAAATATTTTAATAAATAT
* * * *
3588002 TATAAGTCAGGTAAAGA-TA---ATTT-TCTAAAATTACTTTGAATCAACTCTAGAAATCTTAGT
129 TATAAGTCAGGTAAAGATTATTTTTTTATCTAAAATTGCTTTGAATCAACTCCAAAAATCTTA-T
* *
3588062 AAAATATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACTTTATAAATTTAAATCG
193 AAAAAATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATCG
* * * * *
3588127 ATTCAAAACTTATAAATTTTTTATT-TTTTGTCCAATACTAAATACGTTATACCATTTTAGAC-A
258 ATTCAAAACTTAT-AAGTTCTGATTATTTT-TCCAATACTAAATACGTTGTACAATTTTAGACAA
* * * * * * * * *
3588190 GAATAGACGTAATATAAGCCCACAATAATTCTTTCTTTTTTTTTTAAATTTTGTTTAGTTTTTAA
321 G-ATGGACGCAATATAAGCCCACAATAATTC-TT-TTTTCTTTCTCACTGTTGTTTGGTCTTTAA
* * * * * *
3588255 TTTGTTCCTTTAATAATGATTTCTAAAATTTTATTATATGTAATTTTTT-AAAAAATAATTAACA
383 TTTGTTCCTTTGATGATGTTTTCTAAAATTTTATTATCTGTATTTTTTTAAAAAAATAATTAGCA
*
3588319 TTAAATTCATAATTGAGCATAA
448 TTAAATTCATAATTGAGTATAA
3588341 TTTTTTAAAT
Statistics
Matches: 1901, Mismatches: 234, Indels: 89
0.85 0.11 0.04
Matches are distributed among these distances:
560 5 0.00
561 85 0.04
562 58 0.03
563 42 0.02
564 137 0.07
565 118 0.06
566 6 0.00
567 3 0.00
568 108 0.06
569 223 0.12
570 280 0.15
571 243 0.13
572 22 0.01
573 88 0.05
574 174 0.09
575 298 0.16
576 11 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (570 bp):
TTCGTATTATATTAATTTTTATAAAACTAAATTAAATACATGTGATAAAGTCTTATAAAATATAA
AAAATTTTAATTAAAATATATTAAAAATAGTTATAAAATTAAAAAAAATATTTTAATAAATATTA
TAAGTCAGGTAAAGATTATTTTTTTATCTAAAATTGCTTTGAATCAACTCCAAAAATCTTATAAA
AAATCAACTCGTCTCTCTTAAAACTCAAATTTTAAAAATATTTACCTTATAAATTTAAATCGATT
CAAAACTTATAAGTTCTGATTATTTTTCCAATACTAAATACGTTGTACAATTTTAGACAAGATGG
ACGCAATATAAGCCCACAATAATTCTTTTTTCTTTCTCACTGTTGTTTGGTCTTTAATTTGTTCC
TTTGATGATGTTTTCTAAAATTTTATTATCTGTATTTTTTTAAAAAAATAATTAGCATTAAATTC
ATAATTGAGTATAAATATATAATAATTATTTAAATATATTATTTTTTAAAAAATTAAATTTATTT
ATATAAAATATATAGATATTTATATAATATTCATTGAAATCCATATAATA
Found at i:3589094 original size:67 final size:67
Alignment explanation
Indices: 3589011--3589144 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
3589001 AAAAATATAA
* *
3589011 AAAAAAATTAATTTTATACTCAAATTAAAGAACAAAAATGAGTTTACAATAAAAATATTTTAAAT
1 AAAAAAATTAACTTTATACTCAAATTAAAGAACAAAAATGAGTTTACAATAAAAACATTTTAAAT
3589076 AT
66 AT
*
3589078 AAAAAAATTAACTTTATACTCGAATTAAAGAACAAAAATGAGTTTACAATAAAAACATTTTAAAT
1 AAAAAAATTAACTTTATACTCAAATTAAAGAACAAAAATGAGTTTACAATAAAAACATTTTAAAT
3589143 AT
66 AT
3589145 CATTTAAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (67 bp):
AAAAAAATTAACTTTATACTCAAATTAAAGAACAAAAATGAGTTTACAATAAAAACATTTTAAAT
AT
Found at i:3592940 original size:14 final size:15
Alignment explanation
Indices: 3592921--3592952 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3592911 TTTTTATATA
3592921 AAAAATAAA-TAAAT
1 AAAAATAAAGTAAAT
3592935 AAAAATAAAGTAAAT
1 AAAAATAAAGTAAAT
3592950 AAA
1 AAA
3592953 TTATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAAATAAAGTAAAT
Found at i:3593430 original size:16 final size:16
Alignment explanation
Indices: 3593409--3593447 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3593399 AATATGATGC
3593409 TTTTTTGCCTTTAATT
1 TTTTTTGCCTTTAATT
* *
3593425 TTTTTTTCCTTTCATT
1 TTTTTTGCCTTTAATT
*
3593441 TCTTTTG
1 TTTTTTG
3593448 ATTTTTCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTTTGCCTTTAATT
Found at i:3593553 original size:4 final size:4
Alignment explanation
Indices: 3593544--3593569 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3593534 TAATAATAAT
3593544 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
3593570 ATCATTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:3597586 original size:20 final size:21
Alignment explanation
Indices: 3597554--3597605 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3597544 TCAGATTGAT
3597554 TAAAATAAT-TATTTAAA-TAA
1 TAAAA-AATATATTTAAATTAA
3597574 TAAAAAATATATTTAAATTTAA
1 TAAAAAATATATTTAAA-TTAA
*
3597596 TTAAAAATAT
1 TAAAAAATAT
3597606 TAATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
22 12 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAATATATTTAAATTAA
Found at i:3598108 original size:22 final size:22
Alignment explanation
Indices: 3598064--3598125 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
3598054 AAACATAAAA
*
3598064 AATTATTT-TTATTAATATTTAT
1 AATTATTTATAATTAA-ATTTAT
3598086 ATATT-TTTATAATTAAATTTAT
1 A-ATTATTTATAATTAAATTTAT
*
3598108 AATTATTTATTATTAAAT
1 AATTATTTATAATTAAAT
3598126 AATTTGAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.09
22 23 0.66
23 9 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTATTTATAATTAAATTTAT
Found at i:3598421 original size:36 final size:36
Alignment explanation
Indices: 3598381--3598457 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
3598371 TAATTTAAAT
3598381 TATTATTTT-AATAATTAAAA-ATAATTTTTAAATTTA
1 TATTATTTTAAATAA-TAAAATA-AATTTTTAAATTTA
3598417 TATTATTTTAAATAATAAAATAAATTTTTAAATTTA
1 TATTATTTTAAATAATAAAATAAATTTTTAAATTTA
3598453 T-TTAT
1 TATTAT
3598458 AATTAAGCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
35 4 0.10
36 29 0.74
37 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
TATTATTTTAAATAATAAAATAAATTTTTAAATTTA
Found at i:3604728 original size:21 final size:21
Alignment explanation
Indices: 3604703--3604747 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3604693 TTTCAATGTT
*
3604703 AATATCTTTAA-ATTTTTAAAA
1 AATAT-TTTAATATATTTAAAA
3604724 AATATTTTAATATATTTAAAA
1 AATATTTTAATATATTTAAAA
3604745 AAT
1 AAT
3604748 TATATTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATTTTAATATATTTAAAA
Found at i:3605096 original size:6 final size:6
Alignment explanation
Indices: 3605085--3605110 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3605075 TGGAAAATGG
3605085 AGGGGA AGGGGA AGGGGA AGGGGA AG
1 AGGGGA AGGGGA AGGGGA AGGGGA AG
3605111 CAAGATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:3605255 original size:22 final size:22
Alignment explanation
Indices: 3605186--3605256 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
3605176 ACATTCATAT
* *
3605186 TATATTTATATTATTTTTATATA
1 TATATTTTTATTAATTTTA-ATA
* ** *
3605209 TTATAATTTTATTTAA-AATATTA
1 -TATATTTTTA-TTAATTTTAATA
3605232 TATATTTTTATTAATTTTAATA
1 TATATTTTTATTAATTTTAATA
3605254 TAT
1 TAT
3605257 TTATATATTT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
21 4 0.11
22 16 0.46
23 2 0.06
24 10 0.29
25 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATTTTTATTAATTTTAATA
Found at i:3605264 original size:8 final size:8
Alignment explanation
Indices: 3605186--3605272 Score: 57
Period size: 8 Copynumber: 11.6 Consensus size: 8
3605176 ACATTCATAT
3605186 TATATTTA
1 TATATTTA
*
3605194 TATTATTTT
1 TA-TATTTA
3605203 TATATATTA
1 TATAT-TTA
3605212 TA-ATTT-
1 TATATTTA
*
3605218 TAT-TTAA
1 TATATTTA
*
3605225 AATA-TTA
1 TATATTTA
3605232 TATATTT-
1 TATATTTA
3605239 T-TA-TTA
1 TATATTTA
3605245 -AT-TTTAA
1 TATATTT-A
3605252 TATATTTA
1 TATATTTA
3605260 TATATTTA
1 TATATTTA
3605268 TATAT
1 TATAT
3605273 AAACTTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
5 2 0.03
6 9 0.15
7 11 0.18
8 25 0.41
9 14 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:3605272 original size:18 final size:18
Alignment explanation
Indices: 3605186--3605273 Score: 58
Period size: 18 Copynumber: 4.8 Consensus size: 18
3605176 ACATTCATAT
*
3605186 TATATTTATAT-TATTTT
1 TATATTTATATATATTTA
*
3605203 TATATATTATAATTTTATTTA
1 TATAT-TTAT-A-TATATTTA
* *
3605224 -AAATATTATATATTTTTA
1 TATAT-TTATATATATTTA
3605242 T-TAATTT-TAATATATTTA
1 TAT-ATTTAT-ATATATTTA
3605260 TATATTTATATATA
1 TATATTTATATATA
3605274 AACTTATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
17 6 0.11
18 30 0.54
19 6 0.11
20 9 0.16
21 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTATATATATTTA
Found at i:3605815 original size:20 final size:20
Alignment explanation
Indices: 3605790--3605829 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3605780 ATTAAAATAT
3605790 TATTTTTATATTAATATTAA
1 TATTTTTATATTAATATTAA
* *
3605810 TATTTTTATTTTATTATTAA
1 TATTTTTATATTAATATTAA
3605830 ATAATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTATATTAATATTAA
Done.