Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 23 of 39
Found at i:3397934 original size:23 final size:22
Alignment explanation
Indices: 3397908--3397952 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3397898 CTAAAATAAA
*
3397908 ATATAATATATAATTAAAAATAT
1 ATATAATAAATAA-TAAAAATAT
* *
3397931 ATATACTAAATCATAAAAATAT
1 ATATAATAAATAATAAAAATAT
3397953 TATTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAATAAATAATAAAAATAT
Found at i:3398557 original size:15 final size:15
Alignment explanation
Indices: 3398539--3398585 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
3398529 CTTGAACTTA
*
3398539 AAAAAGTCTAAATTC
1 AAAAAGTCTAAACTC
*
3398554 AAAAAGGCTCAAACTC
1 AAAAAGTCT-AAACTC
3398570 AAATAAGTCTAAACTC
1 AAA-AAGTCTAAACTC
3398586 GAAAGATCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAAGTCTAAACTC
Found at i:3398557 original size:16 final size:16
Alignment explanation
Indices: 3398533--3398585 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
3398523 AAAAAGCTTG
*
3398533 AACTTAAAAAAGTCTA
1 AACTCAAAAAAGTCTA
* *
3398549 AATTC-AAAAAGGCTCA
1 AACTCAAAAAAGTCT-A
*
3398565 AACTCAAATAAGTCTA
1 AACTCAAAAAAGTCTA
3398581 AACTC
1 AACTC
3398586 GAAAGATCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 8 0.28
16 14 0.48
17 7 0.24
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.23
Consensus pattern (16 bp):
AACTCAAAAAAGTCTA
Found at i:3398578 original size:32 final size:32
Alignment explanation
Indices: 3398516--3398602 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
3398506 ACTCAAACCC
** *
3398516 AAATTCGAAAAAGCTTGAACTTAAAAAAGTCT
1 AAATTCGAAAAAGCTCAAACTCAAAAAAGTCT
*
3398548 AAATTC-AAAAAGGCTCAAACTCAAATAAGTCT
1 AAATTCGAAAAA-GCTCAAACTCAAAAAAGTCT
* * *
3398580 AAACTCGAAAGATC-CAAACTCAA
1 AAATTCGAAAAAGCTCAAACTCAA
3398603 CATAATTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 14 0.30
32 28 0.61
33 4 0.09
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (32 bp):
AAATTCGAAAAAGCTCAAACTCAAAAAAGTCT
Found at i:3398926 original size:20 final size:20
Alignment explanation
Indices: 3398880--3398928 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3398870 TTGTAAATAA
*
3398880 AATTTTCTTCTAAAAAAATT
1 AATTTTTTTCTAAAAAAATT
*
3398900 AATTTTTTTCTAAAATAATT
1 AATTTTTTTCTAAAAAAATT
3398920 AATTTTTTT
1 AATTTTTTT
3398929 ATATCTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTTTTCTAAAAAAATT
Found at i:3400414 original size:11 final size:10
Alignment explanation
Indices: 3400383--3400442 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
3400373 TTTAATTTCT
*
3400383 AAAAAATAAA
1 AAAAAATATA
3400393 AAATGAAATATTA
1 AAA--AAATA-TA
3400406 AAAAAATATA
1 AAAAAATATA
*
3400416 AAAAACTATA
1 AAAAAATATA
3400426 AAATGAAA-ATA
1 AAA--AAATATA
3400437 AAAAAA
1 AAAAAA
3400443 GAATATGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
9 3 0.07
10 17 0.40
11 11 0.26
12 7 0.17
13 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAAAATATA
Found at i:3400429 original size:33 final size:30
Alignment explanation
Indices: 3400382--3400442 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 30
3400372 TTTTAATTTC
3400382 TAAAAAATAAAAAATGAAATATTAAAAAAATA
1 TAAAAAATAAAAAATGAAA-A-TAAAAAAATA
*
3400414 TAAAAAACTATAAAATGAAAATAAAAAAA
1 TAAAAAA-TAAAAAATGAAAATAAAAAAA
3400443 GAATATGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.30
32 8 0.30
33 11 0.41
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (30 bp):
TAAAAAATAAAAAATGAAAATAAAAAAATA
Found at i:3400448 original size:34 final size:32
Alignment explanation
Indices: 3400382--3400442 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3400372 TTTTAATTTC
*
3400382 TAAAAAATAAAAAATGAAATATTAAAAAAATA
1 TAAAAAATAAAAAATGAAATATAAAAAAAATA
*
3400414 TAAAAAACTATAAAATGAAA-ATAAAAAAA
1 TAAAAAA-TAAAAAATGAAATATAAAAAAA
3400443 GAATATGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (32 bp):
TAAAAAATAAAAAATGAAATATAAAAAAAATA
Found at i:3401217 original size:8 final size:8
Alignment explanation
Indices: 3401193--3401247 Score: 55
Period size: 7 Copynumber: 7.4 Consensus size: 8
3401183 TATGATATTT
3401193 TATAAATA
1 TATAAATA
*
3401201 -ATATA-A
1 TATAAATA
3401207 TATAAATA
1 TATAAATA
3401215 TATAAATA
1 TATAAATA
3401223 TATAAA-A
1 TATAAATA
*
3401230 AATAAAT-
1 TATAAATA
*
3401237 TATTAATA
1 TATAAATA
3401245 TAT
1 TAT
3401248 TTAAATTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
6 1 0.03
7 19 0.50
8 18 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATAAATA
Found at i:3401227 original size:30 final size:33
Alignment explanation
Indices: 3401193--3401265 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 33
3401183 TATGATATTT
3401193 TATAAATAATATAA-TA-TAA-ATATATAAA-TA
1 TATAAATAATA-AATTATTAATATATATAAATTA
* *
3401223 TATAAAAAATAAATTATTAATATATTTAAATTTA
1 TATAAATAATAAATTATTAATATATATAAA-TTA
3401257 TATAAATAA
1 TATAAATAA
3401266 ATTTAATCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 2 0.06
30 12 0.34
31 3 0.09
32 8 0.23
34 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
TATAAATAATAAATTATTAATATATATAAATTA
Found at i:3401574 original size:31 final size:29
Alignment explanation
Indices: 3401524--3401584 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 29
3401514 TATACAATAT
3401524 ATAAATAATAATATAAAAA-TAATATTTTA
1 ATAAATAATAATATAAAAATTAA-ATTTTA
*
3401553 ATAATATAATAAATATTAAAATTAAATTTTA
1 ATAA-ATAAT-AATATAAAAATTAAATTTTA
3401584 A
1 A
3401585 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 5 0.18
31 16 0.57
32 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAAATAATAATATAAAAATTAAATTTTA
Found at i:3402360 original size:18 final size:17
Alignment explanation
Indices: 3402337--3402370 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3402327 GGGTCAAATT
*
3402337 AAAAATTATATTATTTAA
1 AAAAATAATATT-TTTAA
3402355 AAAAATAATATTTTTA
1 AAAAATAATATTTTTA
3402371 TTTAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATAATATTTTTAA
Found at i:3402425 original size:12 final size:12
Alignment explanation
Indices: 3402393--3402436 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3402383 TATAAAATAT
3402393 ATAAATATTAATAA
1 ATAAATATT-A-AA
*
3402407 ATTAATATTAAA
1 ATAAATATTAAA
*
3402419 ATAAATAATAAA
1 ATAAATATTAAA
3402431 ATAAAT
1 ATAAAT
3402437 TTTCAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 18 0.67
13 1 0.04
14 8 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAAATATTAAA
Found at i:3402676 original size:22 final size:23
Alignment explanation
Indices: 3402645--3402745 Score: 59
Period size: 22 Copynumber: 4.4 Consensus size: 23
3402635 ATTTATATAA
3402645 ATTTTA-AT-ATATTAATAATTT
1 ATTTTATATAATATTAATAATTT
* *
3402666 ATTTTATAT-ATTTTAATACGTTT
1 ATTTTATATAATATTAATA-ATTT
* *
3402689 AAATATTTATATAATATTTATTAAATT
1 --AT-TTTATATAATA-TTAATAATTT
* *
3402716 -TTTTATATCATATT-ATATTTT
1 ATTTTATATAATATTAATAATTT
*
3402737 ATATTATAT
1 ATTTTATAT
3402746 TTTATTTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
21 10 0.16
22 19 0.31
23 13 0.21
24 1 0.02
25 2 0.03
26 7 0.11
27 4 0.07
28 5 0.08
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (23 bp):
ATTTTATATAATATTAATAATTT
Found at i:3402737 original size:66 final size:67
Alignment explanation
Indices: 3402593--3402740 Score: 157
Period size: 66 Copynumber: 2.2 Consensus size: 67
3402583 GTATACACAT
* *
3402593 ATATTA-ATTTTTTATATTTTAATTATATTTAAACTATTATATATTTATATAAATTTTAATATAT
1 ATATTATATTTTATATATTTTAATTACATTTAAACTATTATATATTTATATAAATTTTAATATAT
3402657 TA
66 TA
* *
3402659 ATAATT-TATTTTATATATTTTAA-TACGTTTAAA-TATTTATATAATATT-TATTAAATTTT-T
1 AT-ATTATATTTTATATATTTTAATTACATTTAAACTA-TTATAT-AT-TTATA-TAAATTTTAA
*
3402719 TATA-TC
61 TATATTA
3402725 ATATTATATTTTATAT
1 ATATTATATTTTATAT
3402741 TATATTTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
65 5 0.07
66 29 0.41
67 26 0.37
68 10 0.14
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (67 bp):
ATATTATATTTTATATATTTTAATTACATTTAAACTATTATATATTTATATAAATTTTAATATAT
TA
Found at i:3402738 original size:17 final size:17
Alignment explanation
Indices: 3402716--3402753 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3402706 TTATTAAATT
3402716 TTTTATATCATATTATA
1 TTTTATATCATATTATA
* *
3402733 TTTTATATTATATTTTA
1 TTTTATATCATATTATA
3402750 TTTT
1 TTTT
3402754 TTTAATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATCATATTATA
Found at i:3402740 original size:12 final size:12
Alignment explanation
Indices: 3402725--3402750 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3402715 TTTTTATATC
3402725 ATATTATATTTT
1 ATATTATATTTT
3402737 ATATTATATTTT
1 ATATTATATTTT
3402749 AT
1 AT
3402751 TTTTTTAATG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:3402751 original size:22 final size:22
Alignment explanation
Indices: 3402592--3402767 Score: 64
Period size: 20 Copynumber: 8.5 Consensus size: 22
3402582 CGTATACACA
3402592 TATATTA-ATTTT-TTATATTT
1 TATATTATATTTTATTATATTT
3402612 TA-ATTATATTTAAACTATTATATATT
1 TATATTATATTT----TATTATAT-TT
* *
3402638 TATA-TAAATTTTAATATA-TT
1 TATATTATATTTTATTATATTT
*
3402658 AATAATT-TATTTTA-TATATTT
1 TAT-ATTATATTTTATTATATTT
** *
3402679 TA-A-TA-CGTTTA-AATA-TT
1 TATATTATATTTTATTATATTT
* *
3402696 TATATAATA-TTTATTA-AATT
1 TATATTATATTTTATTATATTT
**
3402716 T-T-TTATATCATATTATATTT
1 TATATTATATTTTATTATATTT
3402736 TATATTATATTTTATT-T-TTT
1 TATATTATATTTTATTATATTT
*
3402756 TAATGTTATATT
1 T-ATATTATATT
3402768 ATGTTCTGCA
Statistics
Matches: 116, Mismatches: 18, Indels: 43
0.66 0.10 0.24
Matches are distributed among these distances:
17 4 0.03
18 13 0.11
19 17 0.15
20 26 0.22
21 21 0.18
22 17 0.15
24 1 0.01
25 6 0.05
26 10 0.09
27 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (22 bp):
TATATTATATTTTATTATATTT
Found at i:3404897 original size:53 final size:53
Alignment explanation
Indices: 3404796--3404899 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
3404786 TCATTTCGGG
* * * * *
3404796 TTCAAATCATTTTAAGTTTGAGTTAATTAAGTTTAACTGTTGAATTAATCAGA
1 TTCAAATCATTATAAGTTTGAGTCAATTAAATTTAACTATTCAATTAATCAGA
3404849 TTCAAATCATTAT-AGATTTGAGTCAATTAAATTTAA-TATTCAAGTTAATCA
1 TTCAAATCATTATAAG-TTTGAGTCAATTAAATTTAACTATTCAA-TTAATCA
3404900 ATTAGATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
52 7 0.16
53 37 0.84
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (53 bp):
TTCAAATCATTATAAGTTTGAGTCAATTAAATTTAACTATTCAATTAATCAGA
Found at i:3404900 original size:26 final size:26
Alignment explanation
Indices: 3404871--3404920 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3404861 TAGATTTGAG
*
3404871 TCAATTAAATTTAATATTCAAGTTAA
1 TCAATTAAATTTAATACTCAAGTTAA
*
3404897 TCAATTAGATTTAATACTCAAGTT
1 TCAATTAAATTTAATACTCAAGTT
3404921 TATTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (26 bp):
TCAATTAAATTTAATACTCAAGTTAA
Found at i:3405271 original size:17 final size:16
Alignment explanation
Indices: 3405222--3405271 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
3405212 TTAACTATTC
*
3405222 ATTATATATTTAAAAT
1 ATTATATATTTATAAT
3405238 ATTATTATTATTT-TAAT
1 ATTA-TA-TATTTATAAT
3405255 ATTTATATATTTATAAT
1 A-TTATATATTTATAAT
3405272 TAAATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 9 0.31
17 12 0.41
18 8 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATATATTTATAAT
Found at i:3407262 original size:16 final size:16
Alignment explanation
Indices: 3407241--3407271 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3407231 TTGTATATTG
3407241 AAAAGTAGGGAAAATA
1 AAAAGTAGGGAAAATA
3407257 AAAAGTAGGGAAAAT
1 AAAAGTAGGGAAAAT
3407272 CTTACCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (16 bp):
AAAAGTAGGGAAAATA
Found at i:3411684 original size:22 final size:23
Alignment explanation
Indices: 3411659--3411703 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3411649 TTTTTATTAT
3411659 AATAAAATAGA-AAAATT-ATTTA
1 AATAAAATA-ATAAAATTCATTTA
3411681 AATAAAATAATAAAATTCATTTA
1 AATAAAATAATAAAATTCATTTA
3411704 TTTTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 15 0.71
23 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAAATAATAAAATTCATTTA
Found at i:3411983 original size:24 final size:24
Alignment explanation
Indices: 3411956--3412021 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
3411946 AAATTCAAAG
3411956 TAATATTAAAATTAATTATTATAA
1 TAATATTAAAATTAATTATTATAA
* * * *
3411980 TAATAGTGAAATTAAATATTATAT
1 TAATATTAAAATTAATTATTATAA
*
3412004 TAATTATATTAAATTAAT
1 TAA-TAT-TAAAATTAAT
3412022 AATGCGATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
24 23 0.70
25 2 0.06
26 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
TAATATTAAAATTAATTATTATAA
Found at i:3412110 original size:30 final size:30
Alignment explanation
Indices: 3412076--3412132 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3412066 AATCTATTAA
3412076 TATTTTTA-ATATAAAAATATATTAATAAAT
1 TATTTTTATATATAAAAATAT-TTAATAAAT
*
3412106 TATTTTTATATATAATAATATTTAATA
1 TATTTTTATATATAAAAATATTTAATA
3412133 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTTATATATAAAAATATTTAATAAAT
Found at i:3412520 original size:16 final size:18
Alignment explanation
Indices: 3412501--3412567 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
3412491 ATTAAAAATG
3412501 ATTAATTATAA-AATT-A
1 ATTAATTATAATAATTAA
3412517 ATT-ATTATAATAATTAA
1 ATTAATTATAATAATTAA
* *
3412534 ATTAA-AATAAATATTTAA
1 ATTAATTAT-AATAATTAA
*
3412552 ATTTAATCATAATAAT
1 A-TTAATTATAATAAT
3412568 ATATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.17
16 7 0.17
17 6 0.15
18 10 0.24
19 9 0.22
20 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATTATAATAATTAA
Found at i:3412669 original size:19 final size:20
Alignment explanation
Indices: 3412645--3412704 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
3412635 TATATATGAT
3412645 AAATAATTTATAATTAT-TA
1 AAATAATTTATAATTATATA
* * *
3412664 AAATAAATTATATTTATATT
1 AAATAATTTATAATTATATA
*
3412684 AAATAATAATTAAAATTATAT
1 AAATAAT--TTATAATTATAT
3412705 TTATATTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.47
20 7 0.22
22 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATTTATAATTATATA
Found at i:3412690 original size:32 final size:31
Alignment explanation
Indices: 3412650--3412723 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
3412640 ATGATAAATA
3412650 ATTT-ATAATTATTAAAA-TAAA-TTATATTT
1 ATTTAATAATTATTAAAATTAAATTTATA-TT
* *
3412679 ATATTAAATAATAATTAAAATTATATTTATATT
1 AT-TT-AATAATTATTAAAATTAAATTTATATT
3412712 ATTTAATAATTA
1 ATTTAATAATTA
3412724 AATATTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 2 0.05
30 2 0.05
31 7 0.19
32 14 0.38
33 7 0.19
34 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTTAATAATTATTAAAATTAAATTTATATT
Found at i:3412702 original size:28 final size:28
Alignment explanation
Indices: 3412668--3412772 Score: 130
Period size: 28 Copynumber: 3.9 Consensus size: 28
3412658 TTATTAAAAT
3412668 AAATTATATTTATATTAAATAATAATTA
1 AAATTATATTTATATTAAATAATAATTA
**
3412696 AAATTATATTTATATTATTTAATAATT-
1 AAATTATATTTATATTAAATAATAATTA
*
3412723 AAA-TAT-TTTATA--AAATAAATTATTA
1 AAATTATATTTATATTAAAT-AATAATTA
*
3412748 AAACTATATTTATATTAAATAATAA
1 AAATTATATTTATATTAAATAATAA
3412773 AAAACCTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
23 2 0.03
24 6 0.09
25 9 0.14
26 6 0.09
27 9 0.14
28 29 0.45
29 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATTATATTTATATTAAATAATAATTA
Found at i:3412771 original size:52 final size:52
Alignment explanation
Indices: 3412673--3412772 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
3412663 AAAATAAATT
* * **
3412673 ATATTTATATTAAATAATAATTAAAATTATATTTATATTATTTAATAATTAA
1 ATATTTATATAAAATAATAATTAAAACTATATTTATATTAAATAATAATTAA
*
3412725 ATATTT-TATAAAATAAATTATTAAAACTATATTTATATTAAATAATAA
1 ATATTTATATAAAAT-AATAATTAAAACTATATTTATATTAAATAATAA
3412773 AAAACCTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 7 0.17
52 35 0.83
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (52 bp):
ATATTTATATAAAATAATAATTAAAACTATATTTATATTAAATAATAATTAA
Found at i:3412801 original size:17 final size:17
Alignment explanation
Indices: 3412757--3412848 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
3412747 AAAACTATAT
3412757 TTATATTAAATAATAAA
1 TTATATTAAATAATAAA
** *
3412774 AAACCTATTAAATATTAAA
1 TTA--TATTAAATAATAAA
3412793 TTATATTAAATAATAAA
1 TTATATTAAATAATAAA
3412810 -T-TA--AAATAAT--A
1 TTATATTAAATAATAAA
3412821 TTATATTAAA-AATAAA
1 TTATATTAAATAATAAA
*
3412837 TTA-ATAAAATAA
1 TTATATTAAATAA
3412849 ATATAAAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 9 0.15
14 3 0.05
15 10 0.17
16 7 0.12
17 14 0.24
19 14 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TTATATTAAATAATAAA
Found at i:3412818 original size:13 final size:12
Alignment explanation
Indices: 3412797--3412879 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 12
3412787 ATTAAATTAT
*
3412797 ATTAAATAATAA
1 ATTAAAAAATAA
3412809 ATTAAAATAATATTA
1 ATTAAAA-AATA--A
3412824 TATT-AAAAATAA
1 -ATTAAAAAATAA
3412836 ATTAATAAAATAA
1 ATTAA-AAAATAA
* *
3412849 A-TATAAAA-AC
1 ATTAAAAAATAA
*
3412859 ATTTAAAAAT-A
1 ATTAAAAAATAA
3412870 ATTAAAAAAT
1 ATTAAAAAAT
3412880 TAAAGGAGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
10 2 0.04
11 21 0.38
12 10 0.18
13 12 0.21
14 4 0.07
15 4 0.07
16 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAAAAAATAA
Found at i:3412834 original size:30 final size:28
Alignment explanation
Indices: 3412792--3412848 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
3412782 TAAATATTAA
3412792 ATTATATTAAAT-AATAAATTAAAATAAT
1 ATTATATTAAATAAATAAA-TAAAATAAT
*
3412820 ATTATATTAAAAATAAATTAATAAAATAA
1 ATTATATT--AAATAAATAAATAAAATAA
3412849 ATATAAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATTATATTAAATAAATAAATAAAATAAT
Found at i:3412836 original size:22 final size:22
Alignment explanation
Indices: 3412779--3412842 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
3412769 ATAAAAAACC
* * *
3412779 TATTAAATATTAAATTATATTA
1 TATTAAAAATAAAATAATATTA
*
3412801 -AATAATAAATTAAAATAATATTA
1 TATTAA-AAA-TAAAATAATATTA
*
3412824 TATTAAAAATAAATTAATA
1 TATTAAAAATAAAATAATA
3412843 AAATAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 4 0.12
22 11 0.33
23 14 0.42
24 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTAAAAATAAAATAATATTA
Found at i:3412844 original size:14 final size:15
Alignment explanation
Indices: 3412779--3412850 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 15
3412769 ATAAAAAACC
3412779 TATTAAATATTAAATTA
1 TATTAAA-A-TAAATTA
3412796 TATT-AAAT-AA-TA
1 TATTAAAATAAATTA
*
3412808 AATTAAAATAATATTA
1 TATTAAAATAA-ATTA
3412824 TATTAAAAATAAATTA
1 TATT-AAAATAAATTA
3412840 -A-TAAAATAAAT
1 TATTAAAATAAAT
3412851 ATAAAAACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
12 5 0.10
13 15 0.31
14 3 0.06
15 3 0.06
16 11 0.23
17 11 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAAATAAATTA
Found at i:3414692 original size:19 final size:18
Alignment explanation
Indices: 3414665--3414716 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
3414655 AAATTTATGT
*
3414665 AAAT-ATATAATATTTAA
1 AAATAATATAATATATAA
*
3414682 ATATAATTATAATATATAA
1 AAATAA-TATAATATATAA
3414701 AAATAATATAA-ATATA
1 AAATAATATAATATATA
3414717 CGAATTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.27
18 6 0.20
19 16 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATATAATATATAA
Found at i:3414694 original size:6 final size:7
Alignment explanation
Indices: 3414628--3414716 Score: 59
Period size: 6 Copynumber: 13.6 Consensus size: 7
3414618 TATTAACTTT
3414628 TATATAA
1 TATATAA
3414635 TATA-AA
1 TATATAA
3414641 T-TATTAA
1 TATA-TAA
3414648 TATAATAA
1 TAT-ATAA
* *
3414656 AAT-TTA
1 TATATAA
*
3414662 TGTA-AA
1 TATATAA
3414668 TATATAA
1 TATATAA
*
3414675 TATTTAA
1 TATATAA
3414682 -ATATAA
1 TATATAA
3414688 T-TATAA
1 TATATAA
3414694 TATATAA
1 TATATAA
*
3414701 -AAATAA
1 TATATAA
3414707 TATA-AA
1 TATATAA
3414713 TATA
1 TATA
3414717 CGAATTAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
5 2 0.03
6 32 0.51
7 22 0.35
8 6 0.10
9 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:3414942 original size:2 final size:2
Alignment explanation
Indices: 3414935--3414969 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3414925 TCTCTTTATT
3414935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3414970 CACTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3415440 original size:2 final size:2
Alignment explanation
Indices: 3415433--3415475 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3415423 TATCAAATGA
3415433 AT 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 AT
3415475 A
1 A
3415476 ATAAAAATTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3415941 original size:28 final size:26
Alignment explanation
Indices: 3415910--3415976 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 26
3415900 TTTGAGTTTG
*
3415910 ATTTAATTACTATTTAATTAATAAAAAT
1 ATTTAATTA-AATTTAA-TAATAAAAAT
*
3415938 ATTTTTATTTAAATTTAATAATAAAAAT
1 A--TTTAATTAAATTTAATAATAAAAAT
3415966 A-TTAATATAAA
1 ATTTAAT-TAAA
3415977 AAAATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
25 4 0.12
26 4 0.12
28 12 0.36
29 6 0.18
30 7 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAATTAAATTTAATAATAAAAAT
Found at i:3415972 original size:15 final size:16
Alignment explanation
Indices: 3415948--3415984 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3415938 ATTTTTATTT
*
3415948 AAAT-TTAATA-ATAA
1 AAATATTAATATAAAA
3415962 AAATATTAATATAAAA
1 AAATATTAATATAAAA
3415978 AAATATT
1 AAATATT
3415985 TTAAACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTAATATAAAA
Found at i:3416501 original size:3 final size:3
Alignment explanation
Indices: 3416493--3416517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3416483 TTCAATTAAC
3416493 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3416518 ATGTATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3416638 original size:22 final size:23
Alignment explanation
Indices: 3416611--3416660 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
3416601 TATATTTAAT
3416611 TTATTAAAATGA-AATAAAATAA
1 TTATTAAAATGAGAATAAAATAA
*
3416633 TTATT-ATATGAGAATAAAATAA
1 TTATTAAAATGAGAATAAAATAA
3416655 TT-TTAA
1 TTATTAA
3416661 TAATAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (23 bp):
TTATTAAAATGAGAATAAAATAA
Found at i:3416990 original size:23 final size:24
Alignment explanation
Indices: 3416952--3416997 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3416942 TCTGAATTGT
*
3416952 TTTAATATTATTTTATTTTATATAC
1 TTTAATA-TATTTTATATTATATAC
3416977 TTTAATA-ATTTTATATTATAT
1 TTTAATATATTTTATATTATAT
3416998 TCATATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
25 7 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAATATATTTTATATTATATAC
Found at i:3418026 original size:17 final size:17
Alignment explanation
Indices: 3418006--3418053 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3417996 TACACACTAA
3418006 AAAATTATATATATAAT
1 AAAATTATATATATAAT
3418023 AAAATTATAT-TCATGAAT
1 AAAATTATATAT-AT-AAT
3418041 -AAATTATA-ATATA
1 AAAATTATATATATA
3418054 TCATTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 21 0.75
18 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATTATATATATAAT
Found at i:3418750 original size:24 final size:25
Alignment explanation
Indices: 3418704--3418758 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
3418694 ACAAATTCAA
*
3418704 ATATTTGAATTCGATGTTTATTTAT
1 ATATTTGAATTCGATATTTATTTAT
*
3418729 ATATTT-AATTC-ATATTTGATTTTT
1 ATATTTGAATTCGATATTT-ATTTAT
3418753 ATATTT
1 ATATTT
3418759 TATCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 16 0.59
25 6 0.22
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (25 bp):
ATATTTGAATTCGATATTTATTTAT
Found at i:3418892 original size:24 final size:26
Alignment explanation
Indices: 3418865--3418917 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
3418855 ATATTTAAAT
*
3418865 AATAATGA-ATAA-TAAATTAATTTA
1 AATAATGATATAATTAAATAAATTTA
*
3418889 AAT-ATTATATAATTAAATAAATTTA
1 AATAATGATATAATTAAATAAATTTA
3418914 AATA
1 AATA
3418918 TTATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 3 0.12
24 7 0.29
25 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAATGATATAATTAAATAAATTTA
Found at i:3418911 original size:25 final size:24
Alignment explanation
Indices: 3418873--3418922 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
3418863 ATAATAATGA
*
3418873 ATAATAAATTAATTTAAATATTAT
1 ATAATAAATAAATTTAAATATTAT
3418897 ATAATTAAATAAATTTAAATATTAT
1 ATAA-TAAATAAATTTAAATATTAT
3418922 A
1 A
3418923 AAAATTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATAAATAAATTTAAATATTAT
Found at i:3423641 original size:22 final size:23
Alignment explanation
Indices: 3423611--3423665 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
3423601 TCCACTAATA
*
3423611 AAATAATAA-AAATTTTTAAATT
1 AAATAATAATAAATTTATAAATT
*
3423633 AAATTATAATAAATTTATAAA-T
1 AAATAATAATAAATTTATAAATT
3423655 AAA-AATAATAA
1 AAATAATAATAA
3423666 TTAAAAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATAATAATAAATTTATAAATT
Found at i:3423646 original size:23 final size:22
Alignment explanation
Indices: 3423611--3423665 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
3423601 TCCACTAATA
*
3423611 AAATAATAAAAATTTTTAAATT
1 AAATAATAAAAATTTATAAATT
* *
3423633 AAATTATAATAAATTTATAAATAA
1 AAATAATAA-AAATTTATAAAT-T
3423657 AAATAATAA
1 AAATAATAA
3423666 TTAAAAGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
23 11 0.41
24 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAATAAAAATTTATAAATT
Found at i:3429297 original size:20 final size:22
Alignment explanation
Indices: 3429268--3429307 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3429258 AAAATTTAAA
3429268 TATAATAATTAAAT-ATTTTTT
1 TATAATAATTAAATAATTTTTT
3429289 TATAA-AATTAAATAATTTT
1 TATAATAATTAAATAATTTT
3429308 AGAATCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAATAATTAAATAATTTTTT
Found at i:3435567 original size:6 final size:6
Alignment explanation
Indices: 3435558--3435604 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
3435548 TAATTTTAAA
* *
3435558 AAATTT AAATTT AAATTT AAATTT AAGTAT AAATAATT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT--TT AAATTT AAA
3435605 ATAAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 30 0.86
8 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (6 bp):
AAATTT
Found at i:3435680 original size:14 final size:14
Alignment explanation
Indices: 3435637--3435672 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3435627 TTCTTTTATG
*
3435637 TTAAAAAAATAAAT
1 TTAAATAAATAAAT
*
3435651 TTAATTAAATAAAT
1 TTAAATAAATAAAT
3435665 TTAAATAA
1 TTAAATAA
3435673 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAATAAATAAAT
Found at i:3438322 original size:285 final size:285
Alignment explanation
Indices: 3437812--3438376 Score: 1085
Period size: 285 Copynumber: 2.0 Consensus size: 285
3437802 ATTTTAATCT
3437812 AAAAATCCGTAAATCATGTAAAATACCAATCTCCACTCACAATACATTACTTCAAATAGTCCAAA
1 AAAAATCCGTAAATCATGTAAAATACCAATCTCCACTCACAATACATTACTTCAAATAGTCCAAA
3437877 TAGAAATACAAAAATCAAATAACAAGGAAATGAGTACTACATTTTAACCCAGGAAAACCAGGAAC
66 TAGAAATACAAAAATCAAATAACAAGGAAATGAGTACTACATTTTAACCCAGGAAAACCAGGAAC
3437942 TAGAAATACATCACTTCAAATAATGGCTATTCATCCTAATATCTCAACACCCAGAAATACACAAA
131 TAGAAATACATCACTTCAAATAATGGCTATTCATCCTAATATCTCAACACCCAGAAATACACAAA
3438007 CTTTAAGGAAAGTATTAAAGAAAGCTATGAAAATAGTGAAAAAAAAAATTCACCCCAAATTTTCA
196 CTTTAAGGAAAGTATTAAAGAAAGCTATGAAAATAGTGAAAAAAAAAATTCACCCCAAATTTTCA
*
3438072 ATTTTGATCTAGATATGTGATTTAC
261 ATTTTGATCTAGATACGTGATTTAC
* *
3438097 AAAAATCTGTAAATCATGTAAAATACCAATCTCCACTCACAATACATTACTTCAAATAGTCCAAC
1 AAAAATCCGTAAATCATGTAAAATACCAATCTCCACTCACAATACATTACTTCAAATAGTCCAAA
3438162 TAGAAATACAAAAATCAAATAACAAGGAAATGAGTACTACATTTTAACCCAGGAAAACCAGGAAC
66 TAGAAATACAAAAATCAAATAACAAGGAAATGAGTACTACATTTTAACCCAGGAAAACCAGGAAC
3438227 TAGAAATACATCACTTCAAATAATGGCTATTCATCCTAATATCTCAACACCCAGAAATACACAAA
131 TAGAAATACATCACTTCAAATAATGGCTATTCATCCTAATATCTCAACACCCAGAAATACACAAA
* *
3438292 CTTTAAGGAAAGTATTAGAGAAAGCTATGAACATAGTGAAAAAAAAAATTCACCCCAAATTTTCA
196 CTTTAAGGAAAGTATTAAAGAAAGCTATGAAAATAGTGAAAAAAAAAATTCACCCCAAATTTTCA
3438357 ATTTTGATCTAGATACGTGA
261 ATTTTGATCTAGATACGTGA
3438377 AGAAACAAAA
Statistics
Matches: 275, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
285 275 1.00
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (285 bp):
AAAAATCCGTAAATCATGTAAAATACCAATCTCCACTCACAATACATTACTTCAAATAGTCCAAA
TAGAAATACAAAAATCAAATAACAAGGAAATGAGTACTACATTTTAACCCAGGAAAACCAGGAAC
TAGAAATACATCACTTCAAATAATGGCTATTCATCCTAATATCTCAACACCCAGAAATACACAAA
CTTTAAGGAAAGTATTAAAGAAAGCTATGAAAATAGTGAAAAAAAAAATTCACCCCAAATTTTCA
ATTTTGATCTAGATACGTGATTTAC
Found at i:3439762 original size:206 final size:203
Alignment explanation
Indices: 3439358--3439772 Score: 629
Period size: 206 Copynumber: 2.0 Consensus size: 203
3439348 TGGCGGCATG
* *
3439358 GCCTACTCCTCCGTCATGGATCACATCCTTTCCTCCTCTTCAGCTTTTTTCCAAGCAGCCTGAAA
1 GCCTCCTCCGCCGTCATGGATCACATCCTTTCCTCCTCTTCAGCTTTTTTCCAAGCAGCCTGAAA
* * * * *
3439423 AGGAAAGAACCAACAAATTCATTAGAATTTGTGCTTAAGGAAAACTAATAAAAGTATTCATGTAA
66 AGGAAAGAACCAACAAACTAATTAGAATATGTACTTAAGGAAAACTAATAAAAGTATTCAAGTAA
* *
3439488 TTAGTTGAGAGAAACTTGCCTTTTCTCGTTCAAGTCTGGAGAAATGTGGCTTGTTGGAGTTTCCT
131 TTAGCTGAGAGAAACTTGCCTTTTCTCGTTCAAGTCTGGAGAAATGTGGCTTGATGGAGTTTCCT
3439553 AAGCTTAA
196 AAGCTTAA
**
3439561 GCCTCCTCCGCCGTCATGGATTGCATCCTTTCCTCCTCTTCAGCTTTTTTCCAAGCAGCCTGGAA
1 GCCTCCTCCGCCGTCATGGATCACATCCTTTCCTCCTCTTCAGCTTTTTTCCAAGCAGCCT-GAA
*
3439626 AA-GAAAGAACCAACAAACTAATTAGAATATGTAAAACTTCAGGAAAACTAA-ATAAAGTATTCA
65 AAGGAAAGAACCAACAAACTAATTAGAATATGT---ACTTAAGGAAAACTAATA-AAAGTATTCA
* *
3439689 AGTAATTTGCTGAGAGGAACTTG-CTTTGTCTCGTTCAAGTCTGGAGAAATGTGGCTTGATGGAG
126 AGTAATTAGCTGAGAGAAACTTGCCTTT-TCTCGTTCAAGTCTGGAGAAATGTGGCTTGATGGAG
3439753 TTTCCTAAGCTTAA
190 TTTCCTAAGCTTAA
3439767 GCCTCC
1 GCCTCC
3439773 CCATGCTTCC
Statistics
Matches: 192, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
203 84 0.44
204 5 0.03
205 5 0.03
206 98 0.51
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (203 bp):
GCCTCCTCCGCCGTCATGGATCACATCCTTTCCTCCTCTTCAGCTTTTTTCCAAGCAGCCTGAAA
AGGAAAGAACCAACAAACTAATTAGAATATGTACTTAAGGAAAACTAATAAAAGTATTCAAGTAA
TTAGCTGAGAGAAACTTGCCTTTTCTCGTTCAAGTCTGGAGAAATGTGGCTTGATGGAGTTTCCT
AAGCTTAA
Found at i:3440760 original size:174 final size:174
Alignment explanation
Indices: 3440454--3440804 Score: 512
Period size: 174 Copynumber: 2.0 Consensus size: 174
3440444 TGCCATTGAG
* * *
3440454 CTCATATGTGTTACCATAATTCCTTTTTGCTTCTAGAATTTCCTTTTCAAGTTTTGATGGATGCT
1 CTCATATGTGTTACCAAAATTCCTTTTTGCCTCTAGAATTTCCTTTTCAAGTGTTGATGGATGCT
* * *
3440519 TAACCAATATGCTTCCCAAGTCAGGTATGACCTCAACAGAAGATTCTTCTTCTAACTTTTTATGG
66 TAACCAATATACTTCCCAAGTCAGGTATGACCTCAACAGAAGATTCTTCATCTAACTTTTCATGG
*
3440584 TCCACTCCAGAATTCTCTTTAAAATTTTTTTCTTCCTT-CTGAAT
131 TCCACTCCAGAATTCTCTTTAAAATTTTCTTCTT-CTTCCTGAAT
*
3440628 CTCATATGTGTTACCAAAATTCCTTTTTGCCTCTTGAATTTCCTTTTCAAGTGTTGAT-GAGTGC
1 CTCATATGTGTTACCAAAATTCCTTTTTGCCTCTAGAATTTCCTTTTCAAGTGTTGATGGA-TGC
* * * *
3440692 TTAACCAATATATTTCCGAAGTCAAGG-ATGGCCTCAACAGAAG-TATCTTCATCTGACTTTTCA
65 TTAACCAATATACTTCCCAAGTC-AGGTATGACCTCAACAGAAGAT-TCTTCATCTAACTTTTCA
* *
3440755 TGGTCCACTCCAGAATTCTCTTTGAAATTTTCTTCTTTTTCCTGAAT
128 TGGTCCACTCCAGAATTCTCTTTAAAATTTTCTTCTTCTTCCTGAAT
3440802 CTC
1 CTC
3440805 TTCCTCAAGA
Statistics
Matches: 159, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
173 5 0.03
174 151 0.95
175 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (174 bp):
CTCATATGTGTTACCAAAATTCCTTTTTGCCTCTAGAATTTCCTTTTCAAGTGTTGATGGATGCT
TAACCAATATACTTCCCAAGTCAGGTATGACCTCAACAGAAGATTCTTCATCTAACTTTTCATGG
TCCACTCCAGAATTCTCTTTAAAATTTTCTTCTTCTTCCTGAAT
Found at i:3444142 original size:15 final size:15
Alignment explanation
Indices: 3444091--3444160 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
3444081 TATTTTATAT
*
3444091 TTATATTATATAAT-
1 TTATAATATATAATA
*
3444105 TTAT-ATCATATAAAA
1 TTATAAT-ATATAATA
* *
3444120 ATAAAATATATAATA
1 TTATAATATATAATA
3444135 TTATAATATGA-AATA
1 TTATAATAT-ATAATA
*
3444150 TTAAAATATAT
1 TTATAATATAT
3444161 TAAATTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.02
14 11 0.26
15 28 0.65
16 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
TTATAATATATAATA
Found at i:3444196 original size:20 final size:21
Alignment explanation
Indices: 3444171--3444218 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
3444161 TAAATTTTTT
**
3444171 ATATTTTAAA-ATTTAATAAA
1 ATATTTTAAATATAAAATAAA
*
3444191 ATA-TTTAAATATAAAATAAT
1 ATATTTTAAATATAAAATAAA
3444211 ATATTTTA
1 ATATTTTA
3444219 TTTTTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTTTAAATATAAAATAAA
Found at i:3445531 original size:2 final size:2
Alignment explanation
Indices: 3445524--3445548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3445514 ACTGATCAGA
3445524 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 A
3445549 ATGCCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3449792 original size:14 final size:15
Alignment explanation
Indices: 3449762--3449794 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3449752 TATATTATTT
*
3449762 TTTATAATAATTATA
1 TTTAAAATAATTATA
3449777 TTTAAAATAA-TATA
1 TTTAAAATAATTATA
3449791 TTTA
1 TTTA
3449795 TATAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAAATAATTATA
Found at i:3449824 original size:24 final size:24
Alignment explanation
Indices: 3449782--3449866 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 24
3449772 TTATATTTAA
*
3449782 AATAATATAT-TTATATAAAGT-TT
1 AATAATTTATATTATATAAA-TATT
3449805 AATAATTTATATTATATAAATATT
1 AATAATTTATATTATATAAATATT
*
3449829 AATATATTAATATATT-TATATTATATT
1 AATA-ATT--TATATTATATA-AATATT
*
3449856 TAT-ATTTATAT
1 AATAATTTATAT
3449867 ATTTTATATT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
23 15 0.28
24 15 0.28
25 6 0.11
26 4 0.08
27 13 0.25
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
AATAATTTATATTATATAAATATT
Found at i:3449848 original size:14 final size:13
Alignment explanation
Indices: 3449762--3449905 Score: 77
Period size: 14 Copynumber: 10.8 Consensus size: 13
3449752 TATATTATTT
3449762 TTTATAATAATTATA
1 TTTAT-ATAA-TATA
*
3449777 TTTAAAATAATATA
1 TTT-ATATAATATA
*
3449791 TTTATATAA-A-G
1 TTTATATAATATA
*
3449802 TTTA-ATAATTTA
1 TTTATATAATATA
3449814 TATTATATAA-ATA
1 T-TTATATAATATA
3449827 TTAATATATTAATATA
1 TT--TATA-TAATATA
3449843 TTTATAT--TATA
1 TTTATATAATATA
*
3449854 TTTATATTTATATA
1 TTTATA-TAATATA
* *
3449868 TTT-TATATTATTT
1 TTTATATAATA-TA
*
3449881 TTTATATCATATTTA
1 TTTATAT-A-ATATA
3449896 TTTATATAAT
1 TTTATATAAT
3449906 TAACTTATAC
Statistics
Matches: 101, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
10 4 0.04
11 14 0.14
12 7 0.07
13 20 0.20
14 30 0.30
15 19 0.19
16 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (13 bp):
TTTATATAATATA
Found at i:3449851 original size:33 final size:32
Alignment explanation
Indices: 3449803--3449869 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
3449793 TATATAAAGT
3449803 TTAATAATTTATATTATATAAATATTAATATA
1 TTAATAATTTATATTATATAAATATTAATATA
** *
3449835 TTAATATATTTATATTATATTTATATTTATATA
1 TTAATA-ATTTATATTATATAAATATTAATATA
3449868 TT
1 TT
3449870 TTATATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TTAATAATTTATATTATATAAATATTAATATA
Found at i:3449861 original size:17 final size:17
Alignment explanation
Indices: 3449787--3449902 Score: 68
Period size: 17 Copynumber: 6.9 Consensus size: 17
3449777 TTTAAAATAA
*
3449787 TATATTTATA-TAAAGTT
1 TATATTTATATTATA-TT
*
3449804 TAATAATTTATATTATATA
1 T-AT-ATTTATATTATATT
*
3449823 AATA-TTA-A-TATATT
1 TATATTTATATTATATT
3449837 AATATATTTATATTATATT
1 --TATATTTATATTATATT
3449856 TATATTTATA-TAT-TT
1 TATATTTATATTATATT
* *
3449871 TATA-TTATTTTTTATAT
1 TATATTTATATTATAT-T
*
3449888 CATATTTAT-TTATAT
1 TATATTTATATTATAT
3449903 AATTAACTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
14 9 0.12
15 9 0.12
16 10 0.13
17 24 0.31
18 9 0.12
19 14 0.18
20 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
TATATTTATATTATATT
Found at i:3449867 original size:8 final size:8
Alignment explanation
Indices: 3449786--3449876 Score: 62
Period size: 8 Copynumber: 10.9 Consensus size: 8
3449776 ATTTAAAATA
3449786 ATATATTT
1 ATATATTT
3449794 ATATAAAGTTT
1 ATAT--A-TTT
3449805 A-ATAATTT
1 ATAT-ATTT
*
3449813 ATATTATAT
1 ATA-TATTT
* *
3449822 AAATATTA
1 ATATATTT
*
3449830 ATATATTA
1 ATATATTT
3449838 ATATATTT
1 ATATATTT
3449846 ATATTATATT
1 ATA-TAT-TT
3449856 -TATATTT
1 ATATATTT
3449863 ATATATTT
1 ATATATTT
3449871 -TATATT
1 ATATATT
3449877 ATTTTTTATA
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
7 8 0.12
8 38 0.55
9 13 0.19
10 6 0.09
11 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (8 bp):
ATATATTT
Found at i:3450374 original size:39 final size:41
Alignment explanation
Indices: 3450342--3450439 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 41
3450332 AATTGTTTAT
3450342 ATTATTAA-T-TTA-TATTTTAACATAAATATAATTTTAATA
1 ATTATTAATTATTATTA-TTTAACATAAATATAATTTTAATA
* *
3450381 ATTTTTAATTATTATTATTTAATATAAATATAA-TTTAATA
1 ATTATTAATTATTATTATTTAACATAAATATAATTTTAATA
* * *
3450421 TTTTTTAATTGATTGTTAT
1 ATTATTAATT-ATTATTAT
3450440 ATACACATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
39 7 0.14
40 17 0.33
41 25 0.49
42 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (41 bp):
ATTATTAATTATTATTATTTAACATAAATATAATTTTAATA
Found at i:3450429 original size:40 final size:42
Alignment explanation
Indices: 3450357--3450439 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
3450347 TAATTTATAT
3450357 TTTAACATAAATATAATTTTAATAATTTTTAATT-ATTATTA
1 TTTAACATAAATATAATTTTAATAATTTTTAATTGATTATTA
* * *
3450398 TTTAATATAAATATAA-TTTAATATTTTTTAATTGATTGTTA
1 TTTAACATAAATATAATTTTAATAATTTTTAATTGATTATTA
3450439 T
1 T
3450440 ATACACATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 16 0.42
41 22 0.58
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (42 bp):
TTTAACATAAATATAATTTTAATAATTTTTAATTGATTATTA
Found at i:3454550 original size:21 final size:22
Alignment explanation
Indices: 3454517--3454580 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
3454507 TTATCGTTTT
3454517 ATAATT-ATATTTAA-AATATT-
1 ATAATTAATATTTAATAA-ATTA
3454537 ATATATTAAT-TTTAATAAATTA
1 ATA-ATTAATATTTAATAAATTA
3454559 ATAATTAATATTTATATAAATT
1 ATAATTAATATTTA-ATAAATT
3454581 TAAAATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.08
21 17 0.45
22 11 0.29
23 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTAATATTTAATAAATTA
Found at i:3454648 original size:25 final size:25
Alignment explanation
Indices: 3454592--3454648 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3454582 AAAATATATA
* *
3454592 TTAT-TATATTATATTTTTATTATT
1 TTATATATATTATATTTTTATCAAT
*
3454616 TTATATATATTATTTTTTTATCACAT
1 TTATATATATTATATTTTTATCA-AT
3454642 TTA-ATAT
1 TTATATAT
3454649 TAGTCGGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATATATATTATATTTTTATCAAT
Found at i:3456164 original size:20 final size:21
Alignment explanation
Indices: 3456134--3456172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3456124 AATAAGTTGA
*
3456134 ATTTAAAATTTAAATTTAATT
1 ATTTAAAATTTAAAATTAATT
3456155 ATTT-AAATTTAAAATTAA
1 ATTTAAAATTTAAAATTAA
3456173 AAAATTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAAAATTTAAAATTAATT
Found at i:3456786 original size:21 final size:20
Alignment explanation
Indices: 3456749--3456792 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3456739 TTTTTGTTAA
* * *
3456749 TTATTAATTATATTTAATAT
1 TTATTAATTAAACTTAACAT
3456769 TTATTACATTAAACTTAACAT
1 TTATTA-ATTAAACTTAACAT
3456790 TTA
1 TTA
3456793 AACATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTAATTAAACTTAACAT
Found at i:3457199 original size:16 final size:16
Alignment explanation
Indices: 3457161--3457199 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3457151 AATTTAGTTT
3457161 ATTTA-TTAAATATTA
1 ATTTATTTAAATATTA
*
3457176 ATTAATTTAAATATTA
1 ATTTATTTAAATATTA
*
3457192 TTTTATTT
1 ATTTATTT
3457200 TATAAATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTATTTAAATATTA
Found at i:3457842 original size:2 final size:2
Alignment explanation
Indices: 3457835--3457880 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3457825 AATCTTCATT
3457835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3457877 TA TA
1 TA TA
3457881 GATGCACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3460509 original size:30 final size:30
Alignment explanation
Indices: 3460456--3460540 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
3460446 ATTCTTATAT
*
3460456 ATTTATTTTTAATTTTTTAAATATATAATAAC
1 ATTTA-TTTTAATTTTTT-AATATATAATAAA
3460488 ATTTATTTTAATTTTTTAATATATAATAAA
1 ATTTATTTTAATTTTTTAATATATAATAAA
* ** *
3460518 ATATATGATACTTTTTTAATATA
1 ATTTATTTTAATTTTTTAATATA
3460541 ATAGTCATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 31 0.65
31 12 0.25
32 5 0.10
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (30 bp):
ATTTATTTTAATTTTTTAATATATAATAAA
Found at i:3461145 original size:17 final size:17
Alignment explanation
Indices: 3461108--3461146 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3461098 ATTTTAACTC
*
3461108 AAATTATTATTAATATA
1 AAATTATTATTAATAAA
3461125 AAATTATT-TTAATAAA
1 AAATTATTATTAATAAA
3461141 TAAATT
1 -AAATT
3461147 TTAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTATTATTAATAAA
Found at i:3461227 original size:20 final size:21
Alignment explanation
Indices: 3461177--3461228 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
3461167 ATTATTAAAC
3461177 ATAT-ATATTTATATTTTAATA
1 ATATAATA-TTATATTTTAATA
3461198 ATATAATATTAT-TTTTAATA
1 ATATAATATTATATTTTAATA
3461218 ATA-AATTATTA
1 ATATAA-TATTA
3461229 ATATAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 8 0.28
22 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATAATATTATATTTTAATA
Found at i:3461250 original size:16 final size:17
Alignment explanation
Indices: 3461196--3461279 Score: 54
Period size: 17 Copynumber: 5.1 Consensus size: 17
3461186 TATATTTTAA
* *
3461196 TAATATAATATTATTTT
1 TAATATAAAATTATTAT
*
3461213 TAATA-ATAA--ATTAT
1 TAATATAAAATTATTAT
*
3461227 TAATAT-AATTTATTAT
1 TAATATAAAATTATTAT
3461243 TACA-ATAAAATTATTATT
1 TA-ATATAAAATTATTA-T
*
3461261 TAATA-AAACTATATTAT
1 TAATATAAAAT-TATTAT
3461278 TA
1 TA
3461280 TTTTAATAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
14 10 0.19
16 11 0.21
17 22 0.42
18 9 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAAAATTATTAT
Found at i:3461254 original size:18 final size:18
Alignment explanation
Indices: 3461228--3461279 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3461218 ATAAATTATT
*
3461228 AATATAATTTATTATTAC
1 AATAAAATTTATTATTAC
*
3461246 AATAAAA-TTATTATT-T
1 AATAAAATTTATTATTAC
*
3461262 AATAAAACTATATTATTA
1 AATAAAA-TTTATTATTA
3461280 TTTTAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 13 0.46
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAAATTTATTATTAC
Found at i:3461254 original size:30 final size:31
Alignment explanation
Indices: 3461196--3461258 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
3461186 TATATTTTAA
* *
3461196 TAATATAATATTATTTTTAATAATAAATTAT
1 TAATATAATATTATTATTAACAATAAATTAT
3461227 TAATATAAT-TTATTATT-ACAATAAAATTAT
1 TAATATAATATTATTATTAACAAT-AAATTAT
3461257 TA
1 TA
3461259 TTTAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 16 0.55
31 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATATAATATTATTATTAACAATAAATTAT
Found at i:3461258 original size:17 final size:18
Alignment explanation
Indices: 3461236--3461279 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3461226 TTAATATAAT
3461236 TTATTATTACAATAAAA-
1 TTATTATTACAATAAAAC
*
3461253 TTATTATT-TAATAAAAC
1 TTATTATTACAATAAAAC
3461270 TATATTATTA
1 T-TATTATTA
3461280 TTTTAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 9 0.39
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTATTACAATAAAAC
Found at i:3461583 original size:13 final size:13
Alignment explanation
Indices: 3461540--3461591 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
3461530 TTATTTTAAA
* *
3461540 TATTTAATATTAC
1 TATTAAATATTAT
*
3461553 TA-TAATATTTTAT
1 TATTAA-ATATTAT
*
3461566 CATTAAATATTAT
1 TATTAAATATTAT
3461579 TATTAAATATTAT
1 TATTAAATATTAT
3461592 GATTTTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 2 0.06
13 26 0.84
14 3 0.10
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTAAATATTAT
Found at i:3461603 original size:21 final size:21
Alignment explanation
Indices: 3461579--3461646 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
3461569 TAAATATTAT
3461579 TATTAAATATT-ATGATTTTAA
1 TATTAAATATTAATG-TTTTAA
3461600 TATTAAA-ATTAATGTTTTAA
1 TATTAAATATTAATGTTTTAA
**
3461620 TGA-TAAATAATTTAATAATTTAA
1 T-ATTAAAT-A-TTAATGTTTTAA
3461643 TATT
1 TATT
3461647 TATGTGAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 14 0.36
21 11 0.28
22 2 0.05
23 12 0.31
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TATTAAATATTAATGTTTTAA
Found at i:3462119 original size:11 final size:12
Alignment explanation
Indices: 3462081--3462126 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
3462071 AAATTAAAAT
* *
3462081 TTAAAAATTTAT
1 TTAAAAATATAA
*
3462093 TTAAATATA-AA
1 TTAAAAATATAA
3462104 TTAAAAATATAA
1 TTAAAAATATAA
3462116 -TAAAAATATAA
1 TTAAAAATATAA
3462127 AACTTACCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAAATATAA
Found at i:3463647 original size:14 final size:14
Alignment explanation
Indices: 3463628--3463662 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3463618 TGACGAGATA
3463628 TAATTAAAATTAAT
1 TAATTAAAATTAAT
*
3463642 TAATTAAATTTAAT
1 TAATTAAAATTAAT
*
3463656 TTATTAA
1 TAATTAA
3463663 TAATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTAAAATTAAT
Found at i:3463680 original size:17 final size:18
Alignment explanation
Indices: 3463655--3463690 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3463645 TTAAATTTAA
*
3463655 TTTATTAATAATAA-AAT
1 TTTAATAATAATAATAAT
3463672 TTTAATAATAATAATAAT
1 TTTAATAATAATAATAAT
3463690 T
1 T
3463691 CAATAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAATAATAATAATAAT
Found at i:3464213 original size:14 final size:15
Alignment explanation
Indices: 3464196--3464224 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3464186 TTATTTATTA
3464196 TATTTTAA-AAATAT
1 TATTTTAATAAATAT
3464210 TATTTTAATAAATAT
1 TATTTTAATAAATAT
3464225 AATTCAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAATAAATAT
Found at i:3464214 original size:27 final size:26
Alignment explanation
Indices: 3464156--3464215 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
3464146 ATATTTAACG
3464156 TATTA-TTTTTATTAAATTTTAAAAA
1 TATTATTTTTTATTAAATTTTAAAAA
* *
3464181 -ATAATTTATTTATTATATTTTAAAAA
1 TATTATTT-TTTATTAAATTTTAAAAA
3464207 TATTATTTT
1 TATTATTTT
3464216 AATAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.10
25 2 0.07
26 18 0.62
27 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTTTTTATTAAATTTTAAAAA
Found at i:3464506 original size:32 final size:32
Alignment explanation
Indices: 3464466--3464567 Score: 92
Period size: 32 Copynumber: 3.3 Consensus size: 32
3464456 TGCATTTAAA
3464466 AAAATAATAATAATTTATATAATTATTTTTAT
1 AAAATAATAATAATTTATATAATTATTTTTAT
3464498 AAAATAAT-ATATATTTA-ATAA--ATTTAATT-T
1 AAAATAATAATA-ATTTATATAATTATTT--TTAT
* *
3464528 -AAAT-TTAAAAATTTATAATAATTATTTTTAT
1 AAAATAATAATAATTTAT-ATAATTATTTTTAT
*
3464559 GAAATAATA
1 AAAATAATA
3464568 TATTTTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 21
0.70 0.04 0.26
Matches are distributed among these distances:
28 6 0.11
29 10 0.18
30 7 0.12
31 10 0.18
32 21 0.38
33 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
AAAATAATAATAATTTATATAATTATTTTTAT
Found at i:3464525 original size:20 final size:19
Alignment explanation
Indices: 3464502--3464542 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3464492 TTTTATAAAA
*
3464502 TAATATATATTTAATAAATT
1 TAATATAAATTTAA-AAATT
*
3464522 TAATTTAAATTTAAAAATT
1 TAATATAAATTTAAAAATT
3464541 TA
1 TA
3464543 TAATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATATAAATTTAAAAATT
Found at i:3464558 original size:61 final size:61
Alignment explanation
Indices: 3464477--3464607 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 61
3464467 AAATAATAAT
3464477 AATTTAT-ATAATTATTTTTATAAAATAATATATATTTAATAAAT-T-TAATTTAAATTTAAA
1 AATTTATAATAATTATTTTTATAAAATAATATAT-TTTAATAAATGTGT-ATTTAAATTTAAA
* * *
3464537 AATTTATAATAATTATTTTTATGAAATAATATATTTTAATAAGTGTGTATTTAAATTTTAA
1 AATTTATAATAATTATTTTTATAAAATAATATATTTTAATAAATGTGTATTTAAATTTAAA
3464598 AATTTATAAT
1 AATTTATAAT
3464608 TTTTTAGGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
60 16 0.25
61 48 0.74
62 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (61 bp):
AATTTATAATAATTATTTTTATAAAATAATATATTTTAATAAATGTGTATTTAAATTTAAA
Found at i:3464877 original size:17 final size:17
Alignment explanation
Indices: 3464857--3464891 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3464847 ATATTTTTAT
*
3464857 TATAATTTTATTAAATA
1 TATAATATTATTAAATA
3464874 TATAATATTATTAAATA
1 TATAATATTATTAAATA
3464891 T
1 T
3464892 TTATTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTATTAAATA
Found at i:3465155 original size:2 final size:2
Alignment explanation
Indices: 3465142--3465183 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3465132 GCTCTCGTAA
*
3465142 AT AT AC 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 AT
3465184 GGCATCTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3466126 original size:53 final size:52
Alignment explanation
Indices: 3466063--3466167 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 52
3466053 TCATTAGGTC
3466063 TAAAGTCCTGCAATGAATA-AAAAGAAAGCACATGAATAATTTTTTTTTTCACA
1 TAAAGTCCTGCAATGAA-AGAAAAGAAAGCACATGAAT-ATTTTTTTTTTCACA
3466116 TAAAGTCCTGCAATGAAAGAAAAGAAAGCACATGAATATTTTTTTTTTCACA
1 TAAAGTCCTGCAATGAAAGAAAAGAAAGCACATGAATATTTTTTTTTTCACA
3466168 AAGAAGATCG
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
52 16 0.31
53 35 0.69
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (52 bp):
TAAAGTCCTGCAATGAAAGAAAAGAAAGCACATGAATATTTTTTTTTTCACA
Found at i:3466680 original size:2 final size:2
Alignment explanation
Indices: 3466673--3466698 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3466663 CATTGGGTCA
3466673 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
3466699 CTATGATATC
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:3467396 original size:49 final size:49
Alignment explanation
Indices: 3467319--3467413 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
3467309 GAGGATGGAC
*
3467319 CCTCAATAAAAATATTCATAAATGTAAGGTTAGATGAATTAGTACACAT
1 CCTCAATAAAAATATTCATAAATGTAAGGTCAGATGAATTAGTACACAT
* *
3467368 CCTCCATAAAAATATTCATAAATGTAAGGTCAGATGAATTCGTACA
1 CCTCAATAAAAATATTCATAAATGTAAGGTCAGATGAATTAGTACA
3467414 TACATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (49 bp):
CCTCAATAAAAATATTCATAAATGTAAGGTCAGATGAATTAGTACACAT
Found at i:3468002 original size:15 final size:14
Alignment explanation
Indices: 3467982--3468039 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
3467972 ATTAATTAAA
*
3467982 TTAAATAAAATATTT
1 TTAAATAAAATA-AT
3467997 TTAAATATAAATAAT
1 TTAAATA-AAATAAT
* *
3468012 TTATATAAAATTAT
1 TTAAATAAAATAAT
*
3468026 ATAAATAAATATAA
1 TTAAATAAA-ATAA
3468040 AAATTAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 13 0.37
15 17 0.49
16 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAATAAAATAAT
Found at i:3468003 original size:34 final size:31
Alignment explanation
Indices: 3467928--3468058 Score: 115
Period size: 30 Copynumber: 4.2 Consensus size: 31
3467918 AAAAGGTTAG
* *
3467928 TATTTTTAAATATAAATAATGAAATAAATAG
1 TATTTTTAAATATAAATAATTAAATAAATAA
* *
3467959 TA-TCTTAAATATAATTAATTAAATTAAATAAAA
1 TATTTTTAAATATAAATAATTAAA-TAAAT--AA
* *
3467992 TATTTTTAAATATAAATAATTTATATAAAATTA
1 TATTTTTAAATATAAATAA-TTAAAT-AAATAA
***
3468025 TATAAATAAATATAAA-AATTAAATAAAT-A
1 TATTTTTAAATATAAATAATTAAATAAATAA
3468054 TATTT
1 TATTT
3468059 ATATATAATA
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
29 4 0.05
30 22 0.28
31 12 0.15
32 2 0.03
33 17 0.21
34 15 0.19
35 8 0.10
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (31 bp):
TATTTTTAAATATAAATAATTAAATAAATAA
Found at i:3468648 original size:10 final size:11
Alignment explanation
Indices: 3468608--3468680 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 11
3468598 TAAATTTATT
3468608 TAATATAAATCA
1 TAATATAAAT-A
3468620 TTAATAT--ATA
1 -TAATATAAATA
* *
3468630 AAATTTAAATA
1 TAATATAAATA
3468641 -AATATAAA-A
1 TAATATAAATA
*
3468650 TATTATAAATA
1 TAATATAAATA
3468661 TAATTATAAA-A
1 TAA-TATAAATA
3468672 TAATA-AAAT
1 TAATATAAAT
3468681 TATATTTACG
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
9 8 0.16
10 17 0.35
11 12 0.24
12 6 0.12
13 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATATAAATA
Found at i:3468650 original size:11 final size:11
Alignment explanation
Indices: 3468636--3468675 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
3468626 TATAAAATTT
*
3468636 AAATAAATATA
1 AAATAATTATA
3468647 AAAT-ATTATA
1 AAATAATTATA
3468657 AATATAATTATA
1 AA-ATAATTATA
3468669 AAATAAT
1 AAATAAT
3468676 AAAATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 7 0.27
11 11 0.42
12 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAATTATA
Found at i:3468651 original size:26 final size:28
Alignment explanation
Indices: 3468605--3468684 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 28
3468595 TTTTAAATTT
*
3468605 ATTTAATATAAATCATTAATA-TATAAA
1 ATTTAATATAAATCATAAATATTATAAA
3468632 ATTTAA-ATAAAT-ATAAAATATTAT-AA
1 ATTTAATATAAATCAT-AAATATTATAAA
* *
3468658 ATATAATTATAAAATAATAAA-ATTATA
1 ATTTAA-TAT-AAATCATAAATATTATA
3468685 TTTACGATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
25 2 0.05
26 17 0.39
27 9 0.20
28 7 0.16
29 7 0.16
30 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTTAATATAAATCATAAATATTATAAA
Found at i:3468659 original size:16 final size:16
Alignment explanation
Indices: 3468625--3468663 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3468615 AATCATTAAT
3468625 ATATAAAATTTAAATAA
1 ATATAAAATTT-AATAA
3468642 ATATAAAATATT-ATAA
1 ATATAAAAT-TTAATAA
3468658 ATATAA
1 ATATAA
3468664 TTATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 9 0.43
18 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAAAATTTAATAA
Found at i:3468668 original size:22 final size:21
Alignment explanation
Indices: 3468611--3468673 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
3468601 ATTTATTTAA
3468611 TATAAATCATTAATATATAAA-AT
1 TATAAAT-A-TAATATA-AAATAT
3468634 T-TAAATA-AATATAAAATAT
1 TATAAATATAATATAAAATAT
3468653 TATAAATATAATTATAAAATA
1 TATAAATATAA-TATAAAATA
3468674 ATAAAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.08
19 9 0.25
20 6 0.17
21 3 0.08
22 14 0.39
23 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAAATATAATATAAAATAT
Found at i:3468684 original size:22 final size:22
Alignment explanation
Indices: 3468608--3468680 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
3468598 TAAATTTATT
* *
3468608 TAATATAAATCATTAATATATAA
1 TAATATAAAT-ATAAATATAAAA
*
3468631 -AAT-TTAA-ATAAATATAAAA
1 TAATATAAATATAAATATAAAA
* *
3468650 TATTATAAATATAATTATAAAA
1 TAATATAAATATAAATATAAAA
3468672 TAATA-AAAT
1 TAATATAAAT
3468681 TATATTTACG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 10 0.25
20 2 0.05
21 10 0.25
22 18 0.45
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATATAAATATAAATATAAAA
Found at i:3469409 original size:13 final size:13
Alignment explanation
Indices: 3469391--3469440 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
3469381 TTATTATTTT
*
3469391 TTTAATATTAATG
1 TTTAATATTAATA
*
3469404 TTTAATATTCATA
1 TTTAATATTAATA
*
3469417 TTTAATA-T-ATT
1 TTTAATATTAATA
3469428 TTTAATA-TAATA
1 TTTAATATTAATA
3469440 T
1 T
3469441 AAATAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 10 0.31
12 4 0.12
13 18 0.56
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTAATATTAATA
Found at i:3473999 original size:5 final size:5
Alignment explanation
Indices: 3473984--3474118 Score: 73
Period size: 5 Copynumber: 27.0 Consensus size: 5
3473974 TAAATATTAA
* * * *
3473984 TATAT TTTAT TATAT TATAAT TATAT TTTAT ATATTT TATAT TTTAT TA-AT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT -TATAT TATAT TATAT TATAT
* * * * * *
3474035 TTTAA TATAT TAATAT TA-A- TATTT TATAT TATAT TA-AT TTTAA AATA-
1 TATAT TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * *
3474082 TATAT TCATAT CATAT TATAT TTTAAT TATTT TATAT
1 TATAT T-ATAT TATAT TATAT TAT-AT TATAT TATAT
3474119 ACATCAAAAT
Statistics
Matches: 95, Mismatches: 25, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
3 2 0.02
4 10 0.11
5 62 0.65
6 21 0.22
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:3474023 original size:16 final size:16
Alignment explanation
Indices: 3473983--3474118 Score: 69
Period size: 16 Copynumber: 8.8 Consensus size: 16
3473973 TTAAATATTA
*
3473983 ATATATTTTATTATATT
1 ATATATTTTA-TATTTT
3474000 ATA-A--TTATATTTT
1 ATATATTTTATATTTT
3474013 ATATATTTTATATTTT
1 ATATATTTTATATTTT
*
3474029 AT-TAATTTTAATATATT
1 ATAT-ATTTT-ATATTTT
*
3474046 A-ATA-TTAATATTTT
1 ATATATTTTATATTTT
*
3474060 ATATTATATTA-ATTTT
1 ATA-TATTTTATATTTT
* * *
3474076 A-A-AATATATA-TTC
1 ATATATTTTATATTTT
*
3474089 ATATCATATTATATTTT
1 ATAT-ATTTTATATTTT
3474106 A-ATTATTTTATAT
1 ATA-TATTTTATAT
3474119 ACATCAAAAT
Statistics
Matches: 89, Mismatches: 15, Indels: 31
0.66 0.11 0.23
Matches are distributed among these distances:
13 14 0.16
14 13 0.15
15 5 0.06
16 40 0.45
17 17 0.19
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTTTATATTTT
Found at i:3474047 original size:14 final size:14
Alignment explanation
Indices: 3474028--3474065 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3474018 TTTTATATTT
*
3474028 TATTAATTTTAATA
1 TATTAATATTAATA
3474042 TATTAATATTAATA
1 TATTAATATTAATA
*
3474056 T-TTTATATTA
1 TATTAATATTA
3474066 TATTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTAATATTAATA
Found at i:3474203 original size:23 final size:22
Alignment explanation
Indices: 3474177--3474222 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
3474167 ATTAATATGT
3474177 TAAA-TATGAATACTGAAATAAAA
1 TAAATTATGAATA-TGAAA-AAAA
*
3474200 TAAATTATTAATATGAAAAAAA
1 TAAATTATGAATATGAAAAAAA
3474222 T
1 T
3474223 TTATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAATTATGAATATGAAAAAAA
Found at i:3474514 original size:25 final size:24
Alignment explanation
Indices: 3474459--3474514 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
3474449 TGATATTTTT
3474459 AATTTTTTATATTTTAATAAAATTA
1 AATTTTTTATATTTTAAT-AAATTA
3474484 AATTTTTTATATTTTAAT-AATTA
1 AATTTTTTATATTTTAATAAATTA
*
3474507 TATTTTTT
1 AATTTTTT
3474515 GATAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 12 0.40
25 18 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTTTTATATTTTAATAAATTA
Found at i:3480519 original size:18 final size:18
Alignment explanation
Indices: 3480496--3480621 Score: 57
Period size: 18 Copynumber: 6.8 Consensus size: 18
3480486 TATATATTGG
3480496 TATTTATATTATTTTTTA
1 TATTTATATTATTTTTTA
* *
3480514 TATTTAAAATATTATTTT-
1 TATTTATATTATT-TTTTA
*
3480532 TA--TATA-AATTTTTTA
1 TATTTATATTATTTTTTA
*
3480547 TATATTA-ATAATTTATTT-
1 TAT-TTATATTATTT-TTTA
3480565 TATTTCATATATATATTTTTA
1 TATTT-ATAT-TAT-TTTTTA
* *
3480586 TATGTACATATATTTATTTTA
1 TATTTATAT-TA-TT-TTTTA
**
3480607 TATACATATTATTTT
1 TATTTATATTATTTT
3480622 CATGTTATGT
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
14 4 0.05
15 5 0.06
16 3 0.04
17 3 0.04
18 26 0.31
19 11 0.13
20 14 0.17
21 18 0.21
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (18 bp):
TATTTATATTATTTTTTA
Found at i:3480567 original size:33 final size:32
Alignment explanation
Indices: 3480498--3480565 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
3480488 TATATTGGTA
*
3480498 TTTATATTATTTTTTATATTTAAAATATTATT
1 TTTATATAATTTTTTATATTTAAAATATTATT
3480530 TTTATATAAATTTTTTATATATTAATAAT-TTATT
1 TTTATAT-AATTTTTTATAT-TTAA-AATATTATT
3480564 TT
1 TT
3480566 ATTTCATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.22
33 11 0.34
34 11 0.34
35 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTATATAATTTTTTATATTTAAAATATTATT
Found at i:3480577 original size:40 final size:40
Alignment explanation
Indices: 3480532--3480607 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
3480522 ATATTATTTT
*
3480532 TATATAAATTTTTTATATATTA-ATA-ATTTATTTTATTTCA
1 TATATAAA-TTTTTATAT-GTACATATATTTATTTTATTTCA
*
3480572 TATATATATTTTTATATGTACATATATTTATTTTAT
1 TATATAAATTTTTATATGTACATATATTTATTTTAT
3480608 ATACATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.06
39 12 0.38
40 18 0.56
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (40 bp):
TATATAAATTTTTATATGTACATATATTTATTTTATTTCA
Found at i:3481049 original size:22 final size:22
Alignment explanation
Indices: 3481014--3481055 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3481004 TATATAATAT
3481014 TTTATGTTCTTATATTCATGTCA
1 TTTATGTTCTTATATT-ATGTCA
*
3481037 TTTAT-TTTTTATATTATGT
1 TTTATGTTCTTATATTATGT
3481056 TTTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTATGTTCTTATATTATGTCA
Found at i:3481762 original size:11 final size:11
Alignment explanation
Indices: 3481746--3481770 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3481736 TATATTTTAA
3481746 TATATTCATGT
1 TATATTCATGT
3481757 TATATTCATGT
1 TATATTCATGT
3481768 TAT
1 TAT
3481771 TTTTCACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATTCATGT
Found at i:3482026 original size:16 final size:17
Alignment explanation
Indices: 3481999--3482039 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3481989 ATTTTAAAAT
3481999 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
3482014 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
3482031 AAATTTTAT
1 AAATTTTAT
3482040 AAATATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:3482711 original size:22 final size:21
Alignment explanation
Indices: 3482667--3482733 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
3482657 AAAATGATTG
* *
3482667 AACTTTATTAATTTGAACATTA
1 AACTTAATTAATTT-AAAATTA
*
3482689 AA-TTCGATTAATTTAAAAGTTA
1 AACTT-AATTAATTTAAAA-TTA
*
3482711 AACTTAATTGATTTAAAATTA
1 AACTTAATTAATTTAAAATTA
3482732 AA
1 AA
3482734 ATAATTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 10 0.26
22 26 0.68
23 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (21 bp):
AACTTAATTAATTTAAAATTA
Found at i:3482742 original size:16 final size:16
Alignment explanation
Indices: 3482721--3482751 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3482711 AACTTAATTG
3482721 ATTTAAAATTAAAATA
1 ATTTAAAATTAAAATA
*
3482737 ATTTAAAATTTAAAT
1 ATTTAAAATTAAAAT
3482752 GATTCAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAAATTAAAATA
Found at i:3484167 original size:26 final size:25
Alignment explanation
Indices: 3484137--3484196 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
3484127 TTTTAAAATT
3484137 TAAAATTTAAATCGAAATTAAATAAA
1 TAAAATTTAAAT-GAAATTAAATAAA
* *
3484163 TAAAAAATTAAATTAAATTAAATAAA
1 T-AAAATTTAAATGAAATTAAATAAA
*
3484189 -AAATTTTA
1 TAAAATTTA
3484197 GTTAGGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 6 0.21
26 13 0.45
27 10 0.34
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
TAAAATTTAAATGAAATTAAATAAA
Found at i:3484170 original size:22 final size:22
Alignment explanation
Indices: 3484145--3484192 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3484135 TTTAAAATTT
3484145 AAATCGAAATTAAA-TAAATAAA
1 AAAT-GAAATTAAATTAAATAAA
*
3484167 AAATTAAATTAAATTAAATAAA
1 AAATGAAATTAAATTAAATAAA
3484189 AAAT
1 AAAT
3484193 TTTAGTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATGAAATTAAATTAAATAAA
Found at i:3484193 original size:22 final size:21
Alignment explanation
Indices: 3484151--3484193 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
3484141 ATTTAAATCG
3484151 AAATTAAATAAATAAAAAATT
1 AAATTAAATAAATAAAAAATT
3484172 AAATTAAATTAAATAAAAAATT
1 AAATTAAA-TAAATAAAAAATT
3484194 TTAGTTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAAATAAATAAAAAATT
Done.