Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 20 of 56
Found at i:3605198 original size:18 final size:18
Alignment explanation
Indices: 3605175--3605210 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3605165 CAACTTCAAT
3605175 TGTCAAAATACCATAAGG
1 TGTCAAAATACCATAAGG
3605193 TGTCAAAATACCATAAGG
1 TGTCAAAATACCATAAGG
3605211 CCGGAACGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (18 bp):
TGTCAAAATACCATAAGG
Found at i:3609875 original size:34 final size:33
Alignment explanation
Indices: 3609810--3609875 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
3609800 GCGGGTGTTA
* * * *
3609810 ATGGTGCTCGAGCACCAGGCCCAATTGGTGCTT
1 ATGGTGCTCGAGCACAAAGCCCAACTAGTGCTT
*
3609843 ATGGTGCTCGAGCAACAAAGCCCAGCTAGTGCT
1 ATGGTGCTCGAGC-ACAAAGCCCAACTAGTGCT
3609876 GAAGTTAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (33 bp):
ATGGTGCTCGAGCACAAAGCCCAACTAGTGCTT
Found at i:3611702 original size:2 final size:2
Alignment explanation
Indices: 3611697--3611722 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3611687 AAAAAGAAAA
3611697 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
3611723 TTCAATTTAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3612825 original size:25 final size:26
Alignment explanation
Indices: 3612796--3612844 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3612786 GCTTTCTTTA
3612796 ACTTT-AGCTTTATTTTTTATTTTCG
1 ACTTTGAGCTTTATTTTTTATTTTCG
* * *
3612821 ACTTTGAGTTTTTTTTTTTTTTTT
1 ACTTTGAGCTTTATTTTTTATTTT
3612845 TTTCAAACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.71
Consensus pattern (26 bp):
ACTTTGAGCTTTATTTTTTATTTTCG
Found at i:3613748 original size:11 final size:11
Alignment explanation
Indices: 3613729--3613815 Score: 58
Period size: 11 Copynumber: 8.1 Consensus size: 11
3613719 AGCGTGATAT
*
3613729 TTAATTTTTAA
1 TTAAATTTTAA
3613740 TTAAATTTT-A
1 TTAAATTTTAA
*
3613750 TTAAA-TTTGA
1 TTAAATTTTAA
*
3613760 -TAATATTTTGA
1 TTAA-ATTTTAA
3613771 TTAAGATTTT-A
1 TTAA-ATTTTAA
* *
3613782 TTAAATTTGAG
1 TTAAATTTTAA
*
3613793 TT-GATTTTAA
1 TTAAATTTTAA
3613803 CTTAAATTTTAA
1 -TTAAATTTTAA
3613815 T
1 T
3613816 GTTAATGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
9 6 0.10
10 17 0.28
11 23 0.38
12 15 0.25
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (11 bp):
TTAAATTTTAA
Found at i:3613780 original size:32 final size:30
Alignment explanation
Indices: 3613730--3613813 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 30
3613720 GCGTGATATT
3613730 TAATTTTTAATTAAATTTTATTAAATTTGA
1 TAATTTTTAATTAAATTTTATTAAATTTGA
*
3613760 TAATATTTTGATTAAGATTTTATTAAATTTGA
1 TAAT-TTTTAATTAA-ATTTTATTAAATTTGA
*
3613792 GTTGA-TTTTAACTTAAATTTTA
1 --TAATTTTTAA-TTAAATTTTA
3613814 ATGTTAATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 4 0.09
31 9 0.20
32 27 0.59
33 4 0.09
34 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (30 bp):
TAATTTTTAATTAAATTTTATTAAATTTGA
Found at i:3614330 original size:10 final size:10
Alignment explanation
Indices: 3614315--3614402 Score: 62
Period size: 10 Copynumber: 9.3 Consensus size: 10
3614305 TTACATAATA
3614315 TTTATATATT
1 TTTATATATT
3614325 TTTATATATT
1 TTTATATATT
* * *
3614335 ATAAT-TATA
1 TTTATATATT
3614344 TTTA-A-ATT
1 TTTATATATT
*
3614352 ATTATATATT
1 TTTATATATT
*
3614362 TTTATA-AAT
1 TTTATATATT
*
3614371 TTTA-ATATA
1 TTTATATATT
*
3614380 TTAATA-ATT
1 TTTATATATT
3614389 TATTATATATT
1 T-TTATATATT
3614400 TTT
1 TTT
3614403 TAATAAAATA
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
8 6 0.11
9 19 0.33
10 28 0.49
11 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTATATATT
Found at i:3614358 original size:37 final size:37
Alignment explanation
Indices: 3614316--3614402 Score: 122
Period size: 37 Copynumber: 2.3 Consensus size: 37
3614306 TACATAATAT
*
3614316 TTATATATTTTTATATATTATAATTATATT-TAAATTA
1 TTATATATTTTTATAAATTATAA-TATATTATAAATTA
* *
3614353 TTATATATTTTTATAAATTTTAATATATTAATAATTTA
1 TTATATATTTTTATAAATTATAATATATT-ATAAATTA
3614391 TTATATATTTTT
1 TTATATATTTTT
3614403 TAATAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 6 0.13
37 21 0.47
38 18 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
TTATATATTTTTATAAATTATAATATATTATAAATTA
Found at i:3615612 original size:6 final size:7
Alignment explanation
Indices: 3615583--3615609 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3615573 GTCCTTTTTC
3615583 TTTTTAA
1 TTTTTAA
3615590 TTTTTAA
1 TTTTTAA
3615597 TTTTTAA
1 TTTTTAA
3615604 TTTTTA
1 TTTTTA
3615610 TTTATTTTTT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:3616104 original size:21 final size:20
Alignment explanation
Indices: 3616079--3616119 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3616069 AAAATATTGT
3616079 TTTTAT-ATTAATATTTATAAA
1 TTTTATAATTAA-ATTT-TAAA
3616100 TTTTATAATTAAATTTTAAA
1 TTTTATAATTAAATTTTAAA
3616120 AATATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAATTAAATTTTAAA
Found at i:3616122 original size:22 final size:21
Alignment explanation
Indices: 3616079--3616122 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
3616069 AAAATATTGT
*
3616079 TTTTATATTAATATTTATAAA
1 TTTTATATTAATATTTAAAAA
3616100 TTTTATAATTAA-ATTTTAAAAA
1 TTTTAT-ATTAATA-TTTAAAAA
3616122 T
1 T
3616123 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATATTAATATTTAAAAA
Found at i:3616641 original size:8 final size:8
Alignment explanation
Indices: 3616628--3616720 Score: 71
Period size: 8 Copynumber: 10.8 Consensus size: 8
3616618 GTAATAAAAT
3616628 TAAATATA
1 TAAATATA
3616636 TAAATATA
1 TAAATATA
*
3616644 TAAATTTA
1 TAAATATA
3616652 TATAAT-TA
1 TA-AATATA
*
3616660 TTAATATA
1 TAAATATA
*
3616668 TTAAAATTTA
1 -T-AAATATA
3616678 TAAATATTATA
1 T-AA-A-TATA
3616689 TAAATATA
1 TAAATATA
3616697 TAAATTATA
1 TAAA-TATA
*
3616706 AAAATATA
1 TAAATATA
3616714 TATAATA
1 TA-AATA
3616721 ATTTTTCTGG
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.04
8 35 0.50
9 20 0.29
10 8 0.11
11 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TAAATATA
Found at i:3616674 original size:26 final size:23
Alignment explanation
Indices: 3616604--3616690 Score: 65
Period size: 26 Copynumber: 3.7 Consensus size: 23
3616594 AAATTTTGGA
*
3616604 TATATAATTATTATGTAATAAAA-T
1 TATATAA-TATTATAT-ATAAAATT
* *
3616628 TAAAT-ATA-TAAATATATAAATT
1 TATATAATATTATATATA-AAATT
3616650 TATATAATTATTAATATATTAAAATT
1 TATATAA-TATT-ATATA-TAAAATT
3616676 TATA-AATATTATATA
1 TATATAATATTATATA
3616691 AATATATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
20 3 0.06
21 6 0.12
22 7 0.14
23 7 0.14
24 10 0.20
25 3 0.06
26 13 0.25
27 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
TATATAATATTATATATAAAATT
Found at i:3616720 original size:26 final size:25
Alignment explanation
Indices: 3616629--3616720 Score: 91
Period size: 27 Copynumber: 3.6 Consensus size: 25
3616619 TAATAAAATT
3616629 AAATATATA-AATATATAAATTTATA
1 AAATATATATAATATATAAATTTA-A
* *
3616654 TAAT-TAT-TAATATATTAAAATTTAT
1 AAATATATATAATATA-T-AAATTTAA
3616679 AAATATTATATAAATATATAAATTATAA
1 AAATA-TATAT-AATATATAAATT-TAA
3616707 AAATATATATAATA
1 AAATATATATAATA
3616721 ATTTTTCTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
24 9 0.16
25 7 0.13
26 11 0.20
27 13 0.24
28 9 0.16
29 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATATATAATATATAAATTTAA
Found at i:3617284 original size:19 final size:18
Alignment explanation
Indices: 3617259--3617298 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 18
3617249 TAAACACAAA
3617259 AATATATAATAAATATGACAT
1 AATATAT-AT-AATATG-CAT
3617280 AATATATATAATATGCAT
1 AATATATATAATATGCAT
3617298 A
1 A
3617299 TTAATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 2 0.11
21 7 0.37
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
AATATATATAATATGCAT
Found at i:3617326 original size:17 final size:18
Alignment explanation
Indices: 3617304--3617340 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3617294 GCATATTAAT
3617304 TATATTTAAAATTT-TTA
1 TATATTTAAAATTTATTA
*
3617321 TATATTTAATATTTATTA
1 TATATTTAAAATTTATTA
3617339 TA
1 TA
3617341 CTTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTAAAATTTATTA
Found at i:3617335 original size:15 final size:14
Alignment explanation
Indices: 3617317--3617359 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3617307 ATTTAAAATT
*
3617317 TTTATATATTTAATA
1 TTTATATACTT-ATA
3617332 TTTATTATACTTATA
1 TTTA-TATACTTATA
*
3617347 TTTATATAATTAT
1 TTTATATACTTAT
3617360 CATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 11 0.44
16 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATATACTTATA
Found at i:3619211 original size:26 final size:25
Alignment explanation
Indices: 3619178--3619234 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
3619168 AAAAATTTTG
*
3619178 AATTTAAATTTAAATATAAATAATTA
1 AATTTAAAATTAAATATAAA-AATTA
3619204 AATTTAAAATTAAATATAAAAATTA
1 AATTTAAAATTAAATATAAAAATTA
*
3619229 ATTTTA
1 AATTTA
3619235 TTTTTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTTAAAATTAAATATAAAAATTA
Found at i:3619958 original size:22 final size:21
Alignment explanation
Indices: 3619901--3619962 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
3619891 ATTATTTTAA
3619901 AATATTAAAATATTATTTTATATT
1 AATATT-AAATA--ATTTTATATT
*
3619925 AATATTATATAATTTTATAATT
1 AATATTAAATAATTTTAT-ATT
3619947 AA-ATTTAAATAATTTT
1 AATA-TTAAATAATTTT
3619963 TTGTGAGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.24
22 16 0.47
23 4 0.12
24 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATTAAATAATTTTATATT
Found at i:3621385 original size:30 final size:30
Alignment explanation
Indices: 3621351--3621410 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3621341 TATATATGTT
*
3621351 AAATATAATAATAT-AAATATGATATAAATA
1 AAATAT-ATAATATAAAATATAATATAAATA
*
3621381 AAATATTTAATATAAAATATAATATAAATA
1 AAATATATAATATAAAATATAATATAAATA
3621411 TGTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATATATAATATAAAATATAATATAAATA
Found at i:3621409 original size:25 final size:25
Alignment explanation
Indices: 3621372--3621540 Score: 69
Period size: 25 Copynumber: 6.4 Consensus size: 25
3621362 TATAAATATG
3621372 ATATAA-ATAAAATATTTAATATAAA
1 ATATAATAT-AAATATTTAATATAAA
* * *
3621397 ATATAATATAAATATGTATTTTAAA
1 ATATAATATAAATATTTAATATAAA
* *
3621422 TTTTATATAAAATAAATTATTTATAAATAAA
1 ----ATATAATATAAA-TATTTA-ATATAAA
* ** *
3621453 AT-TTATATAAATATAAAATATTTTAA
1 ATATAATATAAATATTTAATA--TAAA
* *
3621479 ATATAAT-TATAATATAATAAAAT-AA
1 ATATAATATA-AATAT-TTAATATAAA
*
3621504 ATATAATATAAATATATGAATTATTAAA
1 ATATAATATAAATAT-TTAA-TA-TAAA
3621532 AT-TAATATA
1 ATATAATATA
3621541 TCCATAGCAC
Statistics
Matches: 108, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
24 2 0.02
25 40 0.37
26 20 0.19
27 18 0.17
28 8 0.07
29 11 0.10
30 5 0.05
31 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
ATATAATATAAATATTTAATATAAA
Found at i:3621411 original size:11 final size:11
Alignment explanation
Indices: 3621358--3621519 Score: 69
Period size: 11 Copynumber: 15.3 Consensus size: 11
3621348 GTTAAATATA
3621358 ATAATATAAAT
1 ATAATATAAAT
*
3621369 ATGATATAAAT
1 ATAATATAAAT
3621380 A-AA-AT--AT
1 ATAATATAAAT
*
3621387 TTAATATAAAAT
1 ATAATAT-AAAT
3621399 ATAATATAAAT
1 ATAATATAAAT
* *
3621410 ATGTATTTTAAAT
1 A--TAATATAAAT
* *
3621423 TTTATATAAA-
1 ATAATATAAAT
3621433 ATAA-AT---T
1 ATAATATAAAT
*
3621440 AT-TTATAAAT
1 ATAATATAAAT
* * *
3621450 AAAATTTATAT
1 ATAATATAAAT
3621461 A-AATATAAA-
1 ATAATATAAAT
* *
3621470 ATATTTTAAAT
1 ATAATATAAAT
3621481 ATAATTATAATAT
1 ATAA-TATAA-AT
*
3621494 AATAAAATAAAT
1 -ATAATATAAAT
3621506 ATAATATAAAT
1 ATAATATAAAT
3621517 ATA
1 ATA
3621520 TGAATTATTA
Statistics
Matches: 108, Mismatches: 25, Indels: 36
0.64 0.15 0.21
Matches are distributed among these distances:
7 6 0.06
8 2 0.02
9 7 0.06
10 17 0.16
11 44 0.41
12 14 0.13
13 14 0.13
14 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:3621420 original size:30 final size:29
Alignment explanation
Indices: 3621359--3621519 Score: 93
Period size: 30 Copynumber: 5.4 Consensus size: 29
3621349 TTAAATATAA
*
3621359 TAATATAAATATGATATAAATAAAATATT
1 TAATATAAATATAATATAAATAAAATATT
**
3621388 TAATATAAAATATAATATAAAT-ATGTA-T
1 TAATAT-AAATATAATATAAATAAAATATT
* * *
3621416 T--T-TAAATTTTATATAAAATAAATTATT
1 TAATATAAATATAATAT-AAATAAAATATT
* *
3621443 TATAAATAAA-ATTTATATAAATATAAAATATTT
1 TA-ATATAAATA-TAATAT-AA-ATAAAATA-TT
* *
3621476 TAAATATAATTATAATAT-AATAAAATAAATA
1 T-AATATAAATATAATATAAATAAAAT--ATT
3621507 TAATATAAATATA
1 TAATATAAATATA
3621520 TGAATTATTA
Statistics
Matches: 102, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
24 9 0.09
25 5 0.05
26 4 0.04
27 2 0.02
28 2 0.02
29 9 0.09
30 32 0.31
31 16 0.16
32 8 0.08
33 13 0.13
34 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
TAATATAAATATAATATAAATAAAATATT
Found at i:3621439 original size:16 final size:16
Alignment explanation
Indices: 3621418--3621469 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
3621408 ATATGTATTT
3621418 TAAATTTTATATAAAA
1 TAAATTTTATATAAAA
3621434 TAAATTATT-TAT-AAA
1 TAAATT-TTATATAAAA
*
3621449 TAAAATTTATATAAATA
1 TAAATTTTATATAAA-A
3621466 TAAA
1 TAAA
3621470 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.06
15 11 0.35
16 11 0.35
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTATATAAAA
Found at i:3621451 original size:15 final size:16
Alignment explanation
Indices: 3621418--3621488 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
3621408 ATATGTATTT
3621418 TAAATT-TTATATAAAA
1 TAAATTATT-TATAAAA
3621434 TAAATTATTTAT-AAA
1 TAAATTATTTATAAAA
*
3621449 TAAAATT-TATATAAATA
1 T-AAATTATTTATAAA-A
*
3621466 TAAAATATTT-T-AAA
1 TAAATTATTTATAAAA
3621480 TATAATTAT
1 TA-AATTAT
3621489 AATATAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
14 3 0.07
15 15 0.33
16 21 0.47
17 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTATTTATAAAA
Found at i:3621461 original size:31 final size:30
Alignment explanation
Indices: 3621418--3621502 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
3621408 ATATGTATTT
* *
3621418 TAAATTTTATATAAAATAAATTATTTATAAA
1 TAAAATTTATATAAAATAAAATATTT-TAAA
3621449 TAAAATTTATATAAATATAAAATATTTTAAA
1 TAAAATTTATATAAA-ATAAAATATTTTAAA
* *
3621480 TATAA-TTATAATATAATAAAATA
1 TAAAATTTAT-ATAAAATAAAATA
3621503 AATATAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 12 0.25
31 26 0.54
32 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TAAAATTTATATAAAATAAAATATTTTAAA
Found at i:3621496 original size:5 final size:5
Alignment explanation
Indices: 3621478--3621519 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
3621468 AAATATTTTA
*
3621478 AATAT AATTAT AATAT AATAA AATA- AATAT AATAT AAATAT A
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT -AATAT A
3621520 TGAATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 4 0.12
5 19 0.58
6 10 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:3621498 original size:47 final size:46
Alignment explanation
Indices: 3621431--3621520 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 46
3621421 ATTTTATATA
* **
3621431 AAATAAATTATTTATAAATAAAATTTATATAAATATAAA-ATATTTT
1 AAATAAATTATATATAAATAAAATAAATAT-AATATAAATATATTTT
3621477 AAATATAATTATA-ATATAATAAAATAAATATAATATAAATATAT
1 AAATA-AATTATATATA-AATAAAATAAATATAATATAAATATAT
3621521 GAATTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
46 16 0.42
47 22 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (46 bp):
AAATAAATTATATATAAATAAAATAAATATAATATAAATATATTTT
Found at i:3621508 original size:19 final size:20
Alignment explanation
Indices: 3621352--3621514 Score: 67
Period size: 19 Copynumber: 8.3 Consensus size: 20
3621342 ATATATGTTA
3621352 AATATAAT-AATATAAATAT
1 AATATAATAAATATAAATAT
* *
3621371 GATATAAATAAAATATTTAATAT
1 AATAT-AAT-AAATA-TAAATAT
*
3621394 AAAAT-AT-AATATAAATAT
1 AATATAATAAATATAAATAT
* ** **
3621412 -GTATTTTAAAT-TTTATAT
1 AATATAATAAATATAAATAT
* ** *
3621430 AAAATAAATTATTTATAAATAA
1 AATAT-AA-TAAATATAAATAT
*
3621452 AATTTATATAAATATAAA-AT
1 AATATA-ATAAATATAAATAT
* *
3621472 -AT-T-TTAAATATAATTAT
1 AATATAATAAATATAAATAT
3621489 AATATAATAAA-ATAAATAT
1 AATATAATAAATATAAATAT
3621508 AATATAA
1 AATATAA
3621515 ATATATGAAT
Statistics
Matches: 101, Mismatches: 28, Indels: 30
0.64 0.18 0.19
Matches are distributed among these distances:
16 9 0.09
17 4 0.04
18 15 0.15
19 30 0.30
20 8 0.08
21 14 0.14
22 12 0.12
23 9 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
AATATAATAAATATAAATAT
Found at i:3621789 original size:31 final size:30
Alignment explanation
Indices: 3621730--3621798 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
3621720 TAAGATAATT
* *
3621730 TTTAAATATTTAGGTTTGAATTTGATTAAAAA
1 TTTAAATATTTA-GTTTAAATTTAATT-AAAA
*
3621762 TTTAAATATTTTA-TTTAAATTTAATTAAAT
1 TTTAAATA-TTTAGTTTAAATTTAATTAAAA
3621792 TTTAAAT
1 TTTAAAT
3621799 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 10 0.30
31 11 0.33
32 8 0.24
33 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTAAATATTTAGTTTAAATTTAATTAAAA
Found at i:3621924 original size:18 final size:18
Alignment explanation
Indices: 3621880--3621929 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
3621870 TATGTATAAT
3621880 TTTAACTTAAAAATTTATA
1 TTTAA-TTAAAAATTTATA
*
3621899 TTTAAATTAAAATATTTTTA
1 TTT-AATTAAAA-ATTTATA
3621919 -TTAATTAAAAA
1 TTTAATTAAAAA
3621930 AAATGTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 8 0.29
19 11 0.39
20 8 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATTAAAAATTTATA
Found at i:3623904 original size:42 final size:42
Alignment explanation
Indices: 3623841--3623930 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
3623831 CTTTTTTCTA
*
3623841 TAATAAAATTTGTATATTAAATACAAT-ATTAACAATTAATT
1 TAATAAAATTTATATATTAAATACAATAATTAACAATTAATT
* * *
3623882 TAATGAAAATTTATATATTAAATGCACTAATTAATAATTAATT
1 TAAT-AAAATTTATATATTAAATACAATAATTAACAATTAATT
3623925 TAATAA
1 TAATAA
3623931 TTTTAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 4 0.09
42 22 0.51
43 17 0.40
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (42 bp):
TAATAAAATTTATATATTAAATACAATAATTAACAATTAATT
Found at i:3624447 original size:13 final size:14
Alignment explanation
Indices: 3624429--3624465 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
3624419 AATTATAAAA
3624429 ATTATTTTA-TTTT
1 ATTATTTTATTTTT
3624442 ATTATTTTATTTTT
1 ATTATTTTATTTTT
3624456 ATTATATTTA
1 ATTAT-TTTA
3624466 AATAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTATTTTATTTTT
Found at i:3624645 original size:26 final size:26
Alignment explanation
Indices: 3624616--3624675 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
3624606 TAACCCTAAC
3624616 AATTATTTAATAAAAA-AAATTATTTAA
1 AATTATTTAATAAAAATAAA-T-TTTAA
* *
3624643 ATTTAATT-ATAAAAATAAATTTTAA
1 AATTATTTAATAAAAATAAATTTTAA
3624668 AATT-TTTA
1 AATTATTTA
3624676 TTAATTTACG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
24 2 0.07
25 8 0.30
26 8 0.30
27 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTATTTAATAAAAATAAATTTTAA
Found at i:3624840 original size:11 final size:11
Alignment explanation
Indices: 3624824--3624855 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3624814 AATTTATTTT
3624824 AATATAATAAA
1 AATATAATAAA
3624835 AATATAA-AAA
1 AATATAATAAA
3624845 AAT-TAATAAA
1 AATATAATAAA
3624855 A
1 A
3624856 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.15
10 10 0.50
11 7 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AATATAATAAA
Found at i:3624843 original size:28 final size:28
Alignment explanation
Indices: 3624780--3624843 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
3624770 TTTTATTTAG
*
3624780 TTAAAATTTTTTTAGGTATAATTTAAAAA
1 TTAAAATTTTTTTAGATATAA-TTAAAAA
3624809 TTAAAAATTTATTTTA-ATATAA-TAAAAA
1 TT-AAAATTT-TTTTAGATATAATTAAAAA
3624837 TATAAAA
1 T-TAAAA
3624844 AAATTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 11 0.35
29 3 0.10
30 12 0.39
31 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
TTAAAATTTTTTTAGATATAATTAAAAA
Found at i:3627142 original size:12 final size:12
Alignment explanation
Indices: 3627125--3627149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3627115 TAATTTTAAA
3627125 AAATATAAAAAT
1 AAATATAAAAAT
3627137 AAATATAAAAAT
1 AAATATAAAAAT
3627149 A
1 A
3627150 CGATAATAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:3634162 original size:13 final size:12
Alignment explanation
Indices: 3634142--3634180 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
3634132 TTAGCAATAA
3634142 AAAATTATTTTT
1 AAAATTATTTTT
3634154 AATAATTATTTTTT
1 AA-AATTA-TTTTT
3634168 AAAATTATATTTT
1 AAAATTAT-TTTT
3634181 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 14 0.58
14 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:3634193 original size:13 final size:13
Alignment explanation
Indices: 3634141--3634193 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 13
3634131 TTTAGCAATA
*
3634141 AAAAATTATTTTT
1 AAAAATTTTTTTT
*
3634154 AATAATTATTTTTT
1 AAAAATT-TTTTTT
3634168 AAAATTATATTTTTTT
1 AAAA--AT-TTTTTTT
3634184 AAAAATTTTT
1 AAAAATTTTT
3634194 GAAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
16 12 0.36
17 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AAAAATTTTTTTT
Found at i:3635604 original size:26 final size:26
Alignment explanation
Indices: 3635557--3635625 Score: 120
Period size: 26 Copynumber: 2.6 Consensus size: 26
3635547 AATATAATTA
3635557 TATAAAATATAAAAAATTAAAATATAT
1 TATAAAATAT-AAAAATTAAAATATAT
3635584 TATAAAATATAAAAATTAAAATATAT
1 TATAAAATATAAAAATTAAAATATAT
*
3635610 TATATAATATAAAAAT
1 TATAAAATATAAAAAT
3635626 AATATAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 31 0.76
27 10 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TATAAAATATAAAAATTAAAATATAT
Found at i:3635629 original size:11 final size:11
Alignment explanation
Indices: 3635613--3635644 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3635603 AATATATTAT
3635613 ATAATATAAAA
1 ATAATATAAAA
*
3635624 ATAATATAAAC
1 ATAATATAAAA
3635635 ATAATATAAA
1 ATAATATAAA
3635645 TATATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:3635643 original size:55 final size:57
Alignment explanation
Indices: 3635547--3635655 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 57
3635537 TTTTTAATAT
3635547 AATATAATTATATAAAATATAAAAAATTAAAATATATTATAAA-ATATAAAAATTAA
1 AATATAATTATATAAAATATAAAAAATTAAAATATATTATAAATATATAAAAATTAA
* *
3635603 AATAT-ATTATATAATATA-AAAATAATATAAACATA-A-TATAAATATATTAAAAT
1 AATATAATTATATAAAATATAAAA-AAT-TAAA-ATATATTATAAATATATAAAAAT
3635656 ATATAATTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
54 4 0.09
55 21 0.45
56 19 0.40
57 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (57 bp):
AATATAATTATATAAAATATAAAAAATTAAAATATATTATAAATATATAAAAATTAA
Found at i:3635847 original size:25 final size:27
Alignment explanation
Indices: 3635804--3635853 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3635794 ATGAATTTTT
* *
3635804 TTATTTTATATTGATATA-TAAAATAA
1 TTATTTTATATTAAAATATTAAAATAA
3635830 TTATTTT-TATTAAAATATTAAAAT
1 TTATTTTATATTAAAATATTAAAAT
3635854 TTATAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTATTTTATATTAAAATATTAAAATAA
Found at i:3641057 original size:7 final size:7
Alignment explanation
Indices: 3641023--3641051 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3641013 ACTCCAAAAA
3641023 TTTTGTT
1 TTTTGTT
3641030 TTTTGTT
1 TTTTGTT
3641037 TTTTGTT
1 TTTTGTT
3641044 TTTT-TT
1 TTTTGTT
3641050 TT
1 TT
3641052 GTTTTTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTGTT
Found at i:3641150 original size:2 final size:2
Alignment explanation
Indices: 3641143--3641177 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3641133 GGCAATTCTC
3641143 AT AT AT 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 AT AT AT A
3641178 AGAGTTTTTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3641603 original size:12 final size:13
Alignment explanation
Indices: 3641574--3641603 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3641564 AACTAAATAT
3641574 TAAATTTAAAAAA
1 TAAATTTAAAAAA
3641587 TAAATTTAAAAAA
1 TAAATTTAAAAAA
3641600 -AAAT
1 TAAAT
3641604 AAAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAATTTAAAAAA
Found at i:3644818 original size:3 final size:3
Alignment explanation
Indices: 3644810--3644845 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3644800 AATTACTATT
3644810 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3644846 GAAGAAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3645908 original size:21 final size:22
Alignment explanation
Indices: 3645866--3645922 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3645856 TTTAATCACT
*
3645866 ATTTATAAATATAATTTTTATA
1 ATTTATAAATATAATTTATATA
*
3645888 ATTTATAGATA-AATTTATATA
1 ATTTATAAATATAATTTATATA
* *
3645909 TATATATATATATA
1 -ATTTATAAATATA
3645923 TAGAGAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 9 0.31
22 19 0.66
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTATAAATATAATTTATATA
Found at i:3645929 original size:2 final size:2
Alignment explanation
Indices: 3645924--3645948 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3645914 ATATATATAT
3645924 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3645949 ATTTCAACCC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3646354 original size:16 final size:17
Alignment explanation
Indices: 3646333--3646365 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3646323 ATTAATCAAA
3646333 TAAAAATT-CAAATATT
1 TAAAAATTACAAATATT
3646349 TAAAAATTACAAATATT
1 TAAAAATTACAAATATT
3646366 ATATCCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATTACAAATATT
Found at i:3647593 original size:2 final size:2
Alignment explanation
Indices: 3647588--3647637 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
3647578 TATTTTAATG
* * *
3647588 TA TA TA -A TA TA TG TA TA TA TA TA T- TA TG TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3647628 TA TC TA TA TA
1 TA TA TA TA TA
3647638 GATGACTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3647607 original size:8 final size:8
Alignment explanation
Indices: 3647594--3647637 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
3647584 AATGTATATA
3647594 ATATATGT
1 ATATATGT
*
3647602 ATATATAT
1 ATATATGT
3647610 AT-TATGT
1 ATATATGT
3647617 ATATATGT
1 ATATATGT
*
3647625 ATATATCT
1 ATATATGT
3647633 ATATA
1 ATATA
3647638 GATGACTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:3647864 original size:20 final size:20
Alignment explanation
Indices: 3647786--3647864 Score: 51
Period size: 19 Copynumber: 4.0 Consensus size: 20
3647776 AATTAAATTA
*
3647786 ATTTTATATATT-TTTATAA
1 ATTTTATATATTATTTATAT
**
3647805 ATTTT-TATAAAATTTATAT
1 ATTTTATATATTATTTATAT
*
3647824 TTATTTA-AT-TTGA-TTATTAT
1 AT-TTTATATATT-ATTTA-TAT
*
3647844 ATTTTATATTTTATTTATAT
1 ATTTTATATATTATTTATAT
3647864 A
1 A
3647865 GATTACGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
18 4 0.09
19 19 0.42
20 17 0.38
21 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
ATTTTATATATTATTTATAT
Found at i:3649493 original size:21 final size:22
Alignment explanation
Indices: 3649458--3649498 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3649448 TATGTATGTA
*
3649458 TATATATACATAATAAAATAAT
1 TATATATACAAAATAAAATAAT
*
3649480 TATA-ATACAAAATATAATA
1 TATATATACAAAATAAAATA
3649499 TCAATTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
TATATATACAAAATAAAATAAT
Found at i:3649956 original size:2 final size:2
Alignment explanation
Indices: 3649949--3649984 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3649939 TGGAAACCGG
*
3649949 AT AT AT AT AC AT A- 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 AT AT AT AT A
3649985 GACATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3653679 original size:12 final size:12
Alignment explanation
Indices: 3653664--3653727 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
3653654 GATCTGAAAT
*
3653664 TTTATTTTATTA
1 TTTATTATATTA
3653676 TTTATTATATTA
1 TTTATTATATTA
*
3653688 TTTA-AATATTA
1 TTTATTATATTA
3653699 TTT-TTATATTAA
1 TTTATTATATT-A
*
3653711 TATTAATATATT-
1 T-TTATTATATTA
3653723 TTTAT
1 TTTAT
3653728 AATTAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 17 0.40
12 18 0.42
13 2 0.05
14 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:3653707 original size:11 final size:11
Alignment explanation
Indices: 3653671--3653728 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
3653661 AATTTTATTT
3653671 TATTATTTATTA
1 TATTATTT-TTA
**
3653683 TATTATTTAAA
1 TATTATTTTTA
3653694 TATTATTTTTA
1 TATTATTTTTA
* *
3653705 TATTAATATTA
1 TATTATTTTTA
3653716 -ATATATTTTTA
1 TAT-TATTTTTA
3653727 TA
1 TA
3653729 ATTAAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 2 0.06
11 25 0.69
12 9 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:3653708 original size:22 final size:23
Alignment explanation
Indices: 3653671--3653742 Score: 87
Period size: 23 Copynumber: 3.1 Consensus size: 23
3653661 AATTTTATTT
3653671 TATTATTTATTATATT-ATTTAAA
1 TATTATTT-TTATATTAATTTAAA
3653694 TATTATTTTTATATTAATATT-AA
1 TATTATTTTTATATTAAT-TTAAA
3653717 TA-TATTTTTATAATTAAATTTAAA
1 TATTATTTTTAT-ATT-AATTTAAA
3653741 TA
1 TA
3653743 AAAATATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
22 16 0.36
23 19 0.43
24 9 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTATTTTTATATTAATTTAAA
Found at i:3654757 original size:8 final size:8
Alignment explanation
Indices: 3654744--3654844 Score: 56
Period size: 8 Copynumber: 12.9 Consensus size: 8
3654734 GTAATATTAA
*
3654744 ATATAATT
1 ATATAAAT
3654752 ATAT-AA-
1 ATATAAAT
3654758 ATAT-AAT
1 ATATAAAT
*
3654765 ATAAAAAT
1 ATATAAAT
3654773 A-ATTAAA-
1 ATA-TAAAT
3654780 ATATAATAT
1 ATATAA-AT
3654789 ATTATAAAT
1 A-TATAAAT
3654798 ATATAAAT
1 ATATAAAT
*
3654806 ATTTTAAAAT
1 A-TAT-AAAT
*
3654816 TTATATAAT
1 ATATA-AAT
3654825 ATA-AAAT
1 ATATAAAT
3654832 AT-T-AAT
1 ATATAAAT
3654838 ATATAAA
1 ATATAAA
3654845 AATTTATATA
Statistics
Matches: 73, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
6 11 0.15
7 15 0.21
8 25 0.34
9 13 0.18
10 9 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:3654768 original size:11 final size:11
Alignment explanation
Indices: 3654752--3654789 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3654742 AAATATAATT
3654752 ATATAAATATA
1 ATATAAATATA
*
3654763 ATATAAAAATA
1 ATATAAATATA
3654774 AT-TAAAATATA
1 ATAT-AAATATA
3654785 ATATA
1 ATATA
3654790 TTATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAAATATA
Found at i:3654787 original size:27 final size:25
Alignment explanation
Indices: 3654735--3654796 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
3654725 TTTAGCCTCG
* *
3654735 TAATATTAAATATAATTATATAAATA
1 TAATA-TAAAAATAATTAAATAAATA
3654761 TAATATAAAAATAATTAAAATATAATA
1 TAATATAAAAATAATT-AAATA-AATA
*
3654788 TATTATAAA
1 TAATATAAA
3654797 TATATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.32
26 9 0.29
27 12 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TAATATAAAAATAATTAAATAAATA
Found at i:3654799 original size:33 final size:34
Alignment explanation
Indices: 3654737--3654856 Score: 95
Period size: 33 Copynumber: 3.5 Consensus size: 34
3654727 TAGCCTCGTA
*
3654737 ATATT-AAATATAATTATATAAATATAATATAAAAAT
1 ATATTAAAATATAA-TATAT-TATA-AATATAAAAAT
*
3654773 A-ATTAAAATATAATATATTATAAATATATAAAT
1 ATATTAAAATATAATATATTATAAATATAAAAAT
* * * **
3654806 ATTTTAAAAT-TTATATAATATAAA-ATATTAAT
1 ATATTAAAATATAATATATTATAAATATAAAAAT
* *
3654838 ATATAAAAATTTATATATA
1 ATATTAAAATATA-ATATA
3654857 ATATTTTTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
32 15 0.21
33 24 0.34
34 15 0.21
35 8 0.11
36 9 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
ATATTAAAATATAATATATTATAAATATAAAAAT
Found at i:3654846 original size:16 final size:16
Alignment explanation
Indices: 3654777--3654857 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 16
3654767 AAAAATAATT
3654777 AAAATA-TAATATATTA
1 AAAATATTAATATA-TA
* * *
3654793 TAAATATATAAATATTTT
1 -AAA-ATATTAATATATA
3654811 AAAAT-TT-ATATAATA
1 AAAATATTAATAT-ATA
3654826 TAAAATATTAATATATA
1 -AAAATATTAATATATA
3654843 AAAAT-TT-ATATATA
1 AAAATATTAATATATA
3654857 A
1 A
3654858 TATTTTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
14 12 0.23
15 4 0.08
16 12 0.23
17 11 0.21
18 8 0.15
19 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATATTAATATATA
Found at i:3654847 original size:32 final size:32
Alignment explanation
Indices: 3654758--3654854 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 32
3654748 AATTATATAA
* *
3654758 ATATAATATAAAA-A-TAAT-TA-AAATA-TA
1 ATATAATATAAAATATTAATATATAAAAATTT
* * * *
3654785 ATATATTATAAATATATAAATATTTTAAAATTT
1 ATATAATATAAA-ATATTAATATATAAAAATTT
3654818 ATATAATATAAAATATTAATATATAAAAATTT
1 ATATAATATAAAATATTAATATATAAAAATTT
3654850 ATATA
1 ATATA
3654855 TAATATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
27 11 0.20
28 1 0.02
29 1 0.02
30 3 0.06
31 1 0.02
32 25 0.46
33 12 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAATATAAAATATTAATATATAAAAATTT
Found at i:3655234 original size:18 final size:17
Alignment explanation
Indices: 3655211--3655246 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3655201 ATAATTCTTT
*
3655211 AATAATTTTTTCTAAAAA
1 AATAATTTTCT-TAAAAA
3655229 AATAATTTTCTTAAAAA
1 AATAATTTTCTTAAAAA
3655246 A
1 A
3655247 TAAAAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAATTTTCTTAAAAA
Found at i:3655239 original size:16 final size:16
Alignment explanation
Indices: 3655218--3655249 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3655208 TTTAATAATT
3655218 TTTTCTAAAAAAATAA
1 TTTTCTAAAAAAATAA
*
3655234 TTTTCTTAAAAAATAA
1 TTTTCTAAAAAAATAA
3655250 AAATACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTCTAAAAAAATAA
Found at i:3656859 original size:31 final size:31
Alignment explanation
Indices: 3656804--3656864 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
3656794 TATTACTTAT
*
3656804 ATTATAAAAATGGAAAAATGGAAA-TAAAAG
1 ATTAAAAAAATGGAAAAATGGAAATTAAAAG
*
3656834 ATTAAAAAAATTGAAAATATGGAAATTAAAA
1 ATTAAAAAAATGGAAAA-ATGGAAATTAAAA
3656865 AAAAAAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 15 0.56
31 7 0.26
32 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (31 bp):
ATTAAAAAAATGGAAAAATGGAAATTAAAAG
Found at i:3663108 original size:2 final size:2
Alignment explanation
Indices: 3663103--3663132 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3663093 CCCCCCTTTT
3663103 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3663133 AATGAACAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3667239 original size:18 final size:17
Alignment explanation
Indices: 3667216--3667254 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3667206 ATATTATTTT
*
3667216 TTATATCATATTATATAA
1 TTATATCATATT-TAAAA
*
3667234 TTATATTATATTTAAAA
1 TTATATCATATTTAAAA
3667251 TTAT
1 TTAT
3667255 CAAATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATCATATTTAAAA
Found at i:3667327 original size:11 final size:11
Alignment explanation
Indices: 3667306--3667335 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3667296 CAACAAATAA
3667306 TATTCATATTTT
1 TATT-ATATTTT
3667318 TATTATATTTT
1 TATTATATTTT
3667329 TATTATA
1 TATTATA
3667336 ATTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATATTTT
Found at i:3667731 original size:2 final size:2
Alignment explanation
Indices: 3667724--3667759 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3667714 ACTATACATA
3667724 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
3667760 CATACTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3668334 original size:18 final size:17
Alignment explanation
Indices: 3668313--3668354 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3668303 TTATGAAAAA
3668313 TTAAAAT-ATAAAAAATAT
1 TTAAAATAAT-AAAAAT-T
*
3668331 TTAAAGTAATAAAAATT
1 TTAAAATAATAAAAATT
3668348 TTAAAAT
1 TTAAAAT
3668355 TTTAAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 12 0.57
19 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAAAATAATAAAAATT
Found at i:3668365 original size:25 final size:28
Alignment explanation
Indices: 3668324--3668377 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
3668314 TAAAATATAA
3668324 AAAATATTTAAAGTAA-TAAA-AATTTT
1 AAAATATTTAAAGTAATTAAATAATTTT
3668350 AAAAT-TTT-AAGATAATTAAATAATTTT
1 AAAATATTTAAAG-TAATTAAATAATTTT
3668377 A
1 A
3668378 TTTAAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 3 0.12
25 6 0.24
26 9 0.36
27 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATATTTAAAGTAATTAAATAATTTT
Found at i:3668844 original size:10 final size:9
Alignment explanation
Indices: 3668802--3668852 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
3668792 GTGTTTAAAA
3668802 TTATTATTAT
1 TTATTATT-T
*
3668812 TTAATATTT
1 TTATTATTT
*
3668821 TT-TAATTT
1 TTATTATTT
3668829 TATATTATATT
1 T-TATTAT-TT
3668840 TTATTATTT
1 TTATTATTT
3668849 TTAT
1 TTAT
3668853 ATTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 5 0.15
9 10 0.29
10 16 0.47
11 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTATTATTT
Found at i:3668852 original size:21 final size:21
Alignment explanation
Indices: 3668801--3668861 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
3668791 GGTGTTTAAA
*
3668801 ATTATTATTAT-TTAATATTTT
1 ATTATTTTTATATT-ATATTTT
*
3668822 -TTAATTTTATATTATATTTT
1 ATTATTTTTATATTATATTTT
3668842 ATTATTTTTATATTA-ATTTT
1 ATTATTTTTATATTATATTTT
3668862 TATGTTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATTTTTATATTATATTTT
Found at i:3668862 original size:21 final size:22
Alignment explanation
Indices: 3668801--3668864 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 22
3668791 GGTGTTTAAA
*
3668801 ATTATTATTAT-TTAATATTTT
1 ATTATTTTTATATTAATATTTT
*
3668822 -TTAATTTTATATT-ATATTTT
1 ATTATTTTTATATTAATATTTT
3668842 ATTATTTTTATATTAAT-TTTT
1 ATTATTTTTATATTAATATTTT
3668863 AT
1 AT
3668865 GTTATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 15 0.41
21 20 0.54
22 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTATTTTTATATTAATATTTT
Found at i:3668870 original size:38 final size:39
Alignment explanation
Indices: 3668802--3668878 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
3668792 GTGTTTAAAA
*
3668802 TTATTATTATTTAATATTTTTTAATTTTAT-ATTATATT
1 TTATTATTATTTAATATTTTTTAATGTTATAATTATATT
*
3668840 TTATTATT-TTT-ATATTAATTTTTATGTTATAATTATATT
1 TTATTATTATTTAATATT--TTTTAATGTTATAATTATATT
3668879 AAATGTATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 5 0.15
37 3 0.09
38 18 0.53
39 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (39 bp):
TTATTATTATTTAATATTTTTTAATGTTATAATTATATT
Found at i:3668915 original size:21 final size:23
Alignment explanation
Indices: 3668872--3668916 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
3668862 TATGTTATAA
3668872 TTATATTAAATGTATTGTATATT
1 TTATATTAAATGTATTGTATATT
3668895 TTATA-TAAAT-T-TTGATATATT
1 TTATATTAAATGTATTG-TATATT
3668916 T
1 T
3668917 ATTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 5 0.24
23 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
TTATATTAAATGTATTGTATATT
Found at i:3668921 original size:23 final size:24
Alignment explanation
Indices: 3668871--3668921 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
3668861 TTATGTTATA
3668871 ATTATATTAAATGTATTGTATATT
1 ATTATATTAAATGTATTGTATATT
3668895 -TTATA-TAAAT-T-TTGATATATTT
1 ATTATATTAAATGTATTG-TATA-TT
3668917 ATTAT
1 ATTAT
3668922 TTATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 3 0.12
21 5 0.21
22 7 0.29
23 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
ATTATATTAAATGTATTGTATATT
Found at i:3668945 original size:32 final size:32
Alignment explanation
Indices: 3668891--3668951 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3668881 ATGTATTGTA
* * *
3668891 TATTTTATATAAATTTTGATATATTTATTATT
1 TATTTAATATAAAATTTAATATATTTATTATT
*
3668923 TATTTAATTTAAAATTTAATATATTTATT
1 TATTTAATATAAAATTTAATATATTTATT
3668952 TATTAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
TATTTAATATAAAATTTAATATATTTATTATT
Found at i:3668967 original size:28 final size:29
Alignment explanation
Indices: 3668918--3668996 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
3668908 GATATATTTA
*
3668918 TTATTTATTTAAT-TTAAAATTTAAT-ATAT
1 TTATTTA-TTAATATT-ATATTTAATGATAT
3668947 TTATTTATTAATATTATATTT-ATGATAT
1 TTATTTATTAATATTATATTTAATGATAT
* *
3668975 TT-TTTATCATATAATATATTTA
1 TTATTTATTA-ATATTATATTTA
3668997 TATTAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 8 0.19
28 26 0.60
29 9 0.21
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (29 bp):
TTATTTATTAATATTATATTTAATGATAT
Found at i:3669025 original size:20 final size:20
Alignment explanation
Indices: 3668997--3669052 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
3668987 AATATATTTA
*
3668997 TATTAAAATATATTAAATAT
1 TATTTAAATATATTAAATAT
* *
3669017 TATTTAAATAATTTTAAATTT
1 TATTTAAAT-ATATTAAATAT
3669038 TATTT-AATATATTAA
1 TATTTAAATATATTAA
3669053 GTTTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 6 0.19
20 11 0.35
21 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTAAATATATTAAATAT
Found at i:3669063 original size:20 final size:20
Alignment explanation
Indices: 3668992--3669061 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3668982 CATATAATAT
3668992 ATTTATATTAAAATATATTAA
1 ATTTATATT-AAATATATTAA
*
3669013 ATATTAT-TTAAATAATTTTAA
1 AT-TTATATTAAAT-ATATTAA
*
3669034 ATTT-TATTTAATATATTAA
1 ATTTATATTAAATATATTAA
*
3669053 GTTTATATT
1 ATTTATATT
3669062 TATATTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
19 10 0.24
20 15 0.37
21 12 0.29
22 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
ATTTATATTAAATATATTAA
Found at i:3670996 original size:25 final size:25
Alignment explanation
Indices: 3670968--3671041 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
3670958 AATATTATTT
3670968 TTTAAATATTATATATTTATATAAA
1 TTTAAATATTATATATTTATATAAA
* * **
3670993 TTTAAATATT-TTTATTATATTTATT
1 TTTAAATATTATATATT-TATATAAA
*
3671018 TTTATTATATTATAT-TTTATATAA
1 TTTA-AATATTATATATTTATATAA
3671042 TAATTTAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
24 5 0.13
25 24 0.63
26 7 0.18
27 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTAAATATTATATATTTATATAAA
Found at i:3671019 original size:15 final size:16
Alignment explanation
Indices: 3670959--3671035 Score: 70
Period size: 15 Copynumber: 4.8 Consensus size: 16
3670949 TGTATTCGTA
*
3670959 ATATTAT-TTTTTA-A
1 ATATTATATTTTTATT
*
3670973 ATATTATATATTTATAT
1 ATATTATATTTTTAT-T
*
3670990 AAATTTAAATATTTTTATT
1 ATA-TT--ATATTTTTATT
3671009 ATATT-TATTTTTATT
1 ATATTATATTTTTATT
3671024 ATATTATATTTT
1 ATATTATATTTT
3671036 ATATAATAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 7 0.14
15 20 0.39
16 6 0.12
17 2 0.04
18 4 0.08
19 3 0.06
20 9 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTATATTTTTATT
Found at i:3671270 original size:30 final size:28
Alignment explanation
Indices: 3671235--3671305 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
3671225 TAATCCATAT
* *
3671235 ATTTATAAACTTTTTTATTATATTATAATA
1 ATTTATAAAATATTTTA-TAT-TTATAATA
3671265 ATTTATAAAATATTTTATATTTAT-ATAA
1 ATTTATAAAATATTTTATATTTATAAT-A
*
3671293 ATTT-TAATATATT
1 ATTTATAAAATATT
3671306 AACGACTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 10 0.27
28 9 0.24
29 3 0.08
30 15 0.41
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTATAAAATATTTTATATTTATAATA
Found at i:3671302 original size:18 final size:18
Alignment explanation
Indices: 3671254--3671302 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
3671244 CTTTTTTATT
3671254 ATATTATAATAATTTATAAA
1 ATATT-TAAT-ATTTATAAA
*
3671274 ATATTTTATATTTATATAA
1 ATATTTAATATTTATA-AA
3671293 AT-TTTAATAT
1 ATATTTAATAT
3671303 ATTAACGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTAATATTTATAAA
Found at i:3676361 original size:19 final size:19
Alignment explanation
Indices: 3676339--3676401 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
3676329 GTTCCTTGTA
*
3676339 TATTAAATTTTAAATAAAT
1 TATTAAATTTTAAATTAAT
*
3676358 TATTTTAATTTT-AATTAAT
1 TA-TTAAATTTTAAATTAAT
*
3676377 TAATTTAA-TTTAAATTAAT
1 T-ATTAAATTTTAAATTAAT
3676396 TATTAA
1 TATTAA
3676402 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.18
19 22 0.58
20 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTAAATTTTAAATTAAT
Found at i:3676454 original size:23 final size:23
Alignment explanation
Indices: 3676397--3676454 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
3676387 TAAATTAATT
*
3676397 ATTAATTAATAAAAATTATTAAA
1 ATTAATTAATAAAAATTATAAAA
*
3676420 ATTAAATT-AT-AAAAGTATAAAAA
1 ATT-AATTAATAAAAATTAT-AAAA
3676443 ATTAATTAATAA
1 ATTAATTAATAA
3676455 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 11 0.38
23 13 0.45
24 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTAATTAATAAAAATTATAAAA
Found at i:3676883 original size:16 final size:16
Alignment explanation
Indices: 3676864--3676894 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3676854 TGTAATTATT
*
3676864 TAATAATTTTAATAAA
1 TAATAATTTAAATAAA
3676880 TAATAATTTAAATAA
1 TAATAATTTAAATAA
3676895 TTAAAAGAAT
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):
TAATAATTTAAATAAA
Found at i:3677061 original size:2 final size:2
Alignment explanation
Indices: 3677054--3677083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3677044 TTTTTCTTAC
3677054 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
3677084 TTTGTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3677523 original size:14 final size:14
Alignment explanation
Indices: 3677504--3677540 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3677494 CCAAAGGTTC
3677504 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
*
3677518 TTTCTTTCTTTTTT
1 TTTCTTTCTTTCTT
*
3677532 TTTCCTTCT
1 TTTCTTTCT
3677541 ATATTATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTCTT
Found at i:3682898 original size:25 final size:25
Alignment explanation
Indices: 3682864--3682911 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3682854 GCTTTTTTTT
* *
3682864 TTTTTTTTTCCTTTTCTTCGTTTCC
1 TTTTCTTTTCCTCTTCTTCGTTTCC
*
3682889 TTTTCTTTTCCTCTTCTTGGTTT
1 TTTTCTTTTCCTCTTCTTCGTTT
3682912 TAACAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTTCTTTTCCTCTTCTTCGTTTCC
Found at i:3683340 original size:15 final size:16
Alignment explanation
Indices: 3683304--3683337 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3683294 ACCATTTTTA
3683304 AAATAAAAAAGAAAAT
1 AAATAAAAAAGAAAAT
3683320 AAATAAAAACA-AAAAT
1 AAATAAAAA-AGAAAAT
3683336 AA
1 AA
3683338 TAACCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAATAAAAAAGAAAAT
Found at i:3684054 original size:19 final size:21
Alignment explanation
Indices: 3684015--3684065 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
3684005 TTATCCATCA
3684015 AATTTAAATATGATAATTTAT
1 AATTTAAATATGATAATTTAT
*
3684036 AATTTAAAT-T-ATTATTTAT
1 AATTTAAATATGATAATTTAT
*
3684055 ATAATTAAATA
1 A-ATTTAAATA
3684066 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
21 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTTAAATATGATAATTTAT
Found at i:3684070 original size:19 final size:21
Alignment explanation
Indices: 3684015--3684071 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3684005 TTATCCATCA
* *
3684015 AATTTAAATATGATAATT-TAT
1 AATTTAAAT-TAATATTTATAT
*
3684036 AATTTAAATTATTATTTATAT
1 AATTTAAATTAATATTTATAT
3684057 AA-TTAAA-TAATATTT
1 AATTTAAATTAATATTT
3684072 TTATTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.23
20 10 0.32
21 14 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTTAAATTAATATTTATAT
Found at i:3684658 original size:25 final size:26
Alignment explanation
Indices: 3684591--3684661 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 26
3684581 AGCTCATGAG
*
3684591 ATAATAAATGTTTTATTTAATTTTTTT
1 ATAATAAATATTTTA-TTAATTTTTTT
3684618 ATATATGAAATATTTTATTAATTTTATTT
1 ATA-AT-AAATATTTTATTAATTTT-TTT
3684647 ATAA-AAAT-TTTTATT
1 ATAATAAATATTTTATT
3684662 TTTATAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 7 0.17
26 4 0.10
27 3 0.08
28 11 0.28
29 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (26 bp):
ATAATAAATATTTTATTAATTTTTTT
Found at i:3684731 original size:13 final size:13
Alignment explanation
Indices: 3684713--3684753 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3684703 TTAATTAAAA
*
3684713 ATATATTTAATTT
1 ATATATTAAATTT
3684726 ATATATTAAATTT
1 ATATATTAAATTT
*
3684739 ATAT-TTAAAATT
1 ATATATTAAATTT
3684751 ATA
1 ATA
3684754 AAATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATTAAATTT
Found at i:3684747 original size:12 final size:12
Alignment explanation
Indices: 3684714--3684753 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3684704 TAATTAAAAA
3684714 TATATTT-AATT
1 TATATTTAAATT
3684725 TATATATTAAATT
1 TATAT-TTAAATT
*
3684738 TATATTTAAAAT
1 TATATTTAAATT
3684750 TATA
1 TATA
3684754 AAATATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 12 0.46
13 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATTTAAATT
Found at i:3684761 original size:23 final size:22
Alignment explanation
Indices: 3684735--3684787 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
3684725 TATATATTAA
3684735 ATTTATATTTAAAATTATAAAAT
1 ATTTATATTT-AAATTATAAAAT
* * **
3684758 ATTTTTAATTTATATTATATTAT
1 ATTTAT-ATTTAAATTATAAAAT
3684781 ATTTATA
1 ATTTATA
3684788 AAATTAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.04
23 19 0.79
24 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATATTTAAATTATAAAAT
Found at i:3684798 original size:43 final size:44
Alignment explanation
Indices: 3684701--3684804 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 44
3684691 ATTTACGTAT
3684701 AATTAATTAAAAATATATTTAATTTATATATTAAATTTATATTTAA
1 AATTAA-T-AAAATATATTTAATTTATATATTAAATTTATATTTAA
* *
3684747 AATT-ATAAAATATTTTTAA-TT-TATATTATA-TTATATTTATAA
1 AATTAATAAAATATATTTAATTTATATATTAAATTTATA-TT-TAA
3684789 AATTAATAAAAATATA
1 AATTAAT-AAAATATA
3684805 AAATATGATA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
40 5 0.10
41 10 0.20
42 9 0.18
43 14 0.27
44 8 0.16
45 1 0.02
46 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (44 bp):
AATTAATAAAATATATTTAATTTATATATTAAATTTATATTTAA
Found at i:3684806 original size:17 final size:17
Alignment explanation
Indices: 3684784--3684854 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 17
3684774 ATATTATATT
3684784 TATAAAATTAATAAAAA
1 TATAAAATTAATAAAAA
*
3684801 TATAAAATATGATATATAAA
1 TATAAAAT-T-A-ATAAAAA
*
3684821 TATAAATTTTTAATAAAAA
1 TATAAA--ATTAATAAAAA
*
3684840 -ATATGAATTAATAAA
1 TATA-AAATTAATAAA
3684855 TTTAATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
17 16 0.37
18 4 0.09
19 8 0.19
20 13 0.30
21 1 0.02
22 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TATAAAATTAATAAAAA
Found at i:3685344 original size:22 final size:23
Alignment explanation
Indices: 3685319--3685361 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3685309 AATAATTATA
3685319 TAAAATAATTATTTTA-AAAATT
1 TAAAATAATTATTTTATAAAATT
*
3685341 TAAAATAATTTTTTTATAAAA
1 TAAAATAATTATTTTATAAAA
3685362 AATCACGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATAATTATTTTATAAAATT
Found at i:3686239 original size:16 final size:17
Alignment explanation
Indices: 3686197--3686239 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
3686187 TTTAATATTT
*
3686197 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
3686214 ATAAAA-TTATAA-TAA
1 ATAAAATTTATAATTAA
3686229 ATAAAATTTAT
1 ATAAAATTTAT
3686240 TTTGATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3686294 original size:18 final size:19
Alignment explanation
Indices: 3686257--3686306 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
3686247 TAATACGAAT
* *
3686257 ATATTATTAATAATATATAA
1 ATATTATGATTAA-ATATAA
*
3686277 ATTTTAT-ATTAAATATAA
1 ATATTATGATTAAATATAA
3686295 ATATTATGATTA
1 ATATTATGATTA
3686307 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.46
19 8 0.31
20 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTATGATTAAATATAA
Found at i:3687246 original size:22 final size:20
Alignment explanation
Indices: 3687188--3687248 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
3687178 AATATGACAT
*
3687188 TAAAATAATTAAAACATAATA
1 TAAAA-AATAAAAACATAATA
3687209 TAAAAAATAAATAACATGAATA
1 TAAAAAATAAA-AACAT-AATA
*
3687231 TAAAAATATATAAACATA
1 TAAAAA-ATAAAAACATA
3687249 TATGTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 5 0.14
21 11 0.31
22 15 0.43
23 4 0.11
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAAATAAAAACATAATA
Found at i:3687358 original size:12 final size:13
Alignment explanation
Indices: 3687329--3687370 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
3687319 TTAACTTTTC
*
3687329 CTTTTATTTCTCT
1 CTTTTATTTCTTT
*
3687342 ATTTT-TTTCTTT
1 CTTTTATTTCTTT
3687354 CTTTTATTT-TTT
1 CTTTTATTTCTTT
3687366 CTTTT
1 CTTTT
3687371 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTATTTCTTT
Found at i:3687358 original size:25 final size:26
Alignment explanation
Indices: 3687329--3687379 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3687319 TTAACTTTTC
3687329 CTTTTA-TTTCTCTATTTTTTTCTTT
1 CTTTTATTTTCTCTATTTTTTTCTTT
* *
3687354 CTTTTATTTTTTCTTTTTTTTTCTTT
1 CTTTTATTTTCTCTATTTTTTTCTTT
3687380 TCATCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (26 bp):
CTTTTATTTTCTCTATTTTTTTCTTT
Found at i:3687370 original size:22 final size:23
Alignment explanation
Indices: 3687345--3687390 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3687335 TTTCTCTATT
*
3687345 TTTTTCTTTCTTTT-ATTTTTTC
1 TTTTTCTTTCTTTTCATCTTTTC
*
3687367 TTTTTTTTTCTTTTCATCTTTTC
1 TTTTTCTTTCTTTTCATCTTTTC
3687390 T
1 T
3687391 CTCCCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTCTTTTCATCTTTTC
Found at i:3687375 original size:12 final size:12
Alignment explanation
Indices: 3687324--3687375 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3687314 AATACTTAAC
* *
3687324 TTTTCCTTTTAT
1 TTTTCTTTTTTT
*
3687336 TTCTCTATTTTTT
1 TTTTCT-TTTTTT
*
3687349 TCTTTCTTTTATT
1 T-TTTCTTTTTTT
3687362 TTTTCTTTTTTT
1 TTTTCTTTTTTT
3687374 TT
1 TT
3687376 CTTTTCATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:3687380 original size:16 final size:16
Alignment explanation
Indices: 3687344--3687373 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3687334 ATTTCTCTAT
3687344 TTTTTTCTTTCTTTTA
1 TTTTTTCTTTCTTTTA
3687360 TTTTTTCTTT-TTTT
1 TTTTTTCTTTCTTTT
3687374 TTCTTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTCTTTCTTTTA
Found at i:3687388 original size:23 final size:23
Alignment explanation
Indices: 3687344--3687390 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3687334 ATTTCTCTAT
*
3687344 TTTTTTCTTTCTTTTATTTTTTC
1 TTTTTTCTTTCTTTTATCTTTTC
3687367 TTTTTT-TTTCTTTTCATCTTTTC
1 TTTTTTCTTTCTTTT-ATCTTTTC
3687390 T
1 T
3687391 CTCCCATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTCTTTCTTTTATCTTTTC
Found at i:3687573 original size:23 final size:22
Alignment explanation
Indices: 3687538--3687589 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 22
3687528 CCAATACACG
3687538 AATATATTAAAATATAAATAAATT
1 AATA-ATTAAAATATAAA-AAATT
3687562 AATAATTAAAATATAAAAAATT
1 AATAATTAAAATATAAAAAATT
3687584 ATATAA
1 A-ATAA
3687590 ATTTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 6 0.22
23 17 0.63
24 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAATTAAAATATAAAAAATT
Found at i:3689819 original size:2 final size:2
Alignment explanation
Indices: 3689806--3689849 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3689796 TTTGAGGTTC
*
3689806 AT AT AT AG 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
3689848 AT
1 AT
3689850 TTTAAACCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3698981 original size:5 final size:5
Alignment explanation
Indices: 3698967--3698997 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3698957 ATATATATAG
*
3698967 ATTAA GTTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
3698998 AAAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:3699741 original size:28 final size:28
Alignment explanation
Indices: 3699705--3699786 Score: 67
Period size: 31 Copynumber: 2.7 Consensus size: 28
3699695 AATTTTTAAT
3699705 TAAATTTTAATTAAATAAAATTA-AAGTAA
1 TAAA-TTTAATTAAATAAAATTACAA-TAA
* *
3699734 TAAATTTACTTAAGATAATAAAATACAATAA
1 TAAATTTAATTAA-AT-A-AAATTACAATAA
*
3699765 TAAATATTAATCAAAATAAAAT
1 TAAAT-TTAAT-TAAATAAAAT
3699787 AAAATATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
28 8 0.19
29 6 0.14
30 4 0.10
31 14 0.33
32 8 0.19
33 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAATTTAATTAAATAAAATTACAATAA
Found at i:3706941 original size:24 final size:25
Alignment explanation
Indices: 3706911--3706979 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
3706901 TAAAAAAACC
3706911 ATTTATATTAATTTTTTATAATTT-T
1 ATTTATATTAATTTTTT-TAATTTAT
*
3706936 A-TTATATTAAAATTTTTTAATTTAT
1 ATTTATATT-AATTTTTTTAATTTAT
* *
3706961 ATTTAAATAAATTTTTTTA
1 ATTTATATTAATTTTTTTA
3706980 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 13 0.35
25 19 0.51
26 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTATATTAATTTTTTTAATTTAT
Found at i:3707383 original size:21 final size:21
Alignment explanation
Indices: 3707357--3707413 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3707347 AATAATGATG
* *
3707357 ATAAAATTAATTATTATATCA
1 ATAAAATTAAATATTATAACA
3707378 ATAAAATTAAATATTATAACA
1 ATAAAATTAAATATTATAACA
3707399 ATAAAATTAAA-ATTA
1 ATAAAATTAAATATTA
3707414 ATGATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAAATTAAATATTATAACA
Found at i:3708146 original size:2 final size:2
Alignment explanation
Indices: 3708141--3708172 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3708131 GCACACACAC
3708141 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
3708173 CGAGTGCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3715178 original size:60 final size:59
Alignment explanation
Indices: 3715105--3715226 Score: 217
Period size: 60 Copynumber: 2.1 Consensus size: 59
3715095 CTTAATTCCC
*
3715105 AAAAGTTGGATAGGGTGGCATTTAATGTAAGGAAGGATTACACTGACCCCAATTTTTATG
1 AAAAGTTGGATAGGGTGGCATTTAATATAAGGAAGGATTACACTGA-CCCAATTTTTATG
*
3715165 AAAAGTTGGATAGGGTGGCATTTAATATAAGGAAGGATTACATTGACCCAATTTTTATG
1 AAAAGTTGGATAGGGTGGCATTTAATATAAGGAAGGATTACACTGACCCAATTTTTATG
3715224 AAA
1 AAA
3715227 TACAAGGTGC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 16 0.27
60 44 0.73
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (59 bp):
AAAAGTTGGATAGGGTGGCATTTAATATAAGGAAGGATTACACTGACCCAATTTTTATG
Done.