Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 177 of 182
Found at i:53760470 original size:25 final size:25
Alignment explanation
Indices: 53760418--53760468 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
53760408 CATTCAATGT
*
53760418 AATAAATAATTTTAAATGATTATAA
1 AATAAATAATTTAAAATGATTATAA
53760443 AATAAATAA-TTAAAAT-ATTTATAA
1 AATAAATAATTTAAAATGA-TTATAA
53760467 AA
1 AA
53760469 ATTTTATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.58
25 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAAATAATTTAAAATGATTATAA
Found at i:53766518 original size:29 final size:30
Alignment explanation
Indices: 53766462--53766534 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
53766452 AACTACACAT
*
53766462 GAACTATGATTTAATGTGCAATTGTATACAC
1 GAACTTTGATTT-ATGTGCAATTGTATACAC
* * *
53766493 GAACTTTGATTT-TGTGTAATTTTATACAT
1 GAACTTTGATTTATGTGCAATTGTATACAC
*
53766522 GAAATTTTGATTT
1 G-AACTTTGATTT
53766535 GATTCAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.42
30 10 0.28
31 11 0.31
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (30 bp):
GAACTTTGATTTATGTGCAATTGTATACAC
Found at i:53767004 original size:5 final size:5
Alignment explanation
Indices: 53766994--53767018 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53766984 AGTTTCTTAA
53766994 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
53767019 TATCGTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:53770391 original size:17 final size:17
Alignment explanation
Indices: 53770359--53770410 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
53770349 AAACGGTTGA
53770359 CATAGAATAGACAGTTC-G
1 CATA-AATA-ACAGTTCAG
53770377 CATAAAATAACAGTTCATG
1 CAT-AAATAACAGTTCA-G
53770396 CAT-AATAACAGTTCA
1 CATAAATAACAGTTCA
53770411 TTCAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 19 0.61
18 7 0.23
19 5 0.16
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (17 bp):
CATAAATAACAGTTCAG
Found at i:53771737 original size:15 final size:15
Alignment explanation
Indices: 53771713--53771755 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
53771703 TTAAGCACAT
53771713 TAAA-CAAGAATTAA
1 TAAATCAAGAATTAA
* *
53771727 TATATCAAGAA-TAC
1 TAAATCAAGAATTAA
53771741 TAAATCAAGAATTAA
1 TAAATCAAGAATTAA
53771756 GCACACATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (15 bp):
TAAATCAAGAATTAA
Found at i:53772191 original size:25 final size:25
Alignment explanation
Indices: 53772138--53772183 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
53772128 GTTGGATCCA
53772138 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
53772163 AATTAAA-TCTAAACA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
53772184 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:53772256 original size:9 final size:9
Alignment explanation
Indices: 53772244--53772274 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
53772234 TATAAACAAT
53772244 ATAATAATC
1 ATAATAATC
53772253 ATAATAATC
1 ATAATAATC
53772262 ATAATAATC
1 ATAATAATC
53772271 ATAA
1 ATAA
53772275 ATATTAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAATAATC
Found at i:53772256 original size:18 final size:19
Alignment explanation
Indices: 53772235--53772275 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
53772225 AAAGATAAAT
53772235 ATAAACAAT-ATAATAATC
1 ATAAACAATCATAATAATC
*
53772253 AT-AATAATCATAATAATC
1 ATAAACAATCATAATAATC
53772271 ATAAA
1 ATAAA
53772276 TATTAATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAACAATCATAATAATC
Found at i:53773146 original size:25 final size:25
Alignment explanation
Indices: 53773118--53773168 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
53773108 AAAATTGAAA
**
53773118 TGGTTTGCACTGAGAGAAATCAAGG
1 TGGTTTGCACCAAGAGAAATCAAGG
*
53773143 TGGTTTGCGCCAAGAGAAATCAAGG
1 TGGTTTGCACCAAGAGAAATCAAGG
53773168 T
1 T
53773169 TCACATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (25 bp):
TGGTTTGCACCAAGAGAAATCAAGG
Found at i:53777710 original size:60 final size:59
Alignment explanation
Indices: 53777604--53777719 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 59
53777594 AATATATTTT
* * * * * * *
53777604 TTAATTTTTAGAGTTAGGACTAAATTGATAGATTTTATAAATATTGAAGGTTAAATCTA
1 TTAATTTTTAGAATTAGAACTAAAATGACAAATTTTATAAACATTGAAGGCTAAATCTA
* * *
53777663 TTAATTTTATAGAATTAGAATTAAAATGACAAATTTTGTAAACATTGAGGGCTAAAT
1 TTAATTTT-TAGAATTAGAACTAAAATGACAAATTTTATAAACATTGAAGGCTAAAT
53777720 TTGTTGATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
59 8 0.17
60 38 0.83
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (59 bp):
TTAATTTTTAGAATTAGAACTAAAATGACAAATTTTATAAACATTGAAGGCTAAATCTA
Found at i:53779573 original size:24 final size:26
Alignment explanation
Indices: 53779528--53779576 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
53779518 GAGGAAAGAA
*
53779528 AAAAAAAAACATAAGATTTAAAAGTT
1 AAAAAAAAACATAAGATATAAAAGTT
*
53779554 AAAAGAAAACA-AA-ATATAAAAGT
1 AAAAAAAAACATAAGATATAAAAGT
53779577 AAATTGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.18
Consensus pattern (26 bp):
AAAAAAAAACATAAGATATAAAAGTT
Found at i:53781405 original size:20 final size:20
Alignment explanation
Indices: 53781359--53781417 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
53781349 TGACAAAAAA
* *
53781359 ATTTATTAATATAATTTTAAT
1 ATTT-TTAATATATTTTTAAG
*
53781380 AATTTTAATATATTTTTAAG
1 ATTTTTAATATATTTTTAAG
*
53781400 ATTTTTAAAAT-TTTTTAA
1 ATTTTTAATATATTTTTAA
53781418 AATTATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 7 0.21
20 23 0.70
21 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTTTAATATATTTTTAAG
Found at i:53789770 original size:19 final size:20
Alignment explanation
Indices: 53789731--53789770 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53789721 ATTTTGAAAC
*
53789731 TATATTTTTATCAATTATAA
1 TATATTTTAATCAATTATAA
*
53789751 TATATTTTAATTAATT-TAA
1 TATATTTTAATCAATTATAA
53789770 T
1 T
53789771 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATTTTAATCAATTATAA
Found at i:53792417 original size:14 final size:15
Alignment explanation
Indices: 53792392--53792420 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53792382 ATTTTGAAAA
53792392 TAATATAATTTAACT
1 TAATATAATTTAACT
53792407 TAATA-AATTTAACT
1 TAATATAATTTAACT
53792421 GTTATTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATAATTTAACT
Found at i:53792556 original size:15 final size:15
Alignment explanation
Indices: 53792538--53792567 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53792528 GACTAATGGA
*
53792538 ATAATTTAACCTAAT
1 ATAATTTAAACTAAT
53792553 ATAATTTAAACTAAT
1 ATAATTTAAACTAAT
53792568 TCAAATTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTTAAACTAAT
Found at i:53796880 original size:12 final size:13
Alignment explanation
Indices: 53796856--53796884 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
53796846 GTTTTTTTTG
53796856 TTCCCCTTTCCCC
1 TTCCCCTTTCCCC
53796869 TTCCCC-TTCCCC
1 TTCCCCTTTCCCC
53796881 TTCC
1 TTCC
53796885 TGTTCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCCCCTTTCCCC
Found at i:53802060 original size:3 final size:3
Alignment explanation
Indices: 53802054--53802079 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53802044 GCTTTGTTGT
53802054 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
53802080 GGGTTGATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:53803466 original size:2 final size:2
Alignment explanation
Indices: 53803461--53803499 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53803451 TTTCTTTATT
53803461 TA TA 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 TA TA T
53803500 TGACAGGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53803622 original size:3 final size:3
Alignment explanation
Indices: 53803614--53803648 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
53803604 AAGATGGGAA
53803614 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53803649 ACTGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:53806825 original size:29 final size:29
Alignment explanation
Indices: 53806764--53806825 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
53806754 CGTATTGATT
* *
53806764 TTTTAATTATTTTACGAGATCTTAATTAT
1 TTTTAATTATTTTACGAGATCGTAATTAC
* *
53806793 TTTTAATTATTTTACGTGGA-CGTAATTGC
1 TTTTAATTATTTTACG-AGATCGTAATTAC
53806822 TTTT
1 TTTT
53806826 TAGAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (29 bp):
TTTTAATTATTTTACGAGATCGTAATTAC
Found at i:53823488 original size:30 final size:30
Alignment explanation
Indices: 53823454--53823522 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
53823444 TCAATGCCTT
*
53823454 ACAAGGCGAATCCGGTAGCTGAGAAGTACA
1 ACAAGGCGAATCCGGTAGCTAAGAAGTACA
*
53823484 ACAAGGCGAATCCGGTGGCTAAGAAGTACA
1 ACAAGGCGAATCCGGTAGCTAAGAAGTACA
*
53823514 ACACGGCGA
1 ACAAGGCGA
53823523 CATCACCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.30, T:0.12
Consensus pattern (30 bp):
ACAAGGCGAATCCGGTAGCTAAGAAGTACA
Found at i:53825018 original size:26 final size:27
Alignment explanation
Indices: 53824989--53825055 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
53824979 ACCTTAAAAA
53824989 CTTTGCATGTGATTAG-GTGAT-TTATT
1 CTTT-CATGTGATTAGTGTGATCTTATT
* *
53825015 CTTTACATGTGATCAGTTTGATCTTATT
1 CTTT-CATGTGATTAGTGTGATCTTATT
*
53825043 CTTTCATATGATT
1 CTTTCATGTGATT
53825056 CATACCAGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.41
27 11 0.32
28 9 0.26
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (27 bp):
CTTTCATGTGATTAGTGTGATCTTATT
Found at i:53826461 original size:16 final size:17
Alignment explanation
Indices: 53826432--53826468 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
53826422 AAAAAATATA
53826432 TTTT-TAATTATAATTT
1 TTTTATAATTATAATTT
53826448 TTTTATAATT-TAATTT
1 TTTTATAATTATAATTT
53826464 TTTTA
1 TTTTA
53826469 CAAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATAATTATAATTT
Found at i:53826477 original size:16 final size:16
Alignment explanation
Indices: 53826441--53826480 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
53826431 ATTTTTAATT
* *
53826441 ATAATTTTTTTATAAT
1 ATAATTTTTTTACAAA
*
53826457 TTAATTTTTTTACAAA
1 ATAATTTTTTTACAAA
53826473 ATAATTTT
1 ATAATTTT
53826481 AAACATCATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAATTTTTTTACAAA
Found at i:53827354 original size:37 final size:34
Alignment explanation
Indices: 53827289--53827364 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 34
53827279 TATTTTAATA
* * *
53827289 AAATATTAAAAAAATTATTTTTGTAATTAATTTT
1 AAATTTTAAAAAAATTATTTTTGTAATTAAATTC
* *
53827323 AAATTTTAAAAATATTTTTATTGTGTAAATTAAATTC
1 AAATTTTAAAAAAATTATT-TT-TGT-AATTAAATTC
53827360 AAATT
1 AAATT
53827365 GAGCTGGATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 16 0.47
35 2 0.06
36 3 0.09
37 13 0.38
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
AAATTTTAAAAAAATTATTTTTGTAATTAAATTC
Found at i:53828073 original size:19 final size:20
Alignment explanation
Indices: 53828046--53828089 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
53828036 ATTTAATAAC
* *
53828046 CAATCAAATTGATTT-AATT
1 CAATTAAATCGATTTCAATT
53828065 CAATTAAATCGATTTCAATT
1 CAATTAAATCGATTTCAATT
*
53828085 TAATT
1 CAATT
53828090 GATTATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (20 bp):
CAATTAAATCGATTTCAATT
Found at i:53833189 original size:2 final size:2
Alignment explanation
Indices: 53833182--53833226 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
53833172 TATATTGAAA
53833182 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
53833224 AT A
1 AT A
53833227 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53833231 original size:2 final size:2
Alignment explanation
Indices: 53833226--53833269 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
53833216 ATATATATAT
53833226 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
53833268 AG
1 AG
53833270 TCCCCAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53834035 original size:30 final size:31
Alignment explanation
Indices: 53833979--53834036 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
53833969 TTTTTAATCG
* *
53833979 ATTTTTATACTTAAATTTAACAATTAAAGCT
1 ATTTTGATACTTAAATTCAACAATTAAAGCT
53834010 ATTTTGATA-TTAAATTCAA-ATATTAAA
1 ATTTTGATACTTAAATTCAACA-ATTAAA
53834037 AATTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.62
31 8 0.33
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTTTGATACTTAAATTCAACAATTAAAGCT
Found at i:53834909 original size:23 final size:23
Alignment explanation
Indices: 53834868--53834930 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
53834858 AATATATATA
53834868 TAAATA-A-TTATAGATTAAATTT
1 TAAATATATTTATA-ATTAAATTT
* * *
53834890 TATATATTTTTGTAATTAAATTT
1 TAAATATATTTATAATTAAATTT
53834913 TAAATATATTTATAATTA
1 TAAATATATTTATAATTA
53834931 TTTTTCAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 5 0.15
23 24 0.73
24 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
TAAATATATTTATAATTAAATTT
Found at i:53842059 original size:15 final size:16
Alignment explanation
Indices: 53842031--53842061 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53842021 AGGCTCATTC
53842031 ATATTATATTATTTTA
1 ATATTATATTATTTTA
53842047 ATATTAT-TTATTTTA
1 ATATTATATTATTTTA
53842062 TTTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTATATTATTTTA
Found at i:53854800 original size:2 final size:2
Alignment explanation
Indices: 53854793--53854824 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
53854783 ACAAGCCTAT
*
53854793 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53854825 AGAGTGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53860336 original size:30 final size:31
Alignment explanation
Indices: 53860292--53860349 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
53860282 GGGTCTAATT
* * *
53860292 AAAATTTTTCAAAAAATTTG-AGGTTTATTG
1 AAAATTCTTAAAAAAATTAGAAGGTTTATTG
53860322 AAAATTCTTAAAAAAATTAGAAGGTTTA
1 AAAATTCTTAAAAAAATTAGAAGGTTTA
53860350 ATCAAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (31 bp):
AAAATTCTTAAAAAAATTAGAAGGTTTATTG
Found at i:53885163 original size:3 final size:3
Alignment explanation
Indices: 53885155--53885179 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53885145 TTTGTCAATA
53885155 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
53885180 CTTTTGTAGA
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:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:53903306 original size:18 final size:18
Alignment explanation
Indices: 53903283--53903319 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53903273 TTTAAGACTT
53903283 AGTTATATAGGTATCTGA
1 AGTTATATAGGTATCTGA
53903301 AGTTATATAGGTATCTGA
1 AGTTATATAGGTATCTGA
53903319 A
1 A
53903320 AGTTCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (18 bp):
AGTTATATAGGTATCTGA
Found at i:53903703 original size:34 final size:34
Alignment explanation
Indices: 53903664--53903731 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
53903654 GGATCCCCAC
53903664 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
1 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
53903698 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
1 TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
53903732 CTTATTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (34 bp):
TTGTTCACATTCTCTCTTAATAAAAAAGGTTTGT
Found at i:53905606 original size:15 final size:15
Alignment explanation
Indices: 53905515--53905604 Score: 128
Period size: 15 Copynumber: 6.0 Consensus size: 15
53905505 AGACCACTGG
*
53905515 GAACCAAGGAGGTCC
1 GAACCAAGGGGGTCC
53905530 GAACCAAGGGGGTCC
1 GAACCAAGGGGGTCC
*
53905545 GAACCAAGGGGATCC
1 GAACCAAGGGGGTCC
*
53905560 AAACCAAGGGGGTCC
1 GAACCAAGGGGGTCC
*
53905575 GAACCAAGGGGATCC
1 GAACCAAGGGGGTCC
53905590 -AATCCAAGGGGGTCC
1 GAA-CCAAGGGGGTCC
53905605 AACTCAAAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 2 0.03
15 65 0.97
ACGTcount: A:0.31, C:0.27, G:0.34, T:0.08
Consensus pattern (15 bp):
GAACCAAGGGGGTCC
Found at i:53906146 original size:9 final size:9
Alignment explanation
Indices: 53906132--53906156 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53906122 ACAAAGAGCT
53906132 GCAGCTTTA
1 GCAGCTTTA
53906141 GCAGCTTTA
1 GCAGCTTTA
53906150 GCAGCTT
1 GCAGCTT
53906157 CATTTAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (9 bp):
GCAGCTTTA
Found at i:53906562 original size:66 final size:66
Alignment explanation
Indices: 53906448--53906575 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
53906438 ATGCAGAGTC
** ** * *
53906448 GAGTGAAGTGAACCCTTCTGAAGCTGATGATTCTGTAGGGGTTGCTAAAACCAATAAGGAAGTGT
1 GAGTGAAGCAAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTGCTAAAACCAACAAGGAAGTGT
53906513 T
66 T
* *
53906514 GAGTGAAGCAAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTTCTAAAGCCAACAAGGAAG
1 GAGTGAAGCAAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTGCTAAAACCAACAAGGAAG
53906576 AGACAGCAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (66 bp):
GAGTGAAGCAAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTGCTAAAACCAACAAGGAAGTGT
T
Found at i:53914425 original size:32 final size:32
Alignment explanation
Indices: 53914384--53914449 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
53914374 TAAATTCATC
53914384 ATCACTCAATAGTTGACACGCTCTACTTCACA
1 ATCACTCAATAGTTGACACGCTCTACTTCACA
*
53914416 ATCACTCAATAGTTGACACGCTCTGCTTCACA
1 ATCACTCAATAGTTGACACGCTCTACTTCACA
53914448 AT
1 AT
53914450 TTACCGTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (32 bp):
ATCACTCAATAGTTGACACGCTCTACTTCACA
Found at i:53933642 original size:20 final size:21
Alignment explanation
Indices: 53933617--53933656 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53933607 TGTGGAGTTT
*
53933617 ATTAATCAGTA-TTTTATATA
1 ATTAATCAATAGTTTTATATA
*
53933637 ATTAATGAATAGTTTTATAT
1 ATTAATCAATAGTTTTATAT
53933657 TTGAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (21 bp):
ATTAATCAATAGTTTTATATA
Found at i:53944249 original size:29 final size:29
Alignment explanation
Indices: 53944216--53944340 Score: 108
Period size: 29 Copynumber: 4.3 Consensus size: 29
53944206 GATTAAATGC
* * *
53944216 AATTTTTGGATGCCCGAGGGTAAAACGGT
1 AATTTTTGGATACTCGAGGGTAAAAAGGT
* * * *
53944245 AA-TTTTGAACACTTCGAGGGCAAAAGGGT
1 AATTTTTGGATAC-TCGAGGGTAAAAAGGT
* *
53944274 AATTTTTGGATACTCGGGGGTAAAAATGT
1 AATTTTTGGATACTCGAGGGTAAAAAGGT
* * * *
53944303 AATTTTTGGACATTCGAGGGTGAAATGGT
1 AATTTTTGGATACTCGAGGGTAAAAAGGT
*
53944332 GATTTTTGG
1 AATTTTTGG
53944341 GAATTTTGGG
Statistics
Matches: 75, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
28 7 0.09
29 60 0.80
30 8 0.11
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.32
Consensus pattern (29 bp):
AATTTTTGGATACTCGAGGGTAAAAAGGT
Found at i:53944306 original size:58 final size:58
Alignment explanation
Indices: 53944216--53944340 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 58
53944206 GATTAAATGC
* *
53944216 AATTTTTGGATGCCCGAGGGTAAAACGGTAA-TTTTGAACACTTCGAGGGCAAAAGGGT
1 AATTTTTGGATACCCGAGGGTAAAAAGGTAATTTTTGAACA-TTCGAGGGCAAAAGGGT
* * * * ** *
53944274 AATTTTTGGATACTCGGGGGTAAAAATGTAATTTTTGGACATTCGAGGGTGAAATGGT
1 AATTTTTGGATACCCGAGGGTAAAAAGGTAATTTTTGAACATTCGAGGGCAAAAGGGT
*
53944332 GATTTTTGG
1 AATTTTTGG
53944341 GAATTTTGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 48 0.86
59 8 0.14
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.32
Consensus pattern (58 bp):
AATTTTTGGATACCCGAGGGTAAAAAGGTAATTTTTGAACATTCGAGGGCAAAAGGGT
Found at i:53944528 original size:29 final size:29
Alignment explanation
Indices: 53944378--53944546 Score: 152
Period size: 29 Copynumber: 5.8 Consensus size: 29
53944368 TAGGCATTTG
**
53944378 GGGT-AAAATGGTAATTTTTGGAAGGTTCGA
1 GGGTAAAAATGG-AATTTTTGGAAAATTC-A
*
53944408 GGTTAAAAATGGAA-TTTTGGAAAATTCA
1 GGGTAAAAATGGAATTTTTGGAAAATTCA
* *
53944436 GGGGTAAAAATGTG-ATTTTTGGAAAGTTTA
1 -GGGTAAAAATG-GAATTTTTGGAAAATTCA
53944466 GGGTTAAAAATGGAA-TTTTGGAAAATTCA
1 GGG-TAAAAATGGAATTTTTGGAAAATTCA
*
53944495 TGGGT-AAAATGGTAATTTTTGAAAAAATT-A
1 -GGGTAAAAATGG-AATTTTTG-GAAAATTCA
* *
53944525 GGGTTAAAATGGAGTTTTTGGA
1 GGGTAAAAATGGAATTTTTGGA
53944547 TTTTTAGGGT
Statistics
Matches: 117, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
28 9 0.08
29 52 0.44
30 43 0.37
31 13 0.11
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAAATTCA
Found at i:53944533 original size:30 final size:28
Alignment explanation
Indices: 53944381--53944882 Score: 151
Period size: 30 Copynumber: 16.5 Consensus size: 28
53944371 GCATTTGGGG
** *
53944381 TAAAATGGTAATTTTTGGAAGGTTCGAGGT
1 TAAAATGG-AATTTTTGGAAAATTAG-GGT
53944411 TAAAAATGGAA-TTTTGGAAAATTCAGGGGT
1 T-AAAATGGAATTTTTGGAAAATT-A-GGGT
* *
53944441 AAAAATGTG-ATTTTTGGAAAGTTTAGGGT
1 TAAAATG-GAATTTTTGGAAA-ATTAGGGT
53944470 TAAAAATGGAA-TTTTGGAAAATTCATGGG-
1 T-AAAATGGAATTTTTGGAAAATT-A-GGGT
*
53944499 TAAAATGGTAATTTTTGAAAAAATTAGGGT
1 TAAAATGG-AATTTTTG-GAAAATTAGGGT
* ***
53944529 TAAAATGGAGTTTTTGGATTTTTAGGGT
1 TAAAATGGAATTTTTGGAAAATTAGGGT
* *** *
53944557 GGAAAAATCGAGGTCAA-ACAT-GAAATTTTTAGAGGTT
1 --TAAAAT---GG--AATTTTTGGAAA--ATTAG-GG-T
*
53944594 TGGGGGTAAAATGGTAATTTTTGAAAAAATT-GGAGT
1 T------AAAATGG-AATTTTTG-GAAAATTAGG-GT
* ***
53944630 CAAAAATGGAATTTTTGGAGGTTTGAGGGT
1 -TAAAATGGAATTTTTGGAAAATT-AGGGT
* * *
53944660 AAAAATGTAATTTTTGGAAATTTAGGGT
1 TAAAATGGAATTTTTGGAAAATTAGGGT
* *
53944688 TAAAATGTAATTTTTGGAAACTTTAAGGGT
1 TAAAATGGAATTTTTGGAAA-ATT-AGGGT
* * *
53944718 TAAAATGTAATTTTTAGAAAGTTTAAGGGT
1 TAAAATGGAATTTTTGGAAA-ATT-AGGGT
* * *
53944748 TAAAATGTAATTTTTAGAAAGTTTAGGGGT
1 TAAAATGGAATTTTTGGAAA-ATTA-GGGT
* *
53944778 TAAAATGTAA-TTTTGGAAAAGTTTGGAGGT
1 TAAAATGGAATTTTTGGAAAA--TTAG-GGT
*
53944808 TAAAATGTAA-TTTTGGAAAAGTTTAAGGGT
1 TAAAATGGAATTTTTGGAAAA--TT-AGGGT
** *
53944838 TAAAATATAA-TTTTAGAAAAGTTTAGGGGT
1 TAAAATGGAATTTTTGGAAAA--TTA-GGGT
*
53944868 TAAAATGTAATTTTT
1 TAAAATGGAATTTTT
53944883 AGATAGTTTA
Statistics
Matches: 380, Mismatches: 45, Indels: 93
0.73 0.09 0.18
Matches are distributed among these distances:
28 41 0.11
29 82 0.22
30 194 0.51
31 30 0.08
33 4 0.01
34 1 0.00
35 6 0.02
36 4 0.01
37 5 0.01
38 5 0.01
40 3 0.01
41 5 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGAAAATTAGGGT
Found at i:53944546 original size:59 final size:58
Alignment explanation
Indices: 53944377--53944542 Score: 210
Period size: 59 Copynumber: 2.8 Consensus size: 58
53944367 TTAGGCATTT
* * *
53944377 GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTGGAAAATTCA
1 GGGGTAAAATGGTAATTTTTGAAAGATTAG-GGTTAAAAATGGAATTTTGGAAAATTCA
* *
53944436 GGGGTAAAAAT-GTGATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAATTCA
1 GGGGT-AAAATGGTAATTTTT-GAAAGATTAGGGTTAAAAATGGAATTTTGGAAAATTCA
* * *
53944495 TGGGTAAAATGGTAATTTTTGAAAAAATTAGGGTT-AAAATGGAGTTTT
1 GGGGTAAAATGGTAATTTTTG-AAAGATTAGGGTTAAAAATGGAATTTT
53944543 TGGATTTTTA
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
58 18 0.19
59 64 0.68
60 12 0.13
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGAAAGATTAGGGTTAAAAATGGAATTTTGGAAAATTCA
Found at i:53944809 original size:90 final size:89
Alignment explanation
Indices: 53944580--53944881 Score: 341
Period size: 90 Copynumber: 3.4 Consensus size: 89
53944570 TCAAACATGA
* * * * * *
53944580 AATTTTTAG-AGGTTT-GGGGGTAAAATGGTAATTTTTGAAAAAATTGGA-GTCAAAAATGGAAT
1 AATTTTTAGAAAGTTTAGGGGTTAAAAT-GTAATTTTGGAAAAATTTGGAGGT-TAAAATGTAAT
* * * *
53944642 TTTTGGAGGTTTGAGGGTAAAAATGT
64 TTTTGAAAGTTTAAGGGTTAAAATGT
* * *
53944668 AATTTTTGGAAA-TTTA-GGGTTAAAATGTAATTTTTGG-AAACTTT-AAGGGTTAAAATGTAAT
1 AATTTTTAGAAAGTTTAGGGGTTAAAATGTAA-TTTTGGAAAAATTTGGA-GGTTAAAATGTAAT
53944729 TTTTAGAAAGTTTAAGGGTTAAAATGT
64 TTTT-GAAAGTTTAAGGGTTAAAATGT
*
53944756 AATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGAGGTTAAAATGTAATTT
1 AATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAATTTGGAGGTTAAAATGTAATTT
* *
53944821 TGGAAAAGTTTAAGGGTTAAAATAT
66 TTG-AAAGTTTAAGGGTTAAAATGT
53944846 AA-TTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTT
1 AATTTTTAG-AAAGTTTAGGGGTTAAAATGTAATTTT
53944882 TAGATAGTTT
Statistics
Matches: 184, Mismatches: 18, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
86 1 0.01
87 22 0.12
88 56 0.30
89 18 0.10
90 86 0.47
91 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (89 bp):
AATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAATTTGGAGGTTAAAATGTAATTT
TTGAAAGTTTAAGGGTTAAAATGT
Found at i:53944891 original size:30 final size:30
Alignment explanation
Indices: 53944656--53944895 Score: 303
Period size: 30 Copynumber: 8.1 Consensus size: 30
53944646 GGAGGTTTGA
* *
53944656 GGGTAAAAATGTAATTTTTGGAAA-TTTA-
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
* * *
53944684 GGGTTAAAATGTAATTTTTGGAAACTTTAA
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
*
53944714 GGGTTAAAATGTAATTTTTAGAAAGTTTAA
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
53944744 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
*
53944774 GGGTTAAAATGTAA-TTTTGGAAAAGTTT-G
1 GGGTTAAAATGTAATTTTTAG-AAAGTTTAG
* *
53944803 GAGGTTAAAATGTAA-TTTTGGAAAAGTTTAA
1 G-GGTTAAAATGTAATTTTTAG-AAAGTTTAG
*
53944834 GGGTTAAAATATAA-TTTTAGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTTAG-AAAGTTTAG
*
53944864 GGGTTAAAATGTAATTTTTAGATAGTTTAG
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
53944894 GG
1 GG
53944896 ATCTTTTGGG
Statistics
Matches: 195, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
28 23 0.12
29 11 0.06
30 154 0.79
31 7 0.04
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.39
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTTAGAAAGTTTAG
Found at i:53947180 original size:39 final size:37
Alignment explanation
Indices: 53947113--53947232 Score: 100
Period size: 39 Copynumber: 3.2 Consensus size: 37
53947103 AAGATTGGTT
* * *
53947113 GATGG-TGATCTGCCTCAAGCTAGGGGTAAAAGATCG
1 GATGGTTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
* * * * *
53947149 GATGGTTGCAATTTGCCCCAGGCTTGAGGTAAGAGATAAGCT
1 GATGGTTG--ATCTGCCCCAAGCTCGAGGTAAAAGAT---CG
*
53947191 GATGG-TGATCTGCCCCAAGCTCGGGGTAAAAGATCG
1 GATGGTTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
53947227 GATGGT
1 GATGGT
53947233 AATTTTTGGA
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
36 11 0.17
37 2 0.03
39 43 0.67
41 2 0.03
42 6 0.09
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.23
Consensus pattern (37 bp):
GATGGTTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
Found at i:53947405 original size:29 final size:30
Alignment explanation
Indices: 53947373--53947444 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
53947363 GTTTGAGATC
*
53947373 AAAAATGTGATTTTTG-GAAGTTTGGGGGT
1 AAAAATATGATTTTTGAGAAGTTTGGGGGT
**
53947402 AAAAATACAATTTTTGAGAAGTTTGGGGGT
1 AAAAATATGATTTTTGAGAAGTTTGGGGGT
*
53947432 CAAAATATGATTT
1 AAAAATATGATTT
53947445 CTAGATAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 13 0.36
30 23 0.64
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAAATATGATTTTTGAGAAGTTTGGGGGT
Found at i:53949356 original size:58 final size:58
Alignment explanation
Indices: 53949221--53949354 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 58
53949211 TGGATACCCG
* * * * *
53949221 GGGGCAAAATGGTAATTTGGGTTAAATCGAGGTTAAAAATGGGATTTAGGGGAGTTTA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAGGGGATTTAGGGAAGTTTA
* * * *
53949279 AGGGTGAAATGGTAATTTTGGTGAAATCGGGGTTTAAAAGGGGATTTAGGGAAGTTT-
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAGGGGATTTAGGGAAGTTTA
53949336 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
53949355 TGAAAGTTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
57 17 0.26
58 48 0.74
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.31
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAGGGGATTTAGGGAAGTTTA
Found at i:53949424 original size:31 final size:30
Alignment explanation
Indices: 53949330--53949517 Score: 217
Period size: 30 Copynumber: 6.3 Consensus size: 30
53949320 GGATTTAGGG
53949330 AAGTTT-GGGGT-AAAATGGTAATTTTT-GA
1 AAGTTTAGGGGTCAAAAT-GTAATTTTTAGA
* * * *
53949358 AAGTTTCGGGG-AAAAATGCAATTTTTGGA
1 AAGTTTAGGGGTCAAAATGTAATTTTTAGA
53949387 AAGTTTAGGGGTCAAAATGTAATTTTTAGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTTAG-A
*
53949418 AAGTTTAGGGGTTAAAATGTAATTTTTAGA
1 AAGTTTAGGGGTCAAAATGTAATTTTTAGA
* *
53949448 AAGTTTTGGGGTTAAAATGTAATTTTTAGA
1 AAGTTTAGGGGTCAAAATGTAATTTTTAGA
* *
53949478 AAGTTTTA-GGGTCAAAATATAATTTCTAGA
1 AAG-TTTAGGGGTCAAAATGTAATTTTTAGA
53949508 CAA-TTTAGGG
1 -AAGTTTAGGG
53949518 ACTTACAAAG
Statistics
Matches: 141, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.10
29 25 0.18
30 68 0.48
31 34 0.24
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAGTTTAGGGGTCAAAATGTAATTTTTAGA
Found at i:53949450 original size:61 final size:59
Alignment explanation
Indices: 53949330--53949517 Score: 215
Period size: 61 Copynumber: 3.2 Consensus size: 59
53949320 GGATTTAGGG
* * *
53949330 AAGTTT-GGGGTAAAATGGTAATTTTT-GAAAGTTTCGGGG-AAAAATGCAATTTTTGGA
1 AAGTTTAGGGGTAAAAT-GTAATTTTTAGAAAGTTTAGGGGTAAAAATGTAATTTTTAGA
*
53949387 AAGTTTAGGGGTCAAAATGTAATTTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGA
1 AAGTTTAGGGGT-AAAATGTAATTTTTAG-AAAGTTTAGGGGTAAAAATGTAATTTTTAGA
* * * *
53949448 AAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTA-GGGTCAAAATATAATTTCTAGA
1 AAGTTTAGGGG-TAAAATGTAATTTTTAGAAAG-TTTAGGGGTAAAAATGTAATTTTTAGA
53949508 CAA-TTTAGGG
1 -AAGTTTAGGG
53949518 ACTTACAAAG
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
57 6 0.05
58 14 0.12
59 6 0.05
60 40 0.35
61 47 0.41
62 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (59 bp):
AAGTTTAGGGGTAAAATGTAATTTTTAGAAAGTTTAGGGGTAAAAATGTAATTTTTAGA
Found at i:53950638 original size:13 final size:13
Alignment explanation
Indices: 53950620--53950688 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
53950610 TTTTTAATAT
53950620 TATTAATTATTAA
1 TATTAATTATTAA
53950633 TATTAATTA-TAA
1 TATTAATTATTAA
* *
53950645 TCA-TAAATATTTA
1 T-ATTAATTATTAA
53950658 T-TATAATTATTAA
1 TAT-TAATTATTAA
53950671 TTATTATGATTATTAA
1 -TATTA--ATTATTAA
53950687 TA
1 TA
53950689 ATATTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
12 9 0.20
13 21 0.48
14 3 0.07
15 3 0.07
16 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (13 bp):
TATTAATTATTAA
Found at i:53950645 original size:19 final size:18
Alignment explanation
Indices: 53950613--53950693 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 18
53950603 TGTTATATTT
53950613 TTAATATTA-T-TAATTA
1 TTAATATTATTATAATTA
*
53950629 TTAATATTAATTATAATCA
1 TTAATATT-ATTATAATTA
*
53950648 TAAATATTTATTATAATTA
1 TTAATA-TTATTATAATTA
*
53950667 TT-A-ATTATTATGATTA
1 TTAATATTATTATAATTA
*
53950683 TTAATAATATT
1 TTAATATTATT
53950694 TTTATTAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
16 21 0.40
17 3 0.06
18 7 0.13
19 20 0.38
20 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (18 bp):
TTAATATTATTATAATTA
Found at i:53951362 original size:6 final size:6
Alignment explanation
Indices: 53951353--53951409 Score: 71
Period size: 6 Copynumber: 9.3 Consensus size: 6
53951343 GGACTTTAGT
* *
53951353 ATTTTA ATTTAA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
53951402 ATTTAA AT
1 ATTTAA AT
53951410 AAATTCAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.09
6 35 0.78
8 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:53951388 original size:11 final size:12
Alignment explanation
Indices: 53951362--53951409 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 12
53951352 TATTTTAATT
*
53951362 TAAATTTAAATT
1 TAAATTTAAATG
53951374 TAAATTTAAA-G
1 TAAATTTAAATG
*
53951385 TAAATTTAAATAAT
1 TAAATTTAAAT--G
53951399 TAAATTTAAAT
1 TAAATTTAAAT
53951410 AAATTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.32
12 10 0.32
14 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
TAAATTTAAATG
Found at i:53951420 original size:25 final size:26
Alignment explanation
Indices: 53951373--53951425 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
53951363 AAATTTAAAT
*
53951373 TTAAATTTAAAGTAAATTTAAAT-AA
1 TTAAATTTAAAGTAAATTAAAATCAA
53951398 TTAAATTTAAA-TAAATTCAAAATCAA
1 TTAAATTTAAAGTAAATT-AAAATCAA
53951424 TT
1 TT
53951426 TATCTCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (26 bp):
TTAAATTTAAAGTAAATTAAAATCAA
Found at i:53962624 original size:58 final size:57
Alignment explanation
Indices: 53962489--53962622 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 57
53962479 TGGATACCCG
* * * * *
53962489 GGGGCAAAATGGTAATTTGGGTTAAATCGGGGTTAAAAATGGGATTTAGGGGAGTTT
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTT
* *
53962546 GAGGGTGAAATGGTAATTTTGGTGAAATCGGGGTTTAAAAGGGGATTTAGGGAAGTTT
1 G-GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTT
53962604 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
53962623 TGAAAGTTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 18 0.26
58 50 0.74
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTT
Found at i:53962635 original size:58 final size:58
Alignment explanation
Indices: 53962515--53962691 Score: 184
Period size: 58 Copynumber: 3.0 Consensus size: 58
53962505 TTGGGTTAAA
* *
53962515 TCGGGGTTAAAAATGGGATTTAGGGGAGTTTGAGGGTGAAATGGTAATTTTGGTGAAA---
1 TCGGGGTTAAAAATGGGATTTAGGGAAGTTTG-GGGTAAAATGGTAATTTT--TGAAAGTT
* *
53962573 TCGGGGTTTAAAAGGGGATTTAGGGAAGTTTGGGGTAAAATGGTAATTTTTGAAAGTT
1 TCGGGGTTAAAAATGGGATTTAGGGAAGTTTGGGGTAAAATGGTAATTTTTGAAAGTT
** * *
53962631 TCGGGG-TAAAAATGTAATTTTTGGAAAGTTTAGGGGTCAAAAT-GTAATTTTTAGAAAGTT
1 TCGGGGTTAAAAATGGGA-TTTAGGGAAGTTT-GGGGT-AAAATGGTAATTTTT-GAAAGTT
53962691 T
1 T
53962692 AGGGCTCAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
55 5 0.05
57 24 0.24
58 46 0.45
59 14 0.14
60 13 0.13
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.34
Consensus pattern (58 bp):
TCGGGGTTAAAAATGGGATTTAGGGAAGTTTGGGGTAAAATGGTAATTTTTGAAAGTT
Found at i:53962658 original size:30 final size:29
Alignment explanation
Indices: 53962598--53962725 Score: 154
Period size: 30 Copynumber: 4.3 Consensus size: 29
53962588 GGATTTAGGG
53962598 AAGTTT-GGGGT-AAAATGGTAATTTTTGA
1 AAGTTTAGGGGTCAAAAT-GTAATTTTTGA
* *
53962626 AAGTTTCGGGGTAAAAATGTAATTTTTGGA
1 AAGTTTAGGGGTCAAAATGTAATTTTT-GA
53962656 AAGTTTAGGGGTCAAAATGTAATTTTTAGA
1 AAGTTTAGGGGTCAAAATGTAATTTTT-GA
* *
53962686 AAGTTTAGGGCTCAAAATATAATTTTTAGA
1 AAGTTTAGGGGTCAAAATGTAATTTTT-GA
53962716 CAA-TTTAGGG
1 -AAGTTTAGGG
53962726 ACTTACAAAG
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
28 6 0.07
29 14 0.15
30 69 0.76
31 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
AAGTTTAGGGGTCAAAATGTAATTTTTGA
Found at i:53963845 original size:13 final size:13
Alignment explanation
Indices: 53963829--53963897 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
53963819 TTTTTAATAT
53963829 TATTAATTATTAA
1 TATTAATTATTAA
53963842 TATTAATTA-TAA
1 TATTAATTATTAA
* *
53963854 TCA-TAAATATTTA
1 T-ATTAATTATTAA
53963867 T-TATAATTATTAA
1 TAT-TAATTATTAA
53963880 TTATTATGATTATTAA
1 -TATTA--ATTATTAA
53963896 TA
1 TA
53963898 ATATTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
12 9 0.20
13 21 0.48
14 3 0.07
15 3 0.07
16 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (13 bp):
TATTAATTATTAA
Found at i:53963886 original size:19 final size:18
Alignment explanation
Indices: 53963822--53963902 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 18
53963812 GTTATATTTT
53963822 TTAATATTA-T-TAATTA
1 TTAATATTATTATAATTA
*
53963838 TTAATATTAATTATAATCA
1 TTAATATT-ATTATAATTA
*
53963857 TAAATATTTATTATAATTA
1 TTAATA-TTATTATAATTA
*
53963876 TT-A-ATTATTATGATTA
1 TTAATATTATTATAATTA
*
53963892 TTAATAATATT
1 TTAATATTATT
53963903 TTTATTAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
16 21 0.40
17 3 0.06
18 7 0.13
19 20 0.38
20 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (18 bp):
TTAATATTATTATAATTA
Found at i:53964558 original size:16 final size:17
Alignment explanation
Indices: 53964527--53964559 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53964517 ATGGGCCCAT
*
53964527 TTGTAATTGGGCCTTTA
1 TTGTAATTGGGACTTTA
53964544 TTGTAATT-GGACTTTA
1 TTGTAATTGGGACTTTA
53964560 GTATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.48
Consensus pattern (17 bp):
TTGTAATTGGGACTTTA
Found at i:53964571 original size:6 final size:6
Alignment explanation
Indices: 53964562--53964641 Score: 94
Period size: 6 Copynumber: 13.3 Consensus size: 6
53964552 GGACTTTAGT
* *
53964562 ATTTTA ATTTAA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
53964611 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA AT
53964642 AAATTCAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 50 0.77
7 1 0.02
8 6 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:53964597 original size:11 final size:11
Alignment explanation
Indices: 53964571--53964634 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
53964561 TATTTTAATT
*
53964571 TAAATTTAAATT
1 TAAATTTAAA-G
53964583 TAAATTTAAAG
1 TAAATTTAAAG
53964594 TAAATTTAAA-
1 TAAATTTAAAG
*
53964604 T-AA-TTAAATT
1 TAAATTTAAA-G
53964614 TAAATTT-AAG
1 TAAATTTAAAG
53964624 ATAAATTTAAA
1 -TAAATTTAAA
53964635 TTTAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 5 0.11
9 2 0.05
10 2 0.05
11 21 0.48
12 14 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAG
Found at i:53964597 original size:17 final size:17
Alignment explanation
Indices: 53964562--53964646 Score: 90
Period size: 17 Copynumber: 5.2 Consensus size: 17
53964552 GGACTTTAGT
* *
53964562 ATTTTAATTTAAATTTAA
1 ATTTAAATTTAAA-GTAA
53964580 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAGTAA
*
53964597 ATTTAAA--T-AATTAA
1 ATTTAAATTTAAAGTAA
53964611 ATTTAAATTT-AAGATAA
1 ATTTAAATTTAAAG-TAA
53964628 ATTTAAATTTAAA-TAA
1 ATTTAAATTTAAAGTAA
53964644 ATT
1 ATT
53964647 CAAAATCAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.20
15 1 0.02
16 9 0.15
17 23 0.39
18 14 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATTTAAATTTAAAGTAA
Found at i:53964611 original size:37 final size:37
Alignment explanation
Indices: 53964570--53964643 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
53964560 GTATTTTAAT
53964570 TTAAATTTAAATTTAA-ATTTAAA-GTAAATTTAAATAA
1 TTAAATTTAAATTTAAGA--TAAATGTAAATTTAAATAA
*
53964607 TTAAATTTAAATTTAAGATAAATTTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
53964644 ATTCAAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 4 0.12
37 29 0.85
38 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (37 bp):
TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
Found at i:53964614 original size:31 final size:29
Alignment explanation
Indices: 53964567--53964641 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 29
53964557 TTAGTATTTT
53964567 AATTTAAATTTAAATTTAAATTTAA-AGTA
1 AATTTAAATTTAAATTTAAATTTAAGA-TA
53964596 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAAT--TTAAATTTAAATTTAAGATA
53964627 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
53964642 AAATTCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
29 15 0.35
31 27 0.63
32 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
AATTTAAATTTAAATTTAAATTTAAGATA
Found at i:53964652 original size:17 final size:17
Alignment explanation
Indices: 53964608--53964652 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
53964598 TTTAAATAAT
*
53964608 TAAATTTAAATTTAAGA
1 TAAATTAAAATTTAAGA
*
53964625 TAAATTTAAATTTAA-A
1 TAAATTAAAATTTAAGA
53964641 TAAATTCAAAAT
1 TAAATT-AAAAT
53964653 CAATTTATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTAAAATTTAAGA
Found at i:53965332 original size:6 final size:6
Alignment explanation
Indices: 53965321--53965379 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
53965311 CAATTAAACT
** * *
53965321 TTTAAA TTTAAA TTTTTA TTTCAAA -ATAAA TTTAAA TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
*
53965368 TTTAAA CTTAAA
1 TTTAAA TTTAAA
53965380 ATGAATTAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
5 7 0.17
6 33 0.80
7 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:53965365 original size:17 final size:17
Alignment explanation
Indices: 53965338--53965398 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
53965328 TTAAATTTTT
53965338 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
53965356 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* * *
53965373 ACTTAAAATGAATTAAA
1 ATTTAAAATAAATTTAA
*
53965390 ATTAAAAAT
1 ATTTAAAAT
53965399 CTAAAATTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
17 34 0.89
18 4 0.11
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:53986475 original size:34 final size:34
Alignment explanation
Indices: 53986436--53986504 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
53986426 TTAATAAAAT
53986436 TAATGCTTTCAGACATTGAATTGTAATAAGTGGA
1 TAATGCTTTCAGACATTGAATTGTAATAAGTGGA
53986470 TAATGCTTTCAGACATTGAATTGTAATAAGTGGA
1 TAATGCTTTCAGACATTGAATTGTAATAAGTGGA
53986504 T
1 T
53986505 GGACCCCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (34 bp):
TAATGCTTTCAGACATTGAATTGTAATAAGTGGA
Found at i:53999315 original size:9 final size:9
Alignment explanation
Indices: 53999301--53999330 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
53999291 TAATGGGAAA
53999301 GGAATCATG
1 GGAATCATG
53999310 GGAATCATG
1 GGAATCATG
53999319 GGAATCATG
1 GGAATCATG
53999328 GGA
1 GGA
53999331 CCTTTGCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.20
Consensus pattern (9 bp):
GGAATCATG
Found at i:54000552 original size:18 final size:18
Alignment explanation
Indices: 54000529--54000563 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54000519 ATTATAATTC
*
54000529 ATCAAAAATCAAATATTT
1 ATCAAAAATAAAATATTT
54000547 ATCAAAAATAAAATATT
1 ATCAAAAATAAAATATT
54000564 ACCATTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
ATCAAAAATAAAATATTT
Found at i:54001133 original size:3 final size:3
Alignment explanation
Indices: 54001119--54001164 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
54001109 TTTAGGGTTC
54001119 AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
54001165 AATGGGGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54002290 original size:11 final size:12
Alignment explanation
Indices: 54002262--54002291 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54002252 ATTTACAAAA
54002262 AGTTCAACAATC
1 AGTTCAACAATC
54002274 AGTTCAACAAT-
1 AGTTCAACAATC
54002285 AGTTCAA
1 AGTTCAA
54002292 AACAACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (12 bp):
AGTTCAACAATC
Found at i:54002475 original size:20 final size:21
Alignment explanation
Indices: 54002446--54002488 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
54002436 CCATTTGCAA
*
54002446 CTGAGTTGTGCTGCTCA-TTG
1 CTGAGATGTGCTGCTCACTTG
54002466 CTGAGATGTGCTGCTCACTTG
1 CTGAGATGTGCTGCTCACTTG
54002487 CT
1 CT
54002489 AAGTTGGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.37
Consensus pattern (21 bp):
CTGAGATGTGCTGCTCACTTG
Found at i:54005552 original size:47 final size:47
Alignment explanation
Indices: 54005493--54005589 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 47
54005483 TAATAACCCT
* * * *
54005493 AAATCAAAATCAAAAGTGAAAATCGATATTAGA-AAACCCTAAATCAA
1 AAATAAAAATCAAAAGTG-AAATCAAAATTAAATAAACCCTAAATCAA
* *
54005540 AAATAAAAATCAAAATTGAAATCAAAATTAAATAAACCCTAAATTAA
1 AAATAAAAATCAAAAGTGAAATCAAAATTAAATAAACCCTAAATCAA
54005587 AAA
1 AAA
54005590 GCACAATCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 11 0.26
47 32 0.74
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (47 bp):
AAATAAAAATCAAAAGTGAAATCAAAATTAAATAAACCCTAAATCAA
Found at i:54007813 original size:13 final size:13
Alignment explanation
Indices: 54007792--54007825 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54007782 ATATAATAAT
54007792 AATAATAATCCTA
1 AATAATAATCCTA
*
54007805 AATATTAATCCTA
1 AATAATAATCCTA
*
54007818 AAAAATAA
1 AATAATAA
54007826 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:54008777 original size:10 final size:10
Alignment explanation
Indices: 54008750--54008805 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
54008740 CTCAAACATA
*
54008750 TTTTTGTCTT
1 TTTTTCTCTT
54008760 TTTCTTCTCTT
1 TTT-TTCTCTT
54008771 TTTTTCTCAATT
1 TTTTTCTC--TT
*
54008783 TTTTT-TATT
1 TTTTTCTCTT
*
54008792 TTTTTCACTT
1 TTTTTCTCTT
54008802 TTTT
1 TTTT
54008806 CGACTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 7 0.18
10 14 0.37
11 10 0.26
12 7 0.18
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:54009705 original size:5 final size:5
Alignment explanation
Indices: 54009695--54009742 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
54009685 ATTGCATAAT
*
54009695 TAAAA TAAAA TTAAAAA TAAAA TAAAA CAAAA TGAAAA TGAAAA TAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA T-AAAA T-AAAA TAAA
54009743 TATATTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 21 0.55
6 13 0.34
7 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:54009708 original size:11 final size:11
Alignment explanation
Indices: 54009692--54009739 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
54009682 AATATTGCAT
54009692 AATTAAAATAA
1 AATTAAAATAA
54009703 AATTAAAAATAA
1 AATT-AAAATAA
*
54009715 AA-TAAAACAA
1 AATTAAAATAA
*
54009725 AATGAAAATGAA
1 AATTAAAAT-AA
54009737 AAT
1 AAT
54009740 AAATATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 8 0.26
11 9 0.29
12 14 0.45
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (11 bp):
AATTAAAATAA
Found at i:54009720 original size:22 final size:22
Alignment explanation
Indices: 54009695--54009742 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54009685 ATTGCATAAT
*
54009695 TAAAATAAAATTAAAAAT-AAAA
1 TAAAACAAAA-TAAAAATGAAAA
*
54009717 TAAAACAAAATGAAAATGAAAA
1 TAAAACAAAATAAAAATGAAAA
54009739 TAAA
1 TAAA
54009743 TATATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (22 bp):
TAAAACAAAATAAAAATGAAAA
Found at i:54012621 original size:16 final size:16
Alignment explanation
Indices: 54012571--54012615 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
54012561 TGCCAAAAGC
54012571 AAATAAAAATGAAAA-A
1 AAATAAAAAT-AAAATA
54012587 AAATAAAAATAAAATA
1 AAATAAAAATAAAATA
54012603 AAATAATAAATAA
1 AAATAA-AAATAA
54012616 TTAAAAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 17 0.63
17 6 0.22
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (16 bp):
AAATAAAAATAAAATA
Found at i:54022546 original size:20 final size:20
Alignment explanation
Indices: 54022513--54022555 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
54022503 TAGTTTTCAA
*
54022513 TGTAACTATGTTAATTTAGTT
1 TGTAACTATGTTAACTTA-TT
54022534 TGTAACT-TGTTAACTTATT
1 TGTAACTATGTTAACTTATT
54022553 TGT
1 TGT
54022556 TTATGATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (20 bp):
TGTAACTATGTTAACTTATT
Found at i:54028336 original size:21 final size:19
Alignment explanation
Indices: 54028312--54028353 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
54028302 TAATTTTCAA
*
54028312 TGTAACTATGTTAATTTAGTT
1 TGTAACT-TGTTAACTTA-TT
54028333 TGTAACTTGTTAACTTATT
1 TGTAACTTGTTAACTTATT
54028352 TG
1 TG
54028354 GTTATGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (19 bp):
TGTAACTTGTTAACTTATT
Found at i:54040780 original size:5 final size:5
Alignment explanation
Indices: 54040770--54040813 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
54040760 TGTATCAAAA
* *
54040770 TTTAT TTTAT TTTA- TTTAT TTTAG TTTAGT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTA
54040814 ACATTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
4 4 0.12
5 26 0.76
6 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:54055488 original size:28 final size:30
Alignment explanation
Indices: 54055456--54055522 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
54055446 AAATGAGTTT
**
54055456 TTTACTAATTTAATA-AAAA-AAATATTTA
1 TTTACTAAAATAATACAAAATAAATATTTA
* *
54055484 TTTACCAAAATAGTACAAAATAAATATTTA
1 TTTACTAAAATAATACAAAATAAATATTTA
*
54055514 TATACTAAA
1 TTTACTAAA
54055523 TTGGTATCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 11 0.35
29 4 0.13
30 16 0.52
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (30 bp):
TTTACTAAAATAATACAAAATAAATATTTA
Found at i:54055631 original size:29 final size:30
Alignment explanation
Indices: 54055568--54055640 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
54055558 TGTGGATAGG
* *
54055568 ATTTTGGTATATAAATATTTATTTTGTACG
1 ATTTTGGTATATAAATATCTATTTTGTACC
54055598 ATTTTGGTATATAAATATCT-TTTTGTACC
1 ATTTTGGTATATAAATATCTATTTTGTACC
*
54055627 ATTTTGGTAAATAA
1 ATTTTGGTATATAA
54055641 CTCATTTTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (30 bp):
ATTTTGGTATATAAATATCTATTTTGTACC
Found at i:54056885 original size:43 final size:44
Alignment explanation
Indices: 54056789--54056886 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 44
54056779 TATGTTATTC
* * *
54056789 ATTGACATGTTATTAAATTATATTACTTGATTCATGTTAATATG
1 ATTGACATGTTACTAAATTATATTACTTGACTCATATTAATATG
* * *
54056833 GTTG-TATGTTACTAAATTATATTACTTGACTCTTATTAATAT-
1 ATTGACATGTTACTAAATTATATTACTTGACTCATATTAATATG
54056875 ATTGACATGTTA
1 ATTGACATGTTA
54056887 TTAATTCTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
42 3 0.07
43 39 0.87
44 3 0.07
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (44 bp):
ATTGACATGTTACTAAATTATATTACTTGACTCATATTAATATG
Found at i:54058600 original size:24 final size:23
Alignment explanation
Indices: 54058555--54058604 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
54058545 TATATTATAT
54058555 TATTTTAATATTTAATAATTTTA
1 TATTTTAATATTTAATAATTTTA
* **
54058578 TATTTTAATTTATTAATTTTTTTA
1 TATTTTAATAT-TTAATAATTTTA
54058602 TAT
1 TAT
54058605 AGTAATCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTAATATTTAATAATTTTA
Found at i:54075373 original size:5 final size:5
Alignment explanation
Indices: 54075363--54075387 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54075353 AATTTTGATG
54075363 CTCTT CTCTT CTCTT CTCTT CTCTT
1 CTCTT CTCTT CTCTT CTCTT CTCTT
54075388 GCTTTTATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTCTT
Found at i:54076992 original size:42 final size:42
Alignment explanation
Indices: 54076902--54077022 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 42
54076892 CTTGTGCAGA
* * * *
54076902 AGTCACACGGGCGTGTGTCTAGGTCGTGCAAGCCATTGACTTC
1 AGTCACACGGGCGTGTG-CCAGATCGTGTAAGCCACTGACTTC
* * *
54076945 GGTCACACGGGCGTGTGCCAGACCGTGTAAGCCACTGACTTT
1 AGTCACACGGGCGTGTGCCAGATCGTGTAAGCCACTGACTTC
* * * *
54076987 AGTCACACAGACGTGTGCCAGATTGTGTGAGCCACT
1 AGTCACACGGGCGTGTGCCAGATCGTGTAAGCCACT
54077023 ATGAGGAGCC
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 49 0.75
43 16 0.25
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (42 bp):
AGTCACACGGGCGTGTGCCAGATCGTGTAAGCCACTGACTTC
Found at i:54080002 original size:21 final size:21
Alignment explanation
Indices: 54079976--54080028 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
54079966 ATAATTATGC
54079976 TTATTTTCTTTAAATTAA-GGA
1 TTATTTT-TTTAAATTAATGGA
* *
54079997 TTATTTTTTTAATTTAATGTA
1 TTATTTTTTTAAATTAATGGA
*
54080018 TTATTTATTTA
1 TTATTTTTTTA
54080029 TTTTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (21 bp):
TTATTTTTTTAAATTAATGGA
Found at i:54083709 original size:2 final size:2
Alignment explanation
Indices: 54083702--54083732 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54083692 GGACAATCAG
54083702 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 A
54083733 AAGCAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54089622 original size:23 final size:23
Alignment explanation
Indices: 54089555--54089610 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
54089545 TGCTGGGCAA
* * *
54089555 CAGAGAGCACACACAGCGTTAAT
1 CAGAGAGCACACATAGTGCTAAT
54089578 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACATAGTGCTAAT
54089601 CAGAGAGCAC
1 CAGAGAGCAC
54089611 GAGACGTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACATAGTGCTAAT
Found at i:54093849 original size:20 final size:20
Alignment explanation
Indices: 54093820--54093865 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
54093810 CTAGCTCCTT
*
54093820 TCAATTGATCAAATAAATCA
1 TCAATCGATCAAATAAATCA
54093840 TCAATCGATCAAATAAATCA
1 TCAATCGATCAAATAAATCA
54093860 TCAATC
1 TCAATC
54093866 CTGGGTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAATCGATCAAATAAATCA
Found at i:54096727 original size:23 final size:23
Alignment explanation
Indices: 54096697--54096798 Score: 125
Period size: 23 Copynumber: 4.3 Consensus size: 23
54096687 AGTTGGGCAA
*
54096697 CAGAGAGCACACACAGTTCTAAT
1 CAGAGAGCACACACAGTGCTAAT
*
54096720 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
*
54096743 CATAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
* *
54096766 AACAGAGAGCACGAGAC-GTGCTAAA
1 --CAGAGAGCAC-ACACAGTGCTAAT
54096791 CAGAGAGC
1 CAGAGAGC
54096799 GCGCTAGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
23 50 0.72
25 16 0.23
26 3 0.04
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACACAGTGCTAAT
Found at i:54096787 original size:48 final size:46
Alignment explanation
Indices: 54096695--54096798 Score: 129
Period size: 48 Copynumber: 2.2 Consensus size: 46
54096685 ATAGTTGGGC
*
54096695 AACAGAGAGCACACACAGTTCTAATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTA
* * * *
54096741 ATCATAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTA
1 AACAGAGAGCACACACAGTGCTAAT--CAGAGAGCAC-ACAAAGTGCTA
54096789 AACAGAGAGC
1 AACAGAGAGC
54096799 GCGCTAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
46 22 0.46
48 25 0.52
49 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.12
Consensus pattern (46 bp):
AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTA
Found at i:54099575 original size:2 final size:2
Alignment explanation
Indices: 54099568--54099592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54099558 GAGGACAATC
54099568 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
54099593 AAGCAATGAA
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:54120976 original size:3 final size:3
Alignment explanation
Indices: 54120968--54120995 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54120958 CAAAGCCATC
54120968 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
54120996 AGGCCTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:54125052 original size:31 final size:32
Alignment explanation
Indices: 54125017--54125076 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
54125007 ACGGTTATTG
54125017 AACTATTCAAAAG-TTTTAATTTAAGTCACTA
1 AACTATTCAAAAGATTTTAATTTAAGTCACTA
*
54125048 AACTATTCAAAAGATTTTTATTTAAGTCA
1 AACTATTCAAAAGATTTTAATTTAAGTCA
54125077 GAGGACTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (32 bp):
AACTATTCAAAAGATTTTAATTTAAGTCACTA
Found at i:54125987 original size:2 final size:2
Alignment explanation
Indices: 54125980--54126007 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54125970 AAACCAAAAG
54125980 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
54126008 GGTGAGGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54133440 original size:24 final size:24
Alignment explanation
Indices: 54133412--54133498 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
54133402 TAGACTAATA
*
54133412 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * *
54133436 AGAGTTCAATTGAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * *
54133460 AAAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
54133484 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
54133499 GATTATTTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:54135003 original size:168 final size:168
Alignment explanation
Indices: 54134712--54135036 Score: 551
Period size: 168 Copynumber: 1.9 Consensus size: 168
54134702 TGTCCAAACC
* *
54134712 GGTACATCGTTAATCTTGATCCAACCAATTTTATTAATCAATCTAATTCTATTCCAACAACATTA
1 GGTACATCGTCAATCTTGATCCAACCAATTTTATTAATCAATCTAATTCTATTCCAACAACACTA
* *
54134777 CTATTCACCGCACAAACCCAAAATAAAAATAATAATCTCTAAACCGATCAAGCCATCCGTTTTCG
66 CTATTCACCGCACAAACCCAAAATAAAAACAATAATCTCTAAACCGATCAACCCATCCGTTTTCG
*
54134842 ATGCGACTATCGTTCGATTTCAATTAATTCGCTCAAAG
131 ACGCGACTATCGTTCGATTTCAATTAATTCGCTCAAAG
* *
54134880 GGTACATCGTCAATCTTGATCCAACTAATTTTATTAATCAATCTAATTCTATTCCAGCAACACTA
1 GGTACATCGTCAATCTTGATCCAACCAATTTTATTAATCAATCTAATTCTATTCCAACAACACTA
* * *
54134945 TTATTCACCGCACAAACTCAAAATAAAAACAATAATCTCTAAACTGATCAACCCATCCGTTTTCG
66 CTATTCACCGCACAAACCCAAAATAAAAACAATAATCTCTAAACCGATCAACCCATCCGTTTTCG
*
54135010 ACGCGATTATCGTTCGATTTCAATTAA
131 ACGCGACTATCGTTCGATTTCAATTAA
54135037 AGAAATTATT
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 146 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (168 bp):
GGTACATCGTCAATCTTGATCCAACCAATTTTATTAATCAATCTAATTCTATTCCAACAACACTA
CTATTCACCGCACAAACCCAAAATAAAAACAATAATCTCTAAACCGATCAACCCATCCGTTTTCG
ACGCGACTATCGTTCGATTTCAATTAATTCGCTCAAAG
Found at i:54135073 original size:15 final size:16
Alignment explanation
Indices: 54135053--54135082 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54135043 TATTAAAATG
54135053 ATAAAAAA-ATAAAAA
1 ATAAAAAATATAAAAA
54135068 ATAAAAAATATAAAA
1 ATAAAAAATATAAAA
54135083 CATTGTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
ATAAAAAATATAAAAA
Found at i:54140463 original size:29 final size:31
Alignment explanation
Indices: 54140418--54140479 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
54140408 ATTCAAAGTA
** *
54140418 TTTAGAAATTCTTATTACGCC-CT-AAAATT
1 TTTAGAAATTCGCATTAAGCCTCTCAAAATT
54140447 TTTAGAAATTCGCATTAAGCCTCTCAAAATT
1 TTTAGAAATTCGCATTAAGCCTCTCAAAATT
54140478 TT
1 TT
54140480 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.64
30 2 0.07
31 8 0.29
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (31 bp):
TTTAGAAATTCGCATTAAGCCTCTCAAAATT
Found at i:54144162 original size:30 final size:29
Alignment explanation
Indices: 54144123--54144181 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
54144113 TAAATTATTA
*
54144123 AAAATATATTATATTATAAT-TTTGTTAAT
1 AAAATATATTAT-GTATAATATTTGTTAAT
*
54144152 AAAATAATATTATGTATAATATTTTTTAAT
1 AAAAT-ATATTATGTATAATATTTGTTAAT
54144182 TATTGATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
AAAATATATTATGTATAATATTTGTTAAT
Found at i:54147264 original size:16 final size:16
Alignment explanation
Indices: 54147245--54147279 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54147235 TTTTTATAAT
54147245 TTTGGATCATTTTGAG
1 TTTGGATCATTTTGAG
**
54147261 TTTGGATTGTTTTGAG
1 TTTGGATCATTTTGAG
54147277 TTT
1 TTT
54147280 AGATTATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.26, T:0.57
Consensus pattern (16 bp):
TTTGGATCATTTTGAG
Found at i:54147284 original size:16 final size:16
Alignment explanation
Indices: 54147254--54147284 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54147244 TTTTGGATCA
*
54147254 TTTTGAGTTTGGATTG
1 TTTTGAGTTTAGATTG
54147270 TTTTGAGTTTAGATT
1 TTTTGAGTTTAGATT
54147285 ATTTGGTGTG
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:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (16 bp):
TTTTGAGTTTAGATTG
Found at i:54147361 original size:15 final size:16
Alignment explanation
Indices: 54147343--54147383 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
54147333 TATTTGAATA
54147343 ATTTTAAGTTTG-GTT
1 ATTTTAAGTTTGAGTT
*
54147358 ATTTTGTA-TTTGAGTT
1 ATTTT-AAGTTTGAGTT
54147374 ATTTTAAGTT
1 ATTTTAAGTT
54147384 GAGGTTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (16 bp):
ATTTTAAGTTTGAGTT
Found at i:54147526 original size:3 final size:3
Alignment explanation
Indices: 54147507--54147543 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
54147497 TCGAAGTAGA
* *
54147507 ATT AAT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54147544 ATATATAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:54147855 original size:24 final size:24
Alignment explanation
Indices: 54147822--54147873 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54147812 GACTTCACAT
54147822 TTTTGCTGTTTACCGGTTTAATCC
1 TTTTGCTGTTTACCGGTTTAATCC
* * **
54147846 TTTTGTTGTTTATCGGTTTGGTCC
1 TTTTGCTGTTTACCGGTTTAATCC
54147870 TTTT
1 TTTT
54147874 CAGGTGAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (24 bp):
TTTTGCTGTTTACCGGTTTAATCC
Found at i:54148212 original size:30 final size:30
Alignment explanation
Indices: 54148178--54148241 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
54148168 ATATTTGATT
*
54148178 TGAAAATTTAATTCATATGCACACATAATG
1 TGAAAATTTAATTCATATGCACACATAACG
*
54148208 TGAAAATTTAATTCATATGTACACATAACG
1 TGAAAATTTAATTCATATGCACACATAACG
54148238 TGAA
1 TGAA
54148242 CAAAAAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (30 bp):
TGAAAATTTAATTCATATGCACACATAACG
Found at i:54158094 original size:5 final size:5
Alignment explanation
Indices: 54158084--54158108 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54158074 TTTTGGAGAA
54158084 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
54158109 CAGAGGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:54160958 original size:41 final size:40
Alignment explanation
Indices: 54160888--54160965 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
54160878 TTGTATTAAT
*
54160888 TTTTAATTTTGAATTTTAAATTTATTTTGATAAAAATGAG
1 TTTTAATTTTGAATTTTAAATTTATTTTGACAAAAATGAG
* *
54160928 TTTTATTTTATGATTTTTAAATATTA-TTTGACAAAAAT
1 TTTTAATTT-TGAATTTTAAAT-TTATTTTGACAAAAAT
54160966 TTTAAATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 8 0.24
41 22 0.67
42 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.54
Consensus pattern (40 bp):
TTTTAATTTTGAATTTTAAATTTATTTTGACAAAAATGAG
Found at i:54161428 original size:23 final size:23
Alignment explanation
Indices: 54161401--54161458 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 23
54161391 TTTTAAAATC
54161401 AAATTTATATTATTTTTAATTT-TT
1 AAATTTATATT-TTTTT-ATTTATT
54161425 -AATTTAGTATTTTTTTATTTATT
1 AAATTTA-TATTTTTTTATTTATT
54161448 AAAATTTATAT
1 -AAATTTATAT
54161459 ACAGGCAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 4 0.13
23 13 0.43
24 7 0.23
25 6 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
AAATTTATATTTTTTTATTTATT
Found at i:54163360 original size:30 final size:31
Alignment explanation
Indices: 54163326--54163385 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
54163316 ACAGTTTTTT
54163326 ATAATTAAATGATTAA-AATAAAAATTATTG
1 ATAATTAAATGATTAATAATAAAAATTATTG
* * * *
54163356 ATAATTGAGTGATTAATAATATAATTTATT
1 ATAATTAAATGATTAATAATAAAAATTATT
54163386 TTAAATAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (31 bp):
ATAATTAAATGATTAATAATAAAAATTATTG
Found at i:54167260 original size:30 final size:30
Alignment explanation
Indices: 54167204--54167260 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
54167194 TAAACATTAT
* ***
54167204 TAAATTATCTCTAATTTTTTTTTTGGTGAA
1 TAAATTATCTCTAAATTTTAAATTGGTGAA
54167234 TAAATTATCTCTAAATTTTAAATTGGT
1 TAAATTATCTCTAAATTTTAAATTGGT
54167261 CTCTAAACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.53
Consensus pattern (30 bp):
TAAATTATCTCTAAATTTTAAATTGGTGAA
Done.