Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold37
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: 836391
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:472142 original size:20 final size:20
Alignment explanation
Indices: 472084--472150 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
472074 ATATATCAAA
472084 ATTAATATAAATATAAAATAT
1 ATTAA-ATAAATATAAAATAT
* *
472105 TTTAAATTAAT-TAAAAATAT
1 ATTAAATAAATAT-AAAATAT
472125 ATTAAA-AAATATATAAAT-T
1 ATTAAATAAATATA-AAATAT
472144 ATTAAAT
1 ATTAAAT
472151 TTATCTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 12 0.32
20 22 0.58
21 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAAATAAATATAAAATAT
Found at i:472279 original size:7 final size:8
Alignment explanation
Indices: 472262--472291 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
472252 AACCCAAAAC
472262 AAAAATAA
1 AAAAATAA
472270 AAAAATAA
1 AAAAATAA
472278 AAAAATAA
1 AAAAATAA
472286 ATAAAA
1 A-AAAA
472292 AACTCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:473562 original size:2 final size:2
Alignment explanation
Indices: 473555--473581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
473545 TTGTAAGTTC
473555 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
473582 GTGGACAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:475769 original size:31 final size:32
Alignment explanation
Indices: 475734--475799 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
475724 TAAAAAAAGT
* * *
475734 AATAATTTAAAAAT-AATTAATTTTAATTTAA
1 AATAATTTAAAAATAAAATAATTTAAACTTAA
*
475765 AATAATTTAAATATAAAATAATTTAAACTTAA
1 AATAATTTAAAAATAAAATAATTTAAACTTAA
475797 AAT
1 AAT
475800 GATTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
AATAATTTAAAAATAAAATAATTTAAACTTAA
Found at i:475773 original size:15 final size:16
Alignment explanation
Indices: 475751--475809 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
475741 TAAAAATAAT
*
475751 TAATTTTAATTTAAAA
1 TAATTTAAATTTAAAA
*
475767 TAATTTAAATATAAAA
1 TAATTTAAATTTAAAA
*
475783 TAATTTAAACTTAAAA
1 TAATTTAAATTTAAAA
*
475799 TGA-TTAAATTT
1 TAATTTAAATTT
475810 GATAATTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 7 0.19
16 30 0.81
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:475888 original size:31 final size:31
Alignment explanation
Indices: 475853--475947 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
475843 TAAACATGAT
475853 TGATTTGAATTTGAAATATTTATATTTAGAA
1 TGATTTGAATTTGAAATATTTATATTTAGAA
* *
475884 TGATTTGAATTT----T-GTTA-ATCT----
1 TGATTTGAATTTGAAATATTTATATTTAGAA
475905 TGATTTGAATTTGAAATATTTATATTTAGAA
1 TGATTTGAATTTGAAATATTTATATTTAGAA
475936 TGATTTGAATTT
1 TGATTTGAATTT
475948 TGTTAATATG
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
21 12 0.24
25 4 0.08
26 6 0.12
27 4 0.08
31 24 0.48
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.52
Consensus pattern (31 bp):
TGATTTGAATTTGAAATATTTATATTTAGAA
Found at i:475908 original size:52 final size:52
Alignment explanation
Indices: 475852--475954 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
475842 TTAAACATGA
475852 TTGATTTGAATTTGAAATATTTATATTTAGAATGATTTGAATTTTGTTAATC
1 TTGATTTGAATTTGAAATATTTATATTTAGAATGATTTGAATTTTGTTAATC
475904 TTGATTTGAATTTGAAATATTTATATTTAGAATGATTTGAATTTTGTTAAT
1 TTGATTTGAATTTGAAATATTTATATTTAGAATGATTTGAATTTTGTTAAT
475955 ATGTGTGTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.52
Consensus pattern (52 bp):
TTGATTTGAATTTGAAATATTTATATTTAGAATGATTTGAATTTTGTTAATC
Found at i:476053 original size:32 final size:32
Alignment explanation
Indices: 475990--476107 Score: 111
Period size: 32 Copynumber: 3.8 Consensus size: 32
475980 TTTGAAATTA
* * *
475990 TTTAAAAT-TAAA-AATATTAAATTTGAGATAT
1 TTTAAAATCAAAATAAT-TTAAATTTAAAATAT
*
476021 TTTAAAATCAAAGTAATTTAAATTTAAAATAT
1 TTTAAAATCAAAATAATTTAAATTTAAAATAT
* *
476053 TTTAAAA-CATAAATAA-TGAAACTTAAAA-AT
1 TTTAAAATCA-AAATAATTTAAATTTAAAATAT
*
476083 TTTAAAATTTAAAATAATTTAAATT
1 TTTAAAA-TCAAAATAATTTAAATT
476108 AAATTAACTC
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
30 9 0.13
31 26 0.37
32 33 0.46
33 3 0.04
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
TTTAAAATCAAAATAATTTAAATTTAAAATAT
Found at i:476056 original size:16 final size:16
Alignment explanation
Indices: 475990--476107 Score: 64
Period size: 16 Copynumber: 7.5 Consensus size: 16
475980 TTTGAAATTA
*
475990 TTTAAAATTAAAA-AT
1 TTTAAATTTAAAATAT
* * *
476005 ATTAAATTTGAGATAT
1 TTTAAATTTAAAATAT
* * * *
476021 TTTAAAATCAAAGTAA
1 TTTAAATTTAAAATAT
476037 TTTAAATTTAAAATAT
1 TTTAAATTTAAAATAT
**
476053 TTTAAA-ACATAAATA-
1 TTTAAATTTA-AAATAT
* * *
476068 ATGAAACTTAAAA-AT
1 TTTAAATTTAAAATAT
*
476083 TTTAAAATTTAAAATAA
1 TTT-AAATTTAAAATAT
476100 TTTAAATT
1 TTTAAATT
476108 AAATTAACTC
Statistics
Matches: 72, Mismatches: 25, Indels: 11
0.67 0.23 0.10
Matches are distributed among these distances:
14 1 0.01
15 18 0.25
16 49 0.68
17 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAAATAT
Found at i:476252 original size:20 final size:19
Alignment explanation
Indices: 476223--476261 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
476213 TCTATTTACA
476223 TAAAAAATAAAAAATAAAT
1 TAAAAAATAAAAAATAAAT
*
476242 TAAATAAATAAACAATAAAT
1 TAAA-AAATAAAAAATAAAT
476262 AATTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAAAAATAAAAAATAAAT
Found at i:476854 original size:17 final size:15
Alignment explanation
Indices: 476829--476874 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
476819 TGAATTTTAA
*
476829 TATTTATAAAATTTT
1 TATTAATAAAATTTT
*
476844 TAATTAAATAAAATTAT
1 T-ATT-AATAAAATTTT
476861 TATTAATAAAATTT
1 TATTAATAAAATTT
476875 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.38
16 6 0.23
17 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATAAAATTTT
Found at i:476876 original size:16 final size:16
Alignment explanation
Indices: 476824--476877 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
476814 TTGTTTGAAT
* *
476824 TTTAATATTTATAAAA
1 TTTATTATTAATAAAA
476840 TTT-TTAATTAAATAAAA
1 TTTATT-ATT-AATAAAA
476857 -TTATTATTAATAAAA
1 TTTATTATTAATAAAA
476872 TTTATT
1 TTTATT
476878 TAAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.25
16 16 0.50
17 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATTATTAATAAAA
Found at i:477430 original size:16 final size:16
Alignment explanation
Indices: 477394--477429 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
477384 AGTACACAAA
477394 TTTTTCTCTTTTTCTT
1 TTTTTCTCTTTTTCTT
477410 TTTTTC-CTTTTTCTT
1 TTTTTCTCTTTTTCTT
477425 TTTTT
1 TTTTT
477430 TATAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTCTTTTTCTT
Found at i:477853 original size:20 final size:21
Alignment explanation
Indices: 477807--477852 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
477797 TAAATGTACG
*
477807 AAAAATAAAAATATAACATAA
1 AAAAATAAAAACATAACATAA
* *
477828 AAAAATTAAAACATAATATAA
1 AAAAATAAAAACATAACATAA
477849 AAAA
1 AAAA
477853 TGAATATGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAATAAAAACATAACATAA
Found at i:478233 original size:7 final size:7
Alignment explanation
Indices: 478223--478260 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
478213 TAATTTTTTC
478223 TTTTCTT
1 TTTTCTT
478230 TTTTCTTT
1 TTTTC-TT
478238 TTTTCTT
1 TTTTCTT
478245 TTTTCTT
1 TTTTCTT
478252 TCTTTCTT
1 T-TTTCTT
478260 T
1 T
478261 CTTTTTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:478240 original size:19 final size:19
Alignment explanation
Indices: 478216--478266 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
478206 GAATATATAA
*
478216 TTTTTTCTTTTCTTTTTTCT
1 TTTTTTCTTTT-TTCTTTCT
478236 TTTTTTCTTTTTTCTTTCT
1 TTTTTTCTTTTTTCTTTCT
*
478255 TTCTTTCTTTTT
1 TTTTTTCTTTTT
478267 CTACTGAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTCTTTTTTCTTTCT
Found at i:478243 original size:15 final size:15
Alignment explanation
Indices: 478223--478260 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
478213 TAATTTTTTC
478223 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
478238 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
*
478253 CTTTCTTT
1 TTTTCTTT
478261 CTTTTTCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTCTTT
Found at i:478255 original size:4 final size:4
Alignment explanation
Indices: 478219--478264 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
478209 TATATAATTT
*
478219 TTTC TTTTC TTT- TTTC TTTT TTTC TTT- TTTC TTTC TTTC TTTC TTT
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
478265 TTCTACTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
3 6 0.16
4 27 0.73
5 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTC
Found at i:478527 original size:28 final size:30
Alignment explanation
Indices: 478495--478552 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
478485 TAAGAAGTAT
478495 ATTTTAATTTTT-TAT-TATT-AAATTAAAA
1 ATTTTAATTTTTATATAT-TTAAAATTAAAA
*
478523 ATTTTTATTTTTATATATTTAAAATTAAAA
1 ATTTTAATTTTTATATATTTAAAATTAAAA
478553 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTTTAATTTTTATATATTTAAAATTAAAA
Found at i:479090 original size:2 final size:2
Alignment explanation
Indices: 479083--479118 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
479073 CTTATTTTCT
479083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
479119 AGTTTTATTT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:479731 original size:17 final size:18
Alignment explanation
Indices: 479709--479744 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
479699 TTTTTTATTT
479709 ATTTTTTAAAAAA-AATA
1 ATTTTTTAAAAAATAATA
479726 ATTTTTTAAAAAATAATA
1 ATTTTTTAAAAAATAATA
479744 A
1 A
479745 AATTAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTTTTAAAAAATAATA
Found at i:480172 original size:26 final size:28
Alignment explanation
Indices: 480121--480179 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
480111 ATTTTTTAAA
* *
480121 AAATTTAAATATTTTTATATTTATA-TT
1 AAATTTAAATATTTTTATAATCATATTT
*
480148 AAATTTATATA-TTTTATAATCATATTT
1 AAATTTAAATATTTTTATAATCATATTT
480175 AAATT
1 AAATT
480180 ATTATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
AAATTTAAATATTTTTATAATCATATTT
Found at i:480175 original size:32 final size:30
Alignment explanation
Indices: 480136--480241 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 30
480126 TAAATATTTT
*
480136 TATATTTATATTAAATT-TATATATTTTATAA
1 TATATTTATATT-AATTATATAAATTTT-TAA
*
480167 TCATATTTAAATT-ATTATATAAATTTTTAA
1 T-ATATTTATATTAATTATATAAATTTTTAA
*
480197 TACATTTATAATTATATTATATAAATTTTTAA
1 TATATTTAT-ATTA-ATTATATAAATTTTTAA
*
480229 AATATTTATATTA
1 TATATTTATATTA
480242 TTTTTTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.09
30 10 0.16
31 14 0.22
32 34 0.53
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TATATTTATATTAATTATATAAATTTTTAA
Found at i:480255 original size:16 final size:16
Alignment explanation
Indices: 480234--480269 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
480224 TTTAAAATAT
* *
480234 TTATATTATTTTTTTA
1 TTATATTATATTTTAA
480250 TTATATTATATTTTAA
1 TTATATTATATTTTAA
480266 TTAT
1 TTAT
480270 TTTTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:480261 original size:21 final size:21
Alignment explanation
Indices: 480207--480280 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
480197 TACATTTATA
480207 ATTATATTATA-TAAATTTTT
1 ATTATATTATATTAAATTTTT
** **
480227 AAAATATTTATATTATTTTTTT
1 ATTATA-TTATATTAAATTTTT
*
480249 ATTATATTATATTTTAATTATTT
1 ATTATATTATA-TTAAATT-TTT
480272 -TTATATTAT
1 ATTATATTAT
480281 TTTTGATGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.10
21 10 0.24
22 24 0.59
23 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATATTATATTAAATTTTT
Found at i:488694 original size:2 final size:2
Alignment explanation
Indices: 488689--488718 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
488679 ATCTTTTTTA
488689 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
488719 CTTTTGTTTC
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:488906 original size:20 final size:20
Alignment explanation
Indices: 488858--488909 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
488848 AATGGTTCAT
* *
488858 TTTAATAAA-ATGTTAAATG
1 TTTAATAAATATTTTAAATA
* *
488877 TTTAAAAAATATTTTTAATA
1 TTTAATAAATATTTTAAATA
488897 TTTAATAAATATT
1 TTTAATAAATATT
488910 AATTATATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTAATAAATATTTTAAATA
Found at i:489645 original size:40 final size:38
Alignment explanation
Indices: 489579--489654 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 38
489569 TATTATAATA
* *
489579 ATATTTTAAATTAATCGTGTATTATAAATATATATCAT
1 ATATTGTAAATTAATCATGTATTATAAATATATATCAT
489617 ATATTGTAAATATATATCATGTATTATAAATATATATC
1 ATATTGTAAAT-TA-ATCATGTATTATAAATATATATC
489655 GTGTATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 10 0.29
39 2 0.06
40 22 0.65
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (38 bp):
ATATTGTAAATTAATCATGTATTATAAATATATATCAT
Found at i:489659 original size:20 final size:20
Alignment explanation
Indices: 489596--489663 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
489586 AAATTAATCG
489596 TGTATTATAAATATATATCA
1 TGTATTATAAATATATATCA
* *
489616 TATATTGTAAATATATATCA
1 TGTATTATAAATATATATCA
*
489636 TGTATTATAAATATATATCG
1 TGTATTATAAATATATATCA
489656 TGTATTAT
1 TGTATTAT
489664 GACAATTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (20 bp):
TGTATTATAAATATATATCA
Found at i:489779 original size:33 final size:34
Alignment explanation
Indices: 489742--489819 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 34
489732 TGATATCCAA
489742 AAATAATAAA-TA-ATTAAAAGTTATATTTATG-C
1 AAATAATAAATTATATTAAAA-TTATATTTATGTC
*
489774 TAAATAATAAATTATCTATTCAAATTATATTTATGTC
1 -AAATAATAAATTA--TATTAAAATTATATTTATGTC
489811 AAATAATAA
1 AAATAATAA
489820 TTAAAAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 10 0.26
34 2 0.05
36 20 0.51
37 7 0.18
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (34 bp):
AAATAATAAATTATATTAAAATTATATTTATGTC
Found at i:489885 original size:16 final size:16
Alignment explanation
Indices: 489864--489933 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
489854 TAATTTTAAT
489864 AAAATTTAAAAAATAA
1 AAAATTTAAAAAATAA
**
489880 AAAATTTAAAGATTTAA
1 AAAATTTAAA-AAATAA
* *
489897 AAAA-TAAATAAAAGAA
1 AAAATTTAA-AAAATAA
489913 AAAATTTTGAAAAAA-AA
1 AAAA-TTT-AAAAAATAA
489930 AAAA
1 AAAA
489934 GGTTAAAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
16 20 0.48
17 15 0.36
18 5 0.12
19 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (16 bp):
AAAATTTAAAAAATAA
Found at i:489899 original size:17 final size:16
Alignment explanation
Indices: 489858--489901 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
489848 TAAAAATAAT
489858 TTTAATAAAATTTAAAA
1 TTTAA-AAAATTTAAAA
**
489875 AATAAAAAATTTAAAGA
1 TTTAAAAAATTTAAA-A
489892 TTTAAAAAAT
1 TTTAAAAAAT
489902 AAATAAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TTTAAAAAATTTAAAA
Found at i:490273 original size:22 final size:21
Alignment explanation
Indices: 490248--490300 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 21
490238 TATTATAAAT
*
490248 AAGTAATTTTTATTTAATAGAA
1 AAGTAATTTTT-TTTAAGAGAA
490270 AAG---TTTTTTTTAAGAGAA
1 AAGTAATTTTTTTTAAGAGAA
*
490288 AAATAATTTTTTT
1 AAGTAATTTTTTT
490301 AAAAAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
21 7 0.27
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (21 bp):
AAGTAATTTTTTTTAAGAGAA
Found at i:490362 original size:20 final size:20
Alignment explanation
Indices: 490337--490387 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
490327 CGTTAGTTGC
490337 TAAAAGAGTGACAATTTTAT
1 TAAAAGAGTGACAATTTTAT
490357 TAAAAGAGTGACAATTTTAT
1 TAAAAGAGTGACAATTTTAT
490377 TAAAAGAGTGA
1 TAAAAGAGTGA
490388 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (20 bp):
TAAAAGAGTGACAATTTTAT
Found at i:491688 original size:27 final size:28
Alignment explanation
Indices: 491651--491703 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
491641 ACTTCAAAAA
*
491651 TAAAATAATTATTTAATAAAAATAAATT
1 TAAAATAATTATTCAATAAAAATAAATT
491679 TAAAA-AATTATTCAATAAAAATAAA
1 TAAAATAATTATTCAATAAAAATAAA
491704 AATATTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAAATAATTATTCAATAAAAATAAATT
Found at i:494872 original size:47 final size:46
Alignment explanation
Indices: 494803--494896 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 46
494793 TCTTTTACTT
494803 TATTATCTCATAAAAGTAATAATTATGTTCATATATATATATATATA
1 TATTATCTCATAAAAGTAATAATTATGTT-ATATATATATATATATA
494850 TATTATCTCATAAAAGTAATAATTATGTTATATATATATATATATA
1 TATTATCTCATAAAAGTAATAATTATGTTATATATATATATATATA
494896 T
1 T
494897 GAGAATAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 18 0.38
47 29 0.62
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (46 bp):
TATTATCTCATAAAAGTAATAATTATGTTATATATATATATATATA
Found at i:495283 original size:3 final size:3
Alignment explanation
Indices: 495277--495319 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
495267 TCTAAAATCA
495277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
495320 GTGTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:499578 original size:41 final size:42
Alignment explanation
Indices: 499501--499583 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 42
499491 AAAAAAAAAG
*
499501 AAAGAAAGGTGATACATTATTTTACTTGGTGGAAAAGAAACT
1 AAAGAAAGGTCATACATTATTTTACTTGGTGGAAAAGAAACT
*
499543 AAAGAAGGGTCATACATTA-TTTACTTGGTGGAAAAGAAACT
1 AAAGAAAGGTCATACATTATTTTACTTGGTGGAAAAGAAACT
499584 TAGGAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 22 0.56
42 17 0.44
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (42 bp):
AAAGAAAGGTCATACATTATTTTACTTGGTGGAAAAGAAACT
Found at i:502690 original size:16 final size:15
Alignment explanation
Indices: 502672--502725 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
502662 ACCGATCCCA
502672 AATTTAAATTAAATT
1 AATTTAAATTAAATT
*
502687 AAATTTGAAA-TAAAAT
1 -AATTT-AAATTAAATT
*
502703 ATTTTAAATTTAAATT
1 AATTTAAA-TTAAATT
502719 AATTTAA
1 AATTTAA
502726 TTTATTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 3 0.10
15 4 0.13
16 21 0.68
17 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTTAAATTAAATT
Found at i:502700 original size:21 final size:20
Alignment explanation
Indices: 502676--502727 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
502666 ATCCCAAATT
502676 TAAATTAAATTAAATTTGAAA
1 TAAATTAAATTAAATTT-AAA
* **
502697 TAAAATATTTTAAATTTAAA
1 TAAATTAAATTAAATTTAAA
* *
502717 TTAATTTAATT
1 TAAATTAAATT
502728 TATTATTATT
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAAATTAAATTAAATTTAAA
Found at i:502790 original size:17 final size:17
Alignment explanation
Indices: 502770--502804 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
502760 AATTTAATTA
502770 TAAAAATAAAATAATAT
1 TAAAAATAAAATAATAT
*
502787 TAAATATAAAATAATAT
1 TAAAAATAAAATAATAT
502804 T
1 T
502805 TTAATTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATAAAATAATAT
Found at i:510213 original size:19 final size:20
Alignment explanation
Indices: 510185--510243 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
510175 GTCTATTTTA
*
510185 TTATTATTATATT-ATATTT
1 TTATTTTTATATTAATATTT
510204 TTATTTTTATATTAATATTT
1 TTATTTTTATATTAATATTT
*
510224 ATATTTTTATAATTAA-ATTT
1 TTATTTTTAT-ATTAATATTT
510244 AAATAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 12 0.33
20 19 0.53
21 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTTATATTAATATTT
Found at i:511641 original size:21 final size:22
Alignment explanation
Indices: 511609--511658 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
511599 AAAACTTAGT
*
511609 AATATTAAAT-AAAATTA-TAAA
1 AATA-TAAATAAAAATAATTAAA
511630 AATATAATATAAAAATAATTAAA
1 AATATAA-ATAAAAATAATTAAA
511653 AATATA
1 AATATA
511659 TCAGTATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 6 0.24
22 6 0.24
23 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AATATAAATAAAAATAATTAAA
Found at i:514514 original size:2 final size:2
Alignment explanation
Indices: 514507--514556 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
514497 GTACCTTGTT
*
514507 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
514549 TA TA TA TA
1 TA TA TA TA
514557 CCCGATTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:514747 original size:2 final size:2
Alignment explanation
Indices: 514740--514765 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
514730 ATGGTGAATG
514740 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
514766 TTAATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:516345 original size:19 final size:19
Alignment explanation
Indices: 516321--516360 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
516311 GAAATAAAAT
516321 TTATTTTTAATC-AGAATTA
1 TTATTTTTAATCTA-AATTA
516340 TTATTTTTAATCTAAATTA
1 TTATTTTTAATCTAAATTA
516359 TT
1 TT
516361 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATTTTTAATCTAAATTA
Found at i:524646 original size:17 final size:19
Alignment explanation
Indices: 524596--524666 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
524586 TTTATTTTAT
524596 TTATT-ATATATATTAT-AA
1 TTATTAATATAT-TTATAAA
* * *
524614 TAATTTATAT-TTTTTAAAA
1 TTATTAATATATTTAT-AAA
*
524633 TT-TTAATATATTTATATA
1 TTATTAATATATTTATAAA
*
524651 TTATTAATATTTTTAT
1 TTATTAATATATTTAT
524667 TATATTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 3 0.07
18 15 0.37
19 23 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTAATATATTTATAAA
Found at i:524664 original size:28 final size:27
Alignment explanation
Indices: 524588--524680 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 27
524578 AACAAAAATT
*
524588 TATTT-TATTTATTATATATATTATAATA
1 TATTTATATTTATTA-ATAT-TTTTAATA
* *
524616 -ATTTATATTTTTTAA-AATTTTAATA
1 TATTTATATTTATTAATATTTTTAATA
*
524641 TATTTATATATTATTAATATTTTTATTA
1 TATTTATAT-TTATTAATATTTTTAATA
524669 TA-TTAT-TTTATT
1 TATTTATATTTATT
524681 TTTATATCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
25 12 0.22
26 10 0.18
27 15 0.27
28 18 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTATATTTATTAATATTTTTAATA
Found at i:524680 original size:19 final size:20
Alignment explanation
Indices: 524635--524685 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
524625 TTTTAAAATT
*
524635 TTAATATATTTA-TATATTA
1 TTAATATTTTTATTATATTA
524654 TTAATATTTTTATTATATTA
1 TTAATATTTTTATTATATTA
*
524674 TT-TTATTTTTAT
1 TTAATATTTTTAT
524686 ATCATATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAATATTTTTATTATATTA
Found at i:524700 original size:21 final size:19
Alignment explanation
Indices: 524658--524705 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
524648 ATATTATTAA
* *
524658 TATTTTTATTATATTATTT
1 TATTTTTATTATATCATAT
524677 TATTTTTATATCATATCATAT
1 TATTTTTAT-T-ATATCATAT
*
524698 TATATTTA
1 TATTTTTA
524706 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 1 0.04
21 14 0.58
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATTATATCATAT
Found at i:524827 original size:12 final size:12
Alignment explanation
Indices: 524788--524829 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
524778 ATTTATTATA
*
524788 ATAAATATTATT
1 ATAAATATTAAT
524800 AT-AA-ATTAATT
1 ATAAATATTAA-T
524811 ATAAATATTAAT
1 ATAAATATTAAT
524823 ATAAATA
1 ATAAATA
524830 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 12 0.46
13 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAAATATTAAT
Found at i:524839 original size:23 final size:23
Alignment explanation
Indices: 524788--524854 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
524778 ATTTATTATA
* *
524788 ATAAATATTATTATAAATTAATT
1 ATAAATATTAATATAAATAAATT
*
524811 ATAAATATTAATATAAATAAAAT
1 ATAAATATTAATATAAATAAATT
*
524834 -TAAA-ATT-ATA-AAATAATTT
1 ATAAATATTAATATAAATAAATT
524853 AT
1 AT
524855 CGAATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.18
20 4 0.11
21 3 0.08
22 4 0.11
23 20 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAATATTAATATAAATAAATT
Found at i:526061 original size:24 final size:24
Alignment explanation
Indices: 525994--526067 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
525984 AATTAACCTA
* *
525994 AATATTTAT-TTTATAATTTAAAAT
1 AATATTTATAATTA-AATTTAAATT
* ** *
526018 AATATTTAAAATTATTTTTATATT
1 AATATTTATAATTAAATTTAAATT
526042 AATATTTATAATTAAATTTAAATT
1 AATATTTATAATTAAATTTAAATT
526066 AA
1 AA
526068 AAAATTTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 36 0.92
25 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATTTATAATTAAATTTAAATT
Found at i:526100 original size:24 final size:23
Alignment explanation
Indices: 526008--526107 Score: 75
Period size: 24 Copynumber: 4.4 Consensus size: 23
525998 TTTATTTTAT
*
526008 AATTTAAAATAATATTTAAAATTA
1 AATTT-AAATAATAATTAAAATTA
** * * *
526032 TTTTTATATTAATATTTATAATTA
1 AATTTA-AATAATAATTAAAATTA
526056 AATTTAAAT--TAA--AAAATTTA
1 AATTTAAATAATAATTAAAA-TTA
526076 ATATTTAAATAATAATTAAAATTA
1 A-ATTTAAATAATAATTAAAATTA
526100 AA-TTAAAT
1 AATTTAAAT
526108 CGATCTACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
19 3 0.05
20 4 0.07
21 10 0.17
22 6 0.10
23 7 0.12
24 26 0.43
25 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTAAATAATAATTAAAATTA
Found at i:530606 original size:6 final size:6
Alignment explanation
Indices: 530595--530619 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
530585 TAGATATTTG
530595 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
530620 TTATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:531077 original size:13 final size:14
Alignment explanation
Indices: 531056--531119 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 14
531046 GAATTTTTTT
531056 ATTTAAATTTTTAA
1 ATTTAAATTTTTAA
531070 ATTT-AATTTTT--
1 ATTTAAATTTTTAA
531081 ATTTAAAATTATTTAA
1 ATTT-AAATT-TTTAA
*
531097 TATTAAATAATTTTTAA
1 -ATT-TA-AATTTTTAA
531114 ATTTAA
1 ATTTAA
531120 GCAAATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
11 4 0.10
13 11 0.28
14 8 0.20
15 1 0.03
16 3 0.08
17 9 0.22
18 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAAATTTTTAA
Found at i:531699 original size:32 final size:33
Alignment explanation
Indices: 531653--531716 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
531643 ATTTGTATTA
531653 AATTTAAATAATATTTATT-TA-TAATTTAAATT
1 AATTTAAATAATA-TTATTATATTAATTTAAATT
* * *
531685 AATTTATATCATATTATTATATTATTTTAAAT
1 AATTTAAATAATATTATTATATTAATTTAAAT
531717 AATAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 5 0.19
32 13 0.48
33 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (33 bp):
AATTTAAATAATATTATTATATTAATTTAAATT
Found at i:533152 original size:2 final size:2
Alignment explanation
Indices: 533145--533176 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
533135 TAAGAAGACC
533145 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
533177 GTTTTTCAAA
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:533780 original size:2 final size:2
Alignment explanation
Indices: 533773--533809 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
533763 ATCAAAATGC
533773 AT 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 AT A
533810 CATTTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:535860 original size:2 final size:2
Alignment explanation
Indices: 535853--535879 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
535843 TATGAATAAA
535853 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 A
535880 ATGATTAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:536031 original size:13 final size:14
Alignment explanation
Indices: 536003--536035 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
535993 GAAAAAGTTC
536003 AAAGAGAAAAATAA
1 AAAGAGAAAAATAA
*
536017 AAAGGGAAAAA-AA
1 AAAGAGAAAAATAA
536030 AAAGAG
1 AAAGAG
536036 GAGAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (14 bp):
AAAGAGAAAAATAA
Found at i:537793 original size:15 final size:15
Alignment explanation
Indices: 537768--537807 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
537758 ATTATTCTAT
537768 TTAATATAATAATATTA
1 TTAATA-AATAATA-TA
537785 TT-ATAAATAATATA
1 TTAATAAATAATATA
537799 TTAATAAAT
1 TTAATAAAT
537808 TTTGAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 13 0.59
16 3 0.14
17 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATAAATAATATA
Found at i:539975 original size:6 final size:6
Alignment explanation
Indices: 539966--540024 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
539956 AAAACAAAAT
* *
539966 CTTTCA CTTTCA CTTTCA CTTTC- CTTTTC- CTTTTCC CTTTCA CTTTCT
1 CTTTCA CTTTCA CTTTCA CTTTCA C-TTTCA C-TTTCA CTTTCA CTTTCA
540014 CTCTTCA CTTT
1 CT-TTCA CTTT
540025 GCAAAGTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.02
6 40 0.85
7 6 0.13
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (6 bp):
CTTTCA
Found at i:541270 original size:2 final size:2
Alignment explanation
Indices: 541263--541301 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
541253 ATATAGCGCT
* *
541263 TA TA TA TA TA CA TA TA TA TA TA CA 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
541302 GTAGTCATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:541280 original size:12 final size:12
Alignment explanation
Indices: 541263--541301 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
541253 ATATAGCGCT
541263 TATATATATACA
1 TATATATATACA
541275 TATATATATACA
1 TATATATATACA
*
541287 TATATATATATA
1 TATATATATACA
541299 TAT
1 TAT
541302 GTAGTCATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
TATATATATACA
Found at i:541626 original size:23 final size:21
Alignment explanation
Indices: 541586--541640 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
541576 CCTTTTATCC
* *
541586 TTATATAA-TTTTTTAATTTT
1 TTATAAAATTTTTTTAATTGT
*
541606 TTATTTAAATTTTTTTGAATTGT
1 TTA-TAAAATTTTTTT-AATTGT
541629 TTATAAAATTTT
1 TTATAAAATTTT
541641 CTTTTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 3 0.11
22 14 0.50
23 8 0.29
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTATAAAATTTTTTTAATTGT
Found at i:543110 original size:16 final size:16
Alignment explanation
Indices: 543086--543117 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
543076 GCACTTAACC
*
543086 CATTTTTTTTTTCATT
1 CATTCTTTTTTTCATT
543102 CATTCTTTTTTTCATT
1 CATTCTTTTTTTCATT
543118 TCTTTGTTAT
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:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (16 bp):
CATTCTTTTTTTCATT
Found at i:543186 original size:18 final size:17
Alignment explanation
Indices: 543156--543190 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
543146 AAAAATATTC
*
543156 AAATAATTTTATATAAT
1 AAATAATTATATATAAT
543173 AAATAAATTATATATAAT
1 AAAT-AATTATATATAAT
543191 TACATAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATTATATATAAT
Found at i:543619 original size:19 final size:16
Alignment explanation
Indices: 543582--543613 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
543572 TCAAATAAAT
543582 TCTAAATTTTATTATA
1 TCTAAATTTTATTATA
*
543598 TCTAAATTTTAATATA
1 TCTAAATTTTATTATA
543614 ATATCTTTGA
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:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TCTAAATTTTATTATA
Found at i:544519 original size:11 final size:10
Alignment explanation
Indices: 544495--544520 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
544485 TTATTTTATC
544495 AAAAATTCAT
1 AAAAATTCAT
544505 AAAAATTCAT
1 AAAAATTCAT
544515 AAAAAT
1 AAAAAT
544521 AATTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATTCAT
Found at i:544607 original size:2 final size:2
Alignment explanation
Indices: 544602--544655 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
544592 TATTCAAATA
* * *
544602 AT AT AT AA AT AT AA AT CT -T 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
544643 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
544656 ATAAAGCTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:547827 original size:2 final size:2
Alignment explanation
Indices: 547820--547853 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
547810 GTTATTATCC
547820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
547854 CACACACGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:548020 original size:32 final size:32
Alignment explanation
Indices: 547984--548046 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
547974 GTAGGTGTAC
547984 AATCCTAAAAGATATTTTCCAGTTTTCCTTAT
1 AATCCTAAAAGATATTTTCCAGTTTTCCTTAT
*
548016 AATCCTAAAAGATGTTTTCCAGTTTTCCTTA
1 AATCCTAAAAGATATTTTCCAGTTTTCCTTA
548047 CTTCTTCTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (32 bp):
AATCCTAAAAGATATTTTCCAGTTTTCCTTAT
Found at i:550851 original size:3 final size:3
Alignment explanation
Indices: 550843--550878 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
550833 TATTATAATC
550843 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
550879 GGATACAATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:551200 original size:20 final size:20
Alignment explanation
Indices: 551175--551213 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
551165 TTATTATATT
551175 TTAAATA-ATAATTTAAATTA
1 TTAAATATA-AATTTAAATTA
*
551195 TTAAATTTAAATTTAAATT
1 TTAAATATAAATTTAAATT
551214 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATATAAATTTAAATTA
Found at i:551651 original size:22 final size:18
Alignment explanation
Indices: 551603--551638 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
551593 AAGTTTGAAT
551603 TATTT-AATTAATTAAAA
1 TATTTAAATTAATTAAAA
551620 TATTTAAATTAATTAAAA
1 TATTTAAATTAATTAAAA
551638 T
1 T
551639 TTATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTAAATTAATTAAAA
Found at i:554846 original size:18 final size:18
Alignment explanation
Indices: 554820--554860 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
554810 TTAGTATCGC
* *
554820 TATTATAATTTTTTTATA
1 TATTTTAATTTATTTATA
554838 TATTTTAATTTATTTATA
1 TATTTTAATTTATTTATA
*
554856 AATTT
1 TATTT
554861 ATTAATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTAATTTATTTATA
Found at i:558471 original size:14 final size:16
Alignment explanation
Indices: 558452--558491 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
558442 ATTATTCTTC
558452 TTTATATTTAC-T-TT
1 TTTATATTTACATGTT
558466 TTTATATTTACATGTT
1 TTTATATTTACATGTT
*
558482 CTTATATTTA
1 TTTATATTTA
558492 TTCATAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 1 0.04
16 11 0.48
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTATATTTACATGTT
Found at i:558488 original size:16 final size:14
Alignment explanation
Indices: 558453--558491 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
558443 TTATTCTTCT
*
558453 TTATATTTACTTTT
1 TTATATTTACTTTC
558467 TTATATTTACATGTTC
1 TTATATTTAC-T-TTC
558483 TTATATTTA
1 TTATATTTA
558492 TTCATAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 11 0.50
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (14 bp):
TTATATTTACTTTC
Found at i:560115 original size:13 final size:13
Alignment explanation
Indices: 560084--560127 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
560074 CTAAATATAT
*
560084 TAAAATATATAAA
1 TAAAATAGATAAA
560097 -AAAATAGATAAA
1 TAAAATAGATAAA
560109 TAAAATAGATAAA
1 TAAAATAGATAAA
560122 TAAAAT
1 TAAAAT
560128 TTTTCTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (13 bp):
TAAAATAGATAAA
Found at i:560187 original size:2 final size:2
Alignment explanation
Indices: 560180--560208 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
560170 ATACATTATT
560180 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 T
560209 GCGCTTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:560655 original size:14 final size:15
Alignment explanation
Indices: 560632--560670 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
560622 ATAATAGTAT
560632 TATAATTTTATA-AA
1 TATAATTTTATATAA
*
560646 TATTATTTTATATAA
1 TATAATTTTATATAA
560661 TATAATTTTA
1 TATAATTTTA
560671 CAGCATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTTTATATAA
Found at i:561476 original size:13 final size:13
Alignment explanation
Indices: 561436--561478 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
561426 TTTAATTCAA
561436 TAAAAATAATATAT
1 TAAAAATAATA-AT
* * *
561450 TCAATATAAAAAT
1 TAAAAATAATAAT
561463 TAAAAATAATAAT
1 TAAAAATAATAAT
561476 TAA
1 TAA
561479 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATAATAAT
Found at i:561983 original size:15 final size:15
Alignment explanation
Indices: 561961--562000 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
561951 ATTAAAATTT
561961 TATT-ATTTAAAAAA
1 TATTAATTTAAAAAA
561975 TATTAATTTAAAAAA
1 TATTAATTTAAAAAA
* *
561990 AATTAAATTAA
1 TATTAATTTAA
562001 TTTAGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTAATTTAAAAAA
Found at i:562074 original size:21 final size:22
Alignment explanation
Indices: 562049--562102 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
562039 ATTGAATAAG
* *
562049 TTAAATATTTTA-ATATTTCAT
1 TTAAATATTTTACAAATTTAAT
*
562070 TTAAATATATTACAAATTTAAT
1 TTAAATATTTTACAAATTTAAT
562092 TTAAAT-TTTTA
1 TTAAATATTTTA
562103 TTTTTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATATTTTACAAATTTAAT
Found at i:562093 original size:22 final size:21
Alignment explanation
Indices: 562049--562097 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
562039 ATTGAATAAG
* * *
562049 TTAAATATTTTAATATTTCAT
1 TTAAATATATTAAAATTTAAT
562070 TTAAATATATTACAAATTTAAT
1 TTAAATATATTA-AAATTTAAT
562092 TTAAAT
1 TTAAAT
562098 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATATATTAAAATTTAAT
Found at i:562867 original size:14 final size:14
Alignment explanation
Indices: 562848--562876 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
562838 ATTTGAGTTA
562848 AATTAAAATTTTTT
1 AATTAAAATTTTTT
562862 AATTAAAATTTTTT
1 AATTAAAATTTTTT
562876 A
1 A
562877 TTTACAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTAAAATTTTTT
Found at i:563267 original size:3 final size:3
Alignment explanation
Indices: 563259--563286 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
563249 ACAAGTCTGG
563259 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
563287 TTTTGTCACG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:568219 original size:2 final size:2
Alignment explanation
Indices: 568212--568236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
568202 CTCTGCTCAA
568212 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
568237 GCTTAAGATA
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:568706 original size:9 final size:9
Alignment explanation
Indices: 568688--568728 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
568678 TTTATTCACG
*
568688 TAATTTATT
1 TAATTAATT
568697 TAATTAATT
1 TAATTAATT
568706 TAATTTAATT
1 TAA-TTAATT
*
568716 TAATTTATT
1 TAATTAATT
568725 TAAT
1 TAAT
568729 CGATTTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAATTAATT
Found at i:568710 original size:5 final size:5
Alignment explanation
Indices: 568688--568728 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
568678 TTTATTCACG
568688 TAATT T-ATT TAA-T TAATT TAATT TAATT TAATT T-ATT TAAT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAAT
568729 CGATTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.36
5 21 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TAATT
Found at i:568719 original size:28 final size:28
Alignment explanation
Indices: 568688--568744 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
568678 TTTATTCACG
*
568688 TAATTTATTTAATTAATTTAATTTAATT
1 TAATTTATTTAATCAATTTAATTTAATT
* *
568716 TAATTTATTTAATCGATTTGATTTAATT
1 TAATTTATTTAATCAATTTAATTTAATT
568744 T
1 T
568745 TTTTTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (28 bp):
TAATTTATTTAATCAATTTAATTTAATT
Found at i:568900 original size:21 final size:21
Alignment explanation
Indices: 568872--568922 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
568862 TTTATAAATA
* *
568872 ATAAAATAAAAAAATATAAATT
1 ATAATATAAATAAATAT-AATT
*
568894 ATCAATATAAATAGATATAATT
1 AT-AATATAAATAAATATAATT
568916 ATAATAT
1 ATAATAT
568923 GTATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATATAAATAAATATAATT
Found at i:569016 original size:22 final size:21
Alignment explanation
Indices: 568973--569016 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
568963 GTTAAAGTTA
*
568973 TATTTTTTTAAATAAATTATT
1 TATTTTTTTAAATAAATAATT
568994 TATTTTATTT-AATAACATAATT
1 TATTTT-TTTAAATAA-ATAATT
569016 T
1 T
569017 TATTATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTTTTAAATAAATAATT
Found at i:571837 original size:110 final size:110
Alignment explanation
Indices: 571634--571854 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 110
571624 TGTCTATAGC
* * *
571634 GTCTATTTGAGCTTTCTGTTCATGCATGATGTTGGTTTATACTCTAGGCATTTGACTTTTTTAAA
1 GTCTATTTGAGCTCTCTGTTCATGCATGATGTTGGTTTATACTCTAGGCATTTGACGTTTCTAAA
571699 ATAGAAGCTTCAATTTCCCTTTTGTTTTTTATGCTTGATAAGCAG
66 ATAGAAGCTTCAATTTCCCTTTTGTTTTTTATGCTTGATAAGCAG
*
571744 GTCTATTTGAGCTCTCTGTTCATGCATGATGTTGGTTTGTACTCTAGGCATTTGACGTTTCTAAA
1 GTCTATTTGAGCTCTCTGTTCATGCATGATGTTGGTTTATACTCTAGGCATTTGACGTTTCTAAA
571809 ATAGAAGCTTCAA-TTCCCTTTTGTTTTTTATGCTTGATAAGCAG
66 ATAGAAGCTTCAATTTCCCTTTTGTTTTTTATGCTTGATAAGCAG
571853 GT
1 GT
571855 TGGTGCCTCC
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
109 33 0.31
110 74 0.69
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (110 bp):
GTCTATTTGAGCTCTCTGTTCATGCATGATGTTGGTTTATACTCTAGGCATTTGACGTTTCTAAA
ATAGAAGCTTCAATTTCCCTTTTGTTTTTTATGCTTGATAAGCAG
Found at i:576078 original size:2 final size:2
Alignment explanation
Indices: 576071--576102 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
576061 ATTAGATTAC
576071 AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
576103 GGTCCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:576816 original size:16 final size:16
Alignment explanation
Indices: 576795--576938 Score: 155
Period size: 16 Copynumber: 8.9 Consensus size: 16
576785 TAAAATTAAT
* *
576795 TAATTTCAATTTGAAA
1 TAATTTGAATTTAAAA
*
576811 TAATTTGAATATAAAA
1 TAATTTGAATTTAAAA
* *
576827 TGATCTGAATTTAAAAA
1 TAATTTGAATTT-AAAA
*
576844 TAATTTAAATTTAAAA
1 TAATTTGAATTTAAAA
*
576860 TAGTTTGAATTTAAAA
1 TAATTTGAATTTAAAA
*
576876 TAATTTTAATTTAAAA
1 TAATTTGAATTTAAAA
* *
576892 -AGATTCGAATTTGAAA
1 TA-ATTTGAATTTAAAA
576908 TAATTTGAATTTAAAA
1 TAATTTGAATTTAAAA
**
576924 TAATTCAAATTTAAA
1 TAATTTGAATTTAAA
576939 GTGACTCGAA
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
15 1 0.01
16 90 0.86
17 14 0.13
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (16 bp):
TAATTTGAATTTAAAA
Found at i:576867 original size:49 final size:49
Alignment explanation
Indices: 576795--576927 Score: 169
Period size: 49 Copynumber: 2.7 Consensus size: 49
576785 TAAAATTAAT
* * *
576795 TAATTTCAATTTGAAATAATTTGAATATAAAATGATCTGAATTTAAAAA
1 TAATTTAAATTTGAAATAATTTGAATTTAAAATAATCTGAATTTAAAAA
* * * *
576844 TAATTTAAATTTAAAATAGTTTGAATTTAAAATAATTTTAATTTAAAAA
1 TAATTTAAATTTGAAATAATTTGAATTTAAAATAATCTGAATTTAAAAA
* **
576893 -GATTCGAATTTGAAATAATTTGAATTTAAAATAAT
1 TAATTTAAATTTGAAATAATTTGAATTTAAAATAAT
576928 TCAAATTTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
48 30 0.42
49 42 0.58
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (49 bp):
TAATTTAAATTTGAAATAATTTGAATTTAAAATAATCTGAATTTAAAAA
Found at i:577093 original size:16 final size:17
Alignment explanation
Indices: 577057--577095 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
577047 TTAATTAATT
577057 TAAATTTAAAATGATCA
1 TAAATTTAAAATGATCA
*
577074 -AAATTTAGAATGAT-A
1 TAAATTTAAAATGATCA
577089 TAAATTT
1 TAAATTT
577096 GATGAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (17 bp):
TAAATTTAAAATGATCA
Found at i:577149 original size:16 final size:16
Alignment explanation
Indices: 577130--577243 Score: 59
Period size: 16 Copynumber: 7.1 Consensus size: 16
577120 TTAATTCATT
*
577130 ATTAAAATTATTCAAA
1 ATTAAAATAATTCAAA
*
577146 ATTAAAATAATTTAAA
1 ATTAAAATAATTCAAA
* * * *
577162 TTTAAAATGATACTAA
1 ATTAAAATAATTCAAA
** * **
577178 ATCGAAATGATTTTAA
1 ATTAAAATAATTCAAA
* *
577194 TTTAAAATAATTTAAA
1 ATTAAAATAATTCAAA
*
577210 ATTAAAACT-ATTTAAA
1 ATTAAAA-TAATTCAAA
* *
577226 TTTAAAAATAATTTAAA
1 ATT-AAAATAATTCAAA
577243 A
1 A
577244 CTTTTAAAAT
Statistics
Matches: 75, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
16 63 0.84
17 12 0.16
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTAAAATAATTCAAA
Found at i:577162 original size:69 final size:69
Alignment explanation
Indices: 577019--577164 Score: 163
Period size: 69 Copynumber: 2.1 Consensus size: 69
577009 TTTAGTTGAT
* * * * *
577019 TTTAAA-TTGATTAATTTAAGTGTTAAATTTAATTAATTTAAATTTAAAATGATCAAAATTTAGA
1 TTTAAATTTGATGAATTGAAGTGTTAAATCTAATTAATTCAAATTTAAAATGATCAAAATTTAAA
*
577083 ATGA
66 ATAA
* * * *
577087 TATAAATTTGATGAATTGAAGTGTTAAATCTGATTAATTC-ATTATTAAAATTATTCAAAA-TTA
1 TTTAAATTTGATGAATTGAAGTGTTAAATCTAATTAATTCAAAT-TTAAAATGA-TCAAAATTTA
577150 AAATAA
64 AAATAA
577156 TTTAAATTT
1 TTTAAATTT
577165 AAAATGATAC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
68 7 0.11
69 51 0.80
70 6 0.09
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (69 bp):
TTTAAATTTGATGAATTGAAGTGTTAAATCTAATTAATTCAAATTTAAAATGATCAAAATTTAAA
ATAA
Found at i:577167 original size:32 final size:31
Alignment explanation
Indices: 577131--577243 Score: 109
Period size: 32 Copynumber: 3.5 Consensus size: 31
577121 TAATTCATTA
*
577131 TTAAAATTATTCAAAATTAAAATAATTTAAAT
1 TTAAAATAATTCAAAATTAAAAT-ATTTAAAT
* * * ** *
577163 TTAAAATGATACTAAATCGAAATGATTTTAAT
1 TTAAAATAATTCAAAATTAAAAT-ATTTAAAT
*
577195 TTAAAATAATTTAAAATTAAAACTATTTAAAT
1 TTAAAATAATTCAAAATTAAAA-TATTTAAAT
*
577227 TTAAAAATAATTTAAAA
1 TT-AAAATAATTCAAAA
577244 CTTTTAAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (31 bp):
TTAAAATAATTCAAAATTAAAATATTTAAAT
Found at i:577239 original size:17 final size:17
Alignment explanation
Indices: 577182--577242 Score: 72
Period size: 16 Copynumber: 3.7 Consensus size: 17
577172 TACTAAATCG
* *
577182 AAATGATTTTAATTT-A
1 AAATAATTTAAATTTAA
*
577198 AAATAATTTAAAATTAA
1 AAATAATTTAAATTTAA
*
577215 AACT-ATTTAAATTTAA
1 AAATAATTTAAATTTAA
577231 AAATAATTTAAA
1 AAATAATTTAAA
577243 ACTTTTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 26 0.70
17 11 0.30
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATAATTTAAATTTAA
Found at i:577650 original size:3 final size:3
Alignment explanation
Indices: 577631--577663 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
577621 GTCGTGATTA
*
577631 AAT ATT AAT AA- AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
577664 TTTATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:578081 original size:14 final size:13
Alignment explanation
Indices: 578019--578082 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
578009 TAAAATAATC
*
578019 TTTAAAAATATTAA
1 TTTAATAATATT-A
*
578033 TTTAAGAATA-TA
1 TTTAATAATATTA
578045 -TTAATAA-ATTA
1 TTTAATAATATTA
*
578056 TTTAATGTATATTA
1 TTTAAT-AATATTA
578070 TTTTAATAATATT
1 -TTTAATAATATT
578083 TAAAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 1 0.02
11 8 0.20
12 6 0.15
13 2 0.05
14 18 0.44
15 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TTTAATAATATTA
Found at i:578291 original size:19 final size:18
Alignment explanation
Indices: 578232--578291 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
578222 CAAAATATTT
*
578232 TAAAT-AAAATAAATTAA
1 TAAATAAAAATAAACTAA
*
578249 TAAAATGAAAAA-AAAGCTAT
1 T-AAAT-AAAAATAAA-CTAA
578269 TAAATAAAAATGAAACTAA
1 TAAATAAAAAT-AAACTAA
578288 TAAA
1 TAAA
578292 AAATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.26
19 14 0.41
20 10 0.29
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.23
Consensus pattern (18 bp):
TAAATAAAAATAAACTAA
Found at i:578732 original size:16 final size:16
Alignment explanation
Indices: 578713--578743 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
578703 AACTAAATTG
578713 ATTTAAATTTAAAATA
1 ATTTAAATTTAAAATA
578729 ATTTAAATTTAAAAT
1 ATTTAAATTTAAAAT
578744 GACTTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAATTTAAAATA
Found at i:578750 original size:16 final size:16
Alignment explanation
Indices: 578715--578751 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
578705 CTAAATTGAT
*
578715 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAC
*
578731 TTAAATTTAAAATGAC
1 TTAAATTTAAAATAAC
578747 TTAAA
1 TTAAA
578752 CATGATTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAAATAAC
Found at i:578773 original size:22 final size:22
Alignment explanation
Indices: 578747--578800 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
578737 TTAAAATGAC
*
578747 TTAAACATGATTAACTTAAATA
1 TTAAACATAATTAACTTAAATA
* *
578769 TTAAACTTAATTAATTTAAA-A
1 TTAAACATAATTAACTTAAATA
*
578790 ATAAA-ATAATT
1 TTAAACATAATT
578801 TTAAACTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 5 0.19
21 5 0.19
22 17 0.63
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAAACATAATTAACTTAAATA
Found at i:578827 original size:16 final size:16
Alignment explanation
Indices: 578769--578828 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
578759 AACTTAAATA
* *
578769 TTAAACTTAATTAATT
1 TTAAACTAAAATAATT
* *
578785 TAAAAATAAAATAATT
1 TTAAACTAAAATAATT
578801 TTAAACTAAAATAA-T
1 TTAAACTAAAATAATT
578816 TTAAACTCAAAAT
1 TTAAACT-AAAAT
578829 GACACAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
15 8 0.22
16 29 0.78
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAACTAAAATAATT
Found at i:580130 original size:17 final size:16
Alignment explanation
Indices: 580103--580136 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
580093 TAATGTAATT
580103 AATTTATATAATTATA
1 AATTTATATAATTATA
580119 AATTTAATATAATTATA
1 AATTT-ATATAATTATA
580136 A
1 A
580137 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTATATAATTATA
Found at i:580332 original size:3 final size:3
Alignment explanation
Indices: 580324--580351 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
580314 CACATACTTC
580324 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
580352 AAAATATGGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:582007 original size:2 final size:2
Alignment explanation
Indices: 582000--582028 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
581990 TAAACTACAA
582000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
582029 CACGAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:582121 original size:23 final size:25
Alignment explanation
Indices: 582072--582125 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
582062 TATTTAATTT
* *
582072 AAATATTTTTATTTTTATATATTTA
1 AAATATTTTTATTTATATATATATA
*
582097 AAAT-TTTTTA-TTATATTTATATA
1 AAATATTTTTATTTATATATATATA
582120 AAATAT
1 AAATAT
582126 ATGTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 14 0.56
24 7 0.28
25 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATTTTTATTTATATATATATA
Found at i:583261 original size:14 final size:16
Alignment explanation
Indices: 583242--583279 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
583232 ATATTTATAT
583242 TTATTT-TAAAA-AAA
1 TTATTTATAAAAGAAA
583256 TTATTTATAAAAGAAA
1 TTATTTATAAAAGAAA
583272 TTGATTTA
1 TT-ATTTA
583280 ATTACTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 5 0.24
17 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
TTATTTATAAAAGAAA
Found at i:584491 original size:33 final size:32
Alignment explanation
Indices: 584453--584526 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
584443 AATAATTAAA
584453 ATATAATATGAATATATAAATG-ATTCAAAATTT
1 ATATAATATGAATA-ATAAATGTA-TCAAAATTT
* * *
584486 CTATAACATGAATAATTAATGTATCAAAATTT
1 ATATAATATGAATAATAAATGTATCAAAATTT
*
584518 ATTTAATAT
1 ATATAATAT
584527 AAATTATCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 21 0.62
33 13 0.38
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (32 bp):
ATATAATATGAATAATAAATGTATCAAAATTT
Found at i:589837 original size:23 final size:21
Alignment explanation
Indices: 589792--589844 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
589782 AATGCCTTTA
589792 TTTTAA-TTTTA--TAACTAT
1 TTTTAATTTTTAGTTAACTAT
589810 TTTTATATATTTTAGTTAACT-T
1 TTTTA-AT-TTTTAGTTAACTAT
589832 TCTTTAATTTTTA
1 T-TTTAATTTTTA
589845 CATGACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 5 0.17
19 1 0.03
21 10 0.34
22 4 0.14
23 9 0.31
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAATTTTTAGTTAACTAT
Found at i:593800 original size:42 final size:42
Alignment explanation
Indices: 593749--593874 Score: 147
Period size: 37 Copynumber: 3.1 Consensus size: 42
593739 TATTGATTTC
593749 TTAT-TTTAAATGAAAAAAAAAAAAAATCTAGGAAACTTGTA
1 TTATCTTTAAATGAAAAAAAAAAAAAATCTAGGAAACTTGTA
* *
593790 TTATCTTTAAATG-----AAAAAAAATTCTGGGAAACTTGTA
1 TTATCTTTAAATGAAAAAAAAAAAAAATCTAGGAAACTTGTA
* ****
593827 TTATCTTTAAGTGAAAAAAAAAAACCCCCTAGGAAACTTGTA
1 TTATCTTTAAATGAAAAAAAAAAAAAATCTAGGAAACTTGTA
593869 TTATCT
1 TTATCT
593875 ATTATATTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 34 0.48
41 4 0.06
42 33 0.46
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (42 bp):
TTATCTTTAAATGAAAAAAAAAAAAAATCTAGGAAACTTGTA
Found at i:595946 original size:37 final size:36
Alignment explanation
Indices: 595896--595972 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
595886 GTTTATTTCA
* *
595896 TTTAGAATTCTGTTTAGAAT-AAAGTTTATATTTTTAC
1 TTTAGAATTCTGTTGAGAATAAAAGTTT-T-GTTTTAC
*
595933 TTTAG-ATTACTGTTGAGGATAAAAGTTTTGTTTTAC
1 TTTAGAATT-CTGTTGAGAATAAAAGTTTTGTTTTAC
595969 TTTA
1 TTTA
595973 AGATATGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 13 0.37
37 15 0.43
38 7 0.20
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (36 bp):
TTTAGAATTCTGTTGAGAATAAAAGTTTTGTTTTAC
Found at i:600873 original size:3 final size:3
Alignment explanation
Indices: 600865--600901 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
600855 TGTTCTTCCT
600865 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
600902 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.