Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015232.1 Kokia drynarioides strain JFW-HI SEQ_130277, whole genome shotgun sequence
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: 719139
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 336 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:11633 original size:19 final size:20
Alignment explanation
Indices: 11577--11641 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 20
11567 TACAAAATAA
*
11577 TCAAAATAATTTTCAAAAAT
1 TCAAAATAATTTTTAAAAAT
* *
11597 TGAAAATAATTGTT-AAAAT
1 TCAAAATAATTTTTAAAAAT
11616 TCAAAAT-ATTTTTAAAAAT
1 TCAAAATAATTTTTAAAAAT
*
11635 TCTAAAT
1 TCAAAAT
11642 TTTGTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 5 0.13
19 22 0.58
20 11 0.29
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAAAT
Found at i:11669 original size:18 final size:17
Alignment explanation
Indices: 11648--11681 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
11638 AAATTTTGTA
11648 TTTTTTAAAAATTATAAT
1 TTTTTTAAAAA-TATAAT
11666 TTTTTTAAAAATATAA
1 TTTTTTAAAAATATAA
11682 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTTAAAAATATAAT
Found at i:14343 original size:5 final size:5
Alignment explanation
Indices: 14333--14369 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
14323 CCATGTATAC
14333 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CT
1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CT
14370 GATTGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (5 bp):
CTACA
Found at i:23427 original size:19 final size:20
Alignment explanation
Indices: 23391--23430 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23381 GACATTGTAG
23391 TTTTATAATAAATATAAATT
1 TTTTATAATAAATATAAATT
* *
23411 TTTTTTAATATAT-TAAATT
1 TTTTATAATAAATATAAATT
23430 T
1 T
23431 ATAGAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAATAAATATAAATT
Found at i:25841 original size:14 final size:14
Alignment explanation
Indices: 25812--25854 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
25802 TTTTCATGTG
*
25812 ATTTGCATTTTAGTA
1 ATTTG-ATTTTGGTA
*
25827 ATTTGGTTTTGGTA
1 ATTTGATTTTGGTA
*
25841 ATTTTATTTTGGTA
1 ATTTGATTTTGGTA
25855 TAAAAAGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (14 bp):
ATTTGATTTTGGTA
Found at i:46476 original size:30 final size:30
Alignment explanation
Indices: 46442--46502 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
46432 AATGGTTTCA
46442 AATTCTAACACTCACCGATTTAAATTTTTT
1 AATTCTAACACTCACCGATTTAAATTTTTT
46472 AATTCTAACACTCACCGATTTAAATTTTTT
1 AATTCTAACACTCACCGATTTAAATTTTTT
46502 A
1 A
46503 CTTTTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (30 bp):
AATTCTAACACTCACCGATTTAAATTTTTT
Found at i:49012 original size:29 final size:29
Alignment explanation
Indices: 48648--49011 Score: 340
Period size: 29 Copynumber: 12.5 Consensus size: 29
48638 TTTCGGAATC
* * * **
48648 AAAAATGGAATTTTGGGAAGTTTGGGGCC
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
48677 AAAAATAGAATTTTTTTGAAGTTTTGGGGTT
1 AAAAATGGGA-TTTTTGGAAG-TTCGGGGGT
* * * **
48708 AAAAAT-GTAATTTTAGAAGTTTTGGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
48736 CAAAATGGGATTTTTAGAAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
*
48765 AAAAATGGGGTTTTTGGAAGTTTC-GGGGT
1 AAAAATGGGATTTTTGGAAG-TTCGGGGGT
* **
48794 CGAAAATAAGATTTTTGGAAGTTCGGGGGT
1 -AAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
48824 AAAAATGGAATTTTTGGAAGTT-TGGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
48852 AAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
* ** **
48881 GAAAATGATATTTTTGGAAGTTCAAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
*
48910 AAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
48939 -AAAATGGGATTTTTTGGAAGTTCGGGGGT
1 AAAAATGGGA-TTTTTGGAAGTTCGGGGGT
* *
48968 AAAAATGGGATTTTTAGAAGTTCGAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGT
*
48997 AAAAATGAGATTTTT
1 AAAAATGGGATTTTT
49012 AAACAGTTTA
Statistics
Matches: 284, Mismatches: 42, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
28 48 0.17
29 181 0.64
30 42 0.15
31 13 0.05
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:50106 original size:21 final size:23
Alignment explanation
Indices: 50050--50107 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
50040 TTTTAATTTA
* *
50050 ATTAATGCCATTATTAATGATATT
1 ATTAATGCTATTATTAAT-ATACT
**
50074 ATTAATATTATTATT-AT-TACT
1 ATTAATGCTATTATTAATATACT
50095 ATTAATGCTATTA
1 ATTAATGCTATTA
50108 AAATCATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 14 0.50
23 2 0.07
24 12 0.43
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
ATTAATGCTATTATTAATATACT
Found at i:50566 original size:22 final size:19
Alignment explanation
Indices: 50524--50562 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
50514 GGCCATGGCA
50524 GCGGCGGTTGAAGCAGCTG
1 GCGGCGGTTGAAGCAGCTG
50543 GCGGCGGTTGAAGCAGCTG
1 GCGGCGGTTGAAGCAGCTG
50562 G
1 G
50563 TGGCAGTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.49, T:0.15
Consensus pattern (19 bp):
GCGGCGGTTGAAGCAGCTG
Found at i:58418 original size:21 final size:20
Alignment explanation
Indices: 58391--58446 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 20
58381 TGTATTATAA
58391 TAAGAAATAAATAAAAAGAG
1 TAAGAAATAAATAAAAAGAG
58411 TAAGGAAATAAATAAAAAGAG
1 TAA-GAAATAAATAAAAAGAG
58432 TAAGAAA-AAA-AAAAA
1 TAAGAAATAAATAAAAA
58447 CAATAAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.14
19 3 0.09
20 7 0.20
21 20 0.57
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (20 bp):
TAAGAAATAAATAAAAAGAG
Found at i:59791 original size:3 final size:3
Alignment explanation
Indices: 59785--59815 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59775 ACCATGGTGA
59785 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
59816 AGAACGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:67384 original size:21 final size:21
Alignment explanation
Indices: 67358--67399 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
67348 CAAACGAAAA
*
67358 AATGGTGACGGTGTGTGAGTG
1 AATGGTGACAGTGTGTGAGTG
67379 AATGGTGACAGTGTGTGAGTG
1 AATGGTGACAGTGTGTGAGTG
67400 GTGGGAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.45, T:0.29
Consensus pattern (21 bp):
AATGGTGACAGTGTGTGAGTG
Found at i:68805 original size:29 final size:30
Alignment explanation
Indices: 68726--68877 Score: 132
Period size: 29 Copynumber: 5.1 Consensus size: 30
68716 CGCCACTAGA
**
68726 GCTCACATATAACAAAG-GACAGCCACAAATG
1 GCTCACATATAACAAAGTTTC-GCCACAAA-G
** *
68757 TTTCCACATATAAC-AAGTTTCGCCACAAGG
1 GCT-CACATATAACAAAGTTTCGCCACAAAG
* *
68787 GCTCACATATAAC-AGGTTTCGCCACAAGG
1 GCTCACATATAACAAAGTTTCGCCACAAAG
** * *
68816 GCTCACATATAACAAAGAATAGCCACAAAT
1 GCTCACATATAACAAAGTTTCGCCACAAAG
* *
68846 GCTCACATAT-ACTAGGTTTCGCCACAAAG
1 GCTCACATATAACAAAGTTTCGCCACAAAG
68875 GCT
1 GCT
68878 TATACATATA
Statistics
Matches: 98, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
29 54 0.55
30 22 0.22
31 11 0.11
32 11 0.11
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (30 bp):
GCTCACATATAACAAAGTTTCGCCACAAAG
Found at i:68852 original size:59 final size:58
Alignment explanation
Indices: 68761--68877 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 58
68751 CAAATGTTTC
** * * *
68761 CACATATAACAAGTTTCGCCACAAGGGCTCACATATAAC-AGGTTTCGCCACAAGGGCT
1 CACATATAACAAGAATAGCCACAAAGGCTCACATAT-ACTAGGTTTCGCCACAAAGGCT
*
68819 CACATATAACAAAGAATAGCCACAAATGCTCACATATACTAGGTTTCGCCACAAAGGCT
1 CACATATAAC-AAGAATAGCCACAAAGGCTCACATATACTAGGTTTCGCCACAAAGGCT
68878 TATACATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 12 0.24
59 39 0.76
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (58 bp):
CACATATAACAAGAATAGCCACAAAGGCTCACATATACTAGGTTTCGCCACAAAGGCT
Found at i:68887 original size:90 final size:90
Alignment explanation
Indices: 68700--68877 Score: 245
Period size: 90 Copynumber: 2.0 Consensus size: 90
68690 CAAAGGTTTC
* * * *
68700 CACATATAATAGGTCTCGCCACTAGAGCTCACATATAACAAAGGACAGCCACAAATGTTTCCACA
1 CACATATAACAGGTCTCGCCACAAGAGCTCACATATAACAAAGAACAGCCACAAATGTCTCCACA
*
68765 TATAACAAGTTTCGCCACAAGGGCT
66 TATAACAAGTTTCGCCACAAAGGCT
* * *
68790 CACATATAACAGGTTTCGCCACAAGGGCTCACATATAACAAAGAATAGCCACAAATG-CT-CACA
1 CACATATAACAGGTCTCGCCACAAGAGCTCACATATAACAAAGAACAGCCACAAATGTCTCCACA
*
68853 TAT-ACTAGGTTTCGCCACAAAGGCT
66 TATAAC-AAGTTTCGCCACAAAGGCT
68878 TATACATATA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 2 0.03
88 24 0.31
89 1 0.01
90 51 0.65
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (90 bp):
CACATATAACAGGTCTCGCCACAAGAGCTCACATATAACAAAGAACAGCCACAAATGTCTCCACA
TATAACAAGTTTCGCCACAAAGGCT
Found at i:76250 original size:17 final size:18
Alignment explanation
Indices: 76211--76259 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
76201 CTTTCTCTCA
*
76211 GTTGTTTATTTCCTTCTTCT
1 GTTGTTTATTT--TGCTTCT
76231 GTTGTTTATTTTGCTT-T
1 GTTGTTTATTTTGCTTCT
*
76248 GTTGGTTATTTT
1 GTTGTTTATTTT
76260 TTTTTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
20 11 0.41
ACGTcount: A:0.06, C:0.10, G:0.16, T:0.67
Consensus pattern (18 bp):
GTTGTTTATTTTGCTTCT
Found at i:77891 original size:15 final size:16
Alignment explanation
Indices: 77865--77894 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
77855 CCTTTAGTCT
77865 TTTTATAATTTTAAAA
1 TTTTATAATTTTAAAA
77881 TTTTA-AATTTTAAA
1 TTTTATAATTTTAAA
77895 TGAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTATAATTTTAAAA
Found at i:78612 original size:25 final size:24
Alignment explanation
Indices: 78563--78623 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
78553 AATAAAAACA
78563 TAAAAATTAAAAAATATATCATTTT
1 TAAAAA-TAAAAAATATATCATTTT
*
78588 TAAAAATAAAAAATATAAT-TTTTT
1 TAAAAATAAAAAATAT-ATCATTTT
*
78612 TTAAAATAAAAA
1 TAAAAATAAAAA
78624 TTATGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 25 0.76
25 8 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAATAAAAAATATATCATTTT
Found at i:79177 original size:32 final size:31
Alignment explanation
Indices: 79141--79211 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
79131 AGTTATATTC
* * *
79141 TAAAAAATATATATGAAAAACTCTTTAAAATT
1 TAAAAAATAT-TATAAAAAACTATTTAAAATA
* *
79173 TAAAAATTATTTTAAAAAACTATTTAAAATA
1 TAAAAAATATTATAAAAAACTATTTAAAATA
79204 TAAAAAAT
1 TAAAAAAT
79212 TCTAAAATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 24 0.73
32 9 0.27
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (31 bp):
TAAAAAATATTATAAAAAACTATTTAAAATA
Found at i:83701 original size:31 final size:31
Alignment explanation
Indices: 83644--83702 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
83634 TTTACCGTAA
* *
83644 ATACTAATTTGGACCAAAAAATCAAGTTCAG
1 ATACTAATTTGAACCAAAAAACCAAGTTCAG
* *
83675 ATACTAATTTGAACCAATAAGCCAAGTT
1 ATACTAATTTGAACCAAAAAACCAAGTT
83703 TAAGTACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (31 bp):
ATACTAATTTGAACCAAAAAACCAAGTTCAG
Found at i:85644 original size:13 final size:13
Alignment explanation
Indices: 85626--85650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85616 TTTTCATGTT
85626 ATTATATTATTAA
1 ATTATATTATTAA
85639 ATTATATTATTA
1 ATTATATTATTA
85651 CTTTTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATATTATTAA
Found at i:85829 original size:33 final size:33
Alignment explanation
Indices: 85787--85858 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
85777 TACCAAACTC
85787 TGGATTTGAGTTGAGCTCGAGCTGGATAATATT
1 TGGATTTGAGTTGAGCTCGAGCTGGATAATATT
85820 TGGATTTGAGTTGAGCTCGAGCTGGATAATATT
1 TGGATTTGAGTTGAGCTCGAGCTGGATAATATT
85853 TGGATT
1 TGGATT
85859 CAACTGAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.24, C:0.08, G:0.31, T:0.38
Consensus pattern (33 bp):
TGGATTTGAGTTGAGCTCGAGCTGGATAATATT
Found at i:115396 original size:17 final size:18
Alignment explanation
Indices: 115374--115407 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
115364 AAATATGTTG
115374 TTAGT-CCTATACTTTAT
1 TTAGTCCCTATACTTTAT
*
115391 TTAGTCCCTGTACTTTA
1 TTAGTCCCTATACTTTA
115408 AAGATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.50
Consensus pattern (18 bp):
TTAGTCCCTATACTTTAT
Found at i:117206 original size:18 final size:17
Alignment explanation
Indices: 117183--117216 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
117173 TATGCATTGA
117183 TAATTTGATCTTTTTTTG
1 TAATTT-ATCTTTTTTTG
*
117201 TAATTTTTCTTTTTTT
1 TAATTTATCTTTTTTT
117217 ACATTTAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (17 bp):
TAATTTATCTTTTTTTG
Found at i:119194 original size:21 final size:22
Alignment explanation
Indices: 119170--119246 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 22
119160 ACTATTTCAA
*
119170 GGTTCAAGGTTTGT-AATTTAG
1 GGTTCAAGATTTGTGAATTTAG
* *
119191 GGTTTAAGATTTGAGTTTGAGATTTGG
1 GGTTCAAGATTT--G--TGA-ATTTAG
119218 GGTTCAAGATTT-TGAATTTAG
1 GGTTCAAGATTTGTGAATTTAG
119239 GGTTCAAG
1 GGTTCAAG
119247 GTAAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 23 0.51
22 3 0.07
23 1 0.02
25 1 0.02
26 1 0.02
27 16 0.36
ACGTcount: A:0.25, C:0.04, G:0.30, T:0.42
Consensus pattern (22 bp):
GGTTCAAGATTTGTGAATTTAG
Found at i:121494 original size:2 final size:2
Alignment explanation
Indices: 121489--121514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
121479 TTTTTTTCCT
121489 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
121515 CTTGTATAAT
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):
TA
Found at i:128912 original size:6 final size:6
Alignment explanation
Indices: 128902--128936 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
128892 ATTTTTAAAG
*
128902 AAAACTT AAACTT AAAATT AAAATT AAAATT AAAA
1 AAAA-TT AAAATT AAAATT AAAATT AAAATT AAAA
128937 ATGCAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.88
7 3 0.12
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:139409 original size:2 final size:2
Alignment explanation
Indices: 139402--139436 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
139392 TTTTAAATTA
*
139402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
139437 GGTGTAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:139954 original size:29 final size:30
Alignment explanation
Indices: 139908--139965 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
139898 GAATTGGATC
*
139908 AAATTAAAAATTCGTATATAAAATCACACA
1 AAATTAAAAATTAGTATATAAAATCACACA
* *
139938 AAATT-AAAATTATTATATAAAATTACAC
1 AAATTAAAAATTAGTATATAAAATCACAC
139966 GTTAAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATTAAAAATTAGTATATAAAATCACACA
Found at i:144279 original size:19 final size:20
Alignment explanation
Indices: 144255--144294 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
144245 TTTGTATTTT
144255 TTCTTA-ATTTGGACTTTAG
1 TTCTTATATTTGGACTTTAG
**
144274 TTCTTATATTTTTACTTTAG
1 TTCTTATATTTGGACTTTAG
144294 T
1 T
144295 AATTCAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (20 bp):
TTCTTATATTTGGACTTTAG
Found at i:145150 original size:2 final size:2
Alignment explanation
Indices: 145143--145170 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
145133 TCGAATCTCG
145143 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
145171 AACTAATTTA
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):
TA
Found at i:145758 original size:4 final size:4
Alignment explanation
Indices: 145749--145781 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
145739 TATTCACATG
145749 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
145782 AGATGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:148937 original size:16 final size:16
Alignment explanation
Indices: 148906--148935 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
148896 ACAAGGGTGT
148906 TTTTTTTAATTATTTA
1 TTTTTTTAATTATTTA
148922 TTTTTTTAA-TATTT
1 TTTTTTTAATTATTT
148936 TACTACATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTAATTATTTA
Found at i:149105 original size:47 final size:48
Alignment explanation
Indices: 149025--149126 Score: 161
Period size: 47 Copynumber: 2.1 Consensus size: 48
149015 ATGTGAATCT
*
149025 TTATTATAGAGTTTTTTTTTTTTAATTCTTTTAAAGTATCAAATGTGGG
1 TTATTATAGAG-TTTTTTTTTTTAATTCTTTTAAAGTATCAAATGCGGG
*
149074 TTATTATAGAG-TTTTTTTTTTAATTCTTTTAAAGTATCGAATGCGGG
1 TTATTATAGAGTTTTTTTTTTTAATTCTTTTAAAGTATCAAATGCGGG
*
149121 GTATTA
1 TTATTA
149127 CTTTGTTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
47 39 0.78
49 11 0.22
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (48 bp):
TTATTATAGAGTTTTTTTTTTTAATTCTTTTAAAGTATCAAATGCGGG
Found at i:151002 original size:16 final size:16
Alignment explanation
Indices: 150981--151017 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
150971 GATTTTTAAA
*
150981 AAAATATTTAATATGT
1 AAAATATATAATATGT
*
150997 AAAATATATAATATTT
1 AAAATATATAATATGT
151013 AAAAT
1 AAAAT
151018 TAATTAAATT
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:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AAAATATATAATATGT
Found at i:155567 original size:42 final size:42
Alignment explanation
Indices: 155508--155595 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
155498 TCCCGAAGTA
*
155508 AAACCACAGAATGATTATGTTCCAGGAATATTAAACATGCAG
1 AAACCACAGAATGATTATGATCCAGGAATATTAAACATGCAG
*
155550 AAACCACGGAATGATTATGATCCAGGAATATTAAACATGCAG
1 AAACCACAGAATGATTATGATCCAGGAATATTAAACATGCAG
155592 AAAC
1 AAAC
155596 AATCTAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACCACAGAATGATTATGATCCAGGAATATTAAACATGCAG
Found at i:163508 original size:17 final size:17
Alignment explanation
Indices: 163486--163558 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 17
163476 CCAATTTTAG
* *
163486 ATTTTAATTTTTAATTT
1 ATTTTAAGTTTAAATTT
163503 ATTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
* * **
163520 ATTGTAAATTTAAGCTT
1 ATTTTAAGTTTAAATTT
**
163537 ATTTGGAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
163554 ATTTT
1 ATTTT
163559 GAAATAAAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.59
Consensus pattern (17 bp):
ATTTTAAGTTTAAATTT
Found at i:164255 original size:21 final size:21
Alignment explanation
Indices: 164216--164255 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
164206 TTTTTTTATA
* *
164216 TATAATATATTTATTTATTGT
1 TATAATATATTAATGTATTGT
*
164237 TATAATGTATTAATGTATT
1 TATAATATATTAATGTATT
164256 TATTAATGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TATAATATATTAATGTATTGT
Found at i:164307 original size:3 final size:3
Alignment explanation
Indices: 164299--164351 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
164289 CAGAACGTTT
*
164299 TAA TAA TAA TAA TAA TAA -ATA TAA TAA -ATA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA
164344 -AA TAA TAA
1 TAA TAA TAA
164352 CAAAAGGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:165492 original size:29 final size:29
Alignment explanation
Indices: 165456--165743 Score: 148
Period size: 29 Copynumber: 9.7 Consensus size: 29
165446 ACCTTTATTT
165456 TTCC-AAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* ****
165484 TTCCAAAAATT-CCATTTTGGACTCTGCTTTT
1 TTCCAAAAATTACCATTTT--ACCCT-CGAAC
*
165515 TTCAAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
**
165544 TTCCAAAAATTA-CATTTTGACCC-CGATTT
1 TTCCAAAAATTACCATTTT-ACCCTCGA-AC
* *
165573 TTACAAAAAAAAAATTACCATTTTACCCCCGAAC
1 TT-C----CAAAAATTACCATTTTACCCTCGAAC
***
165607 TTCCAAAAATT-CCATTTTTGA-CCTCGCTTT
1 TTCCAAAAATTACCA-TTTT-ACCCTCG-AAC
*
165637 TTCC-AAAATTACCATTTTACCCCCGAA-
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* * *
165664 TGTCTAAAAATT-CCATTCTAAAACCCT-AAAC
1 T-TCCAAAAATTACCATT-T--TACCCTCGAAC
* *
165695 TTTCCCAAAATTACCATTTTACCCTCG-AG
1 -TTCCAAAAATTACCATTTTACCCTCGAAC
*
165724 TGACCAAAAATTACCATTTT
1 T-TCCAAAAATTACCATTTT
165744 GCCCCCTGGG
Statistics
Matches: 195, Mismatches: 36, Indels: 57
0.68 0.12 0.20
Matches are distributed among these distances:
27 1 0.01
28 32 0.16
29 82 0.42
30 19 0.10
31 24 0.12
32 13 0.07
33 1 0.01
34 14 0.07
35 9 0.05
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCTCGAAC
Found at i:165618 original size:123 final size:121
Alignment explanation
Indices: 165460--165680 Score: 338
Period size: 123 Copynumber: 1.8 Consensus size: 121
165450 TTATTTTTCC
*
165460 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTGGA-CTCTGCTTTTTTCAAAAAA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTGGACCTC-GC-TTTTTC-AAAAA
*
165524 TTACCATTTTACCCTCGAACT-TCCAAAAATTACATTTTGACCCCGATTTTTACAAAAAA
63 TTACCATTTTACCCCCGAA-TGTCCAAAAATTACATTTTGACCCCGATTTTTACAAAAAA
* *
165583 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGCTTTTTCCAAAATTA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTGGACCTCGCTTTTTCAAAAATTA
* *
165648 CCATTTTACCCCCGAATGTCTAAAAATTCCATT
66 CCATTTTACCCCCGAATGTCCAAAAATTACATT
165681 CTAAAACCCT
Statistics
Matches: 90, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
120 1 0.01
121 35 0.39
122 6 0.07
123 45 0.50
124 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (121 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTGGACCTCGCTTTTTCAAAAATTA
CCATTTTACCCCCGAATGTCCAAAAATTACATTTTGACCCCGATTTTTACAAAAAA
Found at i:165663 original size:58 final size:58
Alignment explanation
Indices: 165373--165680 Score: 295
Period size: 58 Copynumber: 5.2 Consensus size: 58
165363 TGAGCTTTTT
* * * * * *
165373 AAAATT-CTTTTTTGACCTTGATTTTTCCAAAAATTA-CACTTTAGGCCCCAAACTT-TA
1 AAAATTCCATTTTTGACCTCGATTTTTCC-AAAATTACCATTTTA-CCCCCGAACTTCCA
** *
165430 CAAAATTCCATTTTTGACCTTTATTTTTCCAAAATTACCATTTTACCCTCGAACTTCCA
1 -AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTACCATTTTACCCCCGAACTTCCA
* * * *
165489 AAAATTCCATTTTGGA-CTCTGCTTTTTTCAAAAAATTACCATTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTGACCTC-G-ATTTTTC-CAAAATTACCATTTTACCCCCGAACTTCCA
* * *
165549 AAAATTACA-TTTTGACCCCGATTTTTACAAAAAAAAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTGACCTCGATTTTT-C-----CAAAATTACCATTTTACCCCCGAACTTCCA
* *
165612 AAAATTCCATTTTTGACCTCGCTTTTTCCAAAATTACCATTTTACCCCCGAA-TGTCTA
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTACCATTTTACCCCCGAACT-TCCA
165670 AAAATTCCATT
1 AAAATTCCATT
165681 CTAAAACCCT
Statistics
Matches: 214, Mismatches: 22, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
57 3 0.01
58 78 0.36
59 40 0.19
60 39 0.18
63 39 0.18
64 15 0.07
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTACCATTTTACCCCCGAACTTCCA
Found at i:167534 original size:18 final size:18
Alignment explanation
Indices: 167504--167550 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 18
167494 AGTTCACCGA
167504 ATAAA-AAACTAAAATATT
1 ATAAACAAA-TAAAATATT
167522 ATAAACAAAT-AAATATT
1 ATAAACAAATAAAATATT
167539 -T-AAC-AATAAAAT
1 ATAAACAAATAAAAT
167551 GTGTCATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 1 0.04
17 7 0.26
18 6 0.22
19 3 0.11
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAACAAATAAAATATT
Found at i:168783 original size:12 final size:12
Alignment explanation
Indices: 168762--168789 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
168752 TATTTTTTCC
168762 TTTCATTTTCTT
1 TTTCATTTTCTT
168774 TTTCATTTTCTT
1 TTTCATTTTCTT
168786 TTTC
1 TTTC
168790 TGAATGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:169264 original size:22 final size:22
Alignment explanation
Indices: 169239--169280 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
169229 AATAAAAATA
*
169239 TTTTTAAAATAATATAATTTAC
1 TTTTTAAAATAAGATAATTTAC
*
169261 TTTTTAAAGTAAGATAATTT
1 TTTTTAAAATAAGATAATTT
169281 TCATGTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTTAAAATAAGATAATTTAC
Found at i:178166 original size:9 final size:8
Alignment explanation
Indices: 178145--178180 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
178135 TTTTTCGCCC
178145 CAAAAACT
1 CAAAAACT
178153 CAAAAACT
1 CAAAAACT
*
178161 CAAAAATT
1 CAAAAACT
178169 CAAAAAC-
1 CAAAAACT
178176 CAAAA
1 CAAAA
178181 GAATAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (8 bp):
CAAAAACT
Found at i:178756 original size:14 final size:13
Alignment explanation
Indices: 178728--178752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178718 ACACGTGTTT
178728 TTTTTAATATTTA
1 TTTTTAATATTTA
178741 TTTTTAATATTT
1 TTTTTAATATTT
178753 TATTATATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:182058 original size:158 final size:154
Alignment explanation
Indices: 181766--182076 Score: 415
Period size: 158 Copynumber: 2.0 Consensus size: 154
181756 ATTACGTAAG
** *
181766 AAACGACCTAGCAAACATCGATGAATCAACTTAAATATACAATTCTTTTCTGCTTCTCAAGTTGC
1 AAACGACCTAGCAAACATCGATGAATCAACTTAAATATACAATTCTTTTCCACTTCACAAGTTGC
* * **
181831 TTTCAAAGCTATGTTATTCCAACTCTTCATTTTTATGAAGTATTTGTGTCCTATACCCACGTCTA
66 TTTCAAAGCTATGTTATTCCAACTCTTCACTTTTACGAAGTATTTGTGTCAGATACCCACGTCTA
*
181896 GCACATTTTCAAACATGGGTATAA
131 GCACATTTTCAAACATGAGTATAA
* * *
181920 AAACGACGTAGGAAACATCGATGAATCAACTTAAATATACAATTTTTTTTTTTCCACTTCACAAG
1 AAACGACCTAGCAAACATCGATGAATCAACTTAAATATACAA----TTCTTTTCCACTTCACAAG
* * * ** *
181985 TTGTTTTCAAAGTTATGTTGTTCTGACTCTTCACTTTTACGAAGTATTTGTGTCAGATACCCATG
62 TTGCTTTCAAAGCTATGTTATTCCAACTCTTCACTTTTACGAAGTATTTGTGTCAGATACCCACG
* *
182050 TCTGGCACATTTTCAAACTTGAGTATA
127 TCTAGCACATTTTCAAACATGAGTATA
182077 GGGACATTGC
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
154 40 0.30
158 94 0.70
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (154 bp):
AAACGACCTAGCAAACATCGATGAATCAACTTAAATATACAATTCTTTTCCACTTCACAAGTTGC
TTTCAAAGCTATGTTATTCCAACTCTTCACTTTTACGAAGTATTTGTGTCAGATACCCACGTCTA
GCACATTTTCAAACATGAGTATAA
Found at i:186731 original size:48 final size:48
Alignment explanation
Indices: 186676--186780 Score: 151
Period size: 48 Copynumber: 2.2 Consensus size: 48
186666 AGCGTTCGCA
* *
186676 AACATGTTCGTTTATATGC-TT-GCAAACATGTTCGTTTATATGTTTATG
1 AACATGTTCGTTTATA--CATTCGCAAACATGTTCGTTTATACGTTCATG
*
186724 AACATGTTCGTTTATACATTCGCGAACATGTTCGTTTATACGTTCATG
1 AACATGTTCGTTTATACATTCGCAAACATGTTCGTTTATACGTTCATG
186772 AACATGTTC
1 AACATGTTC
186781 ACGTACATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 1 0.02
47 2 0.04
48 49 0.94
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (48 bp):
AACATGTTCGTTTATACATTCGCAAACATGTTCGTTTATACGTTCATG
Found at i:186764 original size:24 final size:24
Alignment explanation
Indices: 186659--186780 Score: 122
Period size: 24 Copynumber: 5.1 Consensus size: 24
186649 TCGAGCTCGA
* *
186659 TTCGTTTA-GCGTTCGCAAACATG
1 TTCGTTTATACGTTCGCGAACATG
* *
186682 TTCGTTTATATGCTT-GCAAACATG
1 TTCGTTTATACG-TTCGCGAACATG
* ***
186706 TTCGTTTATATGTTTATGAACATG
1 TTCGTTTATACGTTCGCGAACATG
*
186730 TTCGTTTATACATTCGCGAACATG
1 TTCGTTTATACGTTCGCGAACATG
**
186754 TTCGTTTATACGTTCATGAACATG
1 TTCGTTTATACGTTCGCGAACATG
186778 TTC
1 TTC
186781 ACGTACATGT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
23 10 0.12
24 71 0.86
25 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (24 bp):
TTCGTTTATACGTTCGCGAACATG
Found at i:196646 original size:165 final size:164
Alignment explanation
Indices: 196368--196689 Score: 459
Period size: 165 Copynumber: 2.0 Consensus size: 164
196358 AAATAAAATT
** * * *
196368 ACCATGTTAGAGGCTGTTTTCTAGGTCATTGTTAACTAAAGGGGTGTAGTGTTTTGATATTTCAG
1 ACCATGTTAGAGGCCATTGTATAGGTCATTGTTAACTAAAGGGGTGTAGTGTCTTGATATTTCAG
* ** *
196433 GATAGTTTTGGTAGGTTGCATGACAAGGGGAAGGAAGTTCAGAAGGCTACTTAAATTTTTACTAA
66 GATAGCTTTGGTAGGTTGCATGACAAGGGGAAGGAAGTTCAGAAGGCTACAAAAATTTTGACTAA
196498 GCATTTTCCAAATAAAGTTACCATTCATATGCCA
131 GCATTTTCCAAATAAAGTTACCATTCATATGCCA
* * * * *
196532 ACCATGTTAGAGGCCATTGTATATGTTATTGTTAATTTAAGGGGTGT-GATGTCTTGCTATTTTC
1 ACCATGTTAGAGGCCATTGTATAGGTCATTGTTAACTAAAGGGGTGTAG-TGTCTTGATA-TTTC
*
196596 AGGATAGCTTTGGTAGGTTGCATGACAGGGGGAAGGAAGTTCCA-AAGGCTACAAAAATTTTGAC
64 AGGATAGCTTTGGTAGGTTGCATGACAAGGGGAAGGAAGTT-CAGAAGGCTACAAAAATTTTGAC
*
196660 TAAGCTTTTTCCAAATAAAGTTACCATTCA
128 TAAGCATTTTCCAAATAAAGTTACCATTCA
196690 CACGCCACAG
Statistics
Matches: 139, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
163 1 0.01
164 47 0.34
165 89 0.64
166 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (164 bp):
ACCATGTTAGAGGCCATTGTATAGGTCATTGTTAACTAAAGGGGTGTAGTGTCTTGATATTTCAG
GATAGCTTTGGTAGGTTGCATGACAAGGGGAAGGAAGTTCAGAAGGCTACAAAAATTTTGACTAA
GCATTTTCCAAATAAAGTTACCATTCATATGCCA
Found at i:201899 original size:18 final size:18
Alignment explanation
Indices: 201876--201928 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
201866 AGCTACATCA
201876 ATTTTTAATTTAAAAAAT
1 ATTTTTAATTTAAAAAAT
***
201894 ATTTTTATATTT-TTTAAT
1 ATTTTTA-ATTTAAAAAAT
201912 ATTTTTTAATTTAAAAA
1 A-TTTTTAATTTAAAAA
201929 TAGTTTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTAATTTAAAAAAT
Found at i:201925 original size:37 final size:40
Alignment explanation
Indices: 201877--201973 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 40
201867 GCTACATCAA
201877 TTTTTAATTTAAAAAATATTTT-T-ATATTTTT-T-AATAT
1 TTTTTAATTTAAAAAATATTTTATAATATTTTTCTGAAT-T
*
201914 TTTTTAATTTAAAAATAGTTTTTTTATAATATTTTTCTGAATT
1 TTTTTAATTTAAAAA-A--TATTTTATAATATTTTTCTGAATT
*
201957 TTTTAAATTTAAAAAAT
1 TTTTTAATTTAAAAAAT
201974 TAAATGATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
37 15 0.29
38 1 0.02
40 6 0.12
41 1 0.02
42 9 0.18
43 16 0.31
44 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (40 bp):
TTTTTAATTTAAAAAATATTTTATAATATTTTTCTGAATT
Found at i:201930 original size:18 final size:18
Alignment explanation
Indices: 201877--201937 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
201867 GCTACATCAA
201877 TTTTTAATTTAAAAA-AT
1 TTTTTAATTTAAAAATAT
***
201894 ATTTTTATATTTTTTAATAT
1 -TTTTTA-ATTTAAAAATAT
201914 TTTTTAATTTAAAAATAGT
1 TTTTTAATTTAAAAATA-T
201933 TTTTT
1 TTTTT
201938 TATAATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 14 0.41
19 18 0.53
20 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTAATTTAAAAATAT
Found at i:204299 original size:23 final size:23
Alignment explanation
Indices: 204262--204309 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
204252 AGACATATTG
* * **
204262 AATTTATATTTTTAAATCTAAAA
1 AATTTAAATTATTAAAAATAAAA
204285 AATTTAAATTATTAAAAATAAAA
1 AATTTAAATTATTAAAAATAAAA
204308 AA
1 AA
204310 AAAATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTTAAATTATTAAAAATAAAA
Found at i:205784 original size:25 final size:25
Alignment explanation
Indices: 205756--205806 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
205746 AAAAAATGAG
205756 ACTTAACCAACCGATCAAATCCATT
1 ACTTAACCAACCGATCAAATCCATT
205781 ACTTAACCAACCGATCAAATCCATT
1 ACTTAACCAACCGATCAAATCCATT
205806 A
1 A
205807 GCAGAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.31, G:0.04, T:0.24
Consensus pattern (25 bp):
ACTTAACCAACCGATCAAATCCATT
Found at i:212109 original size:57 final size:57
Alignment explanation
Indices: 212021--212134 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
212011 CCAGTCATTT
212021 CATCCTTTCATTCACCACCCACCCAAAGCATTATCAGCTATTAAACAATCAAACACG
1 CATCCTTTCATTCACCACCCACCCAAAGCATTATCAGCTATTAAACAATCAAACACG
212078 CATCCTTTCATTCACCACCCACCCAAAGCATTATCAGCTATTAAACAATCAAACACG
1 CATCCTTTCATTCACCACCCACCCAAAGCATTATCAGCTATTAAACAATCAAACACG
212135 AACACACCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.37, C:0.35, G:0.05, T:0.23
Consensus pattern (57 bp):
CATCCTTTCATTCACCACCCACCCAAAGCATTATCAGCTATTAAACAATCAAACACG
Found at i:216136 original size:147 final size:147
Alignment explanation
Indices: 215869--216162 Score: 579
Period size: 147 Copynumber: 2.0 Consensus size: 147
215859 TTTTGTAACT
215869 TTCCATATTTGGGTGACCAAAAAATAAAAGAAAACACAGTTGGGTGACCTCTATTGTAGTTTACC
1 TTCCATATTTGGGTGACCAAAAAATAAAAGAAAACACAGTTGGGTGACCTCTATTGTAGTTTACC
215934 CTTTAATATTGGCTTCAAACAAGCCTTTACCGCTATGCAGATGTACGTTATTCCAATCCATATTT
66 CTTTAATATTGGCTTCAAACAAGCCTTTACCGCTATGCAGATGTACGTTATTCCAATCCATATTT
215999 CTCAAAGGAACTGTTAA
131 CTCAAAGGAACTGTTAA
*
216016 TTCCATATTTGGGTGACCAAAAATTAAAAGAAAACACAGTTGGGTGACCTCTATTGTAGTTTACC
1 TTCCATATTTGGGTGACCAAAAAATAAAAGAAAACACAGTTGGGTGACCTCTATTGTAGTTTACC
216081 CTTTAATATTGGCTTCAAACAAGCCTTTACCGCTATGCAGATGTACGTTATTCCAATCCATATTT
66 CTTTAATATTGGCTTCAAACAAGCCTTTACCGCTATGCAGATGTACGTTATTCCAATCCATATTT
216146 CTCAAAGGAACTGTTAA
131 CTCAAAGGAACTGTTAA
216163 AACCTATGTT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (147 bp):
TTCCATATTTGGGTGACCAAAAAATAAAAGAAAACACAGTTGGGTGACCTCTATTGTAGTTTACC
CTTTAATATTGGCTTCAAACAAGCCTTTACCGCTATGCAGATGTACGTTATTCCAATCCATATTT
CTCAAAGGAACTGTTAA
Found at i:223341 original size:43 final size:43
Alignment explanation
Indices: 223280--223569 Score: 286
Period size: 43 Copynumber: 6.9 Consensus size: 43
223270 TCACTTGACG
*
223280 TAAATGGAAGACTCATGTCTCGGGATGAGCGTGAGATTATGTA
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
* *
223323 TAAATGGAATACTCATGTCTCGGGATGAGCGTGAGATTATGTA
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
* *
223366 TAAATGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATGTA
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
* * ** *
223409 TAAATGGAAGACTCGTGACTCGAAATGAGCATGAGATTGTGT-
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
* * * * * *
223451 TTAA-GAAAGACTCATGTCTCGGGGTGAGTACGAGATTATAT-
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
** * * * * *
223492 TAAA-GGAAGACTTGTGACTCAGGACGAGCATGAGATTATATT
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
* * * * *
223534 TTAA-GGAAGACTTATGACTCGGTA-GAGCATAAGATT
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATT
223570 GTTTAAAAAG
Statistics
Matches: 212, Mismatches: 34, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
41 69 0.33
42 23 0.11
43 120 0.57
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (43 bp):
TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
Found at i:224231 original size:21 final size:21
Alignment explanation
Indices: 224207--224260 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
224197 AGAGTTTTTA
*
224207 GTATCGATAGAAG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
*
224228 GTATCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTCATACTT
224249 GTATCGGTAGAA
1 GTATCGGTAGAA
224261 CTAGCACGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:225318 original size:87 final size:87
Alignment explanation
Indices: 225209--225385 Score: 336
Period size: 87 Copynumber: 2.0 Consensus size: 87
225199 AACTACTACG
225209 AATAAAAAGGTTGGAAGCAAGTATAGTTTGTTGATTTATTTTTATATAGATTCCGTTATTTCATT
1 AATAAAAAGGTTGGAAGCAAGTATAGTTTGTTGATTTATTTTTATATAGATTCCGTTATTTCATT
*
225274 AATTTGGATCGAATAATGAATT
66 AATTTGGACCGAATAATGAATT
*
225296 AATAAAAAGGTTGGAAGTAAGTATAGTTTGTTGATTTATTTTTATATAGATTCCGTTATTTCATT
1 AATAAAAAGGTTGGAAGCAAGTATAGTTTGTTGATTTATTTTTATATAGATTCCGTTATTTCATT
225361 AATTTGGACCGAATAATGAATT
66 AATTTGGACCGAATAATGAATT
225383 AAT
1 AAT
225386 GAATCTCTTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (87 bp):
AATAAAAAGGTTGGAAGCAAGTATAGTTTGTTGATTTATTTTTATATAGATTCCGTTATTTCATT
AATTTGGACCGAATAATGAATT
Found at i:226286 original size:24 final size:23
Alignment explanation
Indices: 226235--226290 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
226225 AAACCAATAT
*
226235 TATA-TTTTAATATTAATATAAT
1 TATATTTTTAATATTAATATAAA
226257 TATATTATTTAATATTAATATAAA
1 TATATT-TTTAATATTAATATAAA
226281 -ATTATTTTTA
1 TA-TATTTTTA
226291 TTAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 6 0.20
24 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATTTTTAATATTAATATAAA
Found at i:226298 original size:26 final size:24
Alignment explanation
Indices: 226233--226279 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
226223 AAAAACCAAT
226233 ATTATA-T-TTTAATATTAATATA
1 ATTATATTATTTAATATTAATATA
226255 ATTATATTATTTAATATTAATATA
1 ATTATATTATTTAATATTAATATA
226279 A
1 A
226280 AATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.26
23 1 0.04
24 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATATTATTTAATATTAATATA
Found at i:231613 original size:7 final size:7
Alignment explanation
Indices: 231601--231625 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
231591 ATTAAAATAT
231601 TTTGAAG
1 TTTGAAG
231608 TTTGAAG
1 TTTGAAG
231615 TTTGAAG
1 TTTGAAG
231622 TTTG
1 TTTG
231626 GATGAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
TTTGAAG
Found at i:235676 original size:154 final size:154
Alignment explanation
Indices: 235396--235685 Score: 458
Period size: 154 Copynumber: 1.9 Consensus size: 154
235386 GTACTTTTAC
* *
235396 CTACTTTGGTCGATTGTGATGAATATAAGAGGTAGAAAAGGCCGGAATCACAAAATAAGGATCAT
1 CTACTTTGGTCAATTGTGATGAATATAAGAGGTAGAAAAGGCCGCAATCACAAAATAAGGATCAT
*
235461 AACATCATGTTGAAACCGATGTTTAAGTCTCGGAAAAAAGGGTCATTGTTTATTGCAAGTTGTAG
66 AACATCATGTTGAAACCGATGTTTAAGTCCCGGAAAAAAGGGTCATTGTTTATTGCAAGTTGTAG
235526 GCTTTGGTGCATCAATCATACATG
131 GCTTTGGTGCATCAATCATACATG
* * *
235550 CTACTTTGGTCAATTGTGGTGAATATAAGAGGTAG-AAAGAGCTGCAATCACAAAATAATGATCA
1 CTACTTTGGTCAATTGTGATGAATATAAGAGGTAGAAAAG-GCCGCAATCACAAAATAAGGATCA
* **
235614 TAACATCGTGTTGTTACCGATGTTTTAAGTCCCGG-AAAAAGGGTCATTGTTTATTGCAAGTTGT
65 TAACATCATGTTGAAACCGATG-TTTAAGTCCCGGAAAAAAGGGTCATTGTTTATTGCAAGTTGT
*
235678 AGGTTTTG
129 AGGCTTTG
235686 AAATTTTTAC
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
153 4 0.03
154 109 0.88
155 11 0.09
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (154 bp):
CTACTTTGGTCAATTGTGATGAATATAAGAGGTAGAAAAGGCCGCAATCACAAAATAAGGATCAT
AACATCATGTTGAAACCGATGTTTAAGTCCCGGAAAAAAGGGTCATTGTTTATTGCAAGTTGTAG
GCTTTGGTGCATCAATCATACATG
Found at i:239103 original size:7 final size:7
Alignment explanation
Indices: 239091--239117 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
239081 GTTCAACTGA
239091 CTTCTTC
1 CTTCTTC
239098 CTTCTTC
1 CTTCTTC
239105 CTTCTTC
1 CTTCTTC
239112 CTTCTT
1 CTTCTT
239118 TTTCCCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTCTTC
Found at i:240052 original size:21 final size:21
Alignment explanation
Indices: 240028--240072 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
240018 GTTACAATAT
*
240028 ATTTATAAATATTTAATTTAA
1 ATTTATAAATATTTAATTAAA
* * *
240049 ATTTTTAACTATTTGATTAAA
1 ATTTATAAATATTTAATTAAA
240070 ATT
1 ATT
240073 ATTTTAGTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTATAAATATTTAATTAAA
Found at i:244393 original size:58 final size:57
Alignment explanation
Indices: 244285--244538 Score: 273
Period size: 58 Copynumber: 4.4 Consensus size: 57
244275 AAAATCCGAG
* * *
244285 ATAGTTGGGTAACCAAAAAAGAGAAAATTGAATAGTTGAGTGGTCCTTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAGAG--AATT-AATAGTTGAGTGATCATTTTGTAACTTTTC
* *
244345 ATAGTTGGGTGACCAAAAAAGAGAATTGAATAGTTGAGTGGTTATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAGAGAATT-AATAGTTGAGTGATCATTTTGTAACTTTTC
* * *
244403 ATAGTTGTGTGACCAAAAAA-A-ATACTAATAGTTGGGTGATCATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAGAGA-ATTAATAGTTGAGTGATCATTTTGTAACTTTTC
** * * *
244459 ATAGTT-GGTGAATAAAAAAGAAAAAAATTCATAGTTGGGTGATCATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAG---AGAATTAATAGTTGAGTGATCATTTTGTAACTTTTC
**
244518 ATAGTT-GGTGAATAAAAAAGA
1 ATAGTTGGGTGACCAAAAAAGA
244539 AAAAAATTCA
Statistics
Matches: 175, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
55 10 0.06
56 35 0.20
57 3 0.02
58 52 0.30
59 52 0.30
60 23 0.13
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (57 bp):
ATAGTTGGGTGACCAAAAAAGAGAATTAATAGTTGAGTGATCATTTTGTAACTTTTC
Found at i:244463 original size:29 final size:29
Alignment explanation
Indices: 244430--244525 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
244420 AAAAATACTA
244430 ATAGTTGGGTGATCATTTTGTAACTTTTC
1 ATAGTTGGGTGATCATTTTGTAACTTTTC
* **** * ***
244459 ATAGTT-GGTGAATAAAAAAGAAAAAAATTC
1 ATAGTTGGGTG-ATCATTTTG-TAACTTTTC
244489 ATAGTTGGGTGATCATTTTGTAACTTTTC
1 ATAGTTGGGTGATCATTTTGTAACTTTTC
244518 ATAGTTGG
1 ATAGTTGG
244526 TGAATAAAAA
Statistics
Matches: 46, Mismatches: 18, Indels: 6
0.66 0.26 0.09
Matches are distributed among these distances:
28 4 0.09
29 23 0.50
30 15 0.33
31 4 0.09
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (29 bp):
ATAGTTGGGTGATCATTTTGTAACTTTTC
Found at i:244492 original size:30 final size:30
Alignment explanation
Indices: 244456--244555 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
244446 TTTGTAACTT
244456 TTCATAGTTGGTGAATAAAAAAGAAAAAAA
1 TTCATAGTTGGTGAATAAAAAAGAAAAAAA
* **** * ***
244486 TTCATAGTTGGGTG-ATCATTTTG-TAACTT
1 TTCATAGTT-GGTGAATAAAAAAGAAAAAAA
244515 TTCATAGTTGGTGAATAAAAAAGAAAAAAA
1 TTCATAGTTGGTGAATAAAAAAGAAAAAAA
244545 TTCATAGTTGG
1 TTCATAGTTGG
244556 GTGACTACTA
Statistics
Matches: 49, Mismatches: 18, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
28 4 0.08
29 15 0.31
30 26 0.53
31 4 0.08
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (30 bp):
TTCATAGTTGGTGAATAAAAAAGAAAAAAA
Found at i:244510 original size:59 final size:59
Alignment explanation
Indices: 244299--244559 Score: 286
Period size: 59 Copynumber: 4.5 Consensus size: 59
244289 TTGGGTAACC
* * * * **
244299 AAAAAAG-AGAAAATTGAATAGTTGAGTGGTCCTTTTGTAACTTTTCATAGTTGGGTGACC
1 AAAAAAGAAAAAAATT-AATAGTTGGGTGATCATTTTGTAACTTTTCATAGTT-GGTGAAT
* * * *
244359 AAAAAAG---AGAATTGAATAGTTGAGTGGTTATTTTGTAACTTTTCATAGTT-GTG--T
1 AAAAAAGAAAAAAATT-AATAGTTGGGTGATCATTTTGTAACTTTTCATAGTTGGTGAAT
** * *
244413 GACCAAA-AAAAATACTAATAGTTGGGTGATCATTTTGTAACTTTTCATAGTTGGTGAAT
1 -AAAAAAGAAAAAAATTAATAGTTGGGTGATCATTTTGTAACTTTTCATAGTTGGTGAAT
*
244472 AAAAAAGAAAAAAATTCATAGTTGGGTGATCATTTTGTAACTTTTCATAGTTGGTGAAT
1 AAAAAAGAAAAAAATTAATAGTTGGGTGATCATTTTGTAACTTTTCATAGTTGGTGAAT
*
244531 AAAAAAGAAAAAAATTCATAGTTGGGTGA
1 AAAAAAGAAAAAAATTAATAGTTGGGTGA
244560 CTACTAATGT
Statistics
Matches: 176, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
55 4 0.02
56 36 0.20
57 6 0.03
58 44 0.25
59 79 0.45
60 7 0.04
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (59 bp):
AAAAAAGAAAAAAATTAATAGTTGGGTGATCATTTTGTAACTTTTCATAGTTGGTGAAT
Found at i:244535 original size:114 final size:114
Alignment explanation
Indices: 244315--244536 Score: 288
Period size: 114 Copynumber: 1.9 Consensus size: 114
244305 GAGAAAATTG
* * * *
244315 AATAGTTGAGTGGTCCTTTTGTAACTTTTCATAGTTGGGTGACCAAAAAAGAGAATTGAATAGTT
1 AATAGTTGAGTGATCATTTTGTAACTTTTCATAGTTGGGTGAACAAAAAAGAAAATTGAATAGTT
* * *
244380 GAGTGGTTATTTTGTAACTTTTCATAGTTGTGTGACCAAAAAAAATACT
66 GAGTGATCATTTTGTAACTTTTCATAGTTGTGTGAACAAAAAAAATACT
* * *
244429 AATAGTTGGGTGATCATTTTGTAACTTTTCATAGTT-GGTGAATAAAAAAGAAAAAAATT-CATA
1 AATAGTTGAGTGATCATTTTGTAACTTTTCATAGTTGGGTGAACAAAAAAG---AAAATTGAATA
* *
244492 GTTGGGTGATCATTTTGTAACTTTTCATAGTTG-GTGAATAAAAAA
63 GTTGAGTGATCATTTTGTAACTTTTCATAGTTGTGTGAACAAAAAA
244537 GAAAAAAATT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
113 12 0.13
114 43 0.46
115 33 0.35
116 5 0.05
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (114 bp):
AATAGTTGAGTGATCATTTTGTAACTTTTCATAGTTGGGTGAACAAAAAAGAAAATTGAATAGTT
GAGTGATCATTTTGTAACTTTTCATAGTTGTGTGAACAAAAAAAATACT
Found at i:246149 original size:23 final size:23
Alignment explanation
Indices: 246123--246190 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
246113 AATTTATAAT
*
246123 TTTTGGAAATTTTAATTAGGTAC
1 TTTTGAAAATTTTAATTAGGTAC
*** * *
246146 TTTTTTTAATTTTAATTAGGCAAT
1 TTTTGAAAATTTTAATTAGG-TAC
246170 TTTTGAAAATTTTAATTAGGT
1 TTTTGAAAATTTTAATTAGGT
246191 TTCTCAAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 17 0.49
24 18 0.51
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (23 bp):
TTTTGAAAATTTTAATTAGGTAC
Found at i:247446 original size:14 final size:15
Alignment explanation
Indices: 247418--247446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
247408 TTACGGGAAG
247418 AAGATATTGGAATCA
1 AAGATATTGGAATCA
247433 AAGATATT-GAATCA
1 AAGATATTGGAATCA
247447 TTGGGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (15 bp):
AAGATATTGGAATCA
Found at i:248355 original size:22 final size:21
Alignment explanation
Indices: 248302--248349 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
248292 TATTGTTAAT
* *
248302 TTTGTTATTATTTTAGAGGCA
1 TTTGTTATTAATTTAGAGACA
*
248323 TTTGTTATTAATTTAGAGATA
1 TTTGTTATTAATTTAGAGACA
248344 TTTGTT
1 TTTGTT
248350 TGTTAAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (21 bp):
TTTGTTATTAATTTAGAGACA
Found at i:258510 original size:26 final size:26
Alignment explanation
Indices: 258474--258527 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
258464 TGCGTTAGGG
258474 ATTTTTAGATCCAAATAATTTGAGAA
1 ATTTTTAGATCCAAATAATTTGAGAA
258500 ATTTTTAGATCCAAATAATTTGAGAA
1 ATTTTTAGATCCAAATAATTTGAGAA
258526 AT
1 AT
258528 ATACTTTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (26 bp):
ATTTTTAGATCCAAATAATTTGAGAA
Found at i:261201 original size:19 final size:21
Alignment explanation
Indices: 261168--261208 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
261158 ATTTTCTTTA
261168 TTTTTTAAAATTTTA-TGAAT
1 TTTTTTAAAATTTTATTGAAT
*
261188 TTTTTTAATA-TTTATTGAAT
1 TTTTTTAAAATTTTATTGAAT
261208 T
1 T
261209 AAAATAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTTTAAAATTTTATTGAAT
Found at i:261893 original size:21 final size:22
Alignment explanation
Indices: 261862--261902 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
261852 AACTATATTA
261862 ATTTTGTTAAACAATAAATGAT
1 ATTTTGTTAAACAATAAATGAT
*
261884 ATTTT-TTAAACAGTAAATG
1 ATTTTGTTAAACAATAAATG
261903 TTAACTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (22 bp):
ATTTTGTTAAACAATAAATGAT
Found at i:262727 original size:27 final size:28
Alignment explanation
Indices: 262689--262753 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
262679 ATAATATTTG
262689 AAAT-TTATAAAAATA-AAAATATATATA
1 AAATATTATAAAAATAGAAAATATATA-A
* *
262716 AAATATTA-AAAAGTAGAAAATTTATAA
1 AAATATTATAAAAATAGAAAATATATAA
*
262743 AAATATCATAA
1 AAATATTATAA
262754 TTATGCCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATATTATAAAAATAGAAAATATATAA
Found at i:263613 original size:22 final size:22
Alignment explanation
Indices: 263585--263627 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
263575 ATATTAACAT
263585 TGTTTAAAGGCCAAACAAATAC
1 TGTTTAAAGGCCAAACAAATAC
*
263607 TGTTTAAATGCCAAACAAATA
1 TGTTTAAAGGCCAAACAAATA
263628 TTCTACCGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (22 bp):
TGTTTAAAGGCCAAACAAATAC
Found at i:269390 original size:18 final size:19
Alignment explanation
Indices: 269351--269391 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
269341 ACTTCATAAC
* *
269351 ATATTTTATGATTTTTATA
1 ATATTTAATAATTTTTATA
269370 ATATTTAATAATTTTTA-A
1 ATATTTAATAATTTTTATA
269388 ATAT
1 ATAT
269392 GTTTTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATATTTAATAATTTTTATA
Found at i:271840 original size:30 final size:30
Alignment explanation
Indices: 271804--271861 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
271794 TGATATCCCG
271804 AAATTATTATTTACTAAAATAGTATGTTCC
1 AAATTATTATTTACTAAAATAGTATGTTCC
*
271834 AAATTATTATTTATTAAAATAGTATGTT
1 AAATTATTATTTACTAAAATAGTATGTT
271862 TAGTTAAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (30 bp):
AAATTATTATTTACTAAAATAGTATGTTCC
Found at i:272911 original size:18 final size:18
Alignment explanation
Indices: 272888--272922 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
272878 AAATATTAAA
272888 AATATAATAACCAAAAAC
1 AATATAATAACCAAAAAC
*
272906 AATATAATAACTAAAAA
1 AATATAATAACCAAAAA
272923 TGAAAATTAT
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:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (18 bp):
AATATAATAACCAAAAAC
Found at i:274786 original size:13 final size:13
Alignment explanation
Indices: 274768--274792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274758 AATAATTATT
274768 AAATTATTTAAAA
1 AAATTATTTAAAA
274781 AAATTATTTAAA
1 AAATTATTTAAA
274793 TTATCGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTATTTAAAA
Found at i:274793 original size:22 final size:23
Alignment explanation
Indices: 274738--274796 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
274728 TAATTGCTAG
**
274738 AAATT-TTTAAAAAATTATAAAA
1 AAATTATTTAAATTATTATAAAA
*
274760 TAATTA-TTAAATTATT-TAAAA
1 AAATTATTTAAATTATTATAAAA
274781 AAATTATTTAAATTAT
1 AAATTATTTAAATTAT
274797 CGAATTAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATTTAAATTATTATAAAA
Found at i:276033 original size:14 final size:13
Alignment explanation
Indices: 275996--276034 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
275986 TCAATCAAAA
*
275996 TTATATTTATTTT
1 TTATATTAATTTT
*
276009 TTATATCAATTTT
1 TTATATTAATTTT
276022 TTATTATTAATTT
1 TTA-TATTAATTT
276035 ATCCTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATATTAATTTT
Found at i:276306 original size:19 final size:17
Alignment explanation
Indices: 276283--276332 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
276273 ACATTCATAT
276283 AATTATAATTAAAATAA
1 AATTATAATTAAAATAA
276300 AGTATTATAA-T-AAATAA
1 A--ATTATAATTAAAATAA
*
276317 AATGATAATTAAAATA
1 AATTATAATTAAAATA
276333 TATTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 6 0.21
16 1 0.04
17 13 0.46
18 1 0.04
19 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (17 bp):
AATTATAATTAAAATAA
Found at i:276398 original size:35 final size:35
Alignment explanation
Indices: 276358--276430 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
276348 TATAATAAAT
276358 TTAAATAAAAATTAATTAAATAATTTTCACCTCAA
1 TTAAATAAAAATTAATTAAATAATTTTCACCTCAA
276393 TTAAATAAAAATTAATTAAATAATTTTCACCTCAA
1 TTAAATAAAAATTAATTAAATAATTTTCACCTCAA
276428 TTA
1 TTA
276431 CATTCAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (35 bp):
TTAAATAAAAATTAATTAAATAATTTTCACCTCAA
Found at i:276903 original size:26 final size:27
Alignment explanation
Indices: 276866--276916 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
276856 TGCCAATTTT
*
276866 TTTTTAAAAAAAATAGGATTTTGTGCC
1 TTTTTAAAAAAAATAAGATTTTGTGCC
276893 TTTTT-AAAAAAATAAGATTTTGTG
1 TTTTTAAAAAAAATAAGATTTTGTG
276917 TCATTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (27 bp):
TTTTTAAAAAAAATAAGATTTTGTGCC
Found at i:276929 original size:26 final size:26
Alignment explanation
Indices: 276866--276929 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
276856 TGCCAATTTT
* *
276866 TTTTTAAAAAAAATAGGATTTTGTGCC
1 TTTTT-AAAAAAATAAGATTTTGTGCA
276893 TTTTTAAAAAAATAAGATTTTGTGTCA
1 TTTTTAAAAAAATAAGATTTTGTG-CA
*
276920 TTTTTTAAAA
1 TTTTTAAAAA
276930 TATTTAGAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (26 bp):
TTTTTAAAAAAATAAGATTTTGTGCA
Found at i:278726 original size:24 final size:24
Alignment explanation
Indices: 278673--278727 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
278663 AGGTATTTTC
278673 TAATTATTTATCCCTTTTTTGTAA
1 TAATTATTTATCCCTTTTTTGTAA
* *
278697 TAAATTATTTAT-CTTTTTGTTTTAA
1 T-AATTATTTATCCCTTTT-TTGTAA
278722 TAATTA
1 TAATTA
278728 CAACGTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (24 bp):
TAATTATTTATCCCTTTTTTGTAA
Found at i:289858 original size:61 final size:61
Alignment explanation
Indices: 289788--289910 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
289778 TATGAATCAA
* * *
289788 TGATTTATTAATAATTTTCTAGTATTAACCTTCTATTTTGAATTCTAGTTCTGAGTTACAG
1 TGATTTATTAAAAAATTTCTAATATTAACCTTCTATTTTGAATTCTAGTTCTGAGTTACAG
*
289849 TGATTTATTAAAAAATTTCTAATATTAACCTTCTATTTTGAATTTTAGTTCTGAGTTACAG
1 TGATTTATTAAAAAATTTCTAATATTAACCTTCTATTTTGAATTCTAGTTCTGAGTTACAG
289910 T
1 T
289911 TTTTTTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (61 bp):
TGATTTATTAAAAAATTTCTAATATTAACCTTCTATTTTGAATTCTAGTTCTGAGTTACAG
Found at i:292639 original size:160 final size:160
Alignment explanation
Indices: 292116--292712 Score: 742
Period size: 159 Copynumber: 3.8 Consensus size: 160
292106 GTTGACGTGC
* * * * * * *
292116 CTTCAGAGTCGACTTGG-T-GGTTAAATCACTTCCGCTTGTATCATACAATTGTTCCATTCTTAC
1 CTTCAGAGTCAACTTGGTTCGATTCAATCACTTCCGCTTGCATCATATAATTGTTTCATTTTTAC
*
292179 AGTTCAAGATGGTAAAAGCTGTAAGAATACATTCATGAGGAGAAAAGGATAAAGGAAAA-G---A
66 AGTTCAAGATGGTTAAAGCTGTAAGAAT-CATTCATGAGGAGAAAAGGATAAAGGAAAAGGAAAA
* * *
292240 -AAA-AGTAAGAGATGATACGCTTTAACCAT
130 GAAAGAGTAAGACATGATACACTTTAACCGT
* * ** * * *
292269 CTTCAGCGTCAACTTGGTTCGGTTCAATCAAGTCCGCTTGTA-CCT-T-A-TATTTCATTTTTAC
1 CTTCAGAGTCAACTTGGTTCGATTCAATCACTTCCGCTTGCATCATATAATTGTTTCATTTTTAC
*
292330 AGTTCATGATGGTTAAAGCTGTAAGAATTCATTCATGAGGAGAAAAAGGATAAAGGAAAAGGAAA
66 AGTTCAAGATGGTTAAAGCTGTAAGAA-TCATTCATGAGGAG-AAAAGGATAAAGGAAAAGGAAA
*
292395 AGATAGAAGTAAGACATGATACA-TTTAACCGT
129 AGAAAG-AGTAAGACATGATACACTTTAACCGT
* * * *
292427 CTTCACAGTTCAACTTGGTTTGATTCAATCACCTCCGCTTGCATTATATAATTGTTTCATTTTTA
1 CTTCAGAG-TCAACTTGGTTCGATTCAATCACTTCCGCTTGCATCATATAATTGTTTCATTTTTA
* * *
292492 CAGTTCATGATAGTTAAAGCTGTAAGAATCATTCACGAGGAGAAAAGGATAAAGGAAAAGGAAAA
65 CAGTTCAAGATGGTTAAAGCTGTAAGAATCATTCATGAGGAGAAAAGGATAAAGGAAAAGGAAAA
292557 GAAAGATGTAAGACATGATACACTTTAACCGT
130 GAAAGA-GTAAGACATGATACACTTTAACCGT
*
292589 CTTCAGAG-CAACTTGGTTCGATTCAATCACTTCCGCTTGCATCATATAATTGTTTTATTTTTTA
1 CTTCAGAGTCAACTTGGTTCGATTCAATCACTTCCGCTTGCATCATATAATTGTTTCA-TTTTTA
*
292653 CA-TTCAAGATGGTT-AAGCTGTAAGATTCATTCATGAGGAG-AAAGGCATAAAGGAAAAGGA
65 CAGTTCAAGATGGTTAAAGCTGTAAGAATCATTCATGAGGAGAAAAGG-ATAAAGGAAAAGGA
292713 GTAAGAGTAG
Statistics
Matches: 386, Mismatches: 38, Indels: 34
0.84 0.08 0.07
Matches are distributed among these distances:
151 49 0.13
152 19 0.05
153 16 0.04
154 3 0.01
155 19 0.05
156 1 0.00
157 2 0.01
158 19 0.05
159 81 0.21
160 57 0.15
161 51 0.13
162 30 0.08
163 39 0.10
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (160 bp):
CTTCAGAGTCAACTTGGTTCGATTCAATCACTTCCGCTTGCATCATATAATTGTTTCATTTTTAC
AGTTCAAGATGGTTAAAGCTGTAAGAATCATTCATGAGGAGAAAAGGATAAAGGAAAAGGAAAAG
AAAGAGTAAGACATGATACACTTTAACCGT
Found at i:300083 original size:16 final size:16
Alignment explanation
Indices: 300054--300114 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
300044 ATAATAAATA
*
300054 TTTAATGAAGATATTAT
1 TTTAAT-AAAATATTAT
300071 TTTAATAAAATATTAAAT
1 TTTAATAAAATATT--AT
300089 TTTATATAAAAT-TATAT
1 TTTA-ATAAAATAT-TAT
*
300106 TTTATTAAA
1 TTTAATAAA
300115 TGAGAACAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.29
17 12 0.32
18 7 0.18
19 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TTTAATAAAATATTAT
Found at i:301232 original size:25 final size:24
Alignment explanation
Indices: 301171--301234 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
301161 AGCTTGAATT
*
301171 TATTTAAATTTTGA-TTT--TTAA
1 TATTTAAATTTTAAGTTTAATTAA
301192 TATTT-AA-TTTAAGTTTAATTAAA
1 TATTTAAATTTTAAGTTTAATT-AA
301215 TATTTAAATTTTAAGTTTAA
1 TATTTAAATTTTAAGTTTAA
301235 GTACGATAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 5 0.14
22 2 0.06
23 7 0.19
24 2 0.06
25 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (24 bp):
TATTTAAATTTTAAGTTTAATTAA
Found at i:301429 original size:15 final size:16
Alignment explanation
Indices: 301399--301432 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
301389 AAAATAAAAT
301399 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
301415 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
301430 TTT
1 TTT
301433 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:301478 original size:30 final size:31
Alignment explanation
Indices: 301420--301485 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
301410 AATAATTTAT
301420 ATTTTTATAATTTTTAAAAAATTAAAATA-A
1 ATTTTTATAATTTTTAAAAAATTAAAATATA
* ** * *
301450 ATTTTTATTATTTTTTGAAAGTTTAAATATA
1 ATTTTTATAATTTTTAAAAAATTAAAATATA
301481 ATTTT
1 ATTTT
301486 AATTTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAAAATTAAAATATA
Found at i:308255 original size:31 final size:33
Alignment explanation
Indices: 308220--308280 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
308210 TAGCCTAATG
308220 ACTT-AAA-TAAAAA-TTTTCGAATAGTTTAGTA
1 ACTTAAAACTAAAAACTTTT-GAATAGTTTAGTA
308251 ACTTAAAACTAAAAACTTTTGAATAGTTTA
1 ACTTAAAACTAAAAACTTTTGAATAGTTTA
308281 ATAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 4 0.15
32 3 0.11
33 16 0.59
34 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (33 bp):
ACTTAAAACTAAAAACTTTTGAATAGTTTAGTA
Found at i:312812 original size:25 final size:27
Alignment explanation
Indices: 312784--312852 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 27
312774 AATTTAGTTC
*
312784 TTAATGTTTATATCTTTTT-GTT-AAT
1 TTAATCTTTATATCTTTTTAGTTAAAT
* *
312809 TTAATTTTTAT-TTTTTTTAGTTAAAT
1 TTAATCTTTATATCTTTTTAGTTAAAT
312835 TTAATCTTTA-A-CTTTTTA
1 TTAATCTTTATATCTTTTTA
312853 AAAAGAGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 6 0.16
25 19 0.51
26 12 0.32
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (27 bp):
TTAATCTTTATATCTTTTTAGTTAAAT
Found at i:312850 original size:26 final size:24
Alignment explanation
Indices: 312798--312851 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
312788 TGTTTATATC
* **
312798 TTTTTGTTAATTTAATTTTTATTT
1 TTTTTGTTAATTTAATCTTTAACT
312822 TTTTTAGTTAAATTTAATCTTTAACT
1 TTTTT-GTT-AATTTAATCTTTAACT
312848 TTTT
1 TTTT
312852 AAAAAGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.20
25 3 0.12
26 17 0.68
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTTGTTAATTTAATCTTTAACT
Found at i:319919 original size:4 final size:4
Alignment explanation
Indices: 319910--319992 Score: 78
Period size: 4 Copynumber: 20.2 Consensus size: 4
319900 AAATAAACGG
* * *
319910 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
319960 GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
319993 GTAATGTGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
3 3 0.04
4 52 0.78
5 12 0.18
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:319932 original size:17 final size:17
Alignment explanation
Indices: 319910--319992 Score: 90
Period size: 17 Copynumber: 5.3 Consensus size: 17
319900 AAATAAACGG
319910 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
319927 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
*
319943 G-AAG---GAGAGGAAA
1 GAAAGAAAGAAAGGAAA
* *
319956 GAAAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
319973 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
319988 GAAAG
1 GAAAG
319993 GTAATGTGTA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
12 5 0.09
13 3 0.05
14 3 0.05
15 14 0.24
16 5 0.09
17 28 0.48
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:319945 original size:29 final size:30
Alignment explanation
Indices: 319909--319992 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 30
319899 CAAATAAACG
319909 GGAAAGAAAGAAAGGAAAGAAAGAAAGAAA
1 GGAAAGAAAGAAAGGAAAGAAAGAAAGAAA
* * * *
319939 GG-AAGAAGGAGAGGAAAGAAAGAAGGAGA
1 GGAAAGAAAGAAAGGAAAGAAAGAAAGAAA
319968 GGAAAGAAAGAAGAAGGAAAGAAAG
1 GGAAAGAAAG-A-AAGGAAAGAAAG
319993 GTAATGTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 25 0.56
30 8 0.18
31 1 0.02
32 11 0.24
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (30 bp):
GGAAAGAAAGAAAGGAAAGAAAGAAAGAAA
Found at i:321088 original size:21 final size:20
Alignment explanation
Indices: 321046--321093 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
321036 AAATAGGTTT
**
321046 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATAGAAA
*
321066 ATTTAAATTAAAAAATAGAAA
1 ATTTAAAAT-AAAAATAGAAA
321087 A-TTAAAA
1 ATTTAAAA
321094 AATACTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATTTAAAATAAAAATAGAAA
Found at i:321577 original size:12 final size:12
Alignment explanation
Indices: 321560--321601 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
321550 GATTATATTT
321560 TTTTTTTCTAAA
1 TTTTTTTCTAAA
* *
321572 TTTTTTTATATA
1 TTTTTTTCTAAA
*
321584 TTTATTTCT-AA
1 TTTTTTTCTAAA
321595 TTTTTTT
1 TTTTTTT
321602 ATTTTTTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTTCTAAA
Found at i:321922 original size:28 final size:29
Alignment explanation
Indices: 321871--321925 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
321861 TATATTATAA
*
321871 TAGTAATTATATATATGTATTAATATTTT
1 TAGTAATAATATATATGTATTAATATTTT
321900 TAGTAATAATTATATAT-TA-TAATATT
1 TAGTAATAA-TATATATGTATTAATATT
321926 ATATTATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 10 0.42
30 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TAGTAATAATATATATGTATTAATATTTT
Found at i:321956 original size:37 final size:37
Alignment explanation
Indices: 321899--321969 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
321889 ATTAATATTT
* *
321899 TTAGTAATAATTATATATTATAATAT-TATATTATCTA
1 TTAGTAATAATAATACATTATAATATAT-TATTATCTA
*
321936 TTAGTAATACTAATACATTATAATATATTATTAT
1 TTAGTAATAATAATACATTATAATATATTATTAT
321970 ATTATGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (37 bp):
TTAGTAATAATAATACATTATAATATATTATTATCTA
Found at i:322389 original size:17 final size:17
Alignment explanation
Indices: 322367--322418 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
322357 CAAATTTGAG
322367 CTTTTTCAAACTTAAAA
1 CTTTTTCAAACTTAAAA
* **
322384 CTTTTTTAAAC-TCGAA
1 CTTTTTCAAACTTAAAA
*
322400 TTTTTTCAAACTTACAAA
1 CTTTTTCAAACTTA-AAA
322418 C
1 C
322419 CCGGATCAAC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
16 12 0.48
17 11 0.44
18 2 0.08
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (17 bp):
CTTTTTCAAACTTAAAA
Found at i:328528 original size:23 final size:25
Alignment explanation
Indices: 328488--328536 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
328478 TTAGAGTAAT
* *
328488 TTAATAAATAATATAAATTTAATGG
1 TTAAAAAATAATATAAATTAAATGG
328513 TTAAAAAATAA-A-AAATTAAATGG
1 TTAAAAAATAATATAAATTAAATGG
328536 T
1 T
328537 GAGCTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAAATAATATAAATTAAATGG
Found at i:330507 original size:14 final size:15
Alignment explanation
Indices: 330488--330517 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
330478 AGTTCGGATT
330488 TTAGAAAAA-AATTA
1 TTAGAAAAATAATTA
330502 TTAGAAAAATAATTA
1 TTAGAAAAATAATTA
330517 T
1 T
330518 AAATCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
TTAGAAAAATAATTA
Found at i:331031 original size:22 final size:24
Alignment explanation
Indices: 331001--331045 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
330991 TTAGTTTTGT
331001 TATAAAATAAA-AGAAT-AGAGAG
1 TATAAAATAAAGAGAATAAGAGAG
*
331023 TATAGAATAAAGAGAATAAGAGA
1 TATAAAATAAAGAGAATAAGAGA
331046 ATAAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (24 bp):
TATAAAATAAAGAGAATAAGAGAG
Found at i:345593 original size:23 final size:23
Alignment explanation
Indices: 345562--345611 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
345552 GAAAGAAAAA
345562 AAAACCGTGCTATTCAAGCAAAG
1 AAAACCGTGCTATTCAAGCAAAG
* *
345585 AAAATCGTGCTATTCAAGCAGAG
1 AAAACCGTGCTATTCAAGCAAAG
345608 AAAA
1 AAAA
345612 ATTCAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAACCGTGCTATTCAAGCAAAG
Found at i:347568 original size:26 final size:30
Alignment explanation
Indices: 347502--347568 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 30
347492 GGCGCCAAAA
*
347502 AATTTATTTTTATTACTTTAGTCATTTTTT
1 AATTTAATTTTATTACTTTAGTCATTTTTT
* **
347532 ATTTTTGTTTTATTA-TTT-G-CA-TTTTT
1 AATTTAATTTTATTACTTTAGTCATTTTTT
347558 AATTTAATTTT
1 AATTTAATTTT
347569 TCTATTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 13 0.42
27 2 0.06
28 1 0.03
29 3 0.10
30 12 0.39
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (30 bp):
AATTTAATTTTATTACTTTAGTCATTTTTT
Found at i:347569 original size:27 final size:29
Alignment explanation
Indices: 347502--347569 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
347492 GGCGCCAAAA
347502 AATTTATTTTTATTACTTTAGTCATTTTT
1 AATTTATTTTTATTACTTTAGTCATTTTT
* *
347531 TATTTTTGTTTTATTA-TTT-G-CATTTTT
1 AATTTAT-TTTTATTACTTTAGTCATTTTT
347558 AATTTAATTTTT
1 AATTT-ATTTTT
347570 CTATTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 15 0.45
28 2 0.06
29 8 0.24
30 8 0.24
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (29 bp):
AATTTATTTTTATTACTTTAGTCATTTTT
Found at i:350658 original size:29 final size:28
Alignment explanation
Indices: 350616--350672 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
350606 CTATGGTACG
350616 TTTGCTTACCGACGAATGCCTTTTGGATT
1 TTTGCTTACCGACGAATG-CTTTTGGATT
*
350645 TTTGCTTACTGACGAATGCTTTTGGATT
1 TTTGCTTACCGACGAATGCTTTTGGATT
350673 ATGTAATGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (28 bp):
TTTGCTTACCGACGAATGCTTTTGGATT
Found at i:355378 original size:84 final size:84
Alignment explanation
Indices: 355274--355517 Score: 339
Period size: 84 Copynumber: 2.9 Consensus size: 84
355264 TGTATAAATA
* * *
355274 GAAGACTCATGTCTTGGGTTGAGTATGAGAAATTGTATAAATAGAAGACTCATGTCTTGAGATGA
1 GAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATAGAAGACTCATGTCTCGAGATGA
355339 GAATGAGACTATGAATAAG
66 GAATGAGACTATGAATAAG
*
355358 GAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAGATGA
1 GAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATAGAAGACTCATGTCTCGAGATGA
355423 GAATGAGACTATGAATAAG
66 GAATGAGACTATGAATAAG
*** * ** * * * *
355442 GAAGACTCATGTCTCGAAATGAGAATGAGATTTTG-ATTAA-GGAAGACTCATATCTCGAGTTGA
1 GAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATAGAAGACTCATGTCTCGAGATGA
*
355505 GAATGAGAATATG
66 GAATGAGACTATG
355518 GTTAAGGGGA
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
82 33 0.23
83 4 0.03
84 109 0.75
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (84 bp):
GAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATAGAAGACTCATGTCTCGAGATGA
GAATGAGACTATGAATAAG
Found at i:355386 original size:41 final size:40
Alignment explanation
Indices: 355221--355517 Score: 270
Period size: 43 Copynumber: 7.1 Consensus size: 40
355211 ATACTTGGTG
* *
355221 TATGAATAAGGAAGACTCATGTCTCGGGTTGAGCATGAGA
1 TATGAATAAGGAAGACTCATGTCTCGAGTTGAGAATGAGA
* * * * * *
355261 AATTGTATAAATAGAAGACTCATGTCTTGGGTTGAGTATGAGA
1 TA-TGAAT-AA-GGAAGACTCATGTCTCGAGTTGAGAATGAGA
* * * * *
355304 AATTGTATAAATAGAAGACTCATGTCTTGAGATGAGAATGAGA
1 TA-TGAAT-AA-GGAAGACTCATGTCTCGAGTTGAGAATGAGA
* *
355347 CTATGAATAAGGAAGACTCATGTCTCGGGTTGAGCATGAGA
1 -TATGAATAAGGAAGACTCATGTCTCGAGTTGAGAATGAGA
* * *
355388 AATTGTATAAATGGAAGACTCATGTCTCGAGATGAGAATGAGA
1 TA-TGAAT-AA-GGAAGACTCATGTCTCGAGTTGAGAATGAGA
**
355431 CTATGAATAAGGAAGACTCATGTCTCGAAATGAGAATGAGA
1 -TATGAATAAGGAAGACTCATGTCTCGAGTTGAGAATGAGA
* * *
355472 TTTTGATTAAGGAAGACTCATATCTCGAGTTGAGAATGAGAA
1 -TATGAATAAGGAAGACTCATGTCTCGAGTTGAGAATGAG-A
355514 TATG
1 TATG
355518 GTTAAGGGGA
Statistics
Matches: 218, Mismatches: 30, Indels: 17
0.82 0.11 0.06
Matches are distributed among these distances:
40 2 0.01
41 101 0.46
42 9 0.04
43 104 0.48
44 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (40 bp):
TATGAATAAGGAAGACTCATGTCTCGAGTTGAGAATGAGA
Found at i:355523 original size:41 final size:41
Alignment explanation
Indices: 355227--355524 Score: 251
Period size: 41 Copynumber: 7.1 Consensus size: 41
355217 GGTGTATGAA
* * *
355227 TAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAA-ATTGT
1 TAAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
* * * * *
355267 ATAAATAGAAGACTCATGTCTTGGGTTGAGTATGAGAA-ATTGT
1 -T-AA-GGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
* * * * **
355310 ATAAATAGAAGACTCATGTCTTGAGATGAGAATGAGACTATGAA
1 -T-AA-GGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
* * *
355354 TAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAA-ATTGT
1 TAAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
* * **
355394 ATAAATGGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAA
1 -T-AA-GGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
** * * *
355438 TAAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGAT
1 TAAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
*
355479 TAAGGAAGACTCATATCTCGAGTTGAGAATGAGAATATGGT
1 TAAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
355520 TAAGG
1 TAAGG
355525 GGAGACTTAT
Statistics
Matches: 214, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.01
41 102 0.48
42 8 0.04
43 98 0.46
44 4 0.02
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (41 bp):
TAAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGT
Found at i:357901 original size:75 final size:75
Alignment explanation
Indices: 357817--358106 Score: 262
Period size: 75 Copynumber: 3.9 Consensus size: 75
357807 ATGATTTTCA
* * * * * *
357817 AAATAACACACGACCTGGACACTCGGGCGTGTGCTAGACCATGTGTCCACTAGAGCTTAATTTTA
1 AAATGACACACGGCCTAGACACACGGGCATGTGCTAGACCGTGTGTCCACTAGAGCTTAATTTTA
357882 TAAAATTTTG
66 TAAAATTTTG
* * * * * ** * *
357892 AAACGACACACGGCCTAGAGACACGGGCGTGTTCCAGACCGTGTAACCACTAGAGGTTTATTTTA
1 AAATGACACACGGCCTAGACACACGGGCATGTGCTAGACCGTGTGTCCACTAGAGCTTAATTTTA
* **
357957 TGAAATTTCA
66 TAAAATTTTG
* * * *
357967 AAATGATACACGGCCTAGAGACACGGGCATGTGAC-AGACCGTGTGTCCACTGGAGCTTTATTTT
1 AAATGACACACGGCCTAGACACACGGGCATGTG-CTAGACCGTGTGTCCACTAGAGCTTAATTTT
358031 -TACAAATTTTTG
65 ATA-AAA-TTTTG
* * * * * * *
358043 AAGTGGCACACGGCCTGGACACAAGGGCATGTGCTCGACCGTGTGAT-CACTCGAACTTAATTTT
1 AAATGACACACGGCCTAGACACACGGGCATGTGCTAGACCGTGTG-TCCACTAGAGCTTAATTTT
358107 CTAATTTTTT
Statistics
Matches: 173, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
74 1 0.01
75 117 0.68
76 54 0.31
77 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (75 bp):
AAATGACACACGGCCTAGACACACGGGCATGTGCTAGACCGTGTGTCCACTAGAGCTTAATTTTA
TAAAATTTTG
Found at i:358828 original size:3 final size:3
Alignment explanation
Indices: 358820--358903 Score: 91
Period size: 3 Copynumber: 27.7 Consensus size: 3
358810 TTGTTTGATT
* * *
358820 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TT- CTG TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
358865 TTA TTA TTA TTC TTA TTA TTA TT- TTA TATA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TT
358904 TCCATTTCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.04
3 57 0.83
4 9 0.13
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Done.