Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009006.1 Corchorus capsularis cultivar CVL-1 contig09027, 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: 139710
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:463 original size:19 final size:20
Alignment explanation
Indices: 436--473 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
426 TACTATTATT
436 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
456 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
474 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:667 original size:22 final size:22
Alignment explanation
Indices: 639--822 Score: 115
Period size: 22 Copynumber: 8.3 Consensus size: 22
629 TGTCTCTATG
639 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
661 TGGTTATTATAATTTAATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
684 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
705 TGGTTACCAAAATTTCATATAGA
1 TGGTTATCAAAATTTCATA-AGA
*
728 -AGTTATCAAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
* *
749 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
771 TCATGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
795 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
817 TGGTTA
1 TGGTTA
823 ATTATCACAA
Statistics
Matches: 125, Mismatches: 27, Indels: 20
0.73 0.16 0.12
Matches are distributed among these distances:
20 3 0.02
21 1 0.01
22 98 0.78
23 4 0.03
24 19 0.15
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:754 original size:66 final size:66
Alignment explanation
Indices: 637--768 Score: 160
Period size: 66 Copynumber: 2.0 Consensus size: 66
627 CTTGTCTCTA
* * * * *
637 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTAATGAGGAGGTTATCAAAATTCCATA
1 TGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTAATGAGGAGGTTACCAAAATTCCATA
702 G
66 G
* * *
703 TGTGGTTACCAAAATTTCATATAGA-AGTTATCAAAATTTCAT-AGTATGGTTACCAAAATTTCA
1 TGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTAATGAGGA-GGTTACCAAAATTCCA
766 TAG
64 TAG
769 GATCATGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 3 0.05
66 50 0.89
67 3 0.05
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTAATGAGGAGGTTACCAAAATTCCATA
G
Found at i:799 original size:46 final size:43
Alignment explanation
Indices: 641--815 Score: 156
Period size: 44 Copynumber: 4.0 Consensus size: 43
631 TCTCTATGTG
** * * *
641 GTTATCAAAATTTCATAAG-ATGGTTATTATAATTTAATGAGGAG
1 GTTATCAAAATTTCAT-AGTATGGTTACCAAAATTTCAT-AGGAA
* * *
685 GTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATAGAA
1 GTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATA-GGAA
729 GTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGATCA
1 GTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGA--A
* * ***
774 TGTTATTAAAATTTCTTAGGT-TGGTTATTGAAATTTCATAGG
1 -GTTATCAAAATTTCATA-GTATGGTTACCAAAATTTCATAGG
816 GTGGTTAATT
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
43 5 0.05
44 68 0.62
45 1 0.01
46 33 0.30
47 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGAA
Found at i:991 original size:22 final size:22
Alignment explanation
Indices: 946--1163 Score: 87
Period size: 22 Copynumber: 9.7 Consensus size: 22
936 CATGGGGAAT
* *
946 TTATCAAAATTTTATAATG-TGG
1 TTATCAAAATTTCAT-ATGAAGG
968 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATGAAGG
* *
990 TTAT-AAAAGTCTCAATTTCATAAAGAG
1 TTATCAAAA-TTTC-A--T-ATGAAG-G
* *
1017 -TACCAAAATTTGATA-GAAGG
1 TTATCAAAATTTCATATGAAGG
*
1037 TTATC-AAATCTCATA-G-AGTG
1 TTATCAAAATTTCATATGAAG-G
* * *
1057 ATTATCGAAATTTCATAGAGATTAGA
1 -TTATCAAAATTTCATA-TGA--AGG
* **
1083 TTATCAAAATTT-ATAGGAAAA
1 TTATCAAAATTTCATATGAAGG
**
1104 TTATCAAAATTTCATAGTG-TTG
1 TTATCAAAATTTCATA-TGAAGG
*
1126 TTATCAAAATTTCAAACTG-AGG
1 TTATCAAAATTTCATA-TGAAGG
*
1148 TTATCAAAATTACATA
1 TTATCAAAATTTCATA
1164 ATGTGATTAT
Statistics
Matches: 151, Mismatches: 26, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.01
20 11 0.07
21 32 0.21
22 68 0.45
23 5 0.03
24 4 0.03
25 13 0.09
26 9 0.06
27 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATATGAAGG
Found at i:1173 original size:22 final size:22
Alignment explanation
Indices: 1103--1174 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
1093 TTATAGGAAA
*
1103 ATTATCAAAATTTCATAGTGTTG
1 ATTATCAAAATTTCATAATG-TG
*
1126 -TTATCAAAATTTCA-AACTGAG
1 ATTATCAAAATTTCATAA-TGTG
* *
1147 GTTATCAAAATTACATAATGTG
1 ATTATCAAAATTTCATAATGTG
1169 ATTATC
1 ATTATC
1175 TGAATTACGA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
ATTATCAAAATTTCATAATGTG
Found at i:2309 original size:31 final size:31
Alignment explanation
Indices: 2274--2345 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2264 TAAGTTATTG
*
2274 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA
* ** *
2305 CAAATGATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAAAAAAATGAAAGCATTAAATTAAA
2336 CAAATTAAAA
1 CAAATTAAAA
2346 GCTGATAGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGCATTAAATTAAA
Found at i:9519 original size:18 final size:18
Alignment explanation
Indices: 9472--9520 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
9462 TTGGGACATG
* * *
9472 ATCGAGAGCGTGAGCGTT
1 ATCGAGAACGTGACCATT
* *
9490 ATCGTGATCGTGACCATT
1 ATCGAGAACGTGACCATT
9508 ATCGAGAACGTGA
1 ATCGAGAACGTGA
9521 TCGCCATCGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (18 bp):
ATCGAGAACGTGACCATT
Found at i:9576 original size:24 final size:24
Alignment explanation
Indices: 9526--9580 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
9516 CGTGATCGCC
*
9526 ATCGTGATTACGATCATGACCGTG
1 ATCGTGATTACGATCATGACCGGG
* * **
9550 ATCGTGATTATGATCGTGATTGGG
1 ATCGTGATTACGATCATGACCGGG
9574 ATCGTGA
1 ATCGTGA
9581 CCGGGATCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.33
Consensus pattern (24 bp):
ATCGTGATTACGATCATGACCGGG
Found at i:9586 original size:12 final size:12
Alignment explanation
Indices: 9561--9595 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9551 TCGTGATTAT
**
9561 GATCGTGATTGG
1 GATCGTGACCGG
9573 GATCGTGACCGG
1 GATCGTGACCGG
9585 GATCGTGACCG
1 GATCGTGACCG
9596 AGAGAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.40, T:0.23
Consensus pattern (12 bp):
GATCGTGACCGG
Found at i:14169 original size:6 final size:6
Alignment explanation
Indices: 14160--14186 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
14150 CCAGCAAAAT
14160 AATTAG AATTAG AATTAG AATTAG AAT
1 AATTAG AATTAG AATTAG AATTAG AAT
14187 CAGCCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
AATTAG
Found at i:16844 original size:25 final size:25
Alignment explanation
Indices: 16810--16914 Score: 138
Period size: 25 Copynumber: 4.0 Consensus size: 25
16800 ACCGTAATGT
16810 ACCAACTATTATCTTGCAAAAGTGA
1 ACCAACTATTATCTTGCAAAAGTGA
*
16835 ACCAACTATTATCTTACAAAAGTGA
1 ACCAACTATTATCTTGCAAAAGTGA
* *
16860 ACTATTATTGCTATTATCTTGTAAAAGTGA
1 ACCA--A---CTATTATCTTGCAAAAGTGA
16890 ACCAACTATTATCTTGCAAAAGTGA
1 ACCAACTATTATCTTGCAAAAGTGA
16915 GCATGAGATT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
25 46 0.67
27 1 0.01
28 1 0.01
30 21 0.30
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (25 bp):
ACCAACTATTATCTTGCAAAAGTGA
Found at i:17083 original size:24 final size:24
Alignment explanation
Indices: 17056--17103 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
17046 CCCACCATAT
*
17056 TCCACAAACCAAATGCCTTAAGAA
1 TCCACAAACCAAACGCCTTAAGAA
*
17080 TCCACGAACCAAACGCCTTAAGAA
1 TCCACAAACCAAACGCCTTAAGAA
17104 CAGACTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15
Consensus pattern (24 bp):
TCCACAAACCAAACGCCTTAAGAA
Found at i:18683 original size:2 final size:2
Alignment explanation
Indices: 18676--18713 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18666 TTGTTCCTAG
18676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18714 TCTCTATCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24358 original size:2 final size:2
Alignment explanation
Indices: 24351--24377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24341 ATTTTAGAAT
24351 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
24378 TATGTATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:24395 original size:2 final size:2
Alignment explanation
Indices: 24390--24414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24380 TGTATATATG
24390 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
24415 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:24419 original size:2 final size:2
Alignment explanation
Indices: 24414--24439 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24404 TCTCTCTCTC
24414 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
24440 CGAGTTTTTA
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:26821 original size:6 final size:6
Alignment explanation
Indices: 26810--26835 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26800 GCTCTCACTC
26810 CCCAAA CCCAAA CCCAAA CCCAAA CC
1 CCCAAA CCCAAA CCCAAA CCCAAA CC
26836 AGTCTGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.54, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:26849 original size:6 final size:6
Alignment explanation
Indices: 26840--26872 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
26830 CAAACCAGTC
26840 TGGTTA TGGTTA TGGTTA TGGTTA TGGTTA TGG
1 TGGTTA TGGTTA TGGTTA TGGTTA TGGTTA TGG
26873 CTATTGGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
TGGTTA
Found at i:28545 original size:6 final size:6
Alignment explanation
Indices: 28529--28587 Score: 93
Period size: 6 Copynumber: 10.0 Consensus size: 6
28519 TTTTTGTTGA
* *
28529 TGGGTT CGGGTT TGGGTT TGGGTT TGGGTT TTGGTT TGGGTT TGGGTT
1 TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT
28577 TGGG-T TGGGTT
1 TGGGTT TGGGTT
28588 GGGGATGTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.10
6 43 0.90
ACGTcount: A:0.00, C:0.02, G:0.49, T:0.49
Consensus pattern (6 bp):
TGGGTT
Found at i:35157 original size:30 final size:31
Alignment explanation
Indices: 35121--35192 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
35111 GGCGAAAATG
** *
35121 TAATTCAGGATACATTATTAT-GATTTGTGT
1 TAATTCAGGATACAACATTATCGAGTTGTGT
* * *
35151 TAATTCATGAAATAACATTATCGAGTTGTGT
1 TAATTCAGGATACAACATTATCGAGTTGTGT
35182 TAATTCAGGAT
1 TAATTCAGGAT
35193 GAAATCAGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (31 bp):
TAATTCAGGATACAACATTATCGAGTTGTGT
Found at i:36638 original size:31 final size:31
Alignment explanation
Indices: 36600--36673 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
36590 CGTAATCGTG
36600 TATCCTGAATTGCATTTTCACCCAAACGTTA
1 TATCCTGAATTGCATTTTCACCCAAACGTTA
36631 TATCCTGAATTGCATTTTCACCCAAACGTTA
1 TATCCTGAATTGCATTTTCACCCAAACGTTA
36662 TATCCTGAATTG
1 TATCCTGAATTG
36674 AGCATTTAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (31 bp):
TATCCTGAATTGCATTTTCACCCAAACGTTA
Found at i:49231 original size:2 final size:2
Alignment explanation
Indices: 49226--49255 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49216 TCATTTTGAA
49226 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
49256 GAGATGTTCA
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:50775 original size:1 final size:1
Alignment explanation
Indices: 50769--50800 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
50759 AAGCAGGTGG
50769 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
50801 GATTTGAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:56749 original size:16 final size:16
Alignment explanation
Indices: 56728--56761 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56718 GGGTATTGTT
56728 TTGACTATTCCTCCTG
1 TTGACTATTCCTCCTG
56744 TTGACTATTCCTCCTG
1 TTGACTATTCCTCCTG
56760 TT
1 TT
56762 CATAATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.29, G:0.12, T:0.47
Consensus pattern (16 bp):
TTGACTATTCCTCCTG
Found at i:59482 original size:2 final size:2
Alignment explanation
Indices: 59475--59509 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
59465 CACAAGCGAG
59475 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59510 ATAATATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59757 original size:13 final size:14
Alignment explanation
Indices: 59741--59769 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
59731 TTGTATAATA
59741 TACTACTA-TTATT
1 TACTACTACTTATT
59754 TACTACTACTTATT
1 TACTACTACTTATT
59768 TA
1 TA
59770 GTTCATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (14 bp):
TACTACTACTTATT
Found at i:61128 original size:6 final size:6
Alignment explanation
Indices: 61119--61148 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
61109 AAATGAAGGT
*
61119 GACGGA GACGGA GATGGA GACGGA GACGGA
1 GACGGA GACGGA GACGGA GACGGA GACGGA
61149 CGCTGGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.50, T:0.03
Consensus pattern (6 bp):
GACGGA
Found at i:62407 original size:29 final size:29
Alignment explanation
Indices: 62370--62429 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
62360 AGTTGACAAG
62370 TATCATCACCAACCAATGAATTCAAAGTT
1 TATCATCACCAACCAATGAATTCAAAGTT
62399 TATCATCACCAACCAATGAATTCAAAGTT
1 TATCATCACCAACCAATGAATTCAAAGTT
62428 TA
1 TA
62430 AAAGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (29 bp):
TATCATCACCAACCAATGAATTCAAAGTT
Found at i:72544 original size:38 final size:38
Alignment explanation
Indices: 72483--72555 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
72473 GAGCCTTAAA
* ** *
72483 ACTAGCTCTTCTGGAGCTTTCAATCAAATTTGCACAAT
1 ACTAACTCTTCTGGAGCCATCAATCAAAATTGCACAAT
72521 ACTAACTCTTCTGGAGCCATCAATCAAAATTGCAC
1 ACTAACTCTTCTGGAGCCATCAATCAAAATTGCAC
72556 TACCCGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (38 bp):
ACTAACTCTTCTGGAGCCATCAATCAAAATTGCACAAT
Found at i:73953 original size:25 final size:23
Alignment explanation
Indices: 73911--73958 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
73901 ATCGTTTCCG
* *
73911 TTTTTTTGTTTTTTTGTTTTTGT
1 TTTTTTTGTTTTTGTGTTGTTGT
73934 TTTTGTTTCGTTTTTGTGTTGTTGT
1 TTTT-TTT-GTTTTTGTGTTGTTGT
73959 CAAATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 14 0.67
ACGTcount: A:0.00, C:0.02, G:0.19, T:0.79
Consensus pattern (23 bp):
TTTTTTTGTTTTTGTGTTGTTGT
Found at i:80805 original size:18 final size:18
Alignment explanation
Indices: 80770--80805 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
80760 GGCCCCGCCC
* *
80770 ATTTTATATAGTATATAT
1 ATTTTATATAATACATAT
80788 ATTTTATATAATACATAT
1 ATTTTATATAATACATAT
80806 CTTTAACTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTTATATAATACATAT
Found at i:85162 original size:33 final size:34
Alignment explanation
Indices: 85072--85339 Score: 321
Period size: 33 Copynumber: 7.9 Consensus size: 34
85062 TTTTTAGATC
*
85072 AAGTTCTT-TTATTCTACTTAATTACCCTGAATT
1 AAGTTCTTATTACTCTACTTAATTACCCTGAATT
** ***
85105 AAGCCACTTATTAACTCTACTTAATTAGATTGAATT
1 AAG-TTCTTATT-ACTCTACTTAATTACCCTGAATT
*
85141 AAGTTCTT-TTATTCTACTTAATTACCCTGAATT
1 AAGTTCTTATTACTCTACTTAATTACCCTGAATT
*
85174 AAGTGCTTATTAGCTCTACTTAATTACCCTGAATT
1 AAGTTCTTATTA-CTCTACTTAATTACCCTGAATT
** *
85209 AAGCCACTTATTAACTCTACTTAATTACACTGAATT
1 AAG-TTCTTATT-ACTCTACTTAATTACCCTGAATT
*
85245 AAGTTCTT-TTATTCTACTTAATTACCCTGAATT
1 AAGTTCTTATTACTCTACTTAATTACCCTGAATT
*
85278 AAGTGCTTATTAACTCTACTTAATTACCCTGAATT
1 AAGTTCTTATT-ACTCTACTTAATTACCCTGAATT
*
85313 AAGTTCTT-TTATTCTACTTAATT-CCCT
1 AAGTTCTTATTACTCTACTTAATTACCCT
85340 TCCCTGAAAT
Statistics
Matches: 201, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
32 4 0.02
33 69 0.34
34 14 0.07
35 61 0.30
36 52 0.26
37 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (34 bp):
AAGTTCTTATTACTCTACTTAATTACCCTGAATT
Found at i:85205 original size:104 final size:104
Alignment explanation
Indices: 85084--85315 Score: 437
Period size: 104 Copynumber: 2.2 Consensus size: 104
85074 GTTCTTTTAT
* *
85084 TCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTAGATTGAATTAAGTTCTT
1 TCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACACTGAATTAAGTTCTT
*
85149 TTATTCTACTTAATTACCCTGAATTAAGTGCTTATTAGC
66 TTATTCTACTTAATTACCCTGAATTAAGTGCTTATTAAC
85188 TCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACACTGAATTAAGTTCTT
1 TCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACACTGAATTAAGTTCTT
85253 TTATTCTACTTAATTACCCTGAATTAAGTGCTTATTAAC
66 TTATTCTACTTAATTACCCTGAATTAAGTGCTTATTAAC
85292 TCTACTTAATTACCCTGAATTAAG
1 TCTACTTAATTACCCTGAATTAAG
85316 TTCTTTTATT
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 125 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.41
Consensus pattern (104 bp):
TCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTACACTGAATTAAGTTCTT
TTATTCTACTTAATTACCCTGAATTAAGTGCTTATTAAC
Found at i:85310 original size:68 final size:69
Alignment explanation
Indices: 85084--85339 Score: 324
Period size: 68 Copynumber: 3.7 Consensus size: 69
85074 GTTCTTTTAT
** *** *
85084 TCTACTTAATTACCCTGAATTAAGCCACTTATTAACTCTACTTAATTAGATTGAATTAAGTTCTT
1 TCTACTTAATTACCCTGAATTAAG-TTCTTATT-ACTCTACTTAATTACCCTGAATTAAGTACTT
*
85149 -TT-AT
64 ATTAAC
* *
85153 TCTACTTAATTACCCTGAATTAAGTGCTTATTAGCTCTACTTAATTACCCTGAATTAAGCCACTT
1 TCTACTTAATTACCCTGAATTAAGTTCTTATTA-CTCTACTTAATTACCCTGAATTAAG-TACTT
85218 ATTAAC
64 ATTAAC
* * *
85224 TCTACTTAATTACACTGAATTAAGTTCTT-TTATTCTACTTAATTACCCTGAATTAAGTGCTTAT
1 TCTACTTAATTACCCTGAATTAAGTTCTTATTACTCTACTTAATTACCCTGAATTAAGTACTTAT
85288 TAAC
66 TAAC
*
85292 TCTACTTAATTACCCTGAATTAAGTTCTT-TTATTCTACTTAATT-CCCT
1 TCTACTTAATTACCCTGAATTAAGTTCTTATTACTCTACTTAATTACCCT
85340 TCCCTGAAAT
Statistics
Matches: 169, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
67 5 0.03
68 80 0.47
69 51 0.30
70 5 0.03
71 28 0.17
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (69 bp):
TCTACTTAATTACCCTGAATTAAGTTCTTATTACTCTACTTAATTACCCTGAATTAAGTACTTAT
TAAC
Found at i:85418 original size:39 final size:39
Alignment explanation
Indices: 85362--85648 Score: 389
Period size: 39 Copynumber: 7.6 Consensus size: 39
85352 AGCCTGTGCC
*
85362 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAACTTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
* *
85401 TTAGTCTTTCATTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
* * *
85440 TCAGTCTATCTTCACCTAATTTCCCTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
* *
85479 TCAGTCTATCTTTACCTAATTTCCTTCTTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
85518 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
*
85553 TCAGTC-TTCTTTTACTTAA--T--TTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTCCTTGAAATTAAG
85588 TCAGTC-TTCTTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTCCTTGAAATTAAG
85627 TCA-TACTTTCTTTACCTAATTT
1 TCAGT-CTTTCTTTACCTAATTT
85649 AAGTCAGTCT
Statistics
Matches: 226, Mismatches: 15, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
34 3 0.01
35 62 0.27
37 2 0.01
38 1 0.00
39 155 0.69
40 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (39 bp):
TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
Found at i:85425 original size:35 final size:35
Alignment explanation
Indices: 85362--86155 Score: 870
Period size: 35 Copynumber: 22.2 Consensus size: 35
85352 AGCCTGTGCC
*
85362 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAACTTAAG
1 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAG
* *
85401 TTAGTCTTTCATTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAG
* *
85440 TCAGTCTATCTTCACCTAATTTCCCTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAA-TT---TCCTTGAAATTAAG
*
85479 TCAGTCTATCTTTACCTAATTTCCTTCTTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTT-C--C-TTGAAATTAAG
85518 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
*
85553 TCAGTC-TTCTTTTACTTAATTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTGAAATTAAG
85588 TCAGTC-TTCTTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAA--T--TTCCTTGAAATTAAG
85627 TCA-TACTTTCTTTACCTAA------T----TTAAG
1 TCAGT-CTTTCTTTACCTAATTTCCTTGAAATTAAG
85652 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAG
85691 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
85726 TCAGTC-TTCTTTTACCTAATTTCCTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAA--T--TTCCTTGAAATTAAG
85765 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
85800 TCAGT-TTTCTTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTGAAATTAAG
*
85835 TCAGTCTATCTTTACCTAATTTCCTTCTTCGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTT-C--CTT-GAAATTAAG
85874 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
85909 TCAGTCTTTCTTTACCTAATTTCCTTCTTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTT-C--C-TTGAAATTAAG
*
85948 TCAGTCTTTCTTTACCTAATTTCTTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
85983 TCAGTC-TTCTTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTGAAATTAAG
* * *
86018 TAAGTCTATCTTCACCTAA-----TT-AAATT-AG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
*
86046 TC--T-TCT-TTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
*
86077 TCAGTC-TTCTTTTACCTAATTTCTTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTGAAATTAAG
86112 TCAGTCTTTCTTTTACCTAATTTCCTTGAAATTAAG
1 TCAGTCTTTC-TTTACCTAATTTCCTTGAAATTAAG
86148 TCAGTCTT
1 TCAGTCTT
86156 ATTTTGTTCT
Statistics
Matches: 671, Mismatches: 24, Indels: 123
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.01
25 24 0.04
26 2 0.00
28 3 0.00
29 8 0.01
30 7 0.01
31 4 0.01
33 2 0.00
34 13 0.02
35 268 0.40
36 49 0.07
37 4 0.01
38 13 0.02
39 260 0.39
40 6 0.01
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (35 bp):
TCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAG
Found at i:85650 original size:25 final size:25
Alignment explanation
Indices: 85622--85673 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
85612 TTCCTTGAAA
85622 TTAAGTCA-TACTTTCTTTACCTAAT
1 TTAAGTCAGT-CTTTCTTTACCTAAT
85647 TTAAGTCAGTCTTTCTTTACCTAAT
1 TTAAGTCAGTCTTTCTTTACCTAAT
85672 TT
1 TT
85674 CCTTCCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (25 bp):
TTAAGTCAGTCTTTCTTTACCTAAT
Found at i:85740 original size:74 final size:74
Alignment explanation
Indices: 85362--86038 Score: 824
Period size: 74 Copynumber: 9.3 Consensus size: 74
85352 AGCCTGTGCC
* * *
85362 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAACTTAAGTTAGTCTTTCATTACCTAATTTCCTT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAA--T--TT
85427 CCTTGAAATTAAG
62 CCTTGAAATTAAG
* * * *
85440 TCAGTCTATCTTCACCTAATTTCCCTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCTT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTT-C--
85505 CTTTGAAATTAAG
63 C-TTGAAATTAAG
*
85518 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAGTCAGTC-TTCTTTTACTTAATTTCCT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTC-TTTACCTAATTTCCT
85578 TGAAATTAAG
65 TGAAATTAAG
85588 TCAGTC-TTCTTTTACCTAATTTCCTTCCTTGAAATTAAGTCA-TACTTTCTTTACCTAA-----
1 TCAGTCTTTC-TTTACCTAATTTCCTTCCTTGAAATTAAGTCAGT-CTTTCTTTACCTAATTTCC
85646 -T----TTAAG
64 TTGAAATTAAG
85652 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCTT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCTT
85717 GAAATTAAG
66 GAAATTAAG
85726 TCAGTC-TTCTTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCT
1 TCAGTCTTTC-TTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCT
85790 TGAAATTAAG
65 TGAAATTAAG
*
85800 TCAGT-TTTCTTTTACCTAA--T--TTCCTTGAAATTAAGTCAGTCTATCTTTACCTAATTTCCT
1 TCAGTCTTTC-TTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTT-C-
85860 TCTTCGAAATTAAG
63 -CTT-GAAATTAAG
85874 TCAGTCTTTCTTTACCTAA--T--TTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCTT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTT-C--
85935 CTTTGAAATTAAG
63 C-TTGAAATTAAG
85948 TCAGTCTTTCTTTACCTAATTT-C-T--TTGAAATTAAGTCAGTC-TTCTTTTACCTAATTTCCT
1 TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTC-TTTACCTAATTTCCT
86008 TGAAATTAAG
65 TGAAATTAAG
* * *
86018 TAAGTCTATCTTCACCTAATT
1 TCAGTCTTTCTTTACCTAATT
86039 AAATTAGTCT
Statistics
Matches: 545, Mismatches: 18, Indels: 80
0.85 0.03 0.12
Matches are distributed among these distances:
64 57 0.10
65 4 0.01
68 1 0.00
69 3 0.01
70 92 0.17
71 3 0.01
72 2 0.00
73 14 0.03
74 275 0.50
75 10 0.02
76 4 0.01
77 1 0.00
78 79 0.14
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (74 bp):
TCAGTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCAGTCTTTCTTTACCTAATTTCCTT
GAAATTAAG
Found at i:86047 original size:24 final size:24
Alignment explanation
Indices: 86011--86062 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
86001 ATTTCCTTGA
*
86011 AATTAAGTAAGTCTATC-TTCACCT
1 AATTAAATAAGTCT-TCTTTCACCT
* *
86035 AATTAAATTAGTCTTCTTTTACCT
1 AATTAAATAAGTCTTCTTTCACCT
86059 AATT
1 AATT
86063 TCCTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (24 bp):
AATTAAATAAGTCTTCTTTCACCT
Found at i:86049 original size:59 final size:59
Alignment explanation
Indices: 85976--86097 Score: 192
Period size: 59 Copynumber: 2.1 Consensus size: 59
85966 ATTTCTTTGA
*
85976 AATTAAGTCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGTAAGTCTATC-TTCACCT
1 AATTAAATCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGTAAGTCT-TCTTTCACCT
* * *
86035 AATTAAATTAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGTCAGTCTTCTTTTACCT
1 AATTAAATCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGTAAGTCTTCTTTCACCT
86094 AATT
1 AATT
86098 TCTTTGAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 2 0.03
59 56 0.97
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (59 bp):
AATTAAATCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGTAAGTCTTCTTTCACCT
Found at i:86057 original size:94 final size:95
Alignment explanation
Indices: 85941--86133 Score: 300
Period size: 94 Copynumber: 2.0 Consensus size: 95
85931 CCTTCTTTGA
* *
85941 AATTAAGTCAGTCTTTCTTTACCTAATTTCTTTGAAATTAAGTCAGTCTTCTTTTACCTAATTTC
1 AATTAAATCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAATTTC
86006 CTTGAAATTAAGTAAGTCTATC-TTCACCT
66 CTTGAAATTAAGTAAGTCTATCTTTCACCT
*
86035 AATTAAATTAGTC-TTCTTTTACCTAATTTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAATTT
1 AATTAAATCAGTCTTTC-TTTACCTAATTTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAATTT
* * * *
86099 CTTTGAAATTAAGTCAGTCTTTCTTTTACCT
65 CCTTGAAATTAAGTAAGTCTATCTTTCACCT
86130 AATT
1 AATT
86134 TCCTTGAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
93 3 0.03
94 77 0.86
95 10 0.11
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (95 bp):
AATTAAATCAGTCTTTCTTTACCTAATTTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAATTTC
CTTGAAATTAAGTAAGTCTATCTTTCACCT
Found at i:86394 original size:41 final size:41
Alignment explanation
Indices: 86286--86445 Score: 149
Period size: 41 Copynumber: 3.9 Consensus size: 41
86276 TATGCATACT
* * * *
86286 TTTCTTAATTATCCTAAATTAAAACCTTAACTGTGTCTGAC
1 TTTCTTAATTACCCTAAATTAAGACTTTAACTGTGTTTGAC
* * * *
86327 TATCCTAATTACCCTGAATTAGGACTTTAACTGTGTTTGAC
1 TTTCTTAATTACCCTAAATTAAGACTTTAACTGTGTTTGAC
* * * * ***
86368 TTTCTTAATTACCCTAAATTAAGACTTTGATTATATTTTTT
1 TTTCTTAATTACCCTAAATTAAGACTTTAACTGTGTTTGAC
* * * *
86409 TTTCTTAATTACCTTGAATTAAGACTTTGACTCTGTT
1 TTTCTTAATTACCCTAAATTAAGACTTTAACTGTGTT
86446 ACTTAATCAT
Statistics
Matches: 95, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (41 bp):
TTTCTTAATTACCCTAAATTAAGACTTTAACTGTGTTTGAC
Found at i:89612 original size:26 final size:25
Alignment explanation
Indices: 89577--89646 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 25
89567 CCAACAAACT
*
89577 ATGACCAAAATGCCCCTGAAGCAAAA
1 ATGACAAAAATGCCCCTG-AGCAAAA
* * *
89603 ATGACTAAAATACCCCTTGGGCAAAA
1 ATGACAAAAATGCCCC-TGAGCAAAA
89629 ATGACAAAAATGCCCCTG
1 ATGACAAAAATGCCCCTG
89647 GTATTTCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 2 0.05
26 34 0.89
27 2 0.05
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.16
Consensus pattern (25 bp):
ATGACAAAAATGCCCCTGAGCAAAA
Found at i:92754 original size:19 final size:18
Alignment explanation
Indices: 92721--92756 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
92711 TTGAAATAAT
92721 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
92739 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
92757 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:95713 original size:31 final size:31
Alignment explanation
Indices: 95675--95737 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
95665 TTTTGAAAAA
95675 AAGTAACCAAGAAAAATGGAAGATTTCAGAG
1 AAGTAACCAAGAAAAATGGAAGATTTCAGAG
95706 AAGTAACCAAGAAAAATGGAAGATTTCAGAG
1 AAGTAACCAAGAAAAATGGAAGATTTCAGAG
95737 A
1 A
95738 GAGAGAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.16
Consensus pattern (31 bp):
AAGTAACCAAGAAAAATGGAAGATTTCAGAG
Found at i:98404 original size:27 final size:27
Alignment explanation
Indices: 98374--98425 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
98364 AAATGGACCC
*
98374 AAAATTACCAAAATGCCCCTGAATGCG
1 AAAATGACCAAAATGCCCCTGAATGCG
*
98401 AAAATGACCAAAATGTCCCTGAATG
1 AAAATGACCAAAATGCCCCTGAATG
98426 ACCCTAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCG
Found at i:103179 original size:24 final size:23
Alignment explanation
Indices: 103152--103243 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 23
103142 GAAAGTCAAA
*
103152 GAGCAGCAGAAAAAGAAAAAGAGT
1 GAGCAACAGAAAAAGAAAAA-AGT
* *
103176 GAGCAACAGCAGAAGAAGAAAAGT
1 GAGCAACAGAAAAAGAA-AAAAGT
*
103200 GAGCAACA-ACAGAAGAAACAAAGT
1 GAGCAACAGA-AAAAGAAA-AAAGT
103224 GAGCAACAGGAAAAAGAAAA
1 GAGCAACA-GAAAAAGAAAA
103244 GACTGTTGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.02
24 46 0.79
25 10 0.17
26 1 0.02
ACGTcount: A:0.59, C:0.12, G:0.26, T:0.03
Consensus pattern (23 bp):
GAGCAACAGAAAAAGAAAAAAGT
Found at i:103189 original size:21 final size:23
Alignment explanation
Indices: 103164--103232 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 23
103154 GCAGCAGAAA
103164 AAGAAAAAGAGTGAGCAACAGCAG
1 AAGAAAAA-AGTGAGCAACAGCAG
*
103188 AAGAAGAAAAGTGAGCAACAACAG
1 AAGAA-AAAAGTGAGCAACAGCAG
103212 AAGAAACAAAGTGAGCAACAG
1 AAGAAA-AAAGTGAGCAACAG
103233 GAAAAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.02
24 37 0.90
25 3 0.07
ACGTcount: A:0.57, C:0.13, G:0.26, T:0.04
Consensus pattern (23 bp):
AAGAAAAAAGTGAGCAACAGCAG
Found at i:106440 original size:131 final size:131
Alignment explanation
Indices: 106206--106465 Score: 421
Period size: 131 Copynumber: 2.0 Consensus size: 131
106196 CCTTCATATT
* * * *
106206 GAACAAGAAACATACAAATTCGAAAGTGAGGTATGTCATCTTGAGAGAATGGAAAATAATTGCCA
1 GAACAAGAAACATACAAAATCAAAAGTGAGGCATGTCATCTGGAGAGAATGGAAAATAATTGCCA
* * *
106271 TGCGTGAGGCAGTCAGCATATTTTATCACAAAAAGGCCACAATCTACACCGCTGTATATATATTC
66 TGCGTGAGGCAATCAACATATTTTATCACAAAAAGGCCACAATATACACCGCTGTATATATATTC
106336 A
131 A
* *
106337 GAACAAGAAACGTACAAAATCAAAAGTGAGGCATGTCATCTGGAGAGAATGGAAAATAATTTCCA
1 GAACAAGAAACATACAAAATCAAAAGTGAGGCATGTCATCTGGAGAGAATGGAAAATAATTGCCA
* *
106402 TGTGTGAGGCAATCAACATATTTTATCACAAAAAGGCCACAATATACACCGCTGTGTATATATT
66 TGCGTGAGGCAATCAACATATTTTATCACAAAAAGGCCACAATATACACCGCTGTATATATATT
106466 TGTCCACGAG
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 118 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (131 bp):
GAACAAGAAACATACAAAATCAAAAGTGAGGCATGTCATCTGGAGAGAATGGAAAATAATTGCCA
TGCGTGAGGCAATCAACATATTTTATCACAAAAAGGCCACAATATACACCGCTGTATATATATTC
A
Found at i:108082 original size:24 final size:24
Alignment explanation
Indices: 108054--108101 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
108044 GAAATCGTTT
108054 CCAAGCTCCTCCATCCGGAAATGC
1 CCAAGCTCCTCCATCCGGAAATGC
108078 CCAAGCTCCTCCATCCGGAAATGC
1 CCAAGCTCCTCCATCCGGAAATGC
108102 AACCATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.17, T:0.17
Consensus pattern (24 bp):
CCAAGCTCCTCCATCCGGAAATGC
Found at i:110093 original size:30 final size:30
Alignment explanation
Indices: 110057--110115 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
110047 CATATCATAT
110057 TTGTGTTGCTTAACAACAAAATTAAGTAAA
1 TTGTGTTGCTTAACAACAAAATTAAGTAAA
110087 TTGTGTTGCTTAACAACAAAATTAAGTAA
1 TTGTGTTGCTTAACAACAAAATTAAGTAA
110116 GTGTTTGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (30 bp):
TTGTGTTGCTTAACAACAAAATTAAGTAAA
Found at i:113449 original size:71 final size:71
Alignment explanation
Indices: 113372--113551 Score: 299
Period size: 70 Copynumber: 2.5 Consensus size: 71
113362 ATGCATTAAG
*
113372 CAAACACAGTCAAAGTCTTGATTTGGTAATTAAGAAAAAGCAAAGTCTTAATTCAGGGTAATTAA
1 CAAACACAGTCAAAGTCTTAATTTGGTAATTAAGAAAAAGCAAAGTCTTAATTCAGGGTAATTAA
113437 GAAAAA
66 GAAAAA
113443 CAAACACAGTCAAAGTCTTAATTTGGTAATTAAG-AAAAGCAAAGTCTTAATTCAGGGTAATTAA
1 CAAACACAGTCAAAGTCTTAATTTGGTAATTAAGAAAAAGCAAAGTCTTAATTCAGGGTAATTAA
**
113507 GAAAGT
66 GAAAAA
*
113513 CAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAA
1 CAAACACAGTCAAAGTCTTAATT--TGGTAATTAAGAAA
113552 GTTAAACACA
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
70 56 0.55
71 33 0.32
72 11 0.11
73 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.27
Consensus pattern (71 bp):
CAAACACAGTCAAAGTCTTAATTTGGTAATTAAGAAAAAGCAAAGTCTTAATTCAGGGTAATTAA
GAAAAA
Found at i:113486 original size:29 final size:30
Alignment explanation
Indices: 113453--113510 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
113443 CAAACACAGT
*
113453 CAAAGTCTTAATT-TGGTAATTAAGAAAAG
1 CAAAGTCTTAATTAGGGTAATTAAGAAAAG
113482 CAAAGTCTTAATTCAGGGTAATTAAGAAA
1 CAAAGTCTTAATT-AGGGTAATTAAGAAA
113511 GTCAAACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (30 bp):
CAAAGTCTTAATTAGGGTAATTAAGAAAAG
Found at i:113528 original size:41 final size:41
Alignment explanation
Indices: 113482--113676 Score: 196
Period size: 41 Copynumber: 4.7 Consensus size: 41
113472 TTAAGAAAAG
113482 CAAAGTCTTAATTCAGGGTAATTAAGAAAGTCAAACACAGT
1 CAAAGTCTTAATTCAGGGTAATTAAGAAAGTCAAACACAGT
* * *
113523 TAAAGTCTTAATTCATGGTAATTAAGAAAGTTAAACACAGT
1 CAAAGTCTTAATTCAGGGTAATTAAGAAAGTCAAACACAGT
* * * * *
113564 CAGAGTCCTAATTCAGGATAATTAAGAAGAG-CATATACAGT
1 CAAAGTCTTAATTCAGGGTAATTAAGAA-AGTCAAACACAGT
* * * *
113605 CAAGGTCTTAATTCATGGAAATTAAGGAAAAAT-AAACACAGT
1 CAAAGTCTTAATTCAGGGTAATTAA-G-AAAGTCAAACACAGT
* * * **
113647 TAAGGTATTAATTCACAGTAATTAAGAAAG
1 CAAAGTCTTAATTCAGGGTAATTAAGAAAG
113677 GTGATCACAA
Statistics
Matches: 124, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
40 3 0.02
41 88 0.71
42 31 0.25
43 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (41 bp):
CAAAGTCTTAATTCAGGGTAATTAAGAAAGTCAAACACAGT
Found at i:113628 original size:82 final size:83
Alignment explanation
Indices: 113485--113646 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 83
113475 AGAAAAGCAA
* * * *
113485 AGTCTTAATTCAGGGTAATTAAGAAAGTCAAACACAGTTAAAGTCTTAATTCATGGTAATTAA-G
1 AGTCCTAATTCAGGATAATTAAGAAAGTCAAACACAGTCAAAGTCTTAATTCATGGAAATTAAGG
**
113549 AAAGTTAAACACAGTCAG
66 AAAAATAAACACAGTCAG
* * *
113567 AGTCCTAATTCAGGATAATTAAGAAGAG-CATATACAGTCAAGGTCTTAATTCATGGAAATTAAG
1 AGTCCTAATTCAGGATAATTAAGAA-AGTCAAACACAGTCAAAGTCTTAATTCATGGAAATTAAG
113631 GAAAAATAAACACAGT
65 GAAAAATAAACACAGT
113647 TAAGGTATTA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 53 0.77
83 16 0.23
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (83 bp):
AGTCCTAATTCAGGATAATTAAGAAAGTCAAACACAGTCAAAGTCTTAATTCATGGAAATTAAGG
AAAAATAAACACAGTCAG
Found at i:114229 original size:41 final size:41
Alignment explanation
Indices: 113721--114215 Score: 672
Period size: 41 Copynumber: 12.0 Consensus size: 41
113711 AAAAACAGTA
**
113721 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* * * *
113762 AAGTACAGACTTAATTTAAAGGAAGGAAATTAAGTAAAGTC
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* *
113803 AAGCACAGACTTAATTTCAAGGAAGAAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* *
113844 AAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAGAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
*
113884 ATAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 A-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
*
113926 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* *
113966 ATAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAGGT
1 A-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* *
114008 AAGCACAGACTTAATTTTGAAGGAAGGAAATTAGGTAAAGGT
1 AAGCACAGACTTAA-TTTCAAGGAAGGAAATTAGGTAAAGTT
* *
114050 AAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* * *
114091 AAGCGCAAACTTAATTTCAAGGAAGGAAATTAAGTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* **
114131 ATACCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 A-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
* * * * *
114173 AAGCACATAATTAATTTCAGGGAAGGAAATTAAGTAGAGTT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
114214 AA
1 AA
114216 TAAAGGACTT
Statistics
Matches: 408, Mismatches: 39, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
40 5 0.01
41 362 0.89
42 41 0.10
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTT
Found at i:114242 original size:36 final size:35
Alignment explanation
Indices: 114195--114400 Score: 219
Period size: 36 Copynumber: 5.9 Consensus size: 35
114185 AATTTCAGGG
* * *
114195 AAGGAAATTAAGTAGAGTTAATAAAGGACTTAATTC
1 AAGGTAATTAAGT-GAGTCAATAAAGAACTTAATTC
* **
114231 AGGGTAATTAAGTAGAGTCAATAAAGGGCTTAATTC
1 AAGGTAATTAAGT-GAGTCAATAAAGAACTTAATTC
* *
114267 AGGGTAATTAAGTAGAGTCAATAAATG-GCTTAATTC
1 AAGGTAATTAAGT-GAGTCAATAAA-GAACTTAATTC
114303 AAGGTAATTAAGT-AG--AATAAAGAACTTAATTC
1 AAGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
* *
114335 AACGTAATTAAGTG-G--AATAAAGAATTTAATTC
1 AAGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
*
114367 ATGGTAATTAAGTGTAGTCAATAAAGAACTTAAT
1 AAGGTAATTAAGTG-AGTCAATAAAGAACTTAAT
114401 CTAAAAAGAT
Statistics
Matches: 152, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
31 1 0.01
32 55 0.36
34 3 0.02
36 92 0.61
37 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (35 bp):
AAGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
Found at i:114290 original size:72 final size:70
Alignment explanation
Indices: 114200--114400 Score: 236
Period size: 68 Copynumber: 2.9 Consensus size: 70
114190 CAGGGAAGGA
* **
114200 AATTAAGTAGAGTTAATAAAGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGGGCTTAAT
1 AATTAAGTAGAG-TAATAAAGGACTTAATTCAAGGTAATTAAGT-GAGTCAATAAAGAACTTAAT
**
114265 TCAGGGT
64 TCAACGT
114272 AATTAAGTAGAGTCAATAAATGG-CTTAATTCAAGGTAATTAAGT-AG--AATAAAGAACTTAAT
1 AATTAAGTAGAGT-AATAAA-GGACTTAATTCAAGGTAATTAAGTGAGTCAATAAAGAACTTAAT
114333 TCAACGT
64 TCAACGT
* * *
114340 AATTAAGT-G-G-AATAAAGAATTTAATTCATGGTAATTAAGTGTAGTCAATAAAGAACTTAAT
1 AATTAAGTAGAGTAATAAAGGACTTAATTCAAGGTAATTAAGTG-AGTCAATAAAGAACTTAAT
114401 CTAAAAAGAT
Statistics
Matches: 114, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
63 1 0.01
64 25 0.22
66 3 0.03
67 1 0.01
68 41 0.36
70 2 0.02
71 1 0.01
72 38 0.33
73 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (70 bp):
AATTAAGTAGAGTAATAAAGGACTTAATTCAAGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
AACGT
Found at i:116138 original size:2 final size:2
Alignment explanation
Indices: 116131--116159 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
116121 GTTTTGGACA
116131 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116160 TATTTTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116148 original size:13 final size:13
Alignment explanation
Indices: 116130--116156 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
116120 TGTTTTGGAC
116130 AATATATATATAT
1 AATATATATATAT
116143 AATATATATATAT
1 AATATATATATAT
116156 A
1 A
116157 TATTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:117045 original size:2 final size:2
Alignment explanation
Indices: 117038--117069 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
117028 TAGAATGGTA
117038 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
117070 TAATGGCCTA
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:117951 original size:42 final size:42
Alignment explanation
Indices: 117898--117982 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
117888 AGTTCGGTCT
*
117898 GTCCCGCAATCAATGTCACCTAAGTGGCCTCAATACGGTCAA
1 GTCCCGCAATCAATGTCACATAAGTGGCCTCAATACGGTCAA
* * * *
117940 GTCCCGGAATCAATGTCGCATGAGTGGCCTCAATATGGTCAA
1 GTCCCGCAATCAATGTCACATAAGTGGCCTCAATACGGTCAA
117982 G
1 G
117983 AATACTATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (42 bp):
GTCCCGCAATCAATGTCACATAAGTGGCCTCAATACGGTCAA
Found at i:122555 original size:45 final size:45
Alignment explanation
Indices: 122493--122578 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
122483 TGCATTACCT
* *
122493 AAATTCTACTTCCTCATCTCAAGGTAATTCATCAAAATAAAACTA
1 AAATTATACTTCCTCATCTCAAGGCAATTCATCAAAATAAAACTA
*
122538 AAATTATAC-TCCTTCATCTCTAGGCAATTCATCAAAATAAA
1 AAATTATACTTCC-TCATCTCAAGGCAATTCATCAAAATAAA
122579 GTTAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 3 0.08
45 34 0.92
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (45 bp):
AAATTATACTTCCTCATCTCAAGGCAATTCATCAAAATAAAACTA
Found at i:124991 original size:20 final size:18
Alignment explanation
Indices: 124948--124987 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
124938 AGGGAAAAGC
*
124948 AAAAGCATCAGTCCATGT
1 AAAAGAATCAGTCCATGT
*
124966 AAAAGAATCAGTTCATGT
1 AAAAGAATCAGTCCATGT
124984 AAAA
1 AAAA
124988 AAGATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAAGAATCAGTCCATGT
Found at i:128841 original size:2 final size:2
Alignment explanation
Indices: 128801--128825 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128791 AATACATAGG
128801 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
128826 ACATCACAAT
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:129614 original size:78 final size:78
Alignment explanation
Indices: 129391--129621 Score: 336
Period size: 78 Copynumber: 3.0 Consensus size: 78
129381 ATGAGCAGAA
* * * *
129391 CAATAGAGTTACGAAGCTCGGTTTGTCCCACAATCAATGTCGCCTGAGTGGCCTCAATACGGTCA
1 CAATGGAGTTACGGAGCTCGGTCTGTCCCGCAATCAATGTCGCCTGAGTGGCCTCAATACGGTCA
*
129456 AGACGACTATTGG
66 AGGCGACTATTGG
* * * *
129469 CAATGGAGTTACGGAGCTTGGTCTATCCCGCAATCAATGTCGCCTAAGTAGCCTCAATACGGTCA
1 CAATGGAGTTACGGAGCTCGGTCTGTCCCGCAATCAATGTCGCCTGAGTGGCCTCAATACGGTCA
*
129534 AGGTGACTATTGG
66 AGGCGACTATTGG
* * *
129547 CAATGGAGTTACGGAGCTCGGCCTGTCCCGCAATCAATGTCGCATGAGTGGCCTCAATATGGTCA
1 CAATGGAGTTACGGAGCTCGGTCTGTCCCGCAATCAATGTCGCCTGAGTGGCCTCAATACGGTCA
*
129612 AGGGGACTAT
66 AGGCGACTAT
129622 GTAGATCCGA
Statistics
Matches: 135, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 135 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (78 bp):
CAATGGAGTTACGGAGCTCGGTCTGTCCCGCAATCAATGTCGCCTGAGTGGCCTCAATACGGTCA
AGGCGACTATTGG
Found at i:130329 original size:39 final size:39
Alignment explanation
Indices: 130269--130343 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
130259 GTTGTGTCAA
*
130269 TTCGCCAATGGGGCAGCTTGTGTTTTCTCTGATGTCTGG
1 TTCGCCAATGGGGAAGCTTGTGTTTTCTCTGATGTCTGG
* *
130308 TTCGCCAATTGGGAAGTTTGTGTTTTCTCTGATGTC
1 TTCGCCAATGGGGAAGCTTGTGTTTTCTCTGATGTC
130344 AAGTTCCACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.19, G:0.28, T:0.41
Consensus pattern (39 bp):
TTCGCCAATGGGGAAGCTTGTGTTTTCTCTGATGTCTGG
Found at i:138005 original size:2 final size:2
Alignment explanation
Indices: 137998--138032 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
137988 TTGAAACCTT
137998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
138033 AAAAAACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.