Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 5 of 26
Found at i:1584499 original size:26 final size:26
Alignment explanation
Indices: 1584461--1584600 Score: 86
Period size: 26 Copynumber: 5.1 Consensus size: 26
1584451 ATATTAAAAA
* *
1584461 TTTATAATCAAAATTTTAATTTAATT
1 TTTAAAATTAAAATTTTAATTTAATT
**
1584487 TTTAAAATTAAAATTATTTTTTTTGTAATTT
1 TTTAAAATT-AAA--ATTTTAATT-TAA-TT
1584518 ATAATTAAAATTAAAATTTTAATTTAATT
1 -T--TTAAAATTAAAATTTTAATTTAATT
* * * *
1584547 TTTAAATTTAAAATATTATTTTCACA-A
1 TTTAAAATTAAAATTTTAATTT-A-ATT
* *
1584574 TTT-ATATTAAAATTTTAGTTTAATT
1 TTTAAAATTAAAATTTTAATTTAATT
1584599 TT
1 TT
1584601 GAAAGAGAAG
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
24 1 0.01
25 3 0.03
26 39 0.44
27 7 0.08
28 2 0.02
29 9 0.10
30 6 0.07
31 9 0.10
32 1 0.01
33 3 0.03
34 8 0.09
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTAAAATTAAAATTTTAATTTAATT
Found at i:1584534 original size:60 final size:58
Alignment explanation
Indices: 1584470--1584587 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 58
1584460 ATTTATAATC
* ***
1584470 AAAATTTTAATTTAATTTTTAAAATTAAAATTATTTTTTTTGTAATTTATAATTAAAATT
1 AAAATTTTAATTTAATTTTTAAAATTAAAA-TATTATTTTCACAATTTAT-ATTAAAATT
*
1584530 AAAATTTTAATTTAATTTTTAAATTTAAAATATTATTTTCACAATTTATATTAAAATT
1 AAAATTTTAATTTAATTTTTAAAATTAAAATATTATTTTCACAATTTATATTAAAATT
1584588 TTAGTTTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
58 9 0.17
59 15 0.28
60 29 0.55
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (58 bp):
AAAATTTTAATTTAATTTTTAAAATTAAAATATTATTTTCACAATTTATATTAAAATT
Found at i:1584555 original size:19 final size:20
Alignment explanation
Indices: 1584470--1584552 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
1584460 ATTTATAATC
1584470 AAAATTTTAATTTAATTTTT
1 AAAATTTTAATTTAATTTTT
** **
1584490 AAAATTAAAATTATTTTTTTT
1 AAAATTTTAATT-TAATTTTT
** **
1584511 GTAATTTATAA-TTAA-AATT
1 AAAATTT-TAATTTAATTTTT
1584530 AAAATTTTAATTTAATTTTT
1 AAAATTTTAATTTAATTTTT
1584550 AAA
1 AAA
1584553 TTTAAAATAT
Statistics
Matches: 43, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 16 0.37
21 11 0.26
22 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
AAAATTTTAATTTAATTTTT
Found at i:1585467 original size:22 final size:21
Alignment explanation
Indices: 1585442--1585486 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1585432 ACTAAAATAC
*
1585442 TATTTTTATTAATTTAAAAAAT
1 TATTATTATT-ATTTAAAAAAT
*
1585464 TATTATTATTTTTTAAAAAAT
1 TATTATTATTATTTAAAAAAT
1585485 TA
1 TA
1585487 AACAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTATTATTTAAAAAAT
Found at i:1585804 original size:20 final size:19
Alignment explanation
Indices: 1585783--1585832 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1585773 ATGTTCAATA
1585783 AATAATATTTTTTAAAAAT
1 AATAATATTTTTTAAAAAT
1585802 AA-AATATTTATTTTAAAAATT
1 AATAATA-TT-TTTTAAAAA-T
1585823 AATAA-ATTTT
1 AATAATATTTT
1585833 CGTATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 11 0.41
21 4 0.15
22 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATATTTTTTAAAAAT
Found at i:1588370 original size:3 final size:3
Alignment explanation
Indices: 1588362--1588390 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1588352 TTATATGGCT
1588362 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1588391 TTTCCTCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1600395 original size:21 final size:22
Alignment explanation
Indices: 1600370--1600413 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1600360 AAGTGATTAA
1600370 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1600391 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1600413 T
1 T
1600414 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1604794 original size:27 final size:26
Alignment explanation
Indices: 1604763--1604815 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1604753 ACATTTAAGA
* *
1604763 TAAAACTAAAT-ATTAATAATTTTTTC
1 TAAAAATAAATAAATAAT-ATTTTTTC
*
1604789 TAAAAATACATAAATAATATTTTTTC
1 TAAAAATAAATAAATAATATTTTTTC
1604815 T
1 T
1604816 CTCTCTCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAAAATAAATAAATAATATTTTTTC
Found at i:1607143 original size:15 final size:17
Alignment explanation
Indices: 1607120--1607152 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1607110 ATCCTAAACT
1607120 AACTAAAATTAAA-AAA
1 AACTAAAATTAAATAAA
1607136 AACT-AAATTAAATAAA
1 AACTAAAATTAAATAAA
1607152 A
1 A
1607153 TTGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
AACTAAAATTAAATAAA
Found at i:1607868 original size:11 final size:11
Alignment explanation
Indices: 1607852--1607882 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1607842 TGAGAGTCTT
1607852 AAATTGCAAGG
1 AAATTGCAAGG
1607863 AAATTGCAAGG
1 AAATTGCAAGG
1607874 AAATTGCAA
1 AAATTGCAA
1607883 CAATAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (11 bp):
AAATTGCAAGG
Found at i:1611005 original size:14 final size:13
Alignment explanation
Indices: 1610992--1611047 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
1610982 TTTTTTTAAT
1610992 AATATAAAAATAA
1 AATATAAAAATAA
1611005 TAATAAATAATAAATAA
1 -AAT--ATAA-AAATAA
1611022 AATA-AAAAATAA
1 AATATAAAAATAA
*
1611034 AAAATAAAAA-AA
1 AATATAAAAATAA
1611046 AA
1 AA
1611048 GAAAAACACA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 13 0.35
13 7 0.19
14 4 0.11
16 7 0.19
17 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATATAAAAATAA
Found at i:1611025 original size:19 final size:19
Alignment explanation
Indices: 1610989--1611047 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1610979 ATATTTTTTT
* *
1610989 AATAATATAAAAATAATAATA
1 AATAATA-AATAA-AATAAAA
1611010 AATAATAAATAAAATAAAA
1 AATAATAAATAAAATAAAA
*
1611029 AATAAAAAATAAAA-AAAA
1 AATAATAAATAAAATAAAA
1611047 A
1 A
1611048 GAAAAACACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.14
19 19 0.54
20 4 0.11
21 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (19 bp):
AATAATAAATAAAATAAAA
Found at i:1611041 original size:7 final size:7
Alignment explanation
Indices: 1610992--1611044 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
1610982 TTTTTTTAAT
1610992 AATATAAA
1 AATA-AAA
*
1611000 AAT-AAT
1 AATAAAA
*
1611006 AATAAAT
1 AATAAAA
1611013 AATAAATAA
1 AAT-AA-AA
1611022 AATAAAA
1 AATAAAA
1611029 AATAAAA
1 AATAAAA
1611036 AATAAAA
1 AATAAAA
1611043 AA
1 AA
1611045 AAAGAAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 5 0.12
7 24 0.60
8 7 0.17
9 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AATAAAA
Found at i:1611044 original size:16 final size:17
Alignment explanation
Indices: 1610992--1611053 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1610982 TTTTTTTAAT
*
1610992 AATATAAAAATAATAATA
1 AATA-AAAAATAATAAAA
*
1611010 AATAATAAATAAAATAAAA
1 AATAA-AAA-ATAATAAAA
*
1611029 AATAAAAAATAAAAAAA
1 AATAAAAAATAATAAAA
*
1611046 AAGAAAAA
1 AATAAAAA
1611054 CACAGAGAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 15 0.41
18 10 0.27
19 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.18
Consensus pattern (17 bp):
AATAAAAAATAATAAAA
Found at i:1611052 original size:23 final size:23
Alignment explanation
Indices: 1610989--1611053 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1610979 ATATTTTTTT
* * *
1610989 AATAATATAAAAATAATAATAAAT
1 AATAA-ATAAAAAAAAAAATAAAA
*
1611013 AATAAATAAAATAAAAAATAAAA
1 AATAAATAAAAAAAAAAATAAAA
1611036 AATAAA-AAAAAAGAAAAA
1 AATAAATAAAAAA-AAAAA
1611054 CACAGAGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 5 0.14
23 25 0.71
24 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AATAAATAAAAAAAAAAATAAAA
Found at i:1611726 original size:12 final size:13
Alignment explanation
Indices: 1611703--1611732 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1611693 GGCGGGGAGG
1611703 AAGAAGGAAAAAA
1 AAGAAGGAAAAAA
*
1611716 AAGAAGAAAAAAA
1 AAGAAGGAAAAAA
1611729 AAGA
1 AAGA
1611733 GGAGGACAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAGGAAAAAA
Found at i:1620808 original size:2 final size:2
Alignment explanation
Indices: 1620801--1620829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1620791 AATGATTGCC
1620801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1620830 TCAATTTCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1624964 original size:10 final size:10
Alignment explanation
Indices: 1624949--1624982 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1624939 TATTATGCCT
1624949 AAAAAAAAGA
1 AAAAAAAAGA
*
1624959 AAAAAAAA-T
1 AAAAAAAAGA
1624968 AAAAAAAAGA
1 AAAAAAAAGA
1624978 AAAAA
1 AAAAA
1624983 TAATAAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:1624972 original size:19 final size:19
Alignment explanation
Indices: 1624948--1624990 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1624938 GTATTATGCC
1624948 TAAAAAAAAGAAAAAAAAA
1 TAAAAAAAAGAAAAAAAAA
*
1624967 TAAAAAAAAGAAAAAATAA
1 TAAAAAAAAGAAAAAAAAA
1624986 TAAAA
1 TAAAA
1624991 GCAGAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (19 bp):
TAAAAAAAAGAAAAAAAAA
Found at i:1624990 original size:10 final size:9
Alignment explanation
Indices: 1624948--1624990 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1624938 GTATTATGCC
1624948 TAAAAAAAA
1 TAAAAAAAA
*
1624957 GAAAAAAAAA
1 -TAAAAAAAA
1624967 TAAAAAAAA
1 TAAAAAAAA
*
1624976 GAAAAAATAA
1 TAAAAAA-AA
1624986 TAAAA
1 TAAAA
1624991 GCAGAAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1626031 original size:59 final size:58
Alignment explanation
Indices: 1625935--1626591 Score: 855
Period size: 59 Copynumber: 11.1 Consensus size: 58
1625925 TTGGCATTAG
* * * * *
1625935 AATTTTTGAGTCGAACCTATTTTGAGATAGATTGAGCCTAGATCTAGTCTAGGAATCTT
1 AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAAT-TT
* * * *
1625994 AATTTTTAAGTCGAACTTGTTTTGAGATAGGTCGAGCCTAGATCCAGTCTAGGAATTT
1 AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
*
1626052 CAATTTTTAAGTCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTT
1 -AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAA-TTT
* * *
1626112 AATTTTTAAGTCGAACTTATTTTGAGATAAGTCGAGCCTAGATCAAGTCTAGGAATTT
1 AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
*
1626170 CAATTTCTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
1 -AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
* * * *
1626229 CAACTTTTAAATCGAACCTGTTTTGAGATAGGTTGAGCCTAGATCAAGTCGAGGAATTTT
1 -AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAA-TTT
*
1626289 AATTTTTAAATCGAACCTATTTTGAGATAGGACGAGCCTAGATCAAGTCTAGGAATTT
1 AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
* * *
1626347 ACATTTCTAAATCGAACCTATTTTGAGATAAGTCGAGCGTAGATCAAGTCTAGGAATTTT
1 A-ATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAA-TTT
* * * * * *
1626407 GATTTTTAAGTCGAACCTATTTTGGGATAGGTCGAGCCTAGATCAGGTATAAGAATTT
1 AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
* * * * **
1626465 CAATTTCTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAATCTAAAAATTTT
1 -AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAA-TTT
* * * *
1626525 AATTTTTTAAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATAAAGTCTAAGAATTT
1 AA-TTTTT-AAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
*
1626585 CATTTTT
1 AATTTTT
1626592 TTAAAATCGA
Statistics
Matches: 533, Mismatches: 55, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
58 12 0.02
59 458 0.86
60 20 0.04
61 43 0.08
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (58 bp):
AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTT
Found at i:1627348 original size:28 final size:28
Alignment explanation
Indices: 1627314--1627368 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1627304 AAAAGAGAAG
*
1627314 ACCGATCGACATTGAAG-GAAGAGAAACA
1 ACCGATCGACACTGAAGAGAA-AGAAACA
*
1627342 ACCGATCGACGCTGAAGAGAAAGAAAC
1 ACCGATCGACACTGAAGAGAAAGAAAC
1627369 GAAAAGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.09
Consensus pattern (28 bp):
ACCGATCGACACTGAAGAGAAAGAAACA
Found at i:1627390 original size:12 final size:12
Alignment explanation
Indices: 1627373--1627406 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1627363 AGAAACGAAA
1627373 AGAGAGAAGAGG
1 AGAGAGAAGAGG
*
1627385 AGAGAGAAAAGG
1 AGAGAGAAGAGG
*
1627397 AAAGAGAAGA
1 AGAGAGAAGA
1627407 AGGTGCCGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAGAGAAGAGG
Found at i:1627499 original size:26 final size:26
Alignment explanation
Indices: 1627461--1627521 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
1627451 GAAGGCAGGG
*
1627461 AGGAAGAAGGAAAAAAA-AGAAGAAAA
1 AGGAAGAAAGAAAAAAAGA-AAGAAAA
* *
1627487 AGGAGGAAAGAAAGAAAGAAAGAAAA
1 AGGAAGAAAGAAAAAAAGAAAGAAAA
*
1627513 AAGAA-AAAG
1 AGGAAGAAAG
1627522 TAGAGAGAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.14
26 24 0.83
27 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (26 bp):
AGGAAGAAAGAAAAAAAGAAAGAAAA
Found at i:1638442 original size:47 final size:47
Alignment explanation
Indices: 1638373--1638462 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
1638363 ATTACAATCA
* *
1638373 TACCTGGTCTTAATATAAATCCAAACCCCGAAGCACCCAGGTTACGC
1 TACCTGGTCCTAATATAAATCCAAACCCCAAAGCACCCAGGTTACGC
*
1638420 TACCTGGTCCTAATATAAATCCAAGCCCCAAAGCACCCAGGTT
1 TACCTGGTCCTAATATAAATCCAAACCCCAAAGCACCCAGGTT
1638463 GCCTCACCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.21
Consensus pattern (47 bp):
TACCTGGTCCTAATATAAATCCAAACCCCAAAGCACCCAGGTTACGC
Found at i:1648367 original size:27 final size:26
Alignment explanation
Indices: 1648336--1648388 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1648326 ACATTTAAGA
* *
1648336 TAAAACTAAAT-ATTAATAATTTTTTC
1 TAAAAATAAATAAATAAT-ATTTTTTC
*
1648362 TAAAAATACATAAATAATATTTTTTC
1 TAAAAATAAATAAATAATATTTTTTC
1648388 T
1 T
1648389 CTCTCTCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAAAATAAATAAATAATATTTTTTC
Found at i:1650695 original size:15 final size:16
Alignment explanation
Indices: 1650675--1650706 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1650665 ATCCTAAACT
1650675 AACTAAATTAAA-AAA
1 AACTAAATTAAATAAA
1650690 AACTAAATTAAATAAA
1 AACTAAATTAAATAAA
1650706 A
1 A
1650707 TTGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (16 bp):
AACTAAATTAAATAAA
Found at i:1651417 original size:11 final size:11
Alignment explanation
Indices: 1651401--1651431 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1651391 TGAGAGTCTT
1651401 AAATTGCAAGG
1 AAATTGCAAGG
1651412 AAATTGCAAGG
1 AAATTGCAAGG
1651423 AAATTGCAA
1 AAATTGCAA
1651432 CAATAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (11 bp):
AAATTGCAAGG
Found at i:1669323 original size:14 final size:11
Alignment explanation
Indices: 1669288--1669317 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1669278 TGAGTTTCTT
*
1669288 TTATCCTTTTA
1 TTATTCTTTTA
1669299 TTATTCTTTTA
1 TTATTCTTTTA
1669310 TTATTCTT
1 TTATTCTT
1669318 GATTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTCTTTTA
Found at i:1669821 original size:2 final size:2
Alignment explanation
Indices: 1669814--1669844 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1669804 AATTAAGTTA
*
1669814 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1669845 CAATATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1691250 original size:21 final size:20
Alignment explanation
Indices: 1691226--1691265 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1691216 TTTAGAATAA
*
1691226 AATAACATAAAATTAAACTAC
1 AATAAC-TAAAATCAAACTAC
*
1691247 AATAACTTAAATCAAACTA
1 AATAACTAAAATCAAACTA
1691266 ATGAACATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAACTAAAATCAAACTAC
Found at i:1691951 original size:15 final size:16
Alignment explanation
Indices: 1691931--1691960 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1691921 ATTTCAATCT
1691931 TTTTC-TTTTTCTTTC
1 TTTTCTTTTTTCTTTC
1691946 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
1691961 TTCTCAATTT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTTCTTTC
Found at i:1695773 original size:15 final size:17
Alignment explanation
Indices: 1695755--1695793 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1695745 AATTTCTAAA
*
1695755 AAATTAAT-TAAA-ACT
1 AAATTAATGCAAACACT
1695770 AAATTAATGCAAACACT
1 AAATTAATGCAAACACT
1695787 AAATTAA
1 AAATTAA
1695794 CTAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 3 0.14
17 10 0.48
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (17 bp):
AAATTAATGCAAACACT
Found at i:1696947 original size:21 final size:20
Alignment explanation
Indices: 1696923--1696962 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1696913 TCTAAAACAA
1696923 AATAACATAAAATTAAACTAT
1 AATAAC-TAAAATTAAACTAT
*
1696944 AATAACTTAAATTAAACTA
1 AATAACTAAAATTAAACTA
1696963 ATCAACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAACTAAAATTAAACTAT
Found at i:1699612 original size:13 final size:14
Alignment explanation
Indices: 1699594--1699628 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1699584 AAGAGTTTCC
1699594 AAGAAA-AGCATTA
1 AAGAAACAGCATTA
1699607 AAGAAACTAGCATTA
1 AAGAAAC-AGCATTA
1699622 AAGAAAC
1 AAGAAAC
1699629 TGAAACATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
15 14 0.70
ACGTcount: A:0.60, C:0.11, G:0.14, T:0.14
Consensus pattern (14 bp):
AAGAAACAGCATTA
Found at i:1699620 original size:15 final size:15
Alignment explanation
Indices: 1699600--1699629 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1699590 TTCCAAGAAA
1699600 AGCATTAAAGAAACT
1 AGCATTAAAGAAACT
1699615 AGCATTAAAGAAACT
1 AGCATTAAAGAAACT
1699630 GAAACATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
AGCATTAAAGAAACT
Found at i:1702129 original size:17 final size:16
Alignment explanation
Indices: 1702107--1702143 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1702097 CAGTTGTTGT
*
1702107 TTTTAGTTTTAGTTTAA
1 TTTTAGTTTT-CTTTAA
1702124 TTTTAGTTTTCTTTAA
1 TTTTAGTTTTCTTTAA
1702140 TTTT
1 TTTT
1702144 CAATATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.70
Consensus pattern (16 bp):
TTTTAGTTTTCTTTAA
Found at i:1704974 original size:26 final size:25
Alignment explanation
Indices: 1704945--1704993 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1704935 GAGAAATCAT
*
1704945 GTGGTCACAACCATGTATATCAACTC
1 GTGGTC-CAACCATGTATAACAACTC
* *
1704971 GTGGTCTAGCCATGTATAACAAC
1 GTGGTCCAACCATGTATAACAAC
1704994 CAGTGGCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (25 bp):
GTGGTCCAACCATGTATAACAACTC
Found at i:1705007 original size:25 final size:25
Alignment explanation
Indices: 1704955--1705007 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1704945 GTGGTCACAA
* *
1704955 CCATGTATATCAACTCGTGGTCTAG
1 CCATGTATAACAACTCGTGGCCTAG
*
1704980 CCATGTATAACAAC-CAGTGGCCTTG
1 CCATGTATAACAACTC-GTGGCCTAG
1705005 CCA
1 CCA
1705008 CACATAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (25 bp):
CCATGTATAACAACTCGTGGCCTAG
Found at i:1707960 original size:11 final size:11
Alignment explanation
Indices: 1707941--1707974 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
1707931 TCGATAAAAA
1707941 TAATATTATTT
1 TAATATTATTT
*
1707952 TATTATTATTT
1 TAATATTATTT
1707963 TAATATTATTT
1 TAATATTATTT
1707974 T
1 T
1707975 CTCACCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATATTATTT
Found at i:1710918 original size:28 final size:28
Alignment explanation
Indices: 1710862--1711003 Score: 185
Period size: 28 Copynumber: 4.9 Consensus size: 28
1710852 GTCAACTTTC
1710862 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
1710890 ACATGTTTAGTCTTAATTTAGACAAAAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
*
1710919 ATATGTTTGTCTTAATTTAAGACAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
1710949 ATATTTTTTGTCTTAATCTAGACAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* *
1710978 ACATATTTGTCTCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
1711004 TAATATATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
28 38 0.38
29 37 0.37
30 13 0.13
31 13 0.13
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:1710987 original size:59 final size:57
Alignment explanation
Indices: 1710862--1711023 Score: 207
Period size: 59 Copynumber: 2.8 Consensus size: 57
1710852 GTCAACTTTC
* * * *
1710862 ACATGTTTGTCTTAATTTAGACAAGAAAACATGTTTAGTCTTAATTTAGACAAAAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAATATTTTTTGTCTTAATCTAGACAAAAAA
* *
1710919 ATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAAATATTTTTTGTCTTAATCTAGACAAAAAA
* * * *
1710978 ACATATTTGTCTCAATTTAGACAAGATAATATATTTTTGACTTAAT
1 ACATGTTTGTCTTAATTTAGACAAGAAAATAT-TTTTTGTCTTAAT
1711024 TACAGACAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 23 0.25
58 26 0.29
59 42 0.46
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (57 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAATATTTTTTGTCTTAATCTAGACAAAAAA
Found at i:1713163 original size:19 final size:19
Alignment explanation
Indices: 1713139--1713176 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1713129 AAAAGACATT
*
1713139 AATTAT-CATCATACTTTTA
1 AATTATACA-CATAATTTTA
1713158 AATTATACACATAATTTTA
1 AATTATACACATAATTTTA
1713177 TTCATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATACACATAATTTTA
Found at i:1714074 original size:3 final size:3
Alignment explanation
Indices: 1714059--1714145 Score: 61
Period size: 3 Copynumber: 29.0 Consensus size: 3
1714049 AGGGAATTCT
* * * * *
1714059 GGA GGA GGG GGA GGA GGA GGA GGCA GCA -GC GGA GCA -GA CAGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GG-A GGA GGA GGA GGA GGA -GGA GGA
* * * *
1714104 GGT GGA GGT GGA GGA GGA GGA GGA GGA GGA GAA AGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1714146 AACGACGTGG
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
2 1 0.02
3 58 0.92
4 4 0.06
ACGTcount: A:0.32, C:0.06, G:0.60, T:0.02
Consensus pattern (3 bp):
GGA
Found at i:1715551 original size:88 final size:88
Alignment explanation
Indices: 1715434--1715608 Score: 350
Period size: 88 Copynumber: 2.0 Consensus size: 88
1715424 TTTTCTTGTT
1715434 AATGAAGCTTTTTTTCCATACCTTCAATTCAATGGTTTGTTGTAACTCCAAATTTATCTTTATGA
1 AATGAAGCTTTTTTTCCATACCTTCAATTCAATGGTTTGTTGTAACTCCAAATTTATCTTTATGA
1715499 GAATGATATCAGCTCTTCCAATA
66 GAATGATATCAGCTCTTCCAATA
1715522 AATGAAGCTTTTTTTCCATACCTTCAATTCAATGGTTTGTTGTAACTCCAAATTTATCTTTATGA
1 AATGAAGCTTTTTTTCCATACCTTCAATTCAATGGTTTGTTGTAACTCCAAATTTATCTTTATGA
1715587 GAATGATATCAGCTCTTCCAAT
66 GAATGATATCAGCTCTTCCAAT
1715609 TCAATATTTG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (88 bp):
AATGAAGCTTTTTTTCCATACCTTCAATTCAATGGTTTGTTGTAACTCCAAATTTATCTTTATGA
GAATGATATCAGCTCTTCCAATA
Found at i:1722705 original size:15 final size:15
Alignment explanation
Indices: 1722682--1722722 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1722672 TTTTCTAATG
1722682 TAATATGATTATAAA
1 TAATATGATTATAAA
*
1722697 TAATGTGATTATAAA
1 TAATATGATTATAAA
*
1722712 TAATATTATTA
1 TAATATGATTA
1722723 CAAAGAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (15 bp):
TAATATGATTATAAA
Found at i:1722956 original size:33 final size:32
Alignment explanation
Indices: 1722887--1722970 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
1722877 TTTTAATACC
*
1722887 ATATTTTATTTTTATTTCTTAGTATAACCTTAT
1 ATATTTTA-TTTTATTTCTTAATATAACCTTAT
** *
1722920 ATATTTTATTTTCATTTCTTAATATAAGTTTCT
1 ATATTTTATTTT-ATTTCTTAATATAACCTTAT
1722953 ATATTATCTATTTTATTT
1 ATATT-T-TATTTTATTT
1722971 TAATTTCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
32 4 0.09
33 29 0.66
34 5 0.11
35 6 0.14
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (32 bp):
ATATTTTATTTTATTTCTTAATATAACCTTAT
Found at i:1730447 original size:15 final size:15
Alignment explanation
Indices: 1730427--1730456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1730417 GCAATGAGTC
1730427 TCACCAACTCAGTGA
1 TCACCAACTCAGTGA
*
1730442 TCACCAACTCTGTGA
1 TCACCAACTCAGTGA
1730457 ATAGGACGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.23
Consensus pattern (15 bp):
TCACCAACTCAGTGA
Found at i:1731299 original size:15 final size:16
Alignment explanation
Indices: 1731279--1731308 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1731269 AACCTTTTTT
1731279 TGTAAAA-CTTTGCAA
1 TGTAAAACCTTTGCAA
1731294 TGTAAAACCTTTGCA
1 TGTAAAACCTTTGCA
1731309 TGAGGCTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (16 bp):
TGTAAAACCTTTGCAA
Found at i:1732379 original size:24 final size:21
Alignment explanation
Indices: 1732332--1732376 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1732322 ACCTTCCTTC
1732332 CTTTCTCTCTTTTCTTTCTTT
1 CTTTCTCTCTTTTCTTTCTTT
*
1732353 CTTTCCTCTCTTTTCTCT-TTT
1 CTTT-CTCTCTTTTCTTTCTTT
1732374 CTT
1 CTT
1732377 CTTGGTTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
CTTTCTCTCTTTTCTTTCTTT
Found at i:1737667 original size:15 final size:15
Alignment explanation
Indices: 1737644--1737673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1737634 AAGTGATCAT
*
1737644 GGAGGTGAGTTTGAA
1 GGAGATGAGTTTGAA
1737659 GGAGATGAGTTTGAA
1 GGAGATGAGTTTGAA
1737674 AACTTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (15 bp):
GGAGATGAGTTTGAA
Found at i:1743157 original size:73 final size:74
Alignment explanation
Indices: 1743055--1743221 Score: 221
Period size: 73 Copynumber: 2.3 Consensus size: 74
1743045 GACCAAAAGA
* * * * * *
1743055 CATTGTTAGTCGACTAAGAGCTTAATGCCAAAAACTATGTTTAGAGATAGAAATGACTTAATTAA
1 CATTGTTAGTCGACTAAGAGCTCAATGCCAAAAACTAGGTTCAAAGATAGAAAGGACTTAATCAA
1743120 CTAAGAAG-
66 CTAAGAAGC
* * * * *
1743128 CATTGTTAGTCAACTAAGAGCTCATTGCCAAAAATTGGGTTCAAAGATAGAAAGGACTTAATCGA
1 CATTGTTAGTCGACTAAGAGCTCAATGCCAAAAACTAGGTTCAAAGATAGAAAGGACTTAATCAA
1743193 CTAAGAAGC
66 CTAAGAAGC
1743202 CA-TGTTAGTCGACTAAGAGC
1 CATTGTTAGTCGACTAAGAGC
1743222 ATTCTATATG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 79 0.98
74 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (74 bp):
CATTGTTAGTCGACTAAGAGCTCAATGCCAAAAACTAGGTTCAAAGATAGAAAGGACTTAATCAA
CTAAGAAGC
Found at i:1750380 original size:2 final size:2
Alignment explanation
Indices: 1750373--1750397 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1750363 GAGAACAAGT
1750373 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1750398 GATTATATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1758044 original size:16 final size:17
Alignment explanation
Indices: 1758012--1758044 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1758002 TGAACTTAAA
*
1758012 AAAGGTTGTATCTTGAT
1 AAAGGTTGTACCTTGAT
1758029 AAAGGTTGT-CCTTGAT
1 AAAGGTTGTACCTTGAT
1758045 CCAGCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.39
Consensus pattern (17 bp):
AAAGGTTGTACCTTGAT
Found at i:1761024 original size:20 final size:20
Alignment explanation
Indices: 1760995--1761035 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1760985 CCATTGACAA
*
1760995 CATCGTCCTCACCCACAACT
1 CATCGGCCTCACCCACAACT
*
1761015 CATCGGCCTCACCCATAACT
1 CATCGGCCTCACCCACAACT
1761035 C
1 C
1761036 TATAAGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.49, G:0.07, T:0.20
Consensus pattern (20 bp):
CATCGGCCTCACCCACAACT
Found at i:1761315 original size:79 final size:79
Alignment explanation
Indices: 1761154--1761318 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
1761144 GAACATTTTT
*
1761154 ATAAATCATCATCATGCTTAACCCATAGTGCATATGAATATTTCAACACATACATCTCATGGCAT
1 ATAAATCATCATCATGCTTAACCCATAGTGCACATGAATATTTCAACACATACATCTCATGG-AT
* *
1761219 GTATTTCATAATAAC
65 GTATGTCACAATAAC
* * * *
1761234 ATAAATCATTCA-CATGCTT-AGCCATAGTGTACATG-ATATTCTCAATACATGCATCTCATGG-
1 ATAAATCA-TCATCATGCTTAACCCATAGTGCACATGAATATT-TCAACACATACATCTCATGGA
*
1761295 TGTACATGTCACAATCAC
64 TGT--ATGTCACAATAAC
1761313 ATAAAT
1 ATAAAT
1761319 GGAACTCATG
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
77 3 0.04
78 5 0.07
79 47 0.64
80 15 0.21
81 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (79 bp):
ATAAATCATCATCATGCTTAACCCATAGTGCACATGAATATTTCAACACATACATCTCATGGATG
TATGTCACAATAAC
Found at i:1762196 original size:21 final size:21
Alignment explanation
Indices: 1762172--1762239 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
1762162 AATTGTATTC
*
1762172 ATACATTATGAACATGTATCA
1 ATACATTATGAACATGTATCG
* ** * *
1762193 ATACATGA-CCATATGTATTG
1 ATACATTATGAACATGTATCG
*
1762213 ATACATTATGAACATGCATCG
1 ATACATTATGAACATGTATCG
1762234 ATACAT
1 ATACAT
1762240 CTGAAACATA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (21 bp):
ATACATTATGAACATGTATCG
Found at i:1769465 original size:29 final size:29
Alignment explanation
Indices: 1769426--1769725 Score: 331
Period size: 29 Copynumber: 10.4 Consensus size: 29
1769416 CTTTTACATA
1769426 TTTGTCTTAATTTAGACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* * * **
1769455 TATGTGTTAATGTAGACAAGAAAGTATG-
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* *
1769483 TTTGTCTTAATTTGGACAAGAAAACATTT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* *
1769512 TTTATCTTAATTT-GAACAATAAAACATG-
1 TTTGTCTTAATTTAG-ACAAGAAAACATGT
*** *
1769540 TTCACCTTAATCTAGACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
*
1769569 TTTGTCTTAATTTACACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* *
1769598 TTTGTCTCAATTTAAACAAGAAAACATG-
1 TTTGTCTTAATTTAGACAAGAAAACATGT
*
1769626 TTTGTCTTAATTTAAGACAAGAACAATATGT
1 TTTGTCTTAATTT-AGACAAGAA-AACATGT
* * *
1769657 TTTGTCTTAATCTGGATAAGAAAACATG-
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* * *
1769685 CTTGTTTTAATTTAGACAAGATAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
1769714 TTTGTCTTAATT
1 TTTGTCTTAATT
1769726 AAAATAATGC
Statistics
Matches: 222, Mismatches: 41, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
28 78 0.35
29 120 0.54
30 12 0.05
31 12 0.05
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (29 bp):
TTTGTCTTAATTTAGACAAGAAAACATGT
Found at i:1769490 original size:57 final size:57
Alignment explanation
Indices: 1769426--1769725 Score: 327
Period size: 57 Copynumber: 5.2 Consensus size: 57
1769416 CTTTTACATA
* * **
1769426 TTTGTCTTAATTTAGACAAGAAAACATGTTATGTGTTAATGTAGACAAGAAAGTATG-
1 TTTGTCTTAATTTAGACAAGAAAACATGTT-TGTCTTAATTTAGACAAGAAAACATGT
* * * *
1769483 TTTGTCTTAATTTGGACAAGAAAACATTTTTTATCTTAATTT-GAACAATAAAACATG-
1 TTTGTCTTAATTTAGACAAGAAAACA-TGTTTGTCTTAATTTAG-ACAAGAAAACATGT
*** * *
1769540 TTCACCTTAATCTAGACAAGAAAACATGTTTTGTCTTAATTTACACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATG-TTTGTCTTAATTTAGACAAGAAAACATGT
* * *
1769598 TTTGTCTCAATTTAAACAAGAAAACATGTTTGTCTTAATTTAAGACAAGAACAATATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTT-AGACAAGAA-AACATGT
* * * * * *
1769657 TTTGTCTTAATCTGGATAAGAAAACATGCTTGTTTTAATTTAGACAAGATAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGACAAGAAAACATGT
1769714 TTTGTCTTAATT
1 TTTGTCTTAATT
1769726 AAAATAATGC
Statistics
Matches: 201, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
56 2 0.01
57 118 0.59
58 41 0.20
59 40 0.20
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (57 bp):
TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGACAAGAAAACATGT
Found at i:1769575 original size:86 final size:86
Alignment explanation
Indices: 1769434--1769714 Score: 284
Period size: 86 Copynumber: 3.3 Consensus size: 86
1769424 TATTTGTCTT
* ** * *
1769434 AATTTAGACAAGAAAACATGTT-ATGTGTTAATGTAGACAAGAAAGTATG-TTTGTCTTAATTTG
1 AATTTAAACAAGAAAACATGTTCA--CCTTAATCTAGACAAGAAAATATGTTTTGTCTTAATTTG
* *
1769497 GACAAGAAAACATTTTTTATCTT
64 GACAAGAAAACATGTTTTATCTC
* * * **
1769520 AATTTGAACAATAAAACATGTTCACCTTAATCTAGACAAGAAAACATGTTTTGTCTTAATTTACA
1 AATTTAAACAAGAAAACATGTTCACCTTAATCTAGACAAGAAAATATGTTTTGTCTTAATTTGGA
*
1769585 CAAGAAAACATGTTTTGTCTC
66 CAAGAAAACATGTTTTATCTC
*** * *
1769606 AATTTAAACAAGAAAACATGTTTGTCTTAATTTAAGACAAGAACAATATGTTTTGTCTTAATCTG
1 AATTTAAACAAGAAAACATGTTCACCTTAATCT-AGACAAGAA-AATATGTTTTGTCTTAATTTG
*
1769671 GATAAGAAAACATGCTTGTT-T-T-
64 GACAAGAAAACATG-TT-TTATCTC
* *
1769693 AATTTAGACAAGATAACATGTT
1 AATTTAAACAAGAAAACATGTT
1769715 TTGTCTTAAT
Statistics
Matches: 163, Mismatches: 26, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
85 19 0.12
86 78 0.48
87 30 0.18
88 31 0.19
89 3 0.02
90 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (86 bp):
AATTTAAACAAGAAAACATGTTCACCTTAATCTAGACAAGAAAATATGTTTTGTCTTAATTTGGA
CAAGAAAACATGTTTTATCTC
Found at i:1783531 original size:5 final size:5
Alignment explanation
Indices: 1783521--1783616 Score: 52
Period size: 5 Copynumber: 18.4 Consensus size: 5
1783511 ATATTATAAT
* *
1783521 TAAAA TAAAA T-ATA TAATA TAAGAA TAAAAA TTAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAA-AA T-AAAA -TAAAA TAAAA TAAAA
* * ** * *
1783568 TATAA -AAAT TATATT TATAAA TATAGA TAAAA TAAAT TAAAA TAAAA
1 TAAAA TAAAA TA-AAA TA-AAA TA-AAA TAAAA TAAAA TAAAA TAAAA
1783615 TA
1 TA
1783617 TATAATATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
4 5 0.07
5 44 0.60
6 21 0.29
7 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (5 bp):
TAAAA
Found at i:1783551 original size:26 final size:27
Alignment explanation
Indices: 1783507--1783578 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
1783497 AAAAATATTT
* * *
1783507 TATAATATTATAATTAAAA-TAAAATA
1 TATAATATAAGAATAAAAATTAAAATA
1783533 TATAATATAAGAATAAAAATTAAAATA
1 TATAATATAAGAATAAAAATTAAAATA
1783560 -A-AATA-AA-ATATAAAAATTA
1 TATAATATAAGA-ATAAAAATTA
1783579 TATTTATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 12 0.29
25 4 0.10
26 17 0.41
27 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (27 bp):
TATAATATAAGAATAAAAATTAAAATA
Found at i:1783652 original size:54 final size:52
Alignment explanation
Indices: 1783549--1783652 Score: 138
Period size: 54 Copynumber: 2.0 Consensus size: 52
1783539 ATAAGAATAA
* * * *
1783549 AAATTAAAATAAAATAAAATATAAAAATTATATTTATAAATATAGATAAAAT
1 AAATTAAAATAAAATAAAATATAAAAAATATATTAAGAAATATAAATAAAAT
1783601 AAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAATA-AAATAAA
1 AAATTAAAATAAAATA-A-AATATAAAAAATATATT-AAGAAATATAAATAAA
1783653 TATATAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 16 0.36
53 1 0.02
54 22 0.49
55 6 0.13
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (52 bp):
AAATTAAAATAAAATAAAATATAAAAAATATATTAAGAAATATAAATAAAAT
Found at i:1783661 original size:52 final size:49
Alignment explanation
Indices: 1783539--1783661 Score: 122
Period size: 54 Copynumber: 2.4 Consensus size: 49
1783529 AATATATAAT
* * * *
1783539 ATAAGAATAAAAAT-TAAAATAAAATAAAATATAAAAATTATATTTATAA
1 ATAA-AATAAATATATAAAATAAAATAAAATATAAAAAATATATTAAGAA
* *
1783588 ATATAGATAAAATAAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAA
1 ATA-AAAT-AAATATA-TAAAATAAAATA-A-AATATAAAAAATATATT-AAGAA
1783643 ATAAAATAAATATATAAAA
1 ATAAAATAAATATATAAAA
1783662 ATTATAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
49 5 0.08
50 5 0.08
52 17 0.29
53 7 0.12
54 19 0.32
55 6 0.10
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (49 bp):
ATAAAATAAATATATAAAATAAAATAAAATATAAAAAATATATTAAGAA
Found at i:1783687 original size:33 final size:33
Alignment explanation
Indices: 1783607--1783688 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
1783597 AAATAAATTA
* *
1783607 AAATAAAATATATAATATAAAAAATATATTAAAG
1 AAATAAAATAAAT-ATATAAAAAATATAATAAAG
* *
1783641 AAATAAAATAAATATATAAAAATTATAAT-AAT
1 AAATAAAATAAATATATAAAAAATATAATAAAG
1783673 AAATAAAATCAAATAT
1 AAATAAAAT-AAATAT
1783689 TGACATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 11 0.26
33 20 0.47
34 12 0.28
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (33 bp):
AAATAAAATAAATATATAAAAAATATAATAAAG
Found at i:1783712 original size:81 final size:85
Alignment explanation
Indices: 1783516--1783882 Score: 241
Period size: 87 Copynumber: 4.3 Consensus size: 85
1783506 TTATAATATT
*
1783516 ATAATTAAAATAAAATATATAATATAAGAATAA-AAATT--A-AAATAAAATAAAATATAAAAAT
1 ATAATTAAAATAAAATATATAATATAA-AA-AATATATTAAAGAAATAAAATAAAATATAAAAAT
* * *
1783577 TATATTTATAAATATAGATAAA
64 TATAATAATAAATATAAATAAA
1783599 ATAAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAATAAAATAAATATATAAAAAT
1 AT-AATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAATAAAATAAA-ATATAAAAAT
*
1783664 TATAATAATAAATA-AAATCAA
64 TATAATAATAAATATAAATAAA
* * * *
1783685 AT-ATTGACATTAAAA-ATAT-ATTTAAAATATGATATTATATA-AAATTAATAATATAAATATA
1 ATAATT-AAAATAAAATATATAATATAAAAAAT-ATATTA-A-AGAAA-TAA-AATA-AAATATA
1783746 AATATATTA-AA-AATAAATATAAAATATTATA
59 AA-A-ATTATAATAATAAATAT-AAATA--A-A
* * * * * ** **
1783777 ATAATAAATAAATAAAATATATGACAT-TAAAATATATT-TA-AAATATGATATTATATAAAAAT
1 ATAAT-TA-AAATAAAATATATAATATAAAAAATATATTAAAGAAATAAAATAAAATATAAAAAT
1783839 TAATAAT-ATAAATATAAAT---
64 T-ATAATAATAAATATAAATAAA
*
1783858 AT-ATTAAAAATAAAATATAAAATAT
1 ATAATT-AAAATAAAATATATAATAT
1783883 TATAATAATA
Statistics
Matches: 229, Mismatches: 26, Indels: 62
0.72 0.08 0.20
Matches are distributed among these distances:
79 15 0.07
80 3 0.01
81 2 0.01
82 2 0.01
83 17 0.07
84 38 0.17
85 12 0.05
86 26 0.11
87 47 0.21
88 22 0.10
89 11 0.05
90 2 0.01
91 5 0.02
92 3 0.01
93 3 0.01
94 11 0.05
95 8 0.03
96 2 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (85 bp):
ATAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAATAAAATAAAATATAAAAATTA
TAATAATAAATATAAATAAA
Found at i:1783802 original size:109 final size:111
Alignment explanation
Indices: 1783645--1784192 Score: 874
Period size: 110 Copynumber: 5.0 Consensus size: 111
1783635 TTAAAGAAAT
* *
1783645 AAAATAAATATATAAAAATTATAATAATAAATAAAATCAAATAT-TGACATTAAAAATATATTTA
1 AAAATAAATATA-AAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
1783709 AAATATGATATTATAT-AAAATTAATAATATAAATATAAATATATTA
65 AAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1783755 AAAATAAATATAAAATATTATAATAATAAAT-AAATAAAATATATGACATT-AAAATATATTTAA
1 AAAATAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAA
1783818 AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
66 AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
*
1783864 AAAATAAAATATAAAATATTATAATAATAAATAAAA-AATATATATGACATTAAAAATATATTT-
1 AAAAT-AAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
*
1783927 AAATATGATATTATATAAAAATTAAT-ATATAAATGTAAATATATTA
65 AAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1783973 AAAATAAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
1 AAAAT-AAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
*
1784038 AGAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
65 A-AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
* *
1784085 AAAATAAA-ATATAAATA-TATAATAATAAATAAAATAAAATATATGATATT-AAAATATTTTTA
1 AAAATAAATATA-AAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
1784147 AGAA-ATGAT-TT-TATAAAAATTAATAATA-AAATATAAATATATTA
65 A-AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1784191 AA
1 AA
1784193 CTTATATTTT
Statistics
Matches: 419, Mismatches: 9, Indels: 24
0.93 0.02 0.05
Matches are distributed among these distances:
106 18 0.04
107 17 0.04
108 40 0.10
109 135 0.32
110 139 0.33
111 45 0.11
112 25 0.06
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (111 bp):
AAAATAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAA
AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
Found at i:1783914 original size:219 final size:222
Alignment explanation
Indices: 1783645--1784192 Score: 883
Period size: 219 Copynumber: 2.5 Consensus size: 222
1783635 TTAAAGAAAT
1783645 AAAATAAATATATAAAA-ATTATAATAATAAATAAAATCAAATAT-TGACATTAAAAATATATTT
1 AAAATAAA-ATATAAAATATTATAATAATAAATAAAAT-AAATATATGACATTAAAAATATATTT
1783708 AAAATATGATATTATATAAAATTAATAATATAAATATAAATATATTAAAAAT-AAATATAAAATA
64 AAAATATGATATTATATAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATA
1783772 TTATAATAATAAAT-AAATAAAATATATGACATT-AAAATATATTTAA-AATATGATATTATATA
129 TTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAA-ATGATATTATATA
*
1783834 AAAATTAATAATATAAATATAAATATATTA
193 AAAATTAATAATAAAAATATAAATATATTA
1783864 AAAATAAAATATAAAATATTATAATAATAAATAAAA-AATATATATGACATTAAAAATATATTT-
1 AAAATAAAATATAAAATATTATAATAATAAATAAAATAA-ATATATGACATTAAAAATATATTTA
*
1783927 AAATATGATATTATATAAAAATTAAT-ATATAAATGTAAATATATTAAAAATAAAATATAAAATA
65 AAATATGATATTATAT-AAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATA
1783991 TTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAA
129 TTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAA
1784056 AAATTAATAATAAAAATATAAATATATTA
194 AAATTAATAATAAAAATATAAATATATTA
* *
1784085 AAAATAAAATAT-AAATA-TATAATAATAAATAAAATAAAATATATGATATT-AAAATATTTTTA
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAT-AAATATATGACATTAAAAATATATTTA
*
1784147 AGAA-ATGATTTTATA-AAAATTAATAATA-AAATATAAATATATTAAA
65 A-AATATGATATTATATAAAATTAATAATATAAATATAAATATATTAAA
1784193 CTTATATTTT
Statistics
Matches: 310, Mismatches: 6, Indels: 27
0.90 0.02 0.08
Matches are distributed among these distances:
217 2 0.01
218 78 0.25
219 111 0.36
220 46 0.15
221 71 0.23
222 2 0.01
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (222 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAATAAATATATGACATTAAAAATATATTTAA
AATATGATATTATATAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATATT
ATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAA
ATTAATAATAAAAATATAAATATATTA
Found at i:1783917 original size:110 final size:111
Alignment explanation
Indices: 1783645--1784192 Score: 869
Period size: 109 Copynumber: 5.0 Consensus size: 111
1783635 TTAAAGAAAT
1783645 AAAATAAATATATAAAA-ATTATAATAATAAATAAAATCAAATAT-TGACATTAAAAATATATTT
1 AAAATAAA-ATATAAAATATTATAATAATAAATAAAAT-AAATATATGACATTAAAAATATATTT
1783708 AAAATATGATATTATAT-AAAATTAATAATATAAATATAAATATATTA
64 AAAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1783755 AAAAT-AAATATAAAATATTATAATAATAAAT-AAATAAAATATATGACATT-AAAATATATTTA
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAT-AAATATATGACATTAAAAATATATTTA
1783817 AAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
65 AAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1783864 AAAATAAAATATAAAATATTATAATAATAAATAAAA-AATATATATGACATTAAAAATATATTT-
1 AAAATAAAATATAAAATATTATAATAATAAATAAAATAA-ATATATGACATTAAAAATATATTTA
*
1783927 AAATATGATATTATATAAAAATTAAT-ATATAAATGTAAATATATTA
65 AAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1783973 AAAATAAAATATAAAATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAT-AAATATATGACATTAAAAATATATTTA
*
1784038 AGAA-ATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
65 A-AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
* *
1784085 AAAATAAAATAT-AAATA-TATAATAATAAATAAAATAAAATATATGATATT-AAAATATTTTTA
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAT-AAATATATGACATTAAAAATATATTTA
1784147 AGAA-ATGAT-TT-TATAAAAATTAATAATA-AAATATAAATATATTA
65 A-AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1784191 AA
1 AA
1784193 CTTATATTTT
Statistics
Matches: 420, Mismatches: 6, Indels: 28
0.93 0.01 0.06
Matches are distributed among these distances:
106 18 0.04
107 17 0.04
108 48 0.11
109 136 0.32
110 125 0.30
111 44 0.10
112 32 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (111 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAATAAATATATGACATTAAAAATATATTTAA
AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
Found at i:1784124 original size:24 final size:24
Alignment explanation
Indices: 1784052--1784137 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
1784042 ATGATATTAT
*
1784052 ATAAAA-AT-TAATAATAAA-AAT
1 ATAAAATATATAATAATAAATAAA
1784073 AT-AAATATAT--TAA-AAATAAA
1 ATAAAATATATAATAATAAATAAA
1784093 ATATAAATATATAATAATAAATAAA
1 ATA-AAATATATAATAATAAATAAA
* *
1784118 ATAAAATATATGATATTAAA
1 ATAAAATATATAATAATAAA
1784138 ATATTTTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.06
20 10 0.19
21 4 0.07
22 9 0.17
24 18 0.33
25 10 0.19
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (24 bp):
ATAAAATATATAATAATAAATAAA
Found at i:1789399 original size:26 final size:26
Alignment explanation
Indices: 1789370--1789426 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1789360 ATACAGAGCC
1789370 AAATTAAGACACTTGCTTAATGAACT
1 AAATTAAGACACTTGCTTAATGAACT
1789396 AAATTAAGACACTTGCTTAATGAACT
1 AAATTAAGACACTTGCTTAATGAACT
*
1789422 TAATT
1 AAATT
1789427 TGATTGATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (26 bp):
AAATTAAGACACTTGCTTAATGAACT
Found at i:1794321 original size:11 final size:11
Alignment explanation
Indices: 1794305--1794330 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1794295 GGTCCTTGAA
1794305 GCAATACAAAT
1 GCAATACAAAT
1794316 GCAATACAAAT
1 GCAATACAAAT
1794327 GCAA
1 GCAA
1794331 GCACATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (11 bp):
GCAATACAAAT
Found at i:1806747 original size:23 final size:23
Alignment explanation
Indices: 1806717--1806769 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1806707 TGGACTTTGT
1806717 CTTGATCACAAACTTCGCCGTCG
1 CTTGATCACAAACTTCGCCGTCG
* *
1806740 CTTGATCACGAACTTCGCCGTTG
1 CTTGATCACAAACTTCGCCGTCG
1806763 CTTGATC
1 CTTGATC
1806770 TTCACCCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (23 bp):
CTTGATCACAAACTTCGCCGTCG
Found at i:1806849 original size:18 final size:18
Alignment explanation
Indices: 1806806--1806849 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1806796 TTGATCTTTG
1806806 AAATGC-TCTCAATCTTC
1 AAATGCTTCTCAATCTTC
* *
1806823 GAATACTTCTCAATCTTC
1 AAATGCTTCTCAATCTTC
1806841 AAATGCTTC
1 AAATGCTTC
1806850 CGAATGAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (18 bp):
AAATGCTTCTCAATCTTC
Found at i:1807263 original size:80 final size:80
Alignment explanation
Indices: 1807090--1807348 Score: 326
Period size: 80 Copynumber: 3.2 Consensus size: 80
1807080 AATTATATTT
* * * * ** ** *
1807090 TTATCTCTAAATTAATAT-AATTA-TTAGAGATAATTTAAATGACCAATAATTAA-ATTTTAATT
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAGCTAATA-TTTGATT
* *
1807152 GGTCGAAAATATGAAGA
65 GGTC-AAAATATAAATA
*
1807169 TTATCTCCAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAGCTAATATTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAGCTAATATTTGATTG
1807234 GTCAAAATATAAATA
66 GTCAAAATATAAATA
* *
1807249 TTATCTCTAAATTATTTTGATTTGTTTAGAGATTAATTGGATGACCAATAGCTAATATTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAGCTAATATTTGATTG
* *
1807314 GTCCAGATATAAATA
66 GTCAAAATATAAATA
*
1807329 TTATCTTTAAATTATTTTGA
1 TTATCTCTAAATTATTTTGA
1807349 GAGATAAATA
Statistics
Matches: 159, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
79 15 0.09
80 108 0.68
81 35 0.22
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.42
Consensus pattern (80 bp):
TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAGCTAATATTTGATTG
GTCAAAATATAAATA
Found at i:1807792 original size:23 final size:23
Alignment explanation
Indices: 1807762--1807805 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1807752 ATTGGTATTG
1807762 CATTCCTTAATTAACTAGGATAA
1 CATTCCTTAATTAACTAGGATAA
1807785 CATTCCTTAATTAACTAGGAT
1 CATTCCTTAATTAACTAGGAT
1807806 TCTCCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
CATTCCTTAATTAACTAGGATAA
Found at i:1808341 original size:23 final size:23
Alignment explanation
Indices: 1808292--1808344 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1808282 TGGAGTTTGT
* **
1808292 CTTGATCACGAACTTCGCTGTCA
1 CTTGATCACGAACTTCACCATCA
**
1808315 CTTGATCACGAACTTCACCATTG
1 CTTGATCACGAACTTCACCATCA
1808338 CTTGATC
1 CTTGATC
1808345 TTCACCTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (23 bp):
CTTGATCACGAACTTCACCATCA
Found at i:1808408 original size:18 final size:18
Alignment explanation
Indices: 1808381--1808425 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1808371 TTGATCTCTG
1808381 AAATGC-TCTCAATCTTC
1 AAATGCTTCTCAATCTTC
*
1808398 GAATGCTTCTCAATCTTC
1 AAATGCTTCTCAATCTTC
1808416 AAATGCTTCT
1 AAATGCTTCT
1808426 GAATGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (18 bp):
AAATGCTTCTCAATCTTC
Found at i:1808821 original size:42 final size:42
Alignment explanation
Indices: 1808775--1808902 Score: 122
Period size: 42 Copynumber: 3.1 Consensus size: 42
1808765 TTATTTAGAG
*
1808775 ATAAATTGGATGACCAATAGCTAATATTTGATTGGTCAAAAT
1 ATAAATTGGATGACTAATAGCTAATATTTGATTGGTCAAAAT
* ** * * ** * *
1808817 ATAAATAT-TATCTCTAA-A--TTAT-TTTGATTTGTTTAGAG
1 ATAAAT-TGGATGACTAATAGCTAATATTTGATTGGTCAAAAT
1808855 ATAAATTGGATGACTAATAGCTAATATTTGATTGGTCAAAAT
1 ATAAATTGGATGACTAATAGCTAATATTTGATTGGTCAAAAT
1808897 ATAAAT
1 ATAAAT
1808903 ATTATCTCTA
Statistics
Matches: 61, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
37 1 0.02
38 23 0.38
39 4 0.07
41 4 0.07
42 28 0.46
43 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (42 bp):
ATAAATTGGATGACTAATAGCTAATATTTGATTGGTCAAAAT
Found at i:1808839 original size:80 final size:80
Alignment explanation
Indices: 1808724--1808923 Score: 346
Period size: 80 Copynumber: 2.5 Consensus size: 80
1808714 TTAAATTTTA
* * *
1808724 ATTGGTCAAAAATATGAAGATTATCTCCAAATTATTTTGATTTATTTAGAGATAAATTGGATGAC
1 ATTGGTC-AAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGAC
1808789 CAATAGCTAATATTTG
65 CAATAGCTAATATTTG
* *
1808805 ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTGATTTGTTTAGAGATAAATTGGATGACT
1 ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACC
1808870 AATAGCTAATATTTG
66 AATAGCTAATATTTG
1808885 ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTGA
1 ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTGA
1808924 GAGATAAGTA
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 107 0.94
81 7 0.06
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (80 bp):
ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACC
AATAGCTAATATTTG
Found at i:1809195 original size:30 final size:30
Alignment explanation
Indices: 1809161--1809227 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1809151 ACTGAGGATA
* *
1809161 AAGAAGATGACATGTATGGAGATGAAAATG
1 AAGAAGATGACATGGAAGGAGATGAAAATG
* *
1809191 AAGAAGATGGCATGGAAGGAGATGAAGATG
1 AAGAAGATGACATGGAAGGAGATGAAAATG
*
1809221 AAAAAGA
1 AAGAAGA
1809228 AGTTAAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.49, C:0.03, G:0.33, T:0.15
Consensus pattern (30 bp):
AAGAAGATGACATGGAAGGAGATGAAAATG
Found at i:1818850 original size:36 final size:36
Alignment explanation
Indices: 1818787--1818892 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
1818777 ATTCCACACA
* *
1818787 AATATGGCCTAAATGTGGAGG-ATAGAATACCATATG
1 AATATGGCCCAAATGTGGGGGTA-AGAATACCATATG
* **
1818823 AATATGGCCCAAATGTGGGGGTAAGAATACTATACA
1 AATATGGCCCAAATGTGGGGGTAAGAATACCATATG
* * *
1818859 AATATAG--CATATGTGGGGGTAAGAATGCCATATG
1 AATATGGCCCAAATGTGGGGGTAAGAATACCATATG
1818893 CATTTAGAGT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
34 22 0.38
36 35 0.60
37 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (36 bp):
AATATGGCCCAAATGTGGGGGTAAGAATACCATATG
Found at i:1819265 original size:29 final size:29
Alignment explanation
Indices: 1819240--1819313 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
1819230 AAGTTATGTA
1819240 GATGGAAAAATGCTTATTTGACTTATATG
1 GATGGAAAAATGCTTATTTGACTTATATG
* * *
1819269 GATTGAAAAATGCTTTTTTGACCTATATG
1 GATGGAAAAATGCTTATTTGACTTATATG
1819298 GATGGAAAAATGCTTA
1 GATGGAAAAATGCTTA
1819314 AGTACATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (29 bp):
GATGGAAAAATGCTTATTTGACTTATATG
Found at i:1825891 original size:36 final size:35
Alignment explanation
Indices: 1825774--1825891 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 35
1825764 ATATGTGATT
* * *
1825774 TTCCACATGAATATGGTACATATGT-GGGGCATAGAA
1 TTCCACATGAATATGG-CCAAATGTAGGGGTA-AGAA
* * *
1825810 TACCACTTGAATATGGCCCAAATGTGAAGGGTAAGAA
1 TTCCACATGAATATGG-CCAAATGT-AGGGGTAAGAA
* * *
1825847 TGCTACATGAATATGGCCTAGATGTAGGGGTAAGAA
1 TTCCACATGAATATGGCC-AAATGTAGGGGTAAGAA
1825883 TTCCACATG
1 TTCCACATG
1825892 CCTTTAGAGT
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
36 39 0.60
37 22 0.34
38 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (35 bp):
TTCCACATGAATATGGCCAAATGTAGGGGTAAGAA
Found at i:1830679 original size:17 final size:18
Alignment explanation
Indices: 1830639--1830681 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1830629 AAAATATTAT
*
1830639 GAAATAACAACAGAAGGGT
1 GAAA-AACAACAGAAGGGC
*
1830658 TAAAAACAACA-AAGGGC
1 GAAAAACAACAGAAGGGC
1830675 GAAAAAC
1 GAAAAAC
1830682 TCAAAATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 7 0.33
19 3 0.14
ACGTcount: A:0.58, C:0.14, G:0.21, T:0.07
Consensus pattern (18 bp):
GAAAAACAACAGAAGGGC
Found at i:1831227 original size:24 final size:24
Alignment explanation
Indices: 1831199--1831249 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1831189 ACTAATGAAT
*
1831199 AAAGATATAAAAGATTT-CTGTAAA
1 AAAGAAATAAAAGATTTACT-TAAA
**
1831223 AAAGAAATTCAAGATTTACTTAAA
1 AAAGAAATAAAAGATTTACTTAAA
1831247 AAA
1 AAA
1831250 AATTAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (24 bp):
AAAGAAATAAAAGATTTACTTAAA
Found at i:1832471 original size:30 final size:30
Alignment explanation
Indices: 1832437--1832498 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1832427 CTTGGATAAG
1832437 AGTAACATATACTATGAGACTTAACACTAT
1 AGTAACATATACTATGAGACTTAACACTAT
1832467 AGTAACATATACTATGAGACTTAACACTAT
1 AGTAACATATACTATGAGACTTAACACTAT
1832497 AG
1 AG
1832499 ACTTAGCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (30 bp):
AGTAACATATACTATGAGACTTAACACTAT
Found at i:1832502 original size:14 final size:15
Alignment explanation
Indices: 1832447--1832503 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1832437 AGTAACATAT
1832447 ACTATGAGACTTAAC
1 ACTATGAGACTTAAC
* *
1832462 ACTAT-AGTAACAT-AT
1 ACTATGAG--ACTTAAC
1832477 ACTATGAGACTTAAC
1 ACTATGAGACTTAAC
1832492 ACTAT-AGACTTA
1 ACTATGAGACTTA
1832504 GCAATACTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
14 12 0.35
15 17 0.50
16 5 0.15
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (15 bp):
ACTATGAGACTTAAC
Found at i:1833733 original size:33 final size:33
Alignment explanation
Indices: 1833691--1833753 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1833681 CAAATCCTCT
*
1833691 ATTTTTACCATTCCTTAAGTTCCCTTACCTACC
1 ATTTTTACCATTCCTAAAGTTCCCTTACCTACC
*
1833724 ATTTTTACCATTCCTAAAGTTCTCTTACCT
1 ATTTTTACCATTCCTAAAGTTCCCTTACCT
1833754 CTTGGGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.22, C:0.30, G:0.03, T:0.44
Consensus pattern (33 bp):
ATTTTTACCATTCCTAAAGTTCCCTTACCTACC
Found at i:1834327 original size:68 final size:68
Alignment explanation
Indices: 1834118--1834358 Score: 277
Period size: 68 Copynumber: 3.5 Consensus size: 68
1834108 TATGGAAAAC
* * * ** * *
1834118 ACATCATATACATAATCTCATGGCATTTATCATGCATTCTTAATCACCTTATATTGTATATGAAA
1 ACATCATATACATAATCTTATAGAATACATCATGCATACTTAATCACCTTATATTGTATATGGAA
1834183 TTT
66 TTT
* *
1834186 ACATCATATACATAATCTTATAGTATACATCGTGAAAGCATACTTAATCACCTTATATTGTATAT
1 ACATCATATACATAATCTTATAGAATACATC----ATGCATACTTAATCACCTTATATTGTATAT
1834251 GGAATTT
62 GGAATTT
* * * * * *
1834258 ACATCATTTACACAATCTTCTAGAATACATCATGCATACTTAAGCA-TTTCATATCGTATATGGA
1 ACATCATATACATAATCTTATAGAATACATCATGCATACTTAATCACCTT-ATATTGTATATGGA
1834322 ATTT
65 ATTT
* *
1834326 ACATCATATACATAATCTTATAGCATTCATCAT
1 ACATCATATACATAATCTTATAGAATACATCAT
1834359 ACCAAGTATG
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
67 2 0.01
68 84 0.57
72 61 0.41
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (68 bp):
ACATCATATACATAATCTTATAGAATACATCATGCATACTTAATCACCTTATATTGTATATGGAA
TTT
Found at i:1841059 original size:63 final size:64
Alignment explanation
Indices: 1840944--1841074 Score: 147
Period size: 63 Copynumber: 2.1 Consensus size: 64
1840934 TGTAGATTTG
* * ** ** * **
1840944 TGGTTGAGCCCTTTAAAAACCATGGGTTCTGTTTGCTTTCAAAGAAAAGCATTTTTAAGTTTTA
1 TGGTTGAGCCCATTAAAAACCATGAGTTCTACTTGCTCCCAAAGAAAAGCATTTGTAAGGGTTA
** *
1841008 TGGTTGAG-CCATTAAAAACCATGAGTTCTACTTGCTCCCATTGAAAGGCATTTGTAAGGGTTA
1 TGGTTGAGCCCATTAAAAACCATGAGTTCTACTTGCTCCCAAAGAAAAGCATTTGTAAGGGTTA
1841071 TGGT
1 TGGT
1841075 CAATCTCATA
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
63 47 0.85
64 8 0.15
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (64 bp):
TGGTTGAGCCCATTAAAAACCATGAGTTCTACTTGCTCCCAAAGAAAAGCATTTGTAAGGGTTA
Found at i:1848169 original size:21 final size:19
Alignment explanation
Indices: 1848133--1848173 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1848123 ACATGTTGAG
1848133 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
1848152 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
1848173 T
1 T
1848174 GCTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:1850305 original size:17 final size:17
Alignment explanation
Indices: 1850283--1850320 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1850273 CAACATCTAG
1850283 CCACTCACTAAACTTAC
1 CCACTCACTAAACTTAC
1850300 CCACTCACTAAACTTAC
1 CCACTCACTAAACTTAC
1850317 CCAC
1 CCAC
1850321 CTTATGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (17 bp):
CCACTCACTAAACTTAC
Found at i:1852789 original size:19 final size:19
Alignment explanation
Indices: 1852746--1852791 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1852736 AAAATTTTAG
** *
1852746 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
1852765 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
*
1852784 ATTAAAAT
1 AATAAAAT
1852792 TTTATCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:1853772 original size:18 final size:18
Alignment explanation
Indices: 1853733--1853778 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1853723 CACCCATAAC
1853733 AAAGAAGAAAAGAAAAAG
1 AAAGAAGAAAAGAAAAAG
* *
1853751 AAAGAGAGAAAGGAAAGA-
1 AAAGA-AGAAAAGAAAAAG
1853769 AAAGAA-AAAA
1 AAAGAAGAAAA
1853779 AACTTGCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 10 0.42
19 10 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAGAAGAAAAGAAAAAG
Found at i:1854797 original size:12 final size:12
Alignment explanation
Indices: 1854780--1854805 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1854770 AAATTATGGA
1854780 TGAAAGTTGTTT
1 TGAAAGTTGTTT
1854792 TGAAAGTTGTTT
1 TGAAAGTTGTTT
1854804 TG
1 TG
1854806 GATATATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (12 bp):
TGAAAGTTGTTT
Found at i:1861457 original size:34 final size:34
Alignment explanation
Indices: 1861388--1861461 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
1861378 GCTCCCATGG
* ** *
1861388 AAAAGCATTGTAAAGGTTCTATTTGCTCTAGTGA
1 AAAAGCATTGTAAAGGTTCTACTTGCTAAAATGA
*
1861422 AAAAGCATTGTAAAGGCTT-TGCTTGCTAAAATGA
1 AAAAGCATTGTAAAGG-TTCTACTTGCTAAAATGA
1861456 AAAAGC
1 AAAAGC
1861462 GTAATTGAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (34 bp):
AAAAGCATTGTAAAGGTTCTACTTGCTAAAATGA
Found at i:1867127 original size:34 final size:34
Alignment explanation
Indices: 1867088--1867155 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1867078 AGGACTTAGC
*
1867088 TAATATTTAATAACAAAATTGGACTAAACTAATT
1 TAATATTTAATAACAAAATTGAACTAAACTAATT
*
1867122 TAATATTTAATAACAAAATTGAACTAAAGTAATT
1 TAATATTTAATAACAAAATTGAACTAAACTAATT
1867156 CTATAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.35
Consensus pattern (34 bp):
TAATATTTAATAACAAAATTGAACTAAACTAATT
Found at i:1869942 original size:17 final size:17
Alignment explanation
Indices: 1869920--1869952 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1869910 GATAAGGAAT
1869920 TGCTCCCCCTTAATGTG
1 TGCTCCCCCTTAATGTG
1869937 TGCTCCCCCTTAATGT
1 TGCTCCCCCTTAATGT
1869953 ATGCATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.36, G:0.15, T:0.36
Consensus pattern (17 bp):
TGCTCCCCCTTAATGTG
Found at i:1883613 original size:16 final size:16
Alignment explanation
Indices: 1883592--1883626 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1883582 AGATTAGAAA
1883592 AAAAAATGTAGGAAGG
1 AAAAAATGTAGGAAGG
1883608 AAAAAATGTAGGAAGG
1 AAAAAATGTAGGAAGG
1883624 AAA
1 AAA
1883627 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (16 bp):
AAAAAATGTAGGAAGG
Found at i:1895323 original size:75 final size:76
Alignment explanation
Indices: 1895228--1895389 Score: 227
Period size: 77 Copynumber: 2.1 Consensus size: 76
1895218 AATGCCATAT
* * *
1895228 ATTTTAATTTTGGGTGATTCATAAAAAAT-GAAATTGTTTCCAATTTTAAAAGTAATTCCTAAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAATTATTTCCAACTTTAAAAGAAATTCCTAAAA
*
1895292 TTAATGATAGA
66 TTAAGGATAGA
* * * *
1895303 ATTTCAATTTTGGGTGATTCATAAAAAATAAGAAATTATTTTCTACTTTAAAAGAAATTTCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAAT-AGAAATTATTTCCAACTTTAAAAGAAATTCCTAAA
*
1895368 ATTAAGGATAGT
65 ATTAAGGATAGA
1895380 ATTTTAATTT
1 ATTTTAATTT
1895390 GAGAAATTCA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
75 28 0.37
77 47 0.63
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (76 bp):
ATTTTAATTTTGGGTGATTCATAAAAAATAGAAATTATTTCCAACTTTAAAAGAAATTCCTAAAA
TTAAGGATAGA
Found at i:1904424 original size:29 final size:29
Alignment explanation
Indices: 1904378--1904591 Score: 215
Period size: 29 Copynumber: 7.4 Consensus size: 29
1904368 GGTAACTTTT
*
1904378 ACATG-TTTATCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * * *
1904406 AGATGTTTTGTCTTCATTTTGACAAAAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* *
1904435 AC-TAATTTTGTCTTAATTTAGACAAAAAA
1 ACAT-GTTTTGTCTTAATTTAGACAAGAAA
* * * *
1904464 ACATGTTTTGTCATAACTTAGATAGGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * *
1904493 ACAT-ATTTATCTTAATTTAGATAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
1904521 ACATGTTTTGTCTTAATTTAGACAAG-AA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
1904549 ACATG-TTTGTCTTATTTTAAGACAAG-AA
1 ACATGTTTTGTCTTAATTT-AGACAAGAAA
1904577 ACATGTGTTTTGTCT
1 ACA--TGTTTTGTCT
1904592 CAATCAAGAC
Statistics
Matches: 154, Mismatches: 24, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
27 12 0.08
28 47 0.31
29 85 0.55
30 3 0.02
31 7 0.05
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
ACATGTTTTGTCTTAATTTAGACAAGAAA
Found at i:1919258 original size:29 final size:29
Alignment explanation
Indices: 1919204--1919267 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1919194 CTTGATTGAG
*
1919204 GATGAAAAAGATGACATGCAATGAGATAAA
1 GATG-AAAAGATGACATGCAAGGAGATAAA
** *
1919234 GATGAAAAGATGACATGGGAGGAGATGAA
1 GATGAAAAGATGACATGCAAGGAGATAAA
1919263 GATGA
1 GATGA
1919268 GGAAAATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.48, C:0.05, G:0.31, T:0.16
Consensus pattern (29 bp):
GATGAAAAGATGACATGCAAGGAGATAAA
Found at i:1919292 original size:30 final size:30
Alignment explanation
Indices: 1919256--1919318 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1919246 ACATGGGAGG
* *
1919256 AGATGAAGATGAGGAAAATGTTGAAGATAA
1 AGATGAAGATGAAGAAAATGTTGAAGACAA
1919286 AGATGAAGATGAAGAAAATGTTGAAGACAA
1 AGATGAAGATGAAGAAAATGTTGAAGACAA
1919316 AGA
1 AGA
1919319 CGAAAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.29, T:0.17
Consensus pattern (30 bp):
AGATGAAGATGAAGAAAATGTTGAAGACAA
Found at i:1921848 original size:54 final size:54
Alignment explanation
Indices: 1921745--1921848 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
1921735 TGTCCAATGG
* * *
1921745 AATTCCATTGTAAATGTTTTTCCAACAAAAAATTCCTTTGGAATTTTTTTACGA
1 AATTCCATTGTAAATGCTTTTCCAACAAAAAATTCCATTGGAATGTTTTTACGA
*
1921799 AATTCCATTAG-AAATGCTTTTCCAACGAAAAAATTCCATTGGCA-GTTTTT
1 AATTCCATT-GTAAATGCTTTTCCAAC-AAAAAATTCCATTGGAATGTTTTT
1921849 GATGGAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
54 28 0.64
55 16 0.36
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (54 bp):
AATTCCATTGTAAATGCTTTTCCAACAAAAAATTCCATTGGAATGTTTTTACGA
Found at i:1922146 original size:33 final size:33
Alignment explanation
Indices: 1922104--1922190 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
1922094 GGTGGTGTAT
*
1922104 AATGCCTTTTTAAGGAGCATGCACAACCTCTAC
1 AATGCCTTTTTAAGGAGCAAGCACAACCTCTAC
*
1922137 AATGCCTTTTCAAGGAGCAAGCACAACCTCTAC
1 AATGCCTTTTTAAGGAGCAAGCACAACCTCTAC
*
1922170 AATGCCTTTTTAAAGAGCAAG
1 AATGCCTTTTTAAGGAGCAAG
1922191 AATACCTCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (33 bp):
AATGCCTTTTTAAGGAGCAAGCACAACCTCTAC
Found at i:1924624 original size:15 final size:15
Alignment explanation
Indices: 1924604--1924645 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
1924594 ATATGTTAAT
1924604 TTTATATAGTATATA
1 TTTATATAGTATATA
1924619 TTTATAT-GTAT-TA
1 TTTATATAGTATATA
*
1924632 CTTATATA-TATATA
1 TTTATATAGTATATA
1924646 CAAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.46
14 6 0.25
15 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTATATAGTATATA
Found at i:1924857 original size:25 final size:25
Alignment explanation
Indices: 1924823--1924913 Score: 85
Period size: 25 Copynumber: 3.5 Consensus size: 25
1924813 TAAATTAAAT
*
1924823 ATATGTATATATATAATATTTATAC
1 ATATATATATATATAATATTTATAC
* *
1924848 ATATATATAT-TCATAACATTTAATTAA
1 ATATATATATAT-ATAATATTT-A-TAC
*
1924875 ATGTATGTATATATATAATATTTATAC
1 A--TATATATATATATAATATTTATAC
*
1924902 AAATATATATAT
1 ATATATATATAT
1924914 GCATAACATT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
24 1 0.02
25 26 0.50
26 1 0.02
27 6 0.12
28 1 0.02
29 16 0.31
30 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (25 bp):
ATATATATATATATAATATTTATAC
Found at i:1924874 original size:54 final size:55
Alignment explanation
Indices: 1924815--1924924 Score: 186
Period size: 54 Copynumber: 2.0 Consensus size: 55
1924805 CTTATTTATA
*
1924815 AATTAAATATATGTATATATATAATATTTATAC-ATATATATATTCATAACATTT
1 AATTAAATATATGTATATATATAATATTTATACAATATATATATGCATAACATTT
*
1924869 AATTAAATGTATGTATATATATAATATTTATACAAATATATATATGCATAACATTT
1 AATTAAATATATGTATATATATAATATTTATAC-AATATATATATGCATAACATTT
1924925 TTTATTATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 32 0.62
56 20 0.38
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (55 bp):
AATTAAATATATGTATATATATAATATTTATACAATATATATATGCATAACATTT
Found at i:1924905 original size:29 final size:28
Alignment explanation
Indices: 1924819--1924913 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 28
1924809 TTTATAAATT
1924819 AAATATATGTATATATATAATATTTATAC
1 AAAT-TATGTATATATATAATATTTATAC
* * *
1924848 --A-TATATATAT-TCATAACATTTA-ATT
1 AAATTATGTATATAT-ATAATATTTATA-C
1924873 AAATGTATGTATATATATAATATTTATAC
1 AAAT-TATGTATATATATAATATTTATAC
*
1924902 AAA-TATATATAT
1 AAATTATGTATAT
1924914 GCATAACATT
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
24 2 0.04
25 17 0.33
27 10 0.20
29 20 0.39
30 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (28 bp):
AAATTATGTATATATATAATATTTATAC
Found at i:1925022 original size:30 final size:29
Alignment explanation
Indices: 1924964--1925035 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
1924954 AATTATAACA
1924964 TATTAATATGTAACATATTTACTATCATT
1 TATTAATATGTAACATATTTACTATCATT
1924993 TATTAATAT-TAACATATAAGTTA-TATCATT
1 TATTAATATGTAACATAT---TTACTATCATT
*
1925023 TA-AAATATGTAAC
1 TATTAATATGTAAC
1925036 TTGTAATTNN
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 8 0.21
29 14 0.37
30 13 0.34
31 3 0.08
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (29 bp):
TATTAATATGTAACATATTTACTATCATT
Found at i:1927396 original size:32 final size:33
Alignment explanation
Indices: 1927350--1927418 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
1927340 ATTTTATTGC
1927350 TTAACGAAAATTTGAGGATACTTGAAAAAAGGA
1 TTAACGAAAATTTGAGGATACTTGAAAAAAGGA
*
1927383 TTAA-GAAAATTTGAGGATACTTGAAAGAAGGA
1 TTAACGAAAATTTGAGGATACTTGAAAAAAGGA
1927415 TTAA
1 TTAA
1927419 AGTCATTCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (33 bp):
TTAACGAAAATTTGAGGATACTTGAAAAAAGGA
Found at i:1928979 original size:20 final size:19
Alignment explanation
Indices: 1928931--1928973 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1928921 TCTTTTCCTC
1928931 CTTCACTC-TTTCTTTTTT
1 CTTCACTCTTTTCTTTTTT
*
1928949 TTTCACTCTTTTCTTTCTTT
1 CTTCACTCTTTTCTTT-TTT
1928969 CTTCA
1 CTTCA
1928974 TCCTTTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 7 0.33
20 7 0.33
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (19 bp):
CTTCACTCTTTTCTTTTTT
Found at i:1928980 original size:19 final size:19
Alignment explanation
Indices: 1928931--1928980 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1928921 TCTTTTCCTC
1928931 CTTCACT-CTTTCTTTTTT
1 CTTCACTCCTTTCTTTTTT
* *
1928949 TTTCACTCTTTTCTTTCTTT
1 CTTCACTCCTTTCTTT-TTT
1928969 CTTCA-TCCTTTC
1 CTTCACTCCTTTC
1928981 ATGCTTGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.23
19 13 0.50
20 7 0.27
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (19 bp):
CTTCACTCCTTTCTTTTTT
Found at i:1931056 original size:36 final size:36
Alignment explanation
Indices: 1931013--1931086 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
1931003 ATAAGGAAAG
1931013 AAAATGTGACTAGTAGGATTTGAACCTGCACTAAGA
1 AAAATGTGACTAGTAGGATTTGAACCTGCACTAAGA
*
1931049 AAAATGTGACTAGTAGGATTTGAACCTGCACTGAGA
1 AAAATGTGACTAGTAGGATTTGAACCTGCACTAAGA
1931085 AA
1 AA
1931087 GTCATTGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (36 bp):
AAAATGTGACTAGTAGGATTTGAACCTGCACTAAGA
Found at i:1933506 original size:21 final size:21
Alignment explanation
Indices: 1933482--1933560 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
1933472 AGATAAGATA
1933482 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* * * **
1933503 TAAATATAAA-TAAAGATTAAT
1 TAAATTTAAATTTAA-TTTGTT
*
1933524 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
*
1933545 TAAATTTAAATATAAT
1 TAAATTTAAATTTAAT
1933561 ATCATGTCTT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
20 3 0.07
21 37 0.86
22 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:1947598 original size:22 final size:22
Alignment explanation
Indices: 1947570--1947612 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1947560 AGTCATGCAG
*
1947570 CGCTGCGGCGTTACTTCTCCAT
1 CGCTGCGGCGTTACATCTCCAT
1947592 CGCTGCGGCGTTACATCTCCA
1 CGCTGCGGCGTTACATCTCCA
1947613 GGGATGGTGG
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:0.12, C:0.37, G:0.23, T:0.28
Consensus pattern (22 bp):
CGCTGCGGCGTTACATCTCCAT
Found at i:1953119 original size:24 final size:24
Alignment explanation
Indices: 1953086--1953140 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1953076 GCCTAGCTTG
* *
1953086 ACAACGTATCTTCCTTCATATCAC
1 ACAACTTATCTCCCTTCATATCAC
1953110 ACAACTTATCTCCCTTCATATCAC
1 ACAACTTATCTCCCTTCATATCAC
1953134 AC-ACTTA
1 ACAACTTA
1953141 CAAATTCAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.33
Consensus pattern (24 bp):
ACAACTTATCTCCCTTCATATCAC
Found at i:1957597 original size:25 final size:25
Alignment explanation
Indices: 1957568--1957620 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1957558 GTGACCACAA
* *
1957568 CCACGTATATCAACTCATGGCCTAG
1 CCACGTATATCAACCCACGGCCTAG
*
1957593 CCACGTATATCAACCCACGGCCTTG
1 CCACGTATATCAACCCACGGCCTAG
1957618 CCA
1 CCA
1957621 TATATATGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (25 bp):
CCACGTATATCAACCCACGGCCTAG
Found at i:1957626 original size:25 final size:25
Alignment explanation
Indices: 1957568--1957627 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
1957558 GTGACCACAA
* * *
1957568 CCACGTATATCAACTCATGGCCTAG
1 CCACATATATCAACCCACGGCCTAG
* *
1957593 CCACGTATATCAACCCACGGCCTTG
1 CCACATATATCAACCCACGGCCTAG
*
1957618 CCATATATAT
1 CCACATATAT
1957628 GTCACAAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCCACGGCCTAG
Done.