Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 15 of 113
Found at i:4935604 original size:18 final size:18
Alignment explanation
Indices: 4935581--4935627 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
4935571 AATTTTACTT
4935581 ATAAATAATATTATATAA
1 ATAAATAATATTATATAA
* *
4935599 ATAAATAATACTATATTA
1 ATAAATAATATTATATAA
4935617 ATAAATAATAT
1 ATAAATAATAT
4935628 AATAATAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAATATTATATAA
Found at i:4935616 original size:23 final size:23
Alignment explanation
Indices: 4935588--4935631 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
4935578 CTTATAAATA
4935588 ATATTATATAAATAA-ATAATACT
1 ATATTA-ATAAATAATATAATACT
4935611 ATATTAATAAATAATATAATA
1 ATATTAATAAATAATATAATA
4935632 ATAAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATTAATAAATAATATAATACT
Found at i:4935623 original size:15 final size:15
Alignment explanation
Indices: 4935581--4935635 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 15
4935571 AATTTTACTT
4935581 ATAAATAATATTATATAA
1 ATAAATAATA-TA-AT-A
4935599 ATAAATAATACTATATTA
1 ATAAATAATA-TA-A-TA
4935617 ATAAATAATATAATA
1 ATAAATAATATAATA
4935632 ATAA
1 ATAA
4935636 GTATTATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
15 6 0.17
16 1 0.03
17 2 0.06
18 25 0.71
19 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATAATATAATA
Found at i:4935664 original size:22 final size:21
Alignment explanation
Indices: 4935622--4935694 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
4935612 TATTAATAAA
*
4935622 TAATATAATAATAAGTATTAT
1 TAATATAATAATAAATATTAT
* *
4935643 TAATTTAATTAATAAATTTTA-
1 TAATATAA-TAATAAATATTAT
* *
4935664 TAATA-ATTTTATAATATATTAT
1 TAATATA-ATAATAA-ATATTAT
4935686 TAA-ATAATA
1 TAATATAATA
4935695 CAAAGAATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 6 0.16
21 18 0.47
22 14 0.37
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TAATATAATAATAAATATTAT
Found at i:4935673 original size:11 final size:11
Alignment explanation
Indices: 4935652--4935693 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
4935642 TTAATTTAAT
4935652 TAATAAATTTTA
1 TAAT-AATTTTA
4935664 TAATAATTTTA
1 TAATAATTTTA
4935675 TAATATATTATTA
1 TAATA-ATT-TTA
4935688 -AATAAT
1 TAATAAT
4935694 ACAAAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 14 0.50
12 11 0.39
13 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATAATTTTA
Found at i:4935744 original size:19 final size:19
Alignment explanation
Indices: 4935722--4935759 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4935712 TTTTGTTTTA
*
4935722 AATATTTTTATATTAAAAT
1 AATATTTTAATATTAAAAT
4935741 AATATTTTAATATTAAAAT
1 AATATTTTAATATTAAAAT
4935760 TATTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTTAATATTAAAAT
Found at i:4935777 original size:17 final size:18
Alignment explanation
Indices: 4935757--4935795 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4935747 TTAATATTAA
4935757 AATTATTATTAAAAT-AT
1 AATTATTATTAAAATAAT
* *
4935774 AATTATTTTTAATATAAT
1 AATTATTATTAAAATAAT
4935792 AATT
1 AATT
4935796 TTAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTATTATTAAAATAAT
Found at i:4935803 original size:17 final size:17
Alignment explanation
Indices: 4935739--4935817 Score: 78
Period size: 16 Copynumber: 4.9 Consensus size: 17
4935729 TTATATTAAA
*
4935739 ATAAT-ATTTTAATATT
1 ATAATAATTTTAATAAT
* *
4935755 AAAATTATTATTAA-AAT
1 ATAATAATT-TTAATAAT
*
4935772 ATAATTATTTT--TAAT
1 ATAATAATTTTAATAAT
4935787 ATAATAATTTTAATAAT
1 ATAATAATTTTAATAAT
4935804 A-AATAATTTTAATA
1 ATAATAATTTTAATA
4935818 TATTTTAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.24
16 19 0.35
17 18 0.33
18 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATAATTTTAATAAT
Found at i:4935810 original size:34 final size:34
Alignment explanation
Indices: 4935700--4935811 Score: 89
Period size: 34 Copynumber: 3.4 Consensus size: 34
4935690 TAATACAAAG
4935700 AATAATAAATAATT-TTGTTT--TA-AAT-ATTTT
1 AATAATAAATAATTATT-TTTAATATAATAATTTT
* *
4935730 TATATTAAAATAA-TA-TTTTAATATTAA-AATTATT
1 AATAAT-AAATAATTATTTTTAATA-TAATAATT-TT
*
4935764 ATTAA-AATATAATTATTTTTAATATAATAATTTT
1 AATAATAA-ATAATTATTTTTAATATAATAATTTT
4935798 AATAATAAATAATT
1 AATAATAAATAATT
4935812 TTAATATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
29 3 0.05
30 6 0.10
31 8 0.13
32 2 0.03
33 9 0.14
34 21 0.33
35 14 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (34 bp):
AATAATAAATAATTATTTTTAATATAATAATTTT
Found at i:4935824 original size:26 final size:25
Alignment explanation
Indices: 4935788--4935852 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
4935778 ATTTTTAATA
4935788 TAATA-ATTTTAATAATAAATAATTT
1 TAATATATTTTAATAA-AAATAATTT
4935813 TAATATATTTTAATCAAAAATAATTT
1 TAATATATTTTAAT-AAAAATAATTT
*
4935839 TTA-ATATTTTAATA
1 TAATATATTTTAATA
4935853 GTTATATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 1 0.03
25 15 0.41
26 19 0.51
27 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATATTTTAATAAAAATAATTT
Found at i:4935838 original size:16 final size:15
Alignment explanation
Indices: 4935780--4935844 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
4935770 ATATAATTAT
*
4935780 TTTTAAT-ATAATAA
1 TTTTAATAAAAATAA
4935794 TTTTAATAATAAATAA
1 TTTTAATAA-AAATAA
4935810 TTTTAAT----AT-A
1 TTTTAATAAAAATAA
4935820 TTTTAATCAAAAATAA
1 TTTTAAT-AAAAATAA
4935836 TTTTTAATA
1 -TTTTAATA
4935845 TTTTAATAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 16
0.71 0.02 0.28
Matches are distributed among these distances:
10 8 0.20
11 2 0.05
14 7 0.17
15 3 0.07
16 14 0.34
17 7 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATAAAAATAA
Found at i:4937162 original size:21 final size:18
Alignment explanation
Indices: 4937138--4937189 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
4937128 TTAATTTTTT
4937138 AATTTTTTTTACATACAATTA
1 AATTTTTTTTA-A-AC-ATTA
*
4937159 AATTTTATTTAAACATTA
1 AATTTTTTTTAAACATTA
*
4937177 AGTTTTTTATTAA
1 AATTTTTT-TTAA
4937190 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 1 0.04
21 10 0.37
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTTTTTTAAACATTA
Found at i:4956666 original size:20 final size:20
Alignment explanation
Indices: 4956638--4956681 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4956628 ATTTCATTGC
*
4956638 TCATCCAAATGAACCCTAAA
1 TCATACAAATGAACCCTAAA
4956658 TCATACAAATGAACCCTAAA
1 TCATACAAATGAACCCTAAA
4956678 TCAT
1 TCAT
4956682 GTTTTAGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (20 bp):
TCATACAAATGAACCCTAAA
Found at i:4960524 original size:4 final size:4
Alignment explanation
Indices: 4960515--4960544 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
4960505 TAAGTGGAAG
4960515 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
4960545 CGTATCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4965381 original size:34 final size:33
Alignment explanation
Indices: 4965316--4965389 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
4965306 TTTACCATAC
* *
4965316 AAATAGATAAATAAAATGAAAATAGTAATAATT
1 AAATAAATAAATAAAATAAAAATAGTAATAATT
*
4965349 AAATAAATAAATGAATATAAAAATA-TATATAATT
1 AAATAAATAAAT-AAAATAAAAATAGTA-ATAATT
4965383 AAATAAA
1 AAATAAA
4965390 GGCAGTACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 13 0.36
34 23 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.28
Consensus pattern (33 bp):
AAATAAATAAATAAAATAAAAATAGTAATAATT
Found at i:4984220 original size:21 final size:20
Alignment explanation
Indices: 4984196--4984265 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
4984186 TAAATATATA
4984196 TTATTATAATTAATTTTAATT
1 TTATTAT-ATTAATTTTAATT
*
4984217 TTATTACTA-TAATAATTAATTT
1 TTATTA-TATTAAT-TTTAA-TT
*
4984239 CATTATTATTATTATTTTTAATT
1 --TTATTA-TATTAATTTTAATT
4984262 TTAT
1 TTAT
4984266 AAGAACTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
20 4 0.10
21 15 0.38
22 3 0.08
23 2 0.05
24 12 0.31
25 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTATATTAATTTTAATT
Found at i:4984227 original size:24 final size:24
Alignment explanation
Indices: 4984194--4984265 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
4984184 TTTAAATATA
4984194 TATTATTATAATTAATTTTAATTT
1 TATTATTATAATTAATTTTAATTT
*
4984218 TATTACTATAA-TAA--TTAATTT
1 TATTATTATAATTAATTTTAATTT
* * *
4984239 CATTATTATTATTATTTTTAATTT
1 TATTATTATAATTAATTTTAATTT
4984263 TAT
1 TAT
4984266 AAGAACTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 15 0.38
22 2 0.05
23 3 0.08
24 19 0.49
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTATTATAATTAATTTTAATTT
Found at i:5016956 original size:27 final size:24
Alignment explanation
Indices: 5016910--5016980 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
5016900 GTTTTAATAA
5016910 ATTAAAATAATAAATAATAAATTT
1 ATTAAAATAATAAATAATAAATTT
*
5016934 ATTAATATAATACACATATATAAA--T
1 ATTAAAATAATA-A-ATA-ATAAATTT
5016959 A-TAAAATTAAATAAATAATAAA
1 ATTAAAA-T-AATAAATAATAAA
5016981 ATATATATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
23 5 0.12
24 18 0.45
25 5 0.12
26 7 0.17
27 5 0.12
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
ATTAAAATAATAAATAATAAATTT
Found at i:5016966 original size:34 final size:32
Alignment explanation
Indices: 5016884--5016987 Score: 90
Period size: 34 Copynumber: 3.2 Consensus size: 32
5016874 TATTTTAATT
* *
5016884 ATATATAAATAATAATGTTTTAATAAAT--TAAA
1 ATATATAAATAATAA--ATTAAATAAATAATAAA
* * *
5016916 ATA-ATAAATAATAAATTTATTAATATAATACAC
1 ATATATAAATAATAAATTAAATAA-ATAATA-AA
5016949 ATATATAAAT-ATAAAATTAAATAAATAATAAA
1 ATATATAAATAAT-AAATTAAATAAATAATAAA
5016981 ATATATA
1 ATATATA
5016988 TTCTTATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
29 7 0.12
30 2 0.03
31 11 0.18
32 13 0.22
33 12 0.20
34 15 0.25
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (32 bp):
ATATATAAATAATAAATTAAATAAATAATAAA
Found at i:5020771 original size:18 final size:17
Alignment explanation
Indices: 5020747--5020789 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
5020737 AAATGGTTTT
5020747 ATTTTTTTTTTACGAAA
1 ATTTTTTTTTTACGAAA
**
5020764 AGTTTTTTTTTTTTGAAA
1 A-TTTTTTTTTTACGAAA
5020782 ATTTTTTT
1 ATTTTTTT
5020790 CTTTGCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (17 bp):
ATTTTTTTTTTACGAAA
Found at i:5021059 original size:15 final size:14
Alignment explanation
Indices: 5021032--5021071 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
5021022 AGGAAGAAGG
5021032 AGAAGAAAAAAAAA
1 AGAAGAAAAAAAAA
*
5021046 AGAAGGAAAGAAAAA
1 AGAA-GAAAAAAAAA
5021061 AG-AGAAAAAAA
1 AGAAGAAAAAAA
5021072 TAAACAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 5 0.22
15 11 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAAAA
Found at i:5021061 original size:17 final size:19
Alignment explanation
Indices: 5021025--5021061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5021015 TCGGATAAGG
5021025 AAGAAGGAGAAGAAAAAAAA
1 AAGAAGGAGAAG-AAAAAAA
5021045 AAGAAGGA-AAGAAAAAA
1 AAGAAGGAGAAGAAAAAA
5021062 GAGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAAGGAGAAGAAAAAAA
Found at i:5021511 original size:46 final size:47
Alignment explanation
Indices: 5021306--5021812 Score: 428
Period size: 46 Copynumber: 10.6 Consensus size: 47
5021296 TTCCTTTTAA
* * * *
5021306 CAGAGACTCAATAACTTTAAAATTTTTATCTTGAAAAAAGCTC-TTCTTAG
1 CAGAGGCTCAACAACTTTAAAA---TTCTCTTG-AAAAAGCTCATTCTCAG
* * * *
5021356 TAGAGGCTTAATAATTTTAAAAATCTCTATCTTGAAAAAGCTCA-TCTCAG
1 CAGAGGCTCAACAACTTT-AAAAT-TC--TCTTGAAAAAGCTCATTCTCAG
* * * * *
5021406 CAGAGGCTCAACAACTTTAAAATTTTATTTTTGAAAAAACTC-CTCTCAA
1 CAGAGGCTCAACAACTTTAAAA--TT-CTCTTGAAAAAGCTCATTCTCAG
* *
5021455 CAGAAGCTCAACAACTTTAAAATTCTCTTAAAAAAGCT-ATTCTCAG
1 CAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCATTCTCAG
**
5021501 CAGAAACTCAACAACTTTAAAATTCTCTTGAAAAA-CT-ACTT-TCA-
1 CAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCA-TTCTCAG
*
5021545 CTAGAGGCTCAACAACTTTAAAATTCTTTTGAAAAAGCTCATT-TCAG
1 C-AGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCATTCTCAG
* * *
5021592 CAGAGGCTCAACAATTTTAAAATTTTTATCTTAAAAAAAGCTCA-TCTCAG
1 CAGAGGCTCAACAACTTTAAAA---TTCTCTT-GAAAAAGCTCATTCTCAG
* * *
5021642 CAGAGGCTCAACAACTTTAAAAATCTATCATCTTGGAAGAGTTCATT-TCAG
1 CAGAGGCTCAACAACTTT-AAAA--T-TC-TCTTGAAAAAGCTCATTCTCAG
*
5021693 CAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAGGCTCATT-TCAG
1 CAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCATTCTCAG
* * *
5021739 TAGAGGCTCAACAACTTTAAAATTTTCTTAAAAAAGCTCA-TCTCAG
1 CAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCATTCTCAG
** * * *
5021785 CAGAGATTTAACAATTTTAAAAATCTCT
1 CAGAGGCTCAACAACTTTAAAATTCTCT
5021813 CATCTTGGAA
Statistics
Matches: 380, Mismatches: 52, Indels: 54
0.78 0.11 0.11
Matches are distributed among these distances:
44 1 0.00
45 38 0.10
46 155 0.41
47 6 0.02
48 2 0.01
49 49 0.13
50 80 0.21
51 44 0.12
52 5 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (47 bp):
CAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCATTCTCAG
Found at i:5021698 original size:51 final size:46
Alignment explanation
Indices: 5021385--5021812 Score: 432
Period size: 46 Copynumber: 9.1 Consensus size: 46
5021375 AAAATCTCTA
* *
5021385 TCTTGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAAAATTTTAT
1 TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAA--TT-C
* * * * * *
5021434 TTTTGAAAAAACTCCTCTCAACAGAAGCTCAACAACTTTAAAATTC
1 TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAATTC
* **
5021480 TCTTAAAAAAGCT-ATTCTCAGCAGAAACTCAACAACTTTAAAATTC
1 TCTTGAAAAAGCTCATT-TCAGCAGAGGCTCAACAACTTTAAAATTC
5021526 TCTTGAAAAA-CT-ACTTTCA-CTAGAGGCTCAACAACTTTAAAATTC
1 TCTTGAAAAAGCTCA-TTTCAGC-AGAGGCTCAACAACTTTAAAATTC
* * *
5021571 TTTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAATTTTAAAATTTTTA
1 TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAA---TTC
* *
5021620 TCTTAAAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAAAAATCTATC
1 TCTT-GAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTT-AAAA--T-TC
* * *
5021671 ATCTTGGAAGAGTTCATTTCAGCAGAGGCTCAACAACTTTAAAATTC
1 -TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAATTC
* * *
5021718 TCTTGAAAAGGCTCATTTCAGTAGAGGCTCAACAACTTTAAAATTT
1 TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAATTC
* * ** * * *
5021764 TCTTAAAAAAGCTCATCTCAGCAGAGATTTAACAATTTTAAAAATC
1 TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAATTC
5021810 TCT
1 TCT
5021813 CATCTTGGAA
Statistics
Matches: 320, Mismatches: 46, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.00
45 38 0.12
46 154 0.48
47 6 0.02
48 1 0.00
49 43 0.13
50 38 0.12
51 35 0.11
52 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (46 bp):
TCTTGAAAAAGCTCATTTCAGCAGAGGCTCAACAACTTTAAAATTC
Found at i:5021915 original size:49 final size:48
Alignment explanation
Indices: 5021838--5022072 Score: 247
Period size: 49 Copynumber: 4.8 Consensus size: 48
5021828 TTTCTCAGTA
* *
5021838 GAAAAAGCTCCTCTTAGCAGAAGCTTAACAATTTTAAAATTCTTATCTT
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAATT-TTATCTT
* * * *
5021887 GAAAAAGCTCCTTTTAGCAGAAGTTTAACAATTTTAAAACTTTTATCTT
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAA-TTTTATCTT
* * * * *
5021936 GAAAAAGTTCCTCTTAGCCGAGGCTCAATAATTTTAAAATTCTCATTTT
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAATT-TTATCTT
* * * * *
5021985 GGAAAAGCT-CTTTTCGACAGAGGCTCCACAACTTTAAAATTTTCATCTT
1 GAAAAAGCTCCTCTTAG-CAGAGGCTCAACAATTTTAAAATTTT-ATCTT
* * *
5022034 GGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAA
5022073 AAATTCATCT
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
48 8 0.05
49 142 0.91
50 6 0.04
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (48 bp):
GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAATTTTATCTT
Found at i:5022021 original size:98 final size:98
Alignment explanation
Indices: 5021838--5022072 Score: 285
Period size: 98 Copynumber: 2.4 Consensus size: 98
5021828 TTTCTCAGTA
* * *
5021838 GAAAAAGCTCCTCTTAGCAGAAGCTTAACAATTTTAAAATTCTTATCTTGAAAAAGCTCCTTTTA
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAATTCTCATCTTGAAAAAGCTCCTTTTA
* * *
5021903 GCAGAAGTTTAACAATTTTAAAACTTTT-ATCTT
66 GCAGAAGCTCAACAACTTTAAAA-TTTTCATCTT
* * * * * *
5021936 GAAAAAGTTCCTCTTAGCCGAGGCTCAATAATTTTAAAATTCTCATTTTGGAAAAGCT-CTTTTC
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAATTCTCATCTTGAAAAAGCTCCTTTTA
* *
5022000 GACAGAGGCTCCACAACTTTAAAATTTTCATCTT
66 G-CAGAAGCTCAACAACTTTAAAATTTTCATCTT
* * *
5022034 GGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
1 GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAA
5022073 AAATTCATCT
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
97 10 0.09
98 105 0.91
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (98 bp):
GAAAAAGCTCCTCTTAGCAGAGGCTCAACAATTTTAAAATTCTCATCTTGAAAAAGCTCCTTTTA
GCAGAAGCTCAACAACTTTAAAATTTTCATCTT
Found at i:5029036 original size:19 final size:19
Alignment explanation
Indices: 5029014--5029062 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
5029004 GGAGCTTCAC
*
5029014 TTTTCTTTACTCTA-CTTAT
1 TTTTCTTTA-TCGAGCTTAT
5029033 TTTTCTTGTATCGAGCTTAT
1 TTTTCTT-TATCGAGCTTAT
*
5029053 TATTCTTTAT
1 TTTTCTTTAT
5029063 AACACTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.16, C:0.16, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTCTTTATCGAGCTTAT
Found at i:5034337 original size:21 final size:23
Alignment explanation
Indices: 5034312--5034358 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
5034302 TTACATGCAT
* *
5034312 AAATATCAATAATAATA-AT-TA
1 AAATAACAAAAATAATATATATA
5034333 AAATAACAAAAATAATATATATA
1 AAATAACAAAAATAATATATATA
5034356 AAA
1 AAA
5034359 AAATCTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATAACAAAAATAATATATATA
Found at i:5035339 original size:23 final size:21
Alignment explanation
Indices: 5035311--5035392 Score: 77
Period size: 19 Copynumber: 4.0 Consensus size: 21
5035301 ATTGGATAAG
5035311 GAAGAAAAAGAAGGAAAAAGAAA
1 GAAGAAAAAGAA--AAAAAGAAA
5035334 GAAG-AAAAG-AAAAAAGAAA
1 GAAGAAAAAGAAAAAAAGAAA
5035353 GAA-AAAAGAGAAAAAAAAGAAA
1 GAAGAAAA-AG-AAAAAAAGAAA
*
5035375 -ATG-AAAA-AAAAAAAGAAA
1 GAAGAAAAAGAAAAAAAGAAA
5035393 AAAATAATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
18 11 0.21
19 15 0.28
20 3 0.06
21 5 0.09
22 15 0.28
23 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (21 bp):
GAAGAAAAAGAAAAAAAGAAA
Found at i:5035343 original size:12 final size:12
Alignment explanation
Indices: 5035326--5035395 Score: 90
Period size: 11 Copynumber: 5.9 Consensus size: 12
5035316 AAAAGAAGGA
*
5035326 AAAAGAAAGAAG
1 AAAAGAAAAAAG
5035338 AAAAGAAAAAAG
1 AAAAGAAAAAAG
5035350 -AAAGAAAAAAG
1 AAAAGAAAAAAG
*
5035361 AGAA-AAAAAAG
1 AAAAGAAAAAAG
*
5035372 AAAATGAAAAAAA
1 AAAA-GAAAAAAG
5035385 AAAAGAAAAAA
1 AAAAGAAAAAA
5035396 ATAATTAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
11 21 0.41
12 20 0.39
13 10 0.20
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:5035347 original size:18 final size:17
Alignment explanation
Indices: 5035312--5035393 Score: 80
Period size: 18 Copynumber: 4.8 Consensus size: 17
5035302 TTGGATAAGG
*
5035312 AAGAAAAAG-AAGGAAA
1 AAGAAAAAGAAAAGAAA
5035328 AAGAAAGAAGAAAAGAAAA
1 AAGAAA-AAGAAAAG-AAA
*
5035347 AAGAAAGAA-AAAAGAGA
1 AAGAAA-AAGAAAAGAAA
5035364 AA-AAAAAGAAAATGAAA
1 AAGAAAAAGAAAA-GAAA
*
5035381 AAAAAAAAGAAAA
1 AAGAAAAAGAAAA
5035394 AAATAATTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
15 2 0.04
16 13 0.23
17 12 0.21
18 18 0.32
19 12 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AAGAAAAAGAAAAGAAA
Found at i:5035356 original size:29 final size:27
Alignment explanation
Indices: 5035328--5035395 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
5035318 AAGAAGGAAA
5035328 AAGAAAGAAGAAAAGAAAAAAGAAAGAAAA
1 AAGAAAGAA-AAAAG-AAAAAGAAAG-AAA
*
5035358 AAGAGAA-AAAAAAGAAAATGAAA-AAA
1 AAGA-AAGAAAAAAGAAAAAGAAAGAAA
5035384 AA-AAAGAAAAAA
1 AAGAAAGAAAAAA
5035396 ATAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 2 0.06
25 7 0.20
26 5 0.14
28 8 0.23
29 5 0.14
30 6 0.17
31 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (27 bp):
AAGAAAGAAAAAAGAAAAAGAAAGAAA
Found at i:5035396 original size:12 final size:12
Alignment explanation
Indices: 5035324--5035396 Score: 74
Period size: 13 Copynumber: 5.7 Consensus size: 12
5035314 GAAAAAGAAG
*
5035324 GAAAAAGAAAGAA
1 GAAAAA-AAAAAA
*
5035337 GAAAAGAAAAAA
1 GAAAAAAAAAAA
*
5035349 GAAAGAAAAAAGA
1 GAAA-AAAAAAAA
5035362 GAAAAAAAAGAAAA
1 G-AAAAAAA-AAAA
5035376 TGAAAAAAAAAAA
1 -GAAAAAAAAAAA
5035389 GAAAAAAA
1 GAAAAAAA
5035397 TAATTAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
12 17 0.33
13 20 0.39
14 13 0.25
15 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:5036739 original size:7 final size:6
Alignment explanation
Indices: 5036719--5036792 Score: 78
Period size: 6 Copynumber: 12.3 Consensus size: 6
5036709 TGTTTTATGC
* * * *
5036719 TTCTTCT TTCTTT TTCTTT TTCTTT TTCTTG TTCTTG TTCTTG TTCTTG
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
* *
5036768 TTCTTG TTCTTG TTC-TT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT
5036793 TTCTGCGTGG
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
5 4 0.06
6 55 0.86
7 5 0.08
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.74
Consensus pattern (6 bp):
TTCTTT
Found at i:5036792 original size:6 final size:6
Alignment explanation
Indices: 5036726--5036789 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
5036716 TGCTTCTTCT
* * *
5036726 TTCTTT TTCTTT TTCTTT TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG
5036774 TTCTTG TTCTT- TTCTT
1 TTCTTG TTCTTG TTCTT
5036790 TTTTTCTGCG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
5 5 0.09
6 52 0.91
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.73
Consensus pattern (6 bp):
TTCTTG
Found at i:5044631 original size:15 final size:15
Alignment explanation
Indices: 5044611--5044640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5044601 ATATAATTAT
*
5044611 ATATATGAATACTAA
1 ATATATAAATACTAA
5044626 ATATATAAATACTAA
1 ATATATAAATACTAA
5044641 TAATAATAAT
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:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
ATATATAAATACTAA
Found at i:5044646 original size:13 final size:12
Alignment explanation
Indices: 5044588--5044761 Score: 68
Period size: 13 Copynumber: 14.9 Consensus size: 12
5044578 AATATTTTAA
5044588 AAATA-AATAAT
1 AAATATAATAAT
* *
5044599 ATATATAATTAT
1 AAATATAATAAT
* *
5044611 ATATATGAATACT
1 AAATAT-AATAAT
5044624 AAATAT-ATAA-
1 AAATATAATAAT
*
5044634 ATACTAATAATAAT
1 A-AAT-ATAATAAT
5044648 -AAT-TAATAAT
1 AAATATAATAAT
*
5044658 AGATATAATAAT
1 AAATATAATAAT
*
5044670 AAGATATAACAAT
1 AA-ATATAATAAT
5044683 AAA-AT-A-AAT
1 AAATATAATAAT
*
5044692 AAA-AT-ATAAC
1 AAATATAATAAT
*
5044702 AAATAAAATAAAT
1 AAATATAAT-AAT
*
5044715 AAATTATAA-ATTT
1 AAA-TATAATA-AT
* *
5044728 AAAAAT-AGAAT
1 AAATATAATAAT
*
5044739 -AATATAAAAAT
1 AAATATAATAAT
5044750 AAATATTAATAA
1 AAATA-TAATAA
5044762 CATTAATAAC
Statistics
Matches: 123, Mismatches: 21, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
9 9 0.07
10 18 0.15
11 20 0.16
12 34 0.28
13 38 0.31
14 4 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:5044678 original size:22 final size:20
Alignment explanation
Indices: 5044640--5044715 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 20
5044630 ATAAATACTA
* *
5044640 ATAATAATAATTAATAATAGAT
1 ATAATAATAAAT-ATAACA-AT
5044662 ATAATAATAAGATATAACAAT
1 ATAATAATAA-ATATAACAAT
*
5044683 AAAATAAATAAAATATAACAA-
1 ATAAT-AAT-AAATATAACAAT
5044704 ATAA-AATAAATA
1 ATAATAATAAATA
5044716 AATTATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
18 5 0.11
19 3 0.06
21 9 0.19
22 27 0.57
23 3 0.06
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAATAATAAATATAACAAT
Found at i:5044718 original size:22 final size:22
Alignment explanation
Indices: 5044667--5044789 Score: 83
Period size: 23 Copynumber: 5.4 Consensus size: 22
5044657 TAGATATAAT
5044667 AATAAGATATAAC-AATAAAATA
1 AATAA-ATATAACAAATAAAATA
5044689 AATAAAATATAACAAATAAAATA
1 AAT-AAATATAACAAATAAAATA
**
5044712 AATAAATTATAA-ATTTAAAAATA
1 AATAAA-TATAACAAAT-AAAATA
*
5044735 GAAT-AATATAA-AAATAAATATT
1 -AATAAATATAACAAATAAA-ATA
* *
5044757 AATAACATTAATAACAAACAATATA
1 AATAA-A-T-ATAACAAATAAAATA
*
5044782 AATTAATA
1 AATAAATA
5044790 ATTATTGATA
Statistics
Matches: 81, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
21 6 0.07
22 26 0.32
23 29 0.36
24 5 0.06
25 10 0.12
26 5 0.06
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAAATATAACAAATAAAATA
Found at i:5044734 original size:23 final size:23
Alignment explanation
Indices: 5044667--5044723 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
5044657 TAGATATAAT
*
5044667 AATAAGATATAAC-AATAAAATA
1 AATAAAATATAACAAATAAAATA
5044689 AATAAAATATAACAAATAAAATA
1 AATAAAATATAACAAATAAAATA
*
5044712 AATAAATTATAA
1 AATAAAATATAA
5044724 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (23 bp):
AATAAAATATAACAAATAAAATA
Found at i:5044751 original size:28 final size:28
Alignment explanation
Indices: 5044675--5044758 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
5044665 ATAATAAGAT
* *
5044675 ATAACAATAAA-ATAAATAAAATATAACAA
1 ATAA-AATAAATAAAAAT-AAATTTAACAA
*
5044704 ATAAAATAAATAAATTATAAATTTAA-AA
1 ATAAAATAAATAAA-AATAAATTTAACAA
*
5044732 ATAGAATAATATAAAAATAAATATTAA
1 ATAAAATAA-ATAAAAATAAAT-TTAA
5044759 TAACATTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 22 0.48
29 22 0.48
30 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (28 bp):
ATAAAATAAATAAAAATAAATTTAACAA
Found at i:5044857 original size:20 final size:19
Alignment explanation
Indices: 5044818--5044857 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5044808 TAATAACTTG
*
5044818 TAATTTGATTAATTTATAA
1 TAATTTGAATAATTTATAA
*
5044837 TAATTTGAATAGTTATATAA
1 TAATTTGAATAATT-TATAA
5044857 T
1 T
5044858 TTAGATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
TAATTTGAATAATTTATAA
Found at i:5045103 original size:14 final size:14
Alignment explanation
Indices: 5045084--5045111 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5045074 AATATTCGTT
5045084 ATAATTGACTATAA
1 ATAATTGACTATAA
5045098 ATAATTGACTATAA
1 ATAATTGACTATAA
5045112 TTGTAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
ATAATTGACTATAA
Found at i:5051525 original size:30 final size:30
Alignment explanation
Indices: 5051503--5051564 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5051493 AAAATTTTAT
5051503 TTTA-ATAGAAATTAAAAATTAAAAATATA
1 TTTACATAGAAATTAAAAATTAAAAATATA
* *
5051532 TTTACATATAAATTAAAAATTAAAAATCTA
1 TTTACATAGAAATTAAAAATTAAAAATATA
5051562 TTT
1 TTT
5051565 GGATGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (30 bp):
TTTACATAGAAATTAAAAATTAAAAATATA
Found at i:5054376 original size:15 final size:15
Alignment explanation
Indices: 5054356--5054399 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5054346 TAATATTTGA
5054356 AAAATTACATTTAAT
1 AAAATTACATTTAAT
*
5054371 AAAATTAAATTTAAAT
1 AAAATTACATTT-AAT
**
5054387 AATTTTACATTTA
1 AAAATTACATTTA
5054400 TAATTCCATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTACATTTAAT
Found at i:5054398 original size:16 final size:16
Alignment explanation
Indices: 5054356--5054399 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5054346 TAATATTTGA
5054356 AAAATTACATTT-AAT
1 AAAATTACATTTAAAT
*
5054371 AAAATTAAATTTAAAT
1 AAAATTACATTTAAAT
**
5054387 AATTTTACATTTA
1 AAAATTACATTTA
5054400 TAATTCCATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTACATTTAAAT
Found at i:5055972 original size:15 final size:16
Alignment explanation
Indices: 5055934--5055977 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
5055924 TGATCTGAAA
*
5055934 TTAATAAAATATTATTT
1 TTAATATAA-ATTATTT
5055951 TTAAATATAAATT-TTT
1 TT-AATATAAATTATTT
5055967 TTAATATAAAT
1 TTAATATAAAT
5055978 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 5 0.20
18 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATAAATTATTT
Found at i:5056009 original size:35 final size:33
Alignment explanation
Indices: 5055970--5056048 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 33
5055960 AATTTTTTTA
*
5055970 ATATAAATATAAAATTAAATAAATATATAAAATAT
1 ATATAAATAAAAAATTAAA-AAATA-ATAAAATAT
* *
5056005 ATATAAATAAAAAATTAAAAAATAATTATATAT
1 ATATAAATAAAAAATTAAAAAATAATAAAATAT
*
5056038 ATAGAAATAAA
1 ATATAAATAAA
5056049 TTAACCTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 17 0.43
34 5 0.12
35 18 0.45
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (33 bp):
ATATAAATAAAAAATTAAAAAATAATAAAATAT
Found at i:5056047 original size:33 final size:35
Alignment explanation
Indices: 5055974--5056048 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 35
5055964 TTTTTAATAT
* *
5055974 AAATATAAAATTAAATAAATATATAAAATATATAT
1 AAATAAAAAATTAAATAAATATATAAAATATATAG
* *
5056009 AAATAAAAAATTAAA-AAATA-ATTATATATATAG
1 AAATAAAAAATTAAATAAATATATAAAATATATAG
5056042 AAATAAA
1 AAATAAA
5056049 TTAACCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 17 0.47
34 5 0.14
35 14 0.39
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (35 bp):
AAATAAAAAATTAAATAAATATATAAAATATATAG
Found at i:5061703 original size:9 final size:9
Alignment explanation
Indices: 5061689--5061714 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5061679 TTCAACGGGG
5061689 GAAGAAGAT
1 GAAGAAGAT
5061698 GAAGAAGAT
1 GAAGAAGAT
5061707 GAAGAAGA
1 GAAGAAGA
5061715 ATATTCACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (9 bp):
GAAGAAGAT
Found at i:5061773 original size:54 final size:54
Alignment explanation
Indices: 5061691--5061937 Score: 264
Period size: 54 Copynumber: 4.5 Consensus size: 54
5061681 CAACGGGGGA
* *
5061691 AGAAGATGAAGAAGATGAAGAAGAATATTCACTC-ATGCAATCATCATTTTCAAC
1 AGAAGAAGAAGAAGAAGAAGAAGAATATTCAC-CAATGCAATCATCATTTTCAAC
* * * *
5061745 AGAAGAAGAA-AATGAAGAAGAAGAATATTCGCCTATGCGATCGTCATTTTCAAC
1 AGAAGAAGAAGAA-GAAGAAGAAGAATATTCACCAATGCAATCATCATTTTCAAC
* * *
5061799 GGAAGAAGAAGATGAAGATGAAGAAGAATATTCACCAATGCAATCGTCATTTTCAAC
1 ---AGAAGAAGAAGAAGAAGAAGAAGAATATTCACCAATGCAATCATCATTTTCAAC
* * * ** *
5061856 GGAGGAGGAAGAAGAAGAAGAAGAATATTCACCAATGGGATCATTATTTTCAGAAC
1 AGAAGAAGAAGAAGAAGAAGAAGAATATTCACCAATGCAATCATCATTTTC--AAC
*
5061912 GAGAAGACGAAGAAGAAGAAGAAGAA
1 -AGAAGAAGAAGAAGAAGAAGAAGAA
5061938 GAAGAAGAAG
Statistics
Matches: 162, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
53 3 0.02
54 86 0.53
56 3 0.02
57 68 0.42
58 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (54 bp):
AGAAGAAGAAGAAGAAGAAGAAGAATATTCACCAATGCAATCATCATTTTCAAC
Found at i:5061823 original size:111 final size:111
Alignment explanation
Indices: 5061672--5061940 Score: 335
Period size: 111 Copynumber: 2.4 Consensus size: 111
5061662 GAAAAGAAAC
*
5061672 CATCATTTTCAACGGGGGAAGAAGATGAAGAAGATGAAGAAGAATATTCACTC-ATGCAATCATC
1 CATCATTTTCAAC---GGAAGAAGAAGAAGAAGATGAAGAAGAATATTCAC-CAATGCAATCATC
* *
5061736 ATTTTCAACAGAAGAAGAA-AATGAAGAAGAAGAATATTCGCCTATGCGAT
62 ATTTTCAACAGAAGAAGAAGAA-GAAGAAGAAGAATATTCACCAATGCGAT
* * *
5061786 CGTCATTTTCAACGGAAGAAGAAGATGAAGATGAAGAAGAATATTCACCAATGCAATCGTCATTT
1 CATCATTTTCAACGGAAGAAGAAGAAGAAGATGAAGAAGAATATTCACCAATGCAATCATCATTT
* * * *
5061851 TCAACGGAGGAGGAAGAAGAAGAAGAAGAATATTCACCAATGGGAT
66 TCAACAGAAGAAGAAGAAGAAGAAGAAGAATATTCACCAATGCGAT
* * *
5061897 CATTATTTTCAGAACGAGAAGACGAAGAAGAAGAAGAAGAAGAA
1 CATCATTTTC--AACG-GAAGAAGAAGAAGAAGATGAAGAAGAA
5061941 GAAGAAGAAG
Statistics
Matches: 135, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
110 1 0.01
111 92 0.68
112 2 0.01
113 4 0.03
114 36 0.27
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (111 bp):
CATCATTTTCAACGGAAGAAGAAGAAGAAGATGAAGAAGAATATTCACCAATGCAATCATCATTT
TCAACAGAAGAAGAAGAAGAAGAAGAAGAATATTCACCAATGCGAT
Found at i:5061928 original size:3 final size:3
Alignment explanation
Indices: 5061913--5061973 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
5061903 TTTCAGAACG
*
5061913 AGA AGA CGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
5061961 AGA AGC AGA AGA A
1 AGA AGA AGA AGA A
5061974 AATTCACCGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5067258 original size:13 final size:13
Alignment explanation
Indices: 5067240--5067264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5067230 TATCTCTCAA
5067240 AAGCCTTCAAAAC
1 AAGCCTTCAAAAC
5067253 AAGCCTTCAAAA
1 AAGCCTTCAAAA
5067265 GCGATCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (13 bp):
AAGCCTTCAAAAC
Found at i:5079492 original size:59 final size:58
Alignment explanation
Indices: 5079419--5079632 Score: 198
Period size: 59 Copynumber: 3.6 Consensus size: 58
5079409 TTATTCTTAT
5079419 GAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTCTTGATAATTTTTTTTTTTA
1 GAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTT-TTGA-AATTTTTTTTTTTA
* * ** * **
5079479 -AAAAATTGGTAC-TTCAAACTTTTCCTCAAAAAATATTTTTTAAAAAATTTTATTTTCAA
1 GAAAAATTGATACTTTC-AACTTTTCCT-TAAAAATATTTTTT-TGAAATTTTTTTTTTTA
* * *** *
5079538 GAAAAATTGATATTTTTAACTTTTCCTTAAAAATCCCTTATTGAAATTTTTTTTCTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAATTTTTTTT-TTT--A
* *
5079599 GAAAAATTGATACTTTCAATTTTTTTCTTAAAAA
1 GAAAAATTGATACTTTCAA-CTTTTCCTTAAAAA
5079633 ATTATCAATT
Statistics
Matches: 121, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
58 13 0.11
59 43 0.36
60 33 0.27
61 20 0.17
62 12 0.10
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAATTTTTTTTTTTA
Found at i:5079755 original size:55 final size:56
Alignment explanation
Indices: 5079665--5079791 Score: 152
Period size: 55 Copynumber: 2.2 Consensus size: 56
5079655 AAAAATTTTA
* * * *
5079665 AAAAATATTTTTTAAAATTTTTATTTTCAATGGAAATTGATA-ATTTCAACTTT-CTCTC
1 AAAAATATTTTTT--TATTTTTATGTTAAAAGGAAATTGATATA-TTCAACTTTCCT-TC
*
5079723 -AAAATATTTTTTTATTTTTATGTTAAAAGGAAATTTATATATTCAACTTTCCTTC
1 AAAAATATTTTTTTATTTTTATGTTAAAAGGAAATTGATATATTCAACTTTCCTTC
5079778 AAAAATATTTTTTT
1 AAAAATATTTTTTT
5079792 CAAGTTTTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
55 33 0.54
56 16 0.26
57 12 0.20
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (56 bp):
AAAAATATTTTTTTATTTTTATGTTAAAAGGAAATTGATATATTCAACTTTCCTTC
Found at i:5081203 original size:18 final size:18
Alignment explanation
Indices: 5081180--5081241 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
5081170 TGTATTCTTA
5081180 ATTTTTTGATTCTTTTAT
1 ATTTTTTGATTCTTTTAT
5081198 ATTTTTGTGA-TCTTTT-T
1 ATTTTT-TGATTCTTTTAT
*
5081215 TTTTTTTG-TCATCTTTCTAT
1 ATTTTTTGAT--TCTTT-TAT
5081235 ATTTTTT
1 ATTTTTT
5081242 ATGCCAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 2 0.06
17 6 0.17
18 17 0.47
19 4 0.11
20 7 0.19
ACGTcount: A:0.13, C:0.08, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTTTGATTCTTTTAT
Found at i:5081464 original size:18 final size:17
Alignment explanation
Indices: 5081430--5081474 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
5081420 CTATTATCTT
5081430 AAAATAAAATAAAAATA
1 AAAATAAAATAAAAATA
*
5081447 AAAATAAGAATCAAAAT-
1 AAAATAA-AATAAAAATA
5081464 -AAATAAAATAA
1 AAAATAAAATAA
5081475 CAAACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.16
16 6 0.24
17 7 0.28
18 8 0.32
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:5081738 original size:44 final size:42
Alignment explanation
Indices: 5081690--5081812 Score: 167
Period size: 42 Copynumber: 2.9 Consensus size: 42
5081680 AGGCTCAACG
5081690 ACTTTAAAAAAATAAATTAAGCTCCTCTAAACAGAGGCACCACA
1 ACTTTAAAAAAATAAATT--GCTCCTCTAAACAGAGGCACCACA
* * *
5081734 ACTTTGAAAAAATAAATTGCTTCTCTAAACAGAGGCATCACA
1 ACTTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACA
* *
5081776 ACTTTTAAAAAAA-AAATTGCTCATCTAAACAGCGGCA
1 AC-TTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCA
5081813 ACCAAAATTG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
42 45 0.63
43 9 0.13
44 17 0.24
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.24
Consensus pattern (42 bp):
ACTTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACA
Found at i:5081873 original size:42 final size:42
Alignment explanation
Indices: 5081817--5081950 Score: 112
Period size: 42 Copynumber: 3.2 Consensus size: 42
5081807 GCGGCAACCA
* * * **
5081817 AAATTGCTCCTTTAAACATAAGTAACCACGATTTT-GAAAAAT
1 AAATTACTCCTTTAAACAGAAGCAA-CAAAATTTTAGAAAAAT
* * *
5081859 AAATTACTCTTTTAAATAGAGGCAACAAAATTTTAGAAAAAT
1 AAATTACTCCTTTAAACAGAAGCAACAAAATTTTAGAAAAAT
* * * **
5081901 AAATTACTCCTCTAAATAG-AGACAACAGAGCTTT-GAAAAAT
1 AAATTACTCCTTTAAACAGAAG-CAACAAAATTTTAGAAAAAT
5081942 AAATTACTC
1 AAATTACTC
5081951 ATGAACAATC
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
41 24 0.32
42 52 0.68
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (42 bp):
AAATTACTCCTTTAAACAGAAGCAACAAAATTTTAGAAAAAT
Found at i:5082137 original size:31 final size:31
Alignment explanation
Indices: 5082080--5082140 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5082070 TTCTCAAGAA
*
5082080 TTCACTGAAATTTGATTCTCAGAATTTTAGT
1 TTCACTGAAATTTGATTCTCAAAATTTTAGT
5082111 TTCACT-AGAATTTGATTCAT-AAAATTTTAG
1 TTCACTGA-AATTTGATTC-TCAAAATTTTAG
5082141 ATGTGCAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 25 0.93
32 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
TTCACTGAAATTTGATTCTCAAAATTTTAGT
Found at i:5082936 original size:71 final size:71
Alignment explanation
Indices: 5082776--5082964 Score: 218
Period size: 71 Copynumber: 2.7 Consensus size: 71
5082766 CTCTTTAGTA
* * * * * *
5082776 CTAGCAAATTTAGCATAAACTTCATTAATTGACCCACACTATTTTTACCATAATTCATAGGCTTC
1 CTAGCAATTTTAGAATAAACTTCATCAATTGACCCACACTATTTTCACCATAATTCATAAGCGTC
*
5082841 TTAGTG
66 TCAGTG
* *
5082847 CTAGCAATTTCA-ACATAAACTTCATCCATTGACCCACACTATTTTCACCATAATTCATAAGCGT
1 CTAGCAATTTTAGA-ATAAACTTCATCAATTGACCCACACTATTTTCACCATAATTCATAAGCGT
5082911 CTCAGTG
65 CTCAGTG
* * * * * * *
5082918 CTAGCCATTTTAGAATAAATTTTATCATTTGATCCACATTATGTTCA
1 CTAGCAATTTTAGAATAAACTTCATCAATTGACCCACACTATTTTCA
5082965 TCACTTGATC
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
71 97 0.99
72 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (71 bp):
CTAGCAATTTTAGAATAAACTTCATCAATTGACCCACACTATTTTCACCATAATTCATAAGCGTC
TCAGTG
Found at i:5083624 original size:22 final size:22
Alignment explanation
Indices: 5083581--5083626 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5083571 CTTTTTTTTT
*
5083581 TTTTTTTCTTTTTTTCTTTTCA
1 TTTTTTTCTTTTTTTCTCTTCA
5083603 TTTTTTTCATTTTTTTC-CTTCA
1 TTTTTTTC-TTTTTTTCTCTTCA
5083625 TT
1 TT
5083627 CATTCGTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTCTCTTCA
Found at i:5087021 original size:58 final size:60
Alignment explanation
Indices: 5086931--5087187 Score: 210
Period size: 58 Copynumber: 4.3 Consensus size: 60
5086921 TTATTCTAAA
* *
5086931 AAAAATTGATACTTTCAACTTTTTCGT-AAAAATATTTTTCTTGATAATTTTATTTT-AAG
1 AAAAATTGATACTTTCAA-TTTTTCCTAAAAAATATTTTTCTTGAAAATTTTATTTTCAAG
* * *
5086990 -AAAATTCATA-TTTCAATTTTTCCTCAAAAAATGTTTTTTTTGAAAATTTTATTTTCAAG
1 AAAAATTGATACTTTCAATTTTTCCT-AAAAAATATTTTTCTTGAAAATTTTATTTTCAAG
* * * *** *
5087049 AAAAATTGATATTTTCAATTTTTTCTTAAAAAT-CCCTTCTT-AAAATCTTTTTTTCTTTCAAG
1 AAAAATTGATACTTTCAATTTTTCCTAAAAAATATTTTTCTTGAAAA---TTTTAT-TTTCAAG
* * * * *
5087111 AAAAATTGATATTTTTAACTTTTCCTTTAAAAATA--TTT-TTAAAAATTTTTATTTTCAA-
1 AAAAATTGATACTTTCAATTTTTCC-TAAAAAATATTTTTCTTGAAAA-TTTTATTTTCAAG
5087169 AAGAAATTGATACTTTCAA
1 AA-AAATTGATACTTTCAA
5087188 CTTTCCCTCT
Statistics
Matches: 165, Mismatches: 20, Indels: 26
0.78 0.09 0.12
Matches are distributed among these distances:
56 7 0.04
57 6 0.04
58 41 0.25
59 27 0.16
60 21 0.13
61 20 0.12
62 35 0.21
63 8 0.05
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (60 bp):
AAAAATTGATACTTTCAATTTTTCCTAAAAAATATTTTTCTTGAAAATTTTATTTTCAAG
Found at i:5087156 original size:62 final size:58
Alignment explanation
Indices: 5086871--5087264 Score: 233
Period size: 59 Copynumber: 6.8 Consensus size: 58
5086861 CATGCTTTCA
* * * ** *
5086871 CAAGAAAAATTGATACTTTTCAACTTTT-TTTTAAATACA-TTTTAAGGTTTTTATTCT
1 CAAGAAAAATTGATA-TTTTCAACTTTTCCTTTAAAAATATTTTTAAAATTTTTATTTT
* * * * *
5086928 -AAAAAAAATTGATACTTTCAACTTTTTC-GTAAAAATATTTTTCTTGATAA-TTTTATTTT
1 CAAGAAAAATTGATATTTTCAACTTTTCCTTTAAAAATA--TTT-TT-AAAATTTTTATTTT
* * ** *
5086987 -AAG-AAAATTCATA-TTTCAATTTTTCCTCAAAAAATGTTTTTTTTGAAAA-TTTTATTTT
1 CAAGAAAAATTGATATTTTCAACTTTTCCTTTAAAAA---TATTTTT-AAAATTTTTATTTT
* * * * *
5087045 CAAGAAAAATTGATATTTTCAATTTTTTC-TTAAAAATCCCTTCTTAAAATCTTTTTTTCTTT
1 CAAGAAAAATTGATATTTTCAACTTTTCCTTTAAAAAT--ATTTTTAAAA--TTTTTAT-TTT
*
5087107 CAAGAAAAATTGATATTTTTAACTTTTCCTTTAAAAATATTTTTAAAAATTTTTATTTT
1 CAAGAAAAATTGATATTTTCAACTTTTCCTTTAAAAATATTTTT-AAAATTTTTATTTT
* * * * ** *
5087166 CAA-AAGAAATTGATACTTTCAACTTTCCCTCTAAATATATTTTT-TTA-TTTTATGTT
1 CAAGAA-AAATTGATATTTTCAACTTTTCCTTTAAAAATATTTTTAAAATTTTTATTTT
* ** *
5087222 CAA-AGAAAATTCATACATTCAAC-TTTCCTTCAAAAATATTTTT
1 CAAGA-AAAATTGATATTTTCAACTTTTCCTTTAAAAATATTTTT
5087265 TTTCAAATTT
Statistics
Matches: 269, Mismatches: 45, Indels: 48
0.74 0.12 0.13
Matches are distributed among these distances:
55 33 0.12
56 40 0.15
57 14 0.05
58 37 0.14
59 61 0.23
60 21 0.08
61 22 0.08
62 33 0.12
63 8 0.03
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (58 bp):
CAAGAAAAATTGATATTTTCAACTTTTCCTTTAAAAATATTTTTAAAATTTTTATTTT
Found at i:5087267 original size:56 final size:56
Alignment explanation
Indices: 5087157--5087266 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
5087147 TTTTAAAAAT
* * * *
5087157 TTTTATTTTCAAAAGAAATTGATACTTTCAACTTTCCCTCTAAATATATTTTTTTA
1 TTTTATGTTCAAAAGAAATTCATACATTCAACTTTCCCTCAAAATATATTTTTTTA
*
5087213 TTTTATGTTC-AAAGAAAATTCATACATTCAACTTTCCTTCAAAA-ATATTTTTTT
1 TTTTATGTTCAAAAG-AAATTCATACATTCAACTTTCCCTCAAAATATATTTTTTT
5087267 TCAAATTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
55 14 0.29
56 34 0.71
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.48
Consensus pattern (56 bp):
TTTTATGTTCAAAAGAAATTCATACATTCAACTTTCCCTCAAAATATATTTTTTTA
Found at i:5088094 original size:16 final size:17
Alignment explanation
Indices: 5088073--5088105 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5088063 TCTCATCTTT
5088073 TCTCATCT-GTTTTTGA
1 TCTCATCTAGTTTTTGA
*
5088089 TCTCATTTAGTTTTTGA
1 TCTCATCTAGTTTTTGA
5088106 CTTTAGCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (17 bp):
TCTCATCTAGTTTTTGA
Found at i:5088896 original size:4 final size:5
Alignment explanation
Indices: 5088867--5088903 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
5088857 CTTATTATCT
5088867 TAAAA TAAAA TAAAA T-AAA TCAAAA T-AAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAA
5088904 CAAACAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.28
5 17 0.59
6 4 0.14
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:5097879 original size:2 final size:2
Alignment explanation
Indices: 5097867--5097900 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5097857 TAATGATAGC
*
5097867 AT AT CT 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
5097901 CAAGGATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5120291 original size:2 final size:2
Alignment explanation
Indices: 5120284--5120310 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5120274 CGTTTTCTTT
5120284 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 T
5120311 TTAAGCATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5121627 original size:24 final size:21
Alignment explanation
Indices: 5121584--5121636 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 21
5121574 TACACCAAGT
5121584 TTAATAAAATTTTGAATAAATAAA
1 TTAATAAAATTTTG-AT-AA-AAA
5121608 TTAATAAAATTTAATG-TAAAAA
1 TTAATAAAATTT--TGATAAAAA
5121630 TTAATAA
1 TTAATAA
5121637 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 10 0.37
23 2 0.07
24 13 0.48
26 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TTAATAAAATTTTGATAAAAA
Found at i:5121743 original size:15 final size:14
Alignment explanation
Indices: 5121718--5121747 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5121708 TCGATATTTT
5121718 TATTTATAAATATA
1 TATTTATAAATATA
5121732 TATTTAATAAATATA
1 TATTT-ATAAATATA
5121747 T
1 T
5121748 TAAAAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTATAAATATA
Found at i:5123929 original size:30 final size:30
Alignment explanation
Indices: 5123893--5123953 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5123883 TTCCAACAAA
5123893 ATAATCATATTTAAATCGTTAATAAAAATT
1 ATAATCATATTTAAATCGTTAATAAAAATT
*
5123923 ATAATCATATTTAAATTGTTAATAAAAATT
1 ATAATCATATTTAAATCGTTAATAAAAATT
5123953 A
1 A
5123954 AGTAGTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
ATAATCATATTTAAATCGTTAATAAAAATT
Found at i:5125277 original size:19 final size:20
Alignment explanation
Indices: 5125253--5125291 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5125243 TTAAATCATA
5125253 ATAAAAGCAGTT-AAACTTT
1 ATAAAAGCAGTTAAAACTTT
*
5125272 ATAAAAGGAGTTAAAACTTT
1 ATAAAAGCAGTTAAAACTTT
5125292 TCTATCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (20 bp):
ATAAAAGCAGTTAAAACTTT
Found at i:5131978 original size:16 final size:17
Alignment explanation
Indices: 5131947--5131979 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5131937 ATATTTTATT
5131947 AATTAAAATAATAAAAA
1 AATTAAAATAATAAAAA
*
5131964 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
5131980 TTCGATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAATAATAAAAA
Found at i:5136526 original size:16 final size:16
Alignment explanation
Indices: 5136507--5136540 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5136497 TTATTTATTA
5136507 TTACAATT-ATTAATAT
1 TTACAATTAATT-ATAT
5136523 TTACAATTAATTATAT
1 TTACAATTAATTATAT
5136539 TT
1 TT
5136541 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTACAATTAATTATAT
Found at i:5140227 original size:18 final size:18
Alignment explanation
Indices: 5140204--5140238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5140194 TACTTAATAT
*
5140204 TTTAAAATTAATAAATTA
1 TTTAAAAATAATAAATTA
*
5140222 TTTAAAAATATTAAATT
1 TTTAAAAATAATAAATT
5140239 GTTTTTAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAAAATAATAAATTA
Found at i:5152167 original size:2 final size:2
Alignment explanation
Indices: 5152160--5152198 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5152150 TGCCCAACCC
*
5152160 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5152199 AGAGATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5155903 original size:32 final size:32
Alignment explanation
Indices: 5155857--5155929 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
5155847 TATATTTGAA
*
5155857 TCGATCCGACTTGATATTATATAAAATCATAT
1 TCGATTCGACTTGATATTATATAAAATCATAT
*
5155889 TCGATTCGATTTGATATTATATAAAATCATAT
1 TCGATTCGACTTGATATTATATAAAATCATAT
5155921 TCGATTCGA
1 TCGATTCGA
5155930 AATTAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (32 bp):
TCGATTCGACTTGATATTATATAAAATCATAT
Found at i:5155934 original size:27 final size:29
Alignment explanation
Indices: 5155870--5155941 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 29
5155860 ATCCGACTTG
5155870 ATATTATATAAAATCATATTCGATTCGATTT
1 ATATTATATAAAATCATATTCGATTCGA--T
5155901 GATATTATATAAAATCATATTCGATTCGA-
1 -ATATTATATAAAATCATATTCGATTCGAT
5155930 A-ATTA-ATAAAAT
1 ATATTATATAAAAT
5155942 ATTATTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.17
27 4 0.10
28 1 0.03
32 28 0.70
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (29 bp):
ATATTATATAAAATCATATTCGATTCGAT
Found at i:5155991 original size:21 final size:22
Alignment explanation
Indices: 5155954--5156021 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 22
5155944 TATTTTTAAT
*
5155954 ATAAATTAAAATTAAATATATATAAA
1 ATAAA-TAAAAAT-AAT-TATA-AAA
*
5155980 ATATATAAAAATAATTATAAAA
1 ATAAATAAAAATAATTATAAAA
5156002 ATAAAT--AAATAATT-TAAAA
1 ATAAATAAAAATAATTATAAAA
5156021 A
1 A
5156022 ATTATTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 6 0.15
20 8 0.21
22 8 0.21
23 4 0.10
24 3 0.08
25 6 0.15
26 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAATAAAAATAATTATAAAA
Found at i:5156013 original size:20 final size:20
Alignment explanation
Indices: 5155974--5156021 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5155964 ATTAAATATA
5155974 TATAAAATATATAAAAATAAT
1 TATAAAA-ATATAAAAATAAT
5155995 TATAAAAATA-AATAAATAAT
1 TATAAAAATATAA-AAATAAT
5156015 T-TAAAAA
1 TATAAAAA
5156022 ATTATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.31
20 11 0.42
21 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TATAAAAATATAAAAATAAT
Found at i:5158121 original size:7 final size:7
Alignment explanation
Indices: 5158109--5158141 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5158099 TTGCTGTGTC
5158109 TGTGGAG
1 TGTGGAG
5158116 TGTGGAG
1 TGTGGAG
5158123 TGTGGAG
1 TGTGGAG
*
5158130 TGTGGAA
1 TGTGGAG
5158137 TGTGG
1 TGTGG
5158142 TTGAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (7 bp):
TGTGGAG
Found at i:5160574 original size:28 final size:28
Alignment explanation
Indices: 5160534--5160598 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
5160524 CCAACTGAAG
5160534 CTCTTGCCTTTCGCTCATGCTTTCTTCA
1 CTCTTGCCTTTCGCTCATGCTTTCTTCA
5160562 CTCTTGCCTTTCGCTCATGCTTTCTTCA
1 CTCTTGCCTTTCGCTCATGCTTTCTTCA
5160590 CTCTTGCCT
1 CTCTTGCCT
5160599 CAAACAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.06, C:0.37, G:0.11, T:0.46
Consensus pattern (28 bp):
CTCTTGCCTTTCGCTCATGCTTTCTTCA
Found at i:5161030 original size:126 final size:126
Alignment explanation
Indices: 5160821--5161053 Score: 376
Period size: 126 Copynumber: 1.8 Consensus size: 126
5160811 TGAAAGCCGC
* * * *
5160821 TAAAACGACAGAGTTTTGAAGCACATTTCCCGTGGTATAAAATTATAACCCTCCATCTCTTTCGA
1 TAAAACGACAGAGTTTTGAAGCACATTTCCCATAGTATAAAACTATAACCCTCCATCTCTTCCGA
* *
5160886 CAATCTGAAACGAGCTCTCCTTCTCTCTGCTTATCAACGGCCATGGTGCTCGGAAAGCTTG
66 CAATCTGAAACGAACTCTCCTTCTCTCTGCTTATCAAAGGCCATGGTGCTCGGAAAGCTTG
* * *
5160947 TAAAACGACAGAGTTTTGAAGCACATTTCCCATAGTATAAAACTATAGCCGTCCATTTCTTCCGA
1 TAAAACGACAGAGTTTTGAAGCACATTTCCCATAGTATAAAACTATAACCCTCCATCTCTTCCGA
*
5161012 CAATCTGAAACGAACTCTCCTTCTTTCTGCTTATCAAAGGCC
66 CAATCTGAAACGAACTCTCCTTCTCTCTGCTTATCAAAGGCC
5161054 GAAAACATGG
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 97 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (126 bp):
TAAAACGACAGAGTTTTGAAGCACATTTCCCATAGTATAAAACTATAACCCTCCATCTCTTCCGA
CAATCTGAAACGAACTCTCCTTCTCTCTGCTTATCAAAGGCCATGGTGCTCGGAAAGCTTG
Found at i:5161618 original size:3 final size:3
Alignment explanation
Indices: 5161610--5161646 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
5161600 GAAGTAGTTA
* *
5161610 AAG AAG AAG AAC AAG AAG ACG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5161647 GAAAGACAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.05, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5163819 original size:2 final size:2
Alignment explanation
Indices: 5163814--5163838 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5163804 TGCGTCAGTC
5163814 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
5163839 ACCATACACA
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5166448 original size:129 final size:129
Alignment explanation
Indices: 5166218--5166470 Score: 452
Period size: 129 Copynumber: 2.0 Consensus size: 129
5166208 CTTATCACTA
* * *
5166218 ACTAACTGGCCATCTGTTTCCTTTTGAGATCTTGGGACTTACCAAATCTGCAGCTAAATGCAACG
1 ACTAACCGGCCATCTGTTTCCTTTTGAAATCTTGGGACTTACCAAATCCGCAGCTAAATGCAACG
**
5166283 TGGAGCTTTTTCCCACCTCCTGCATTTTTTGAATCTCCTGTAGGATAAATATTACAGTTGTATC
66 CAGAGCTTTTTCCCACCTCCTGCATTTTTTGAATCTCCTGTAGGATAAATATTACAGTTGTATC
5166347 ACTAACCGGCCATCTGTTTCCTTTTGAAATCTTGGGACTTACCAAATCCGCAGCTAAATGCAACG
1 ACTAACCGGCCATCTGTTTCCTTTTGAAATCTTGGGACTTACCAAATCCGCAGCTAAATGCAACG
*
5166412 CAGAGCTTTTTCCCGCCTCCTGCATTTTTTGAATCTCCTGTAGGATAAATATTACAGTT
66 CAGAGCTTTTTCCCACCTCCTGCATTTTTTGAATCTCCTGTAGGATAAATATTACAGTT
5166471 CTATTCTACT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 118 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (129 bp):
ACTAACCGGCCATCTGTTTCCTTTTGAAATCTTGGGACTTACCAAATCCGCAGCTAAATGCAACG
CAGAGCTTTTTCCCACCTCCTGCATTTTTTGAATCTCCTGTAGGATAAATATTACAGTTGTATC
Found at i:5172091 original size:109 final size:108
Alignment explanation
Indices: 5171901--5172130 Score: 343
Period size: 109 Copynumber: 2.1 Consensus size: 108
5171891 GGTTTACTGA
* * * *
5171901 TCAACCAAGTTCAATGACCTATGTATGTTTTTAATGGTTTTAGGGCTCCAGTTGACAGATTTTGC
1 TCAACCAAGTTGAATGACCTATGTATGTTTTTAATGATTGTAGGGCTCCAATTGACAGATTTTGC
* * *
5171966 ATCTCAGTCTTCTTATCAATTAATTATACAATGTCTAAAAGTT
66 ATCTCAATCTTCTTATCAATTAATTATACAATCTCTAAAAATT
*
5172009 TCAACCAAGTTGAATGACCTATGTATGTTTTTTAATGATTGTAGGGCTCTAATTGACAGATTTTG
1 TCAACCAAGTTGAATGACCTATGTATG-TTTTTAATGATTGTAGGGCTCCAATTGACAGATTTTG
* *
5172074 CATCTCAATCTTCTTATCAATTAATTATACTATCTTTAAAAATT
65 CATCTCAATCTTCTTATCAATTAATTATACAATCTCTAAAAATT
*
5172118 TCTACCAATGTTG
1 TCAACCAA-GTTG
5172131 TTGTTTAAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 26 0.24
109 79 0.72
110 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (108 bp):
TCAACCAAGTTGAATGACCTATGTATGTTTTTAATGATTGTAGGGCTCCAATTGACAGATTTTGC
ATCTCAATCTTCTTATCAATTAATTATACAATCTCTAAAAATT
Found at i:5181727 original size:20 final size:19
Alignment explanation
Indices: 5181689--5181729 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5181679 TCATAGGTGG
*
5181689 ATGAATAACCTCTACACCA
1 ATGAATAACCTCAACACCA
*
5181708 ATGAATAACTTCAAACACCA
1 ATGAATAACCTC-AACACCA
5181728 AT
1 AT
5181730 ATCATGGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (19 bp):
ATGAATAACCTCAACACCA
Found at i:5183918 original size:2 final size:2
Alignment explanation
Indices: 5183913--5183937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5183903 TCTCTCTCTT
5183913 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
5183938 GCAATCTAAT
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:5184163 original size:15 final size:16
Alignment explanation
Indices: 5184128--5184168 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
5184118 ATAAGATAGG
*
5184128 ATAAAATTATATTACAA
1 ATAAAATTAAATTA-AA
5184145 ATAAAATTAAATT-AA
1 ATAAAATTAAATTAAA
5184160 ATAAAATTA
1 ATAAAATTA
5184169 GTTTATTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
17 12 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAATTAAATTAAA
Found at i:5202500 original size:71 final size:73
Alignment explanation
Indices: 5202373--5202511 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 73
5202363 AATTTTAATT
* * * * *
5202373 TATTATATATTAAATTAATTTGTGACTTATGTGATATATATGTTAATTTTATTTATTTGAATATA
1 TATTATATATTAAATTAATTTATGACTCATGTGATACATATGTTAATTTTACTTATTTAAATATA
5202438 TGTTTTTA
66 TGTTTTTA
*
5202446 TATTATATATTAAATTAATTTATGACTCATGT-A-ACATGTGTTAATTTTACTTATTTAAATATA
1 TATTATATATTAAATTAATTTATGACTCATGTGATACATATGTTAATTTTACTTATTTAAATATA
5202509 TGT
66 TGT
5202512 CTTCACACAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 29 0.48
72 1 0.02
73 30 0.50
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (73 bp):
TATTATATATTAAATTAATTTATGACTCATGTGATACATATGTTAATTTTACTTATTTAAATATA
TGTTTTTA
Found at i:5208980 original size:13 final size:14
Alignment explanation
Indices: 5208962--5208994 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5208952 ATATTATGTT
*
5208962 TTTAAAAGA-TGAA
1 TTTAAAAGAGAGAA
5208975 TTTAAAAGAGAGAA
1 TTTAAAAGAGAGAA
5208989 TTTAAA
1 TTTAAA
5208995 TTTGATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TTTAAAAGAGAGAA
Found at i:5209333 original size:21 final size:21
Alignment explanation
Indices: 5209307--5209346 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5209297 TCTGAAACTG
*
5209307 TTAAAATTTAAATTATAATTA
1 TTAAAATTAAAATTATAATTA
*
5209328 TTAAAATTAAAATTTTAAT
1 TTAAAATTAAAATTATAAT
5209347 ATTCTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAATTAAAATTATAATTA
Found at i:5210665 original size:22 final size:23
Alignment explanation
Indices: 5210616--5210669 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5210606 TCATTTAAAA
5210616 ATAAAATATAAAAATATTTAGTTT
1 ATAAAATATAAAAATATTTA-TTT
* *
5210640 -TAAATTATAAAATTATTT-TTT
1 ATAAAATATAAAAATATTTATTT
5210661 ATAAAATAT
1 ATAAAATAT
5210670 TTTATATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 7 0.27
23 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATAAAATATAAAAATATTTATTT
Found at i:5210672 original size:14 final size:15
Alignment explanation
Indices: 5210644--5210672 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5210634 TAGTTTTAAA
5210644 TTATAAAATTATTTT
1 TTATAAAATTATTTT
5210659 TTATAAAA-TATTTT
1 TTATAAAATTATTTT
5210673 ATATGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATAAAATTATTTT
Found at i:5211209 original size:2 final size:2
Alignment explanation
Indices: 5211202--5211229 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5211192 TATGTGAAAA
5211202 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
5211230 TTGTCATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5226507 original size:2 final size:2
Alignment explanation
Indices: 5226500--5226526 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5226490 GTTTTAATAT
5226500 TC 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 TC T
5226527 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5226531 original size:2 final size:2
Alignment explanation
Indices: 5226526--5226555 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5226516 TCTCTCTCTC
5226526 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5226556 GGGATTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5227455 original size:26 final size:26
Alignment explanation
Indices: 5227400--5227448 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
5227390 TTTGGATTAG
5227400 TTTTTATATTTTATTGTATTTAAATA
1 TTTTTATATTTTATTGTATTTAAATA
5227426 TTTTTA-ATTTT-TT-TATTTAAATA
1 TTTTTATATTTTATTGTATTTAAATA
5227449 AAATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.43
24 2 0.09
25 5 0.22
26 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTTATATTTTATTGTATTTAAATA
Found at i:5227585 original size:29 final size:29
Alignment explanation
Indices: 5227526--5227601 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
5227516 TAAAGGCTTA
* * * *
5227526 TAATTTAGATACAAATTAAAATTTAAGAAT
1 TAATTTAAATAC-AATAAAAATATAAAAAT
*
5227556 TTATTTAAATACAATAAAAATATAAAAAT
1 TAATTTAAATACAATAAAAATATAAAAAT
* *
5227585 TAATCTAAATAAAATAA
1 TAATTTAAATACAATAA
5227602 TAAAATTTAG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 28 0.74
30 10 0.26
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (29 bp):
TAATTTAAATACAATAAAAATATAAAAAT
Found at i:5230050 original size:18 final size:18
Alignment explanation
Indices: 5230027--5230065 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5230017 AAATATGAAT
5230027 AATATAGAATTAAAAATC
1 AATATAGAATTAAAAATC
* *
5230045 AATATAGACTTAAAATTC
1 AATATAGAATTAAAAATC
5230063 AAT
1 AAT
5230066 TAAACCCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (18 bp):
AATATAGAATTAAAAATC
Found at i:5245631 original size:22 final size:22
Alignment explanation
Indices: 5245606--5245648 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5245596 GATCCGACCC
5245606 AAAAT-TAATAAAATATTTTTTA
1 AAAATATAA-AAAATATTTTTTA
*
5245628 AAAATATAAAAATTATTTTTT
1 AAAATATAAAAAATATTTTTT
5245649 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATATAAAAAATATTTTTTA
Found at i:5249841 original size:16 final size:17
Alignment explanation
Indices: 5249812--5249855 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
5249802 TTGATTTTTG
*
5249812 AAAA-TATATAAAT-AT
1 AAAATTATATTAATAAT
5249827 AAAATTATATTAATAAT
1 AAAATTATATTAATAAT
5249844 AAAATATATATT
1 AAAAT-TATATT
5249856 TTTATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 7 0.28
18 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTATATTAATAAT
Found at i:5252049 original size:23 final size:22
Alignment explanation
Indices: 5252023--5252069 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5252013 ATTGATTTAG
* *
5252023 TTTTAGAGAAAGAGAGTATGAAT
1 TTTTAGAGAAA-AAAATATGAAT
5252046 TTTTAGAGAAAAAAATATGAAT
1 TTTTAGAGAAAAAAATATGAAT
5252068 TT
1 TT
5252070 AGATGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (22 bp):
TTTTAGAGAAAAAAATATGAAT
Found at i:5252093 original size:34 final size:35
Alignment explanation
Indices: 5252055--5252131 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
5252045 TTTTTAGAGA
*
5252055 AAAAAATATGAATTTAGA-T-GAAAAATAAAAAAAT
1 AAAAAATATGAATTTAGAGTAAAAAAAT-AAAAAAT
* * *
5252089 AAAAAAAATTAATTTTGAGTAAAAAAATAAAAAAT
1 AAAAAATATGAATTTAGAGTAAAAAAATAAAAAAT
5252124 AAAAAATA
1 AAAAAATA
5252132 ATTAAGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 15 0.42
35 15 0.42
36 6 0.17
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (35 bp):
AAAAAATATGAATTTAGAGTAAAAAAATAAAAAAT
Found at i:5252096 original size:36 final size:35
Alignment explanation
Indices: 5252054--5252136 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
5252044 ATTTTTAGAG
* *
5252054 AAAAAAATATGAATTTAGA-T-GAAAAATAAAAAAAT
1 AAAAAAA-ATTAATTTAGAGTAAAAAAAT-AAAAAAT
*
5252089 AAAAAAAATTAATTTTGAGTAAAAAAATAAAAAAT
1 AAAAAAAATTAATTTAGAGTAAAAAAATAAAAAAT
5252124 AAAAAATAATTAA
1 AAAAAA-AATTAA
5252137 GTGTTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 9 0.21
35 21 0.50
36 12 0.29
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (35 bp):
AAAAAAAATTAATTTAGAGTAAAAAAATAAAAAAT
Found at i:5262291 original size:25 final size:25
Alignment explanation
Indices: 5262263--5262329 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 25
5262253 AAAACATCTT
* *
5262263 AATAATACT-TTTTAAAAATGTCATA
1 AATAAT-CTCTTTTAAAAACGACATA
*
5262288 AATAATCTCTTTT-AAAACGACTTA
1 AATAATCTCTTTTAAAAACGACATA
5262312 AATAATCTCTTTTAAAAA
1 AATAATCTCTTTTAAAAA
5262330 ACGTTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 23 0.62
25 14 0.38
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (25 bp):
AATAATCTCTTTTAAAAACGACATA
Found at i:5262409 original size:27 final size:26
Alignment explanation
Indices: 5262386--5262456 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
5262376 GTTTTTAGAT
5262386 AAAAATATCTTAAATAATACTTTAAA
1 AAAAATATCTTAAATAATACTTTAAA
* * ** *
5262412 AAAAGATTAT-TTAAGTTATTTTTTAAC
1 AAAA-A-TATCTTAAATAATACTTTAAA
5262439 AAAAATATCTTAAATAAT
1 AAAAATATCTTAAATAAT
5262457 CTTAATTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
25 3 0.09
26 12 0.34
27 17 0.49
28 3 0.09
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (26 bp):
AAAAATATCTTAAATAATACTTTAAA
Found at i:5262581 original size:13 final size:14
Alignment explanation
Indices: 5262559--5262595 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5262549 TTTGAGTATT
*
5262559 TATTATTAATAAAA
1 TATTAATAATAAAA
5262573 -ATTAATAATAAAA
1 TATTAATAATAAAA
5262586 TATT-ATAATA
1 TATTAATAATA
5262596 TATTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 18 0.86
14 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATTAATAATAAAA
Found at i:5272456 original size:2 final size:2
Alignment explanation
Indices: 5272449--5272490 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5272439 CCCACCCCCA
*
5272449 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5272491 TATGATGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5275096 original size:17 final size:16
Alignment explanation
Indices: 5275059--5275097 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5275049 GAATTTAAAA
5275059 AAAAATTAAAAAACAG
1 AAAAATTAAAAAACAG
* *
5275075 CAAAATTAAGAAACAAG
1 AAAAATTAAAAAAC-AG
5275092 AAAAAT
1 AAAAAT
5275098 ACCCAGATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.13
Consensus pattern (16 bp):
AAAAATTAAAAAACAG
Found at i:5275771 original size:20 final size:21
Alignment explanation
Indices: 5275731--5275771 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5275721 TTTATTTAAA
*
5275731 ATTATCAAAATTTAAACTTTT
1 ATTATCAAAATTTAAAATTTT
*
5275752 ATTATTAAAA-TTAAAATTTT
1 ATTATCAAAATTTAAAATTTT
5275772 CAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATCAAAATTTAAAATTTT
Found at i:5275778 original size:21 final size:21
Alignment explanation
Indices: 5275737--5275778 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
5275727 TAAAATTATC
* *
5275737 AAAATTTAAACTTTTATTATT
1 AAAATTTAAAATTTTAATATT
5275758 AAAA-TTAAAATTTTCAATATT
1 AAAATTTAAAATTTT-AATATT
5275779 TTATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATTTAAAATTTTAATATT
Found at i:5280351 original size:27 final size:24
Alignment explanation
Indices: 5280282--5280364 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 24
5280272 ATATATATTG
*
5280282 ATATATATATT-TTTACATAAAAAT
1 ATATTTATATTATTTA-ATAAAAAT
* * *
5280306 ATATTAATTTTAATTAATATAAAAT
1 ATATTTATATTATTTAATA-AAAAT
5280331 AATAATTTATATTATTTAATAACAAAT
1 -AT-ATTTATATTATTTAATAA-AAAT
5280358 ATATTTA
1 ATATTTA
5280365 CTAAATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
24 11 0.23
25 13 0.28
26 5 0.11
27 18 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATTTATATTATTTAATAAAAAT
Found at i:5280420 original size:20 final size:20
Alignment explanation
Indices: 5280387--5280427 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5280377 AAAATATATA
*
5280387 TGATACTATGTTACTCGTTT
1 TGATACTATATTACTCGTTT
*
5280407 TGATATTATATTACTCGTTT
1 TGATACTATATTACTCGTTT
5280427 T
1 T
5280428 CATTTTTGTT
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:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (20 bp):
TGATACTATATTACTCGTTT
Found at i:5281163 original size:2 final size:2
Alignment explanation
Indices: 5281158--5281186 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5281148 AACTACAATC
5281158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5281187 ATTAAAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5291155 original size:37 final size:37
Alignment explanation
Indices: 5291114--5291189 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
5291104 GTCCAGTAAA
5291114 GGGACTTAATACGCAGGTCTTCAGCAACATGTTTAAG
1 GGGACTTAATACGCAGGTCTTCAGCAACATGTTTAAG
5291151 GGGACTTAATACGCAGGTCTTCAGCAACATGTTTAAG
1 GGGACTTAATACGCAGGTCTTCAGCAACATGTTTAAG
5291188 GG
1 GG
5291190 TATTGTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (37 bp):
GGGACTTAATACGCAGGTCTTCAGCAACATGTTTAAG
Found at i:5300025 original size:18 final size:18
Alignment explanation
Indices: 5300002--5300051 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
5299992 ATTTAATTTA
5300002 TAATTAAATTAAATAAAT
1 TAATTAAATTAAATAAAT
*
5300020 TAATT-ATTATAAAT-AAT
1 TAATTAAAT-TAAATAAAT
* *
5300037 TAAATAAATTTAATA
1 TAATTAAATTAAATA
5300052 TCAAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATTAAATTAAATAAAT
Done.