Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 6 of 106
Found at i:2719686 original size:24 final size:24
Alignment explanation
Indices: 2719659--2719706 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2719649 ACATAATTTT
2719659 AAGAAAAGA-AGAAAAAAAAGAAAA
1 AAGAAAAGAGAG-AAAAAAAGAAAA
*
2719683 AAGAAAAGAGAGAAGAAAAGAAAA
1 AAGAAAAGAGAGAAAAAAAGAAAA
2719707 GAAACCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (24 bp):
AAGAAAAGAGAGAAAAAAAGAAAA
Found at i:2732422 original size:13 final size:13
Alignment explanation
Indices: 2732396--2732434 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2732386 AATAATTATT
2732396 TTTTAAAAATAAAA
1 TTTTAAAAA-AAAA
2732410 TTTTAAAAAAAAA
1 TTTTAAAAAAAAA
*
2732423 GTTTAAGAAAAA
1 TTTTAA-AAAAA
2732435 GCTCCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (13 bp):
TTTTAAAAAAAAA
Found at i:2751547 original size:24 final size:24
Alignment explanation
Indices: 2751497--2751548 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2751487 TATTTATTAT
*
2751497 TAATTTTTTATATAATATTTAAAA
1 TAATTTTTTATATAATATTGAAAA
* *
2751521 TAATTTTTTATCTAA-ATGTGAAGA
1 TAATTTTTTATATAATAT-TGAAAA
2751545 TAAT
1 TAAT
2751549 ATGATAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (24 bp):
TAATTTTTTATATAATATTGAAAA
Found at i:2751700 original size:19 final size:18
Alignment explanation
Indices: 2751658--2751700 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2751648 AAAAAACACT
2751658 TATTTAAATGTTTTTAAA
1 TATTTAAATGTTTTTAAA
2751676 TAATTT-AATAGTTTTTCAAA
1 T-ATTTAAAT-GTTTTT-AAA
2751696 TATTT
1 TATTT
2751701 TTAAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (18 bp):
TATTTAAATGTTTTTAAA
Found at i:2752196 original size:28 final size:29
Alignment explanation
Indices: 2752163--2752229 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
2752153 TGACGTAATA
**
2752163 ATATTTTTAAAATAATT-TTATCATTCATT
1 ATATTTTTAAAATAATTCTTAT-ATAAATT
* *
2752192 A-ATTTTAAAAATTATTCTTATATAAATT
1 ATATTTTTAAAATAATTCTTATATAAATT
2752220 ATATTTTTAA
1 ATATTTTTAA
2752230 TTTTTTTCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
ATATTTTTAAAATAATTCTTATATAAATT
Found at i:2754492 original size:26 final size:27
Alignment explanation
Indices: 2754462--2754582 Score: 93
Period size: 26 Copynumber: 4.4 Consensus size: 27
2754452 ATTTCATTTT
2754462 TAAATATTAAAATTTATAATTTAATTA
1 TAAATATTAAAATTTATAATTTAATTA
* *
2754489 -AAATATTAATAATTGATAATTTAAATA
1 TAAATATTAA-AATTTATAATTTAATTA
* ** *
2754516 TTAATATT-TTATTTATAATTTAATCA
1 TAAATATTAAAATTTATAATTTAATTA
* * *
2754542 TTAATATTTTAAAATATTAATATTTTATTTA
1 -TAA-ATATTAAAAT-TT-ATAATTTAATTA
*
2754573 CAAATATTAA
1 TAAATATTAA
2754583 TGTGGATAGA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
26 22 0.31
27 17 0.24
28 10 0.14
29 8 0.11
30 4 0.06
31 9 0.13
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (27 bp):
TAAATATTAAAATTTATAATTTAATTA
Found at i:2754563 original size:42 final size:43
Alignment explanation
Indices: 2754468--2754583 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 43
2754458 TTTTTAAATA
* * *
2754468 TTAAAAT-TT-ATAATTTAATTAAAATATTAATAATTGATAAT
1 TTAAAATATTAATATTTTATTTAAAATATTAATAATTAATAAT
* * *
2754509 TT-AAATATTAATATTTTATTTATAAT-TTAATCATTAATATT
1 TTAAAATATTAATATTTTATTTAAAATATTAATAATTAATAAT
2754550 TTAAAATATTAATATTTTATTTACAAATATTAAT
1 TTAAAATATTAATATTTTATTTA-AAATATTAAT
2754584 GTGGATAGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.06
41 18 0.29
42 33 0.52
43 3 0.05
44 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (43 bp):
TTAAAATATTAATATTTTATTTAAAATATTAATAATTAATAAT
Found at i:2754583 original size:21 final size:20
Alignment explanation
Indices: 2754468--2754583 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 20
2754458 TTTTTAAATA
* *
2754468 TTAAAAT-TT-ATAATTTAA
1 TTAAAATATTAATATTTTAT
*
2754486 TTAAAATATTAATAATTGATAAT
1 TTAAAATATTAAT-ATT--TTAT
2754509 TT-AAATATTAATATTTTAT
1 TTAAAATATTAATATTTTAT
* *
2754528 TTATAAT-TTAATCATTAATATT
1 TTAAAATATTAAT-ATT-TTA-T
2754550 TTAAAATATTAATATTTTAT
1 TTAAAATATTAATATTTTAT
2754570 TTACAAATATTAAT
1 TTA-AAATATTAAT
2754584 GTGGATAGAG
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
18 7 0.09
19 12 0.15
20 12 0.15
21 19 0.24
22 20 0.25
23 9 0.11
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (20 bp):
TTAAAATATTAATATTTTAT
Found at i:2759766 original size:21 final size:19
Alignment explanation
Indices: 2759720--2759768 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2759710 GACTGATCCT
* *
2759720 TTTTTACTTTTGTTTTTTG
1 TTTTTATTTTTGTTTTTTA
2759739 TTATTTATTTTTGTTTTTCTA
1 TT-TTTATTTTTGTTTTT-TA
2759760 TCTTTTATT
1 T-TTTTATT
2759769 ATATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 14 0.56
21 8 0.32
22 1 0.04
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTTGTTTTTTA
Found at i:2760586 original size:11 final size:12
Alignment explanation
Indices: 2760566--2760597 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
2760556 AACTCTTAAA
2760566 AAATAATAAAAT
1 AAATAATAAAAT
2760578 AAA-AAT-AAAT
1 AAATAATAAAAT
2760588 AAATAATAAA
1 AAATAATAAA
2760598 TATTTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.39
11 6 0.33
12 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:2760598 original size:11 final size:11
Alignment explanation
Indices: 2760562--2760599 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2760552 CTATAACTCT
2760562 TAAA-AAATAA
1 TAAATAAATAA
2760572 TAAAATAAA-AA
1 T-AAATAAATAA
2760583 TAAATAAATAA
1 TAAATAAATAA
2760594 TAAATA
1 TAAATA
2760600 TTTACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.32
11 14 0.56
12 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:2765768 original size:23 final size:21
Alignment explanation
Indices: 2765726--2765779 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
2765716 TTTTTAATTT
*
2765726 TAAATAAAT-AAAAAATATAA
1 TAAAAAAATAAAAAAATATAA
* *
2765746 TGAAAAGATAAAAAATATAATAA
1 TAAAAAAATAAAAAA-AT-ATAA
2765769 TAAAAAAATAA
1 TAAAAAAATAA
2765780 TAAAGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 6 0.23
21 5 0.19
22 2 0.08
23 13 0.50
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATATAA
Found at i:2765779 original size:14 final size:15
Alignment explanation
Indices: 2765753--2765782 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2765743 TAATGAAAAG
2765753 ATAAAAAATATAATA
1 ATAAAAAATATAATA
2765768 ATAAAAAA-ATAATA
1 ATAAAAAATATAATA
2765782 A
1 A
2765783 AGTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAAAATATAATA
Found at i:2765780 original size:11 final size:11
Alignment explanation
Indices: 2765727--2765783 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
2765717 TTTTAATTTT
2765727 AAATAAATAAAA
1 AAAT-AATAAAA
*
2765739 AATATAATGAAA
1 AA-ATAATAAAA
*
2765751 AGATAA-AAAA
1 AAATAATAAAA
2765761 TATAATAATAAAA
1 -A-AATAATAAAA
2765774 AAATAATAAA
1 AAATAATAAA
2765784 GTAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 3 0.08
11 14 0.38
12 14 0.38
13 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:2769216 original size:23 final size:23
Alignment explanation
Indices: 2769188--2769260 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
2769178 AGTTATAAAT
*
2769188 ACATCTGTTGAAATACAATAGAC
1 ACATCTGTTGAAATACAAAAGAC
2769211 ACATCTGTTGAAAATA-AAAAGGAC
1 ACATCTGTTG-AAATACAAAA-GAC
* * *
2769235 GCATCTGTTGAAAGACAACAGAC
1 ACATCTGTTGAAATACAAAAGAC
2769258 ACA
1 ACA
2769261 ACCTCTCACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (23 bp):
ACATCTGTTGAAATACAAAAGAC
Found at i:2772256 original size:47 final size:47
Alignment explanation
Indices: 2772189--2772284 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
2772179 CGACTGTTAC
2772189 TTAATTTCAAATATAAATACTACCTCGTTGGATTTATGCATTTCTTG
1 TTAATTTCAAATATAAATACTACCTCGTTGGATTTATGCATTTCTTG
2772236 TTAATTTCAAATATAAATACTACCTCGTTGGATTTATGCATTTCTTG
1 TTAATTTCAAATATAAATACTACCTCGTTGGATTTATGCATTTCTTG
2772283 TT
1 TT
2772285 GAGGGATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (47 bp):
TTAATTTCAAATATAAATACTACCTCGTTGGATTTATGCATTTCTTG
Found at i:2774080 original size:19 final size:20
Alignment explanation
Indices: 2774056--2774094 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2774046 GGCCCAACAG
*
2774056 GCAAATA-TATGGCAAAATC
1 GCAAATACTACGGCAAAATC
2774075 GCAAATACTACGGCAAAATC
1 GCAAATACTACGGCAAAATC
2774095 AAGATCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (20 bp):
GCAAATACTACGGCAAAATC
Found at i:2779626 original size:43 final size:43
Alignment explanation
Indices: 2779565--2779648 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
2779555 CGTAAGATTT
2779565 CTCCTATAAAGCAAGGAAATATATAAGAAAACATGTTCGAATC
1 CTCCTATAAAGCAAGGAAATATATAAGAAAACATGTTCGAATC
2779608 CTCCTATAAAGCAAGGAAATATATAAGAAAACATGTTCGAA
1 CTCCTATAAAGCAAGGAAATATATAAGAAAACATGTTCGAA
2779649 CTACGTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (43 bp):
CTCCTATAAAGCAAGGAAATATATAAGAAAACATGTTCGAATC
Found at i:2813860 original size:29 final size:28
Alignment explanation
Indices: 2813827--2813915 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
2813817 ATAAAATTGA
2813827 AATAAATCACTAAAAAATAAACT-AATTAT
1 AATAAAT-ACTAAAAAATAAA-TAAATTAT
2813856 AATAAAATAAC-AAAAAATAAATAAATTAT
1 AAT-AAAT-ACTAAAAAATAAATAAATTAT
* * *
2813885 AAAAAATA-TAAAAATTTAATAAA--AT
1 AATAAATACTAAAAAATAAATAAATTAT
2813910 AATAAA
1 AATAAA
2813916 AATAATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
25 7 0.13
27 13 0.25
28 5 0.10
29 21 0.40
30 6 0.12
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (28 bp):
AATAAATACTAAAAAATAAATAAATTAT
Found at i:2813889 original size:19 final size:19
Alignment explanation
Indices: 2813867--2813917 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2813857 ATAAAATAAC
2813867 AAAAAATAAATAAATT-ATA
1 AAAAAATAAA-AAATTAATA
*
2813886 AAAAATATAAAAATTTAATA
1 AAAAA-ATAAAAAATTAATA
*
2813906 AAATAATAAAAA
1 AAAAAATAAAAA
2813918 TAATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAATAAAAAATTAATA
Found at i:2813909 original size:28 final size:28
Alignment explanation
Indices: 2813850--2813933 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
2813840 AAAATAAACT
* *
2813850 AATTATAATAAAATAACAAAAAATAA-ATA
1 AATTATAA-AAAATAATAAAAATTAATA-A
2813879 AATTATAAAAAAT-ATAAAAATTTAATAA
1 AATTATAAAAAATAATAAAAA-TTAATAA
* *
2813907 AATAAT-AAAAATAATAATAATTAATAA
1 AATTATAAAAAATAATAAAAATTAATAA
2813934 TTAATAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
27 19 0.40
28 20 0.42
29 9 0.19
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (28 bp):
AATTATAAAAAATAATAAAAATTAATAA
Found at i:2813918 original size:19 final size:19
Alignment explanation
Indices: 2813854--2813933 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 19
2813844 TAAACTAATT
* *
2813854 ATAAT-AAAATAACAAAAA
1 ATAATAAAAATTATAAAAA
*
2813872 ATAA-ATAAATTATAAAAA
1 ATAATAAAAATTATAAAAA
2813890 AT-ATAAAAATT-TAATAAA
1 ATAATAAAAATTATAA-AAA
* *
2813908 ATAATAAAAATAATAATAA
1 ATAATAAAAATTATAAAAA
*
2813927 TTAATAA
1 ATAATAA
2813934 TTAATAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
17 4 0.08
18 27 0.54
19 16 0.32
20 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAATAAAAATTATAAAAA
Found at i:2814809 original size:21 final size:21
Alignment explanation
Indices: 2814785--2814825 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2814775 TAATCATGAT
* * *
2814785 AATAATGATTATTTAAAAAAG
1 AATAATCAATATTCAAAAAAG
2814806 AATAATCAATATTCAAAAAA
1 AATAATCAATATTCAAAAAA
2814826 TTTATTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AATAATCAATATTCAAAAAAG
Found at i:2818651 original size:2 final size:2
Alignment explanation
Indices: 2818646--2818685 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2818636 TTATATAGAA
2818646 AT AT AT AT -T AT AT AT AT AT AT AT -T AT AT AT AT -T 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
2818685 A
1 A
2818686 AATAGAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2818656 original size:17 final size:16
Alignment explanation
Indices: 2818634--2818684 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
2818624 NNNNNNNNNN
2818634 TATTATATAGAAATATA
1 TATTATATA-AAATATA
*
2818651 TATTATAT-ATATATA
1 TATTATATAAAATATA
* *
2818666 TATTATATATATTATA
1 TATTATATAAAATATA
2818682 TAT
1 TAT
2818685 AAATAGAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 14 0.48
16 7 0.24
17 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TATTATATAAAATATA
Found at i:2818660 original size:9 final size:8
Alignment explanation
Indices: 2818646--2818685 Score: 59
Period size: 7 Copynumber: 5.4 Consensus size: 8
2818636 TTATATAGAA
2818646 ATATATAT
1 ATATATAT
2818654 -TATATAT
1 ATATATAT
2818661 ATATATAT
1 ATATATAT
2818669 -TATATAT
1 ATATATAT
2818676 AT-TATAT
1 ATATATAT
2818683 ATA
1 ATA
2818686 AATAGAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 21 0.72
8 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATATATAT
Found at i:2818662 original size:11 final size:11
Alignment explanation
Indices: 2818646--2818685 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
2818636 TTATATAGAA
2818646 ATATATATTAT
1 ATATATATTAT
2818657 ATATATATATATT
1 ATATATAT-TA-T
2818670 ATATATATTAT
1 ATATATATTAT
2818681 ATATA
1 ATATA
2818686 AATAGAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 14 0.52
12 4 0.15
13 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATATATTAT
Found at i:2819762 original size:130 final size:126
Alignment explanation
Indices: 2819584--2819833 Score: 333
Period size: 130 Copynumber: 2.0 Consensus size: 126
2819574 TTGAGGAGGT
* * * **
2819584 AAAAATAAAAAATTTAATATTTAGAGAGATGAAATTATAAATTTTTTTTTAAAAA-ATAAAGATA
1 AAAAACAAAAAATTCAACATTTAGAGAGATGAAATTATAAATAATTTTTTAAAAATA-AAAG-TA
* *
2819648 AAATTATAAAATTTTTAAAAACAAAACAAAAACAAAAATTATAAATTTTTGAAATTTTAGGTGGA
64 AAATT-TAAAA-ATTTAAAAACAAAACAAAAAC-AAAATTATAAATTTTTGAAACTTTAGGTGGA
2819713 C
126 C
* *
2819714 AAAAACAAAAAGTTCAACATTTAGAGGGATGAAATTATAACA-AATTTTTTAAAAATAAAAGTAA
1 AAAAACAAAAAATTCAACATTTAGAGAGATGAAATTATAA-ATAATTTTTTAAAAATAAAAGTAA
* *
2819778 AATTTAAAAATTTAAAAACTAAACAAAGACAAAATTATAAATTTTTGAAACTTTAG
65 AATTTAAAAATTTAAAAACAAAACAAAAACAAAATTATAAATTTTTGAAACTTTAG
2819834 AGGGGGCGGA
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
126 25 0.23
127 18 0.17
128 5 0.05
129 7 0.07
130 50 0.47
131 2 0.02
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.32
Consensus pattern (126 bp):
AAAAACAAAAAATTCAACATTTAGAGAGATGAAATTATAAATAATTTTTTAAAAATAAAAGTAAA
ATTTAAAAATTTAAAAACAAAACAAAAACAAAATTATAAATTTTTGAAACTTTAGGTGGAC
Found at i:2833209 original size:19 final size:19
Alignment explanation
Indices: 2833185--2833224 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2833175 TTTATGAGTT
2833185 CGTGTTGGTAAAACGGCTG
1 CGTGTTGGTAAAACGGCTG
2833204 CGTGTTGGTAAAACGGCTG
1 CGTGTTGGTAAAACGGCTG
2833223 CG
1 CG
2833225 AGTTTAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.38, T:0.25
Consensus pattern (19 bp):
CGTGTTGGTAAAACGGCTG
Found at i:2833323 original size:17 final size:18
Alignment explanation
Indices: 2833292--2833329 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2833282 AAGCCGCTTC
2833292 TTCCCTCTCTTTCGAATCT
1 TTCCCTCTC-TTCGAATCT
*
2833311 TTCCCTCTC-TCGATTCT
1 TTCCCTCTCTTCGAATCT
2833328 TT
1 TT
2833330 TACTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.37, G:0.05, T:0.50
Consensus pattern (18 bp):
TTCCCTCTCTTCGAATCT
Found at i:2833345 original size:10 final size:10
Alignment explanation
Indices: 2833332--2833393 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
2833322 GATTCTTTTA
2833332 CTCTCTTTCC
1 CTCTCTTTCC
2833342 CTCTCTTT-C
1 CTCTCTTTCC
**
2833351 GACTCTTTCC
1 CTCTCTTTCC
2833361 CTCTCTTTCC
1 CTCTCTTTCC
2833371 CTCTCTTT-C
1 CTCTCTTTCC
**
2833380 GACTCTTTCC
1 CTCTCTTTCC
2833390 CTCT
1 CTCT
2833394 TTCCCAAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 14 0.33
10 28 0.67
ACGTcount: A:0.03, C:0.45, G:0.03, T:0.48
Consensus pattern (10 bp):
CTCTCTTTCC
Found at i:2833356 original size:19 final size:19
Alignment explanation
Indices: 2833292--2833393 Score: 75
Period size: 19 Copynumber: 5.4 Consensus size: 19
2833282 AAGCCGCTTC
*
2833292 TTCCCTCTCTTTCGAATCT
1 TTCCCTCTCTTTCGACTCT
*
2833311 TTCCCTCTC--TCGATTCT
1 TTCCCTCTCTTTCGACTCT
** **
2833328 TTTACTCTCTTTCCCTCTCT
1 TTCCCTCTCTTT-CGACTCT
* * **
2833348 TTCGACTCT-TTCCCTCTCT
1 TTC-CCTCTCTTTCGACTCT
2833367 TTCCCTCTCTTTCGACTCT
1 TTCCCTCTCTTTCGACTCT
2833386 TTCCCTCT
1 TTCCCTCT
2833394 TTCCCAAGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.21
18 4 0.06
19 35 0.53
20 8 0.12
21 5 0.08
ACGTcount: A:0.06, C:0.41, G:0.04, T:0.49
Consensus pattern (19 bp):
TTCCCTCTCTTTCGACTCT
Found at i:2833357 original size:29 final size:29
Alignment explanation
Indices: 2833308--2833398 Score: 127
Period size: 29 Copynumber: 3.3 Consensus size: 29
2833298 CTCTTTCGAA
* *
2833308 TCTTTCCCTCTC--TCGATTCTTTTACTC
1 TCTTTCCCTCTCTTTCGACTCTTTCACTC
*
2833335 TCTTTCCCTCTCTTTCGACTCTTTCCCTC
1 TCTTTCCCTCTCTTTCGACTCTTTCACTC
2833364 TCTTTCCCTCTCTTTCGACTCTTTC-C-C
1 TCTTTCCCTCTCTTTCGACTCTTTCACTC
2833391 TCTTTCCC
1 TCTTTCCC
2833399 AAGAAAATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
27 21 0.36
28 1 0.02
29 37 0.63
ACGTcount: A:0.04, C:0.43, G:0.03, T:0.49
Consensus pattern (29 bp):
TCTTTCCCTCTCTTTCGACTCTTTCACTC
Found at i:2834363 original size:80 final size:80
Alignment explanation
Indices: 2834225--2834386 Score: 288
Period size: 80 Copynumber: 2.0 Consensus size: 80
2834215 ATTAAACTGA
* *
2834225 TGGGATTTATTTTATTTAATGGCTCTTGCATTGATAGAATCTGCTATAATTAATTTCTCTATTAG
1 TGGGATTTATTTTATTTAATGGCTCTTGCATTGATAGAATCTGCTATAATTAACTTCTCCATTAG
2834290 AATAAGGCTGTGACT
66 AATAAGGCTGTGACT
* *
2834305 TGGGATTTATTTTATTTAATGTCTCTTGCATTGATTGAATCTGCTATAATTAACTTCTCCATTAG
1 TGGGATTTATTTTATTTAATGGCTCTTGCATTGATAGAATCTGCTATAATTAACTTCTCCATTAG
2834370 AATAAGGCTGTGACT
66 AATAAGGCTGTGACT
2834385 TG
1 TG
2834387 CGTACGACCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (80 bp):
TGGGATTTATTTTATTTAATGGCTCTTGCATTGATAGAATCTGCTATAATTAACTTCTCCATTAG
AATAAGGCTGTGACT
Found at i:2839100 original size:2 final size:2
Alignment explanation
Indices: 2839093--2839128 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2839083 ATACACATGC
2839093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2839129 CAGTATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2839965 original size:48 final size:48
Alignment explanation
Indices: 2839894--2840035 Score: 248
Period size: 48 Copynumber: 3.0 Consensus size: 48
2839884 CTGGATCGAG
2839894 CGGCTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAT
1 CGGCTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAT
* *
2839942 CGGCTAGCCCTTGTGCCACTAGCTTCTCAATTTCCCTATTTCCAACGT
1 CGGCTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAT
* *
2839990 CGGCTAGCCCTTGTACCACTAGCTTCTCTATTTCCCTATCTCCAAC
1 CGGCTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAAC
2840036 TTCTAATGTC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 89 1.00
ACGTcount: A:0.18, C:0.37, G:0.12, T:0.33
Consensus pattern (48 bp):
CGGCTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAT
Found at i:2841035 original size:75 final size:75
Alignment explanation
Indices: 2840912--2841054 Score: 232
Period size: 75 Copynumber: 1.9 Consensus size: 75
2840902 CCAGAAACTA
* *
2840912 TAAAGGGTTTCATAAATGGTTCATAGATGCCGTATCAAAATGGGACACTATGTTAAAGGAATTTG
1 TAAAGGGTTTCATAAATGGTTCATAGATACCGTATCAAAATGGGACACTATGTTAAAGGAAGTTG
2840977 CAGAACGTCC
66 CAGAACGTCC
* * * *
2840987 TAAAGGGTTTCATAAATGGTTCTTCGATACCTTATCAGAATGGGACACTATGTTAAAGGAAGTTG
1 TAAAGGGTTTCATAAATGGTTCATAGATACCGTATCAAAATGGGACACTATGTTAAAGGAAGTTG
2841052 CAG
66 CAG
2841055 GCCATGGACA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (75 bp):
TAAAGGGTTTCATAAATGGTTCATAGATACCGTATCAAAATGGGACACTATGTTAAAGGAAGTTG
CAGAACGTCC
Found at i:2843790 original size:26 final size:23
Alignment explanation
Indices: 2843761--2843809 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
2843751 AAGTTAAATG
*
2843761 TTATTATATTTGATGTTATTATAATT
1 TTATTATAATT-AT-TT-TTATAATT
2843787 TTATTATAATTATTTTTATAATT
1 TTATTATAATTATTTTTATAATT
2843810 ATTGATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 2 0.09
25 2 0.09
26 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
TTATTATAATTATTTTTATAATT
Found at i:2843807 original size:12 final size:12
Alignment explanation
Indices: 2843776--2843812 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2843766 ATATTTGATG
2843776 TTATTATAATT-
1 TTATTATAATTA
2843787 TTATTATAATTA
1 TTATTATAATTA
*
2843799 TTTTTATAATTA
1 TTATTATAATTA
2843811 TT
1 TT
2843813 GATTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTATAATTA
Found at i:2860068 original size:53 final size:54
Alignment explanation
Indices: 2859993--2860147 Score: 181
Period size: 53 Copynumber: 2.9 Consensus size: 54
2859983 GCTATTATAC
* * ** *
2859993 AGCTATTAATGAAAAACCATGAATGTCCATTTCTTGAAGTGAAT-CTGACAAACG
1 AGCTACTAATAAAAAATTATGAATGTTCATTTCTTGAAGTGAATGC-GACAAACG
* *
2860047 AGCTACTAAT-AAAAATTATGAATGTTCATTTCCTGAAGTAAATGCGACAAACG
1 AGCTACTAATAAAAAATTATGAATGTTCATTTCTTGAAGTGAATGCGACAAACG
*
2860100 AGCTACTAATAAAAAATTATAAATCTGTTCATTT-TCTGAAGTGAATGC
1 AGCTACTAATAAAAAATTATGAA--TGTTCATTTCT-TGAAGTGAATGC
2860148 TACATCATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
53 46 0.53
54 21 0.24
56 20 0.23
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (54 bp):
AGCTACTAATAAAAAATTATGAATGTTCATTTCTTGAAGTGAATGCGACAAACG
Found at i:2860292 original size:26 final size:26
Alignment explanation
Indices: 2860260--2860347 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 26
2860250 TATTTTAATT
*
2860260 ATAATTTTACCACCAGAAGTGGATAG
1 ATAATTTTACCACTAGAAGTGGATAG
** * *
2860286 ATAA-TTTACCATCTA-AA-TTTAAAA
1 ATAATTTTACCA-CTAGAAGTGGATAG
2860310 ATAATTTTACCACTAGAAGTGGATAG
1 ATAATTTTACCACTAGAAGTGGATAG
*
2860336 ACAATTTTACCA
1 ATAATTTTACCA
2860348 TCAAAAGTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
24 10 0.21
25 18 0.38
26 20 0.42
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (26 bp):
ATAATTTTACCACTAGAAGTGGATAG
Found at i:2860513 original size:27 final size:28
Alignment explanation
Indices: 2860431--2860515 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
2860421 ATCACTCACC
* * * *
2860431 AAAAGTGGATATATACTTGTAACCTACT
1 AAAAGTAGATAGATACTTTTAACCCACT
*
2860459 ACAAA-TAGAT-GAATACTTTTAACACACT
1 A-AAAGTAGATAG-ATACTTTTAACCCACT
2860487 AAAAGTAGATAGATA-TTTTAACCCACT
1 AAAAGTAGATAGATACTTTTAACCCACT
2860514 AA
1 AA
2860516 CTCACTATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
27 16 0.34
28 27 0.57
29 4 0.09
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (28 bp):
AAAAGTAGATAGATACTTTTAACCCACT
Found at i:2862971 original size:2 final size:2
Alignment explanation
Indices: 2862959--2863002 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2862949 AACCAGTTAG
*
2862959 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2863001 AT
1 AT
2863003 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2863029 original size:2 final size:2
Alignment explanation
Indices: 2863022--2863056 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2863012 NNNNNNNNNN
2863022 TA TA TA 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 TA TA TA T
2863057 GAGAGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2875640 original size:24 final size:24
Alignment explanation
Indices: 2875604--2875651 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2875594 CCTGATGAAA
2875604 ACAATGCAACTATTGAAACTAAAG
1 ACAATGCAACTATTGAAACTAAAG
* * *
2875628 ACAATGGAGCTATTGGAACTAAAG
1 ACAATGCAACTATTGAAACTAAAG
2875652 CCTCACCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (24 bp):
ACAATGCAACTATTGAAACTAAAG
Found at i:2882410 original size:18 final size:19
Alignment explanation
Indices: 2882368--2882415 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2882358 AGTACTGGGG
*
2882368 GGGTTTTGGCGGTGGTTTA
1 GGGTTTTGGCGGTGATTTA
* *
2882387 GGGTTTTGG-GGTTATTTT
1 GGGTTTTGGCGGTGATTTA
*
2882405 GGGTTTAGGCG
1 GGGTTTTGGCG
2882416 TTTGGAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.06, C:0.04, G:0.46, T:0.44
Consensus pattern (19 bp):
GGGTTTTGGCGGTGATTTA
Found at i:2889909 original size:19 final size:21
Alignment explanation
Indices: 2889885--2889923 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2889875 TTTAAATAGA
2889885 AGATCA-AATATTTA-ATTTG
1 AGATCACAATATTTAGATTTG
*
2889904 AGATCACAATGTTTAGATTT
1 AGATCACAATATTTAGATTT
2889924 TTATCCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (21 bp):
AGATCACAATATTTAGATTTG
Found at i:2890254 original size:55 final size:55
Alignment explanation
Indices: 2890186--2890359 Score: 208
Period size: 55 Copynumber: 3.2 Consensus size: 55
2890176 CATAATGATT
* * * *
2890186 TGTAACAACTAAATCTTCAATATAATGTGTAACAATTATATTTTTTAACATGACG
1 TGTAACAATTAAATTTTCAATATAACGTGTAACAATTATATTTTTCAACATGACG
* * * * *
2890241 TGTAACAATTAAATTTTTAACATAACGTGTAATACTTATATTTTTCAATATGACG
1 TGTAACAATTAAATTTTCAATATAACGTGTAACAATTATATTTTTCAACATGACG
* * * * *
2890296 TATAATAATTAAATTTTCAATATAACGTATAACAATTATA-TTTTCAACATAACA
1 TGTAACAATTAAATTTTCAATATAACGTGTAACAATTATATTTTTCAACATGACG
2890350 TG-AACAATTA
1 TGTAACAATTA
2890360 TTTCTAACAT
Statistics
Matches: 98, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
53 7 0.07
54 12 0.12
55 79 0.81
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (55 bp):
TGTAACAATTAAATTTTCAATATAACGTGTAACAATTATATTTTTCAACATGACG
Found at i:2890256 original size:28 final size:27
Alignment explanation
Indices: 2890186--2890390 Score: 157
Period size: 27 Copynumber: 7.6 Consensus size: 27
2890176 CATAATGATT
* * * *
2890186 TGTAACAACTAAATCTTCAATATAATG
1 TGTAACAATTAAATTTTCAACATAACG
* * *
2890213 TGTAACAATTATATTTTTTAACATGACG
1 TGTAACAATTA-AATTTTCAACATAACG
*
2890241 TGTAACAATTAAATTTTTAACATAACG
1 TGTAACAATTAAATTTTCAACATAACG
* * * * *
2890268 TGTAATACTTATATTTTTCAATATGACG
1 TGTAACAATTA-AATTTTCAACATAACG
* * *
2890296 TATAATAATTAAATTTTCAATATAACG
1 TGTAACAATTAAATTTTCAACATAACG
* * *
2890323 TATAACAATTATATTTTCAACATAACA
1 TGTAACAATTAAATTTTCAACATAACG
* *
2890350 TG-AACAATT--A-TTTCTAACATGACA
1 TGTAACAATTAAATTTTC-AACATAACG
*
2890374 TATAACAATTAAATTTT
1 TGTAACAATTAAATTTT
2890391 AAAATATAGC
Statistics
Matches: 145, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
23 4 0.03
24 10 0.07
25 7 0.05
26 7 0.05
27 72 0.50
28 45 0.31
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (27 bp):
TGTAACAATTAAATTTTCAACATAACG
Found at i:2890440 original size:78 final size:79
Alignment explanation
Indices: 2890279--2890455 Score: 177
Period size: 78 Copynumber: 2.3 Consensus size: 79
2890269 GTAATACTTA
* * * * *
2890279 TATTTTTCAATATGACGTATAATAATTAAATTTTCAATATAACGTATAACAATTATATTTTCAAC
1 TATTTCTCAACATGACATATAACAATTAAATTTTAAATATAACGTATAACAATTATATTTTCAAC
*
2890344 ATAACATGAACAAT
66 ATAAAATGAACAAT
* *
2890358 TATTTCT-AACATGACATATAACAATTAAATTTTAAAATATAGCGT-TAACAA-TATTTTTTTC-
1 TATTTCTCAACATGACATATAACAATTAAATTTT-AAATATAACGTATAACAATTA-TATTTTCA
2890419 ACA-AAAA-GTAACAAT
64 ACATAAAATG-AACAAT
* *
2890434 AATATTTTTCAACATGCCATAT
1 --TATTTCTCAACATGACATAT
2890456 CATTAGCTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
75 1 0.01
76 9 0.11
77 5 0.06
78 41 0.50
79 26 0.32
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.38
Consensus pattern (79 bp):
TATTTCTCAACATGACATATAACAATTAAATTTTAAATATAACGTATAACAATTATATTTTCAAC
ATAAAATGAACAAT
Found at i:2891301 original size:32 final size:32
Alignment explanation
Indices: 2891241--2891324 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
2891231 AACGTGTTAC
* * * *
2891241 TCGTATCTGACACGT-TAAGACACGAAAATTT
1 TCGTATCTTAAACGTGTCAGACACAAAAATTT
2891272 TCGTATCTTAAACGTGTCAGACACAAAAATTT
1 TCGTATCTTAAACGTGTCAGACACAAAAATTT
*
2891304 TTGTGAT-TTAAACGTGTCAGA
1 TCGT-ATCTTAAACGTGTCAGA
2891325 TACGATTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.28
32 31 0.67
33 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
TCGTATCTTAAACGTGTCAGACACAAAAATTT
Found at i:2906521 original size:2 final size:2
Alignment explanation
Indices: 2906514--2906543 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2906504 GTTCAACACA
2906514 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
2906544 TATTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2908423 original size:18 final size:21
Alignment explanation
Indices: 2908388--2908425 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
2908378 AGTTGTGTAA
2908388 AAGCTGTTTTTATATTTCAAT
1 AAGCTGTTTTTATATTTCAAT
2908409 AAGCT-TTTTT-T-TTTCAA
1 AAGCTGTTTTTATATTTCAA
2908426 ACTCAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 1 0.06
20 5 0.29
21 5 0.29
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (21 bp):
AAGCTGTTTTTATATTTCAAT
Found at i:2911370 original size:48 final size:48
Alignment explanation
Indices: 2911303--2911409 Score: 196
Period size: 48 Copynumber: 2.2 Consensus size: 48
2911293 AGGATGTTTA
*
2911303 TATTTCATTCAAGTAATTATACCAGATATTTTCATCTTAGCGTTAGAAT
1 TATTT-ATTTAAGTAATTATACCAGATATTTTCATCTTAGCGTTAGAAT
2911352 TATTTATTTAAGTAATTATACCAGATATTTTCATCTTAGCGTTAGAAT
1 TATTTATTTAAGTAATTATACCAGATATTTTCATCTTAGCGTTAGAAT
2911400 TATTTATTTA
1 TATTTATTTA
2911410 CTTATTAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
48 52 0.91
49 5 0.09
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (48 bp):
TATTTATTTAAGTAATTATACCAGATATTTTCATCTTAGCGTTAGAAT
Found at i:2912650 original size:13 final size:13
Alignment explanation
Indices: 2912634--2912660 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2912624 CAAATTATCA
2912634 AATTAATAAAAAT
1 AATTAATAAAAAT
2912647 AATTAATAAAAAT
1 AATTAATAAAAAT
2912660 A
1 A
2912661 TTTAGACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATTAATAAAAAT
Found at i:2914709 original size:33 final size:33
Alignment explanation
Indices: 2914653--2914770 Score: 128
Period size: 33 Copynumber: 3.6 Consensus size: 33
2914643 ACGGGAGTCA
* * * *
2914653 GTGATGGTGATGTGGATCCTGCTACTAGAGTTG
1 GTGATGATGATGTGAATGCTGCTACTGGAGTTG
* *
2914686 GTGGTGATGATGTGAATGTTGCTACTGGAGTTG
1 GTGATGATGATGTGAATGCTGCTACTGGAGTTG
** ** * *
2914719 GTGATGACAATGTGGGTGCTACTACTGGATTTG
1 GTGATGATGATGTGAATGCTGCTACTGGAGTTG
2914752 GTGATGATGATGTGAATGC
1 GTGATGATGATGTGAATGC
2914771 CATTAACCAA
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.20, C:0.09, G:0.36, T:0.34
Consensus pattern (33 bp):
GTGATGATGATGTGAATGCTGCTACTGGAGTTG
Found at i:2916032 original size:52 final size:53
Alignment explanation
Indices: 2915833--2916040 Score: 255
Period size: 52 Copynumber: 4.0 Consensus size: 53
2915823 CGGCGTTTTT
* * * *
2915833 TGTGAATAGCAAACCATGACCAAGAAGTGAG-AGATAAAACTTG-AGGCCAATT
1 TGTGAATAGCAAACTATGGCCAAGAAGTGAGTAGATAAAGCTTGCA-GCCAATA
* * *
2915885 TGTGAATAACAAACTATGGCCAAGAAGTGAGT-GATAAAGCTTGCGGCTAATA
1 TGTGAATAGCAAACTATGGCCAAGAAGTGAGTAGATAAAGCTTGCAGCCAATA
* * * *
2915937 TGTGAACAGCAAACTATGGTCAAGAAGTGAGCA-ATAAAGCTTGCAGCCAATG
1 TGTGAATAGCAAACTATGGCCAAGAAGTGAGTAGATAAAGCTTGCAGCCAATA
* *
2915989 TGTAAATAGCAAACTATGGCCAAGAAGTGAGTAG-TAAAGCTTGCAACCAATA
1 TGTGAATAGCAAACTATGGCCAAGAAGTGAGTAGATAAAGCTTGCAGCCAATA
2916041 ACATAATATT
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
52 132 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (53 bp):
TGTGAATAGCAAACTATGGCCAAGAAGTGAGTAGATAAAGCTTGCAGCCAATA
Found at i:2918657 original size:26 final size:27
Alignment explanation
Indices: 2918602--2918670 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
2918592 CCCCTGAGCA
* *
2918602 CTTTTGTGCTTGGAACGCCCCTAGGTG
1 CTTTTATGCTTGGAACGCCCCTAGGCG
* *
2918629 CTTTTATGCTTGGAATG-CCCTTGGCG
1 CTTTTATGCTTGGAACGCCCCTAGGCG
* *
2918655 CTTTCACGCTTGGAAC
1 CTTTTATGCTTGGAAC
2918671 ATTCTGATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.35
Consensus pattern (27 bp):
CTTTTATGCTTGGAACGCCCCTAGGCG
Found at i:2924751 original size:27 final size:27
Alignment explanation
Indices: 2924721--2924778 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2924711 CTTTATCGAA
*
2924721 CTTGCTTGCATGACTTGGTTTCTTAGG
1 CTTGCTTGCATGACTTAGTTTCTTAGG
2924748 CTTGCTTGCATGACTTAGTTTCTTAGG
1 CTTGCTTGCATGACTTAGTTTCTTAGG
2924775 CTTG
1 CTTG
2924779 GCTTATCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (27 bp):
CTTGCTTGCATGACTTAGTTTCTTAGG
Found at i:2925213 original size:30 final size:30
Alignment explanation
Indices: 2925179--2925239 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2925169 CCAACATTTA
*
2925179 CTCTGGAATTTGAGAGCCAACCGCTAAAAC
1 CTCTGGAATTTGAGAGCCAACCACTAAAAC
*
2925209 CTCTGGAATTTGAGAGCTAACCACTAAAAC
1 CTCTGGAATTTGAGAGCCAACCACTAAAAC
2925239 C
1 C
2925240 CCATCTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (30 bp):
CTCTGGAATTTGAGAGCCAACCACTAAAAC
Found at i:2927037 original size:43 final size:43
Alignment explanation
Indices: 2926976--2927057 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
2926966 TGTATTGGCA
* *
2926976 ATGTTTTAGATCCTAACTATAATCCTAACAAATTGGTTATGGG
1 ATGTTTTAGATCCTAACTATAATCATAACAAAATGGTTATGGG
2927019 ATGTTTTAGATCCTAACTATAATCATAACAAAATGGTTA
1 ATGTTTTAGATCCTAACTATAATCATAACAAAATGGTTA
2927058 GGGGTGATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (43 bp):
ATGTTTTAGATCCTAACTATAATCATAACAAAATGGTTATGGG
Found at i:2938196 original size:29 final size:27
Alignment explanation
Indices: 2938156--2938216 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
2938146 TATTAAATAA
*
2938156 TTTAAATATTAATATTTTAAGTTAA-ATTT
1 TTTAAATATTAA-ATGTTAA--TAATATTT
2938185 TTTAAA-AGTTAAATGTTAATAATATTT
1 TTTAAATA-TTAAATGTTAATAATATTT
2938212 TTTAA
1 TTTAA
2938217 TTTTTTAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 3 0.10
27 9 0.31
28 7 0.24
29 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
TTTAAATATTAAATGTTAATAATATTT
Found at i:2940929 original size:26 final size:26
Alignment explanation
Indices: 2940886--2940938 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2940876 CAAATTCAAG
* *
2940886 AATCTTTTTCAAATACTTATTTTTGC
1 AATCTTTTTCAAACACTTACTTTTGC
* *
2940912 AATCTTTTTCGAGCACTTACTTTTGC
1 AATCTTTTTCAAACACTTACTTTTGC
2940938 A
1 A
2940939 TTAAGGGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.49
Consensus pattern (26 bp):
AATCTTTTTCAAACACTTACTTTTGC
Found at i:2941601 original size:43 final size:41
Alignment explanation
Indices: 2941522--2941601 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
2941512 TCAACGGAAG
* *
2941522 TTTGAGCAGCATGGCAGCCCAAAACAATCGAAGTTTGAGGC
1 TTTGAGCAGCATGACAGCCCAAAACAATAGAAGTTTGAGGC
**
2941563 TTTGAGCAGCATGACAGACCCATTGACAATAGAAGTTTG
1 TTTGAGCAGCATGACAG-CCCA-AAACAATAGAAGTTTG
2941602 GAAAAGGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 16 0.48
42 4 0.12
43 13 0.39
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (41 bp):
TTTGAGCAGCATGACAGCCCAAAACAATAGAAGTTTGAGGC
Found at i:2943128 original size:24 final size:24
Alignment explanation
Indices: 2943101--2943147 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2943091 AACCGTCGGA
*
2943101 ATATTCCCCTCC-AAATCCAGCGGC
1 ATATTCCCC-CCGAAAACCAGCGGC
2943125 ATATTCCCCCCGAAAACCAGCGG
1 ATATTCCCCCCGAAAACCAGCGG
2943148 AGGGTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.28, C:0.40, G:0.15, T:0.17
Consensus pattern (24 bp):
ATATTCCCCCCGAAAACCAGCGGC
Found at i:2943586 original size:55 final size:56
Alignment explanation
Indices: 2943496--2943600 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 56
2943486 TCTTGGAAAA
2943496 AATGAGTTTTCTTCGGCAGAAGAGGTAAAGCGTTTCTAACAGATTTTAGACGAGAG
1 AATGAGTTTTCTTCGGCAGAAGAGGTAAAGCGTTTCTAACAGATTTTAGACGAGAG
* * * * *
2943552 AATG-GTTTTCTTTGGCGGAGGAGGTAAAGGGTTTCTAACAGGTTTTAGA
1 AATGAGTTTTCTTCGGCAGAAGAGGTAAAGCGTTTCTAACAGATTTTAGA
2943601 GGTTTTCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 40 0.91
56 4 0.09
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.31
Consensus pattern (56 bp):
AATGAGTTTTCTTCGGCAGAAGAGGTAAAGCGTTTCTAACAGATTTTAGACGAGAG
Found at i:2943631 original size:43 final size:45
Alignment explanation
Indices: 2943555--2943643 Score: 137
Period size: 43 Copynumber: 2.0 Consensus size: 45
2943545 ACGAGAGAAT
*
2943555 GGTTTTCTTTGGCGGAGGAGGTAAAGGGTTTCTAACAGGTTTTAGA
1 GGTTTTCTTTGGC-GAGGAGATAAAGGGTTTCTAACAGGTTTTAGA
*
2943601 GGTTTTCTTTGGC-A-GAGATAAAGGGTTTCTAATAGGTTTTAGA
1 GGTTTTCTTTGGCGAGGAGATAAAGGGTTTCTAACAGGTTTTAGA
2943644 CGAGAGAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 27 0.66
44 1 0.02
46 13 0.32
ACGTcount: A:0.24, C:0.08, G:0.31, T:0.37
Consensus pattern (45 bp):
GGTTTTCTTTGGCGAGGAGATAAAGGGTTTCTAACAGGTTTTAGA
Found at i:2954021 original size:23 final size:23
Alignment explanation
Indices: 2953971--2954021 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
2953961 ACAAAGTTTA
*
2953971 TAGAAAATTCATACGAATTTCAT
1 TAGAAAATTCAAACGAATTTCAT
2953994 T-GAAAATTCAAAACG-ATTTCAT
1 TAGAAAATTC-AAACGAATTTCAT
2954016 TAGAAA
1 TAGAAA
2954022 TGGCAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (23 bp):
TAGAAAATTCAAACGAATTTCAT
Found at i:2962347 original size:2 final size:2
Alignment explanation
Indices: 2962340--2962364 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2962330 TGAAGTGGCA
2962340 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
2962365 AGTGTAGAAA
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:2965486 original size:18 final size:18
Alignment explanation
Indices: 2965444--2965486 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2965434 AATTATCAAA
* *
2965444 AGAGAGAAAAAAACAGGG
1 AGAGAAAAAAAAACAGAG
2965462 A-AGGAAAAAAAAACAGAG
1 AGA-GAAAAAAAAACAGAG
2965480 AGAGAAA
1 AGAGAAA
2965487 TAAACAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAGAAAAAAAAACAGAG
Found at i:2977549 original size:9 final size:9
Alignment explanation
Indices: 2977537--2977566 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2977527 TTATAACATA
2977537 TATATTTTT
1 TATATTTTT
2977546 TATATTTTT
1 TATATTTTT
2977555 ATATATTTTT
1 -TATATTTTT
2977565 TA
1 TA
2977567 ATGACCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATATTTTT
Found at i:2977559 original size:10 final size:10
Alignment explanation
Indices: 2977535--2977564 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2977525 TTTTATAACA
2977535 TATATATTTT
1 TATATATTTT
2977545 T-TATATTTT
1 TATATATTTT
2977554 TATATATTTT
1 TATATATTTT
2977564 T
1 T
2977565 TAATGACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATATATTTT
Found at i:2978697 original size:34 final size:33
Alignment explanation
Indices: 2978655--2978718 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
2978645 TAAGTTGTTG
*
2978655 TTTGGATATTTGTTTTT-AGTTATTTAAATTATA
1 TTTGGATATTTATTTTTGA-TTATTTAAATTATA
2978688 TTTGAGATATTTATTTTTGATTATTTAAATT
1 TTTG-GATATTTATTTTTGATTATTTAAATT
2978719 TAAATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 23 0.82
35 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (33 bp):
TTTGGATATTTATTTTTGATTATTTAAATTATA
Found at i:2979832 original size:64 final size:64
Alignment explanation
Indices: 2979755--2979928 Score: 215
Period size: 64 Copynumber: 2.7 Consensus size: 64
2979745 TTCCCATGAT
* * * * *
2979755 AAAAATATCAATATTTATTAATTGTGTAAGACATTCAAAACCTATGTTTATATGTACTCACTAC
1 AAAAATATTAATATTTATCAATTATGTAAGACATTCAAAACCTATATTCATATGTACTCACTAC
* * * * * * *
2979819 AAAAATATTAATATTTATCAATTATGTAAGATA-TCAAAAACTTATATTCATGTGTATTTATTAT
1 AAAAATATTAATATTTATCAATTATGTAAGACATTC-AAAACCTATATTCATATGTACTCACTAC
*
2979883 AAAAATATTAATATTTATCAATTATGTAAAACATTCAAAACCTATA
1 AAAAATATTAATATTTATCAATTATGTAAGACATTCAAAACCTATA
2979929 ATTATATATA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.02
64 89 0.96
65 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (64 bp):
AAAAATATTAATATTTATCAATTATGTAAGACATTCAAAACCTATATTCATATGTACTCACTAC
Found at i:2980090 original size:16 final size:17
Alignment explanation
Indices: 2980056--2980095 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
2980046 ATTTTTTAAT
2980056 TTTAATAATATTAAATAA
1 TTTAA-AATATTAAATAA
2980074 TTTAAAATATT-AATAA
1 TTTAAAATATTAAATAA
2980090 TTTAAA
1 TTTAAA
2980096 TTAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.50
17 6 0.27
18 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAAATATTAAATAA
Found at i:3000156 original size:2 final size:2
Alignment explanation
Indices: 3000151--3000192 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3000141 TTTTTCAAAA
3000151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3000193 GTATCCACTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3011809 original size:30 final size:30
Alignment explanation
Indices: 3011765--3011827 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3011755 TACGTTCAAT
*
3011765 TAAACCCTTATATTTTTATTTTGAACTAAA
1 TAAACCCTTATATTTGTATTTTGAACTAAA
* * *
3011795 TAAACTCTTGTATTTGTATTTTGAATTAAA
1 TAAACCCTTATATTTGTATTTTGAACTAAA
3011825 TAA
1 TAA
3011828 GCTTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (30 bp):
TAAACCCTTATATTTGTATTTTGAACTAAA
Found at i:3031441 original size:23 final size:23
Alignment explanation
Indices: 3031397--3031442 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3031387 CTATGCTTCT
* *
3031397 GATTTCTCTTTCCTGCGTTTTTA
1 GATTTCTCTTTCCTGAGCTTTTA
*
3031420 GATTTCTCTTTCTTGAGCTTTTA
1 GATTTCTCTTTCCTGAGCTTTTA
3031443 AGACACCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.13, T:0.57
Consensus pattern (23 bp):
GATTTCTCTTTCCTGAGCTTTTA
Found at i:3031922 original size:60 final size:57
Alignment explanation
Indices: 3031852--3032026 Score: 148
Period size: 52 Copynumber: 3.1 Consensus size: 57
3031842 GTAATGTAAC
* * **
3031852 AACAATATTTTTTCAA-CATGACGTGTGAAAACAATA-TTTTTTTATTTCAACACGGTGTGT
1 AACAACATTTTTT-AACCATGACGTGT---AACAATAGTATTTTT-TTTCAACACGACGTGT
* *
3031912 AACAACATTTTTTAACCATGGCGTGTAACAATAGTATTTTTTTTCAACATGACGTGT
1 AACAACATTTTTTAACCATGACGTGTAACAATAGTATTTTTTTTCAACACGACGTGT
* * * * *
3031969 AACAAC-----TTAACCATGACGTGTAATAACAGTATTTTTTTTTAACATGATGTGT
1 AACAACATTTTTTAACCATGACGTGTAACAATAGTATTTTTTTTCAACACGACGTGT
*
3032021 ACCAAC
1 AACAAC
3032027 CTAATAATGG
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
52 46 0.46
57 26 0.26
58 6 0.06
59 2 0.02
60 21 0.21
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (57 bp):
AACAACATTTTTTAACCATGACGTGTAACAATAGTATTTTTTTTCAACACGACGTGT
Found at i:3031989 original size:52 final size:52
Alignment explanation
Indices: 3031923--3032026 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
3031913 ACAACATTTT
* *
3031923 TTAACCATGGCGTGTAACAATAGTATTTTTTTTCAACATGACGTGTAACAAC
1 TTAACCATGACGTGTAACAACAGTATTTTTTTTCAACATGACGTGTAACAAC
* * * *
3031975 TTAACCATGACGTGTAATAACAGTATTTTTTTTTAACATGATGTGTACCAAC
1 TTAACCATGACGTGTAACAACAGTATTTTTTTTCAACATGACGTGTAACAAC
3032027 CTAATAATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (52 bp):
TTAACCATGACGTGTAACAACAGTATTTTTTTTCAACATGACGTGTAACAAC
Found at i:3032082 original size:21 final size:21
Alignment explanation
Indices: 3032057--3032101 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3032047 GTTTTTGTAC
*
3032057 ATGGCATGTAACAACCTAATT
1 ATGGCATGTAACAACCTAACT
*
3032078 ATGGCGTGTAACAACCTAACT
1 ATGGCATGTAACAACCTAACT
3032099 ATG
1 ATG
3032102 ACTTGTTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGGCATGTAACAACCTAACT
Found at i:3032123 original size:66 final size:66
Alignment explanation
Indices: 3032017--3032141 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
3032007 TTAACATGAT
* * * *
3032017 GTGTACCAACCTAATAATGGCTTGTCACATGTTTTTGTACATGGCATGTAACAACCTAATTATGG
1 GTGTAACAACCTAATAATGACTTGTCACATATTTTTGTACATGACATGTAACAACCTAATTATGG
3032082 C
66 C
* * *
3032083 GTGTAACAACCTAACT-ATGACTTGTTACATATTTTTGTACATGACGTGTAATAACCTAA
1 GTGTAACAACCTAA-TAATGACTTGTCACATATTTTTGTACATGACATGTAACAACCTAA
3032142 CCATGACTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 50 0.98
67 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (66 bp):
GTGTAACAACCTAATAATGACTTGTCACATATTTTTGTACATGACATGTAACAACCTAATTATGG
C
Found at i:3032148 original size:45 final size:45
Alignment explanation
Indices: 3032082--3032214 Score: 176
Period size: 45 Copynumber: 3.0 Consensus size: 45
3032072 CTAATTATGG
* * *
3032082 CGTGTAACAACCTAACTATGACTTGTTACATATTTTTGTACATGA
1 CGTGTAATAACCTAACCATGACTTGTAACATATTTTTGTACATGA
* * * * *
3032127 CGTGTAATAACCTAACCATGACTTATCACATTTTTTTGTATATGG
1 CGTGTAATAACCTAACCATGACTTGTAACATATTTTTGTACATGA
* *
3032172 CGTGTAATAACCTAACCATGACGTGTAACATATTTTTGCACAT
1 CGTGTAATAACCTAACCATGACTTGTAACATATTTTTGTACAT
3032215 AACATATAAC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (45 bp):
CGTGTAATAACCTAACCATGACTTGTAACATATTTTTGTACATGA
Found at i:3034645 original size:16 final size:16
Alignment explanation
Indices: 3034626--3034662 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3034616 AAATTTTAAA
*
3034626 AATAAAAAATTTAATT
1 AATAAAAAATATAATT
*
3034642 AATAAAAACTATAATT
1 AATAAAAAATATAATT
3034658 AATAA
1 AATAA
3034663 TTTTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAAAAATATAATT
Found at i:3046723 original size:16 final size:16
Alignment explanation
Indices: 3046699--3046734 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3046689 GTTTAATGCC
*
3046699 TGTTTTTGGTAGACCT
1 TGTTCTTGGTAGACCT
*
3046715 TGTTCTTGGTAGATCT
1 TGTTCTTGGTAGACCT
3046731 TGTT
1 TGTT
3046735 GTTGCCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.25, T:0.53
Consensus pattern (16 bp):
TGTTCTTGGTAGACCT
Found at i:3054045 original size:18 final size:17
Alignment explanation
Indices: 3054024--3054058 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3054014 TCTCTCTCTC
3054024 TCTCTCTTTCTTTCTTTT
1 TCTCT-TTTCTTTCTTTT
*
3054042 TCTCTTTTTTTTCTTTT
1 TCTCTTTTCTTTCTTTT
3054059 GGGTTTTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTCTTTTCTTTCTTTT
Found at i:3058059 original size:27 final size:26
Alignment explanation
Indices: 3058007--3058084 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 26
3057997 AGGATAAGCA
* *
3058007 AGAGAGAGAGA-G-AGAGAGAGAGAG
1 AGAGAGAGAGAGGAAGGGAGGGAGAG
*
3058031 AGAGAGAGG-AGG-AGGGAGGGNAGAG
1 AGAGAGAGAGAGGAAGGGAGGG-AGAG
*
3058056 AGAGAGAGAGAGGAAGGGAGGGGGAG
1 AGAGAGAGAGAGGAAGGGAGGGAGAG
3058082 AGA
1 AGA
3058085 TTAAAGACGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.02
24 15 0.33
25 12 0.27
26 9 0.20
27 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.00
Consensus pattern (26 bp):
AGAGAGAGAGAGGAAGGGAGGGAGAG
Found at i:3058084 original size:2 final size:2
Alignment explanation
Indices: 3058007--3058067 Score: 81
Period size: 2 Copynumber: 31.0 Consensus size: 2
3057997 AGGATAAGCA
*
3058007 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG -G AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
3058047 AG GG NAG AG AG AG AG AG AG AG
1 AG AG -AG AG AG AG AG AG AG AG
3058068 GAAGGGAGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 2 0.04
2 49 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3063289 original size:2 final size:2
Alignment explanation
Indices: 3063282--3063317 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3063272 ATAAATGCAC
*
3063282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3063318 GTCACAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3071220 original size:124 final size:123
Alignment explanation
Indices: 3070931--3071156 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 123
3070921 AACCTTATCT
* ** * *
3070931 AAATGGACATACAAGGAGAAGATGGTAAGAATACTATTATAAGCAGATACCATGTTGCAATTTTA
1 AAATGGACAGACAAGGAGAAGATACTAAGAATACAAATATAAGCAGATACCATGTTGCAATTTTA
***
3070996 TATGAATAAACATAACAGAGAAATACCAATAAACGAAAACAGTATCACAAACCTTATCT
66 TATGAATAAACATAACAGAGAAATACCAATAAACGAAAACAGTATCACAAA-CTTAGAG
* * * *
3071055 AAATGGACATACAAGGAGAAGATAGTAAGAATACTATTATAAGCAGATACCATGTTGCAATTTTA
1 AAATGGACAGACAAGGAGAAGATACTAAGAATACAAATATAAGCAGATACCATGTTGCAATTTTA
3071120 TATGGAATAAACATAACAGAGAAATACCAATAAACGA
66 TAT-GAATAAACATAACAGAGAAATACCAATAAACGA
3071157 CAAGCATATT
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 67 0.67
125 33 0.33
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (123 bp):
AAATGGACAGACAAGGAGAAGATACTAAGAATACAAATATAAGCAGATACCATGTTGCAATTTTA
TATGAATAAACATAACAGAGAAATACCAATAAACGAAAACAGTATCACAAACTTAGAG
Found at i:3076787 original size:17 final size:17
Alignment explanation
Indices: 3076765--3076830 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
3076755 TAATTATACT
3076765 AATTATTTATATAAATA
1 AATTATTTATATAAATA
**
3076782 AATTA-TTATATATCTA
1 AATTATTTATATAAATA
* *
3076798 TAATTATTTATTTATACT-
1 -AATTATTTATATA-AATA
3076816 AATTATTTATA-AAAT
1 AATTATTTATATAAAT
3076831 CACATCCTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.05
16 10 0.25
17 20 0.50
18 6 0.15
19 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTTATATAAATA
Found at i:3077370 original size:17 final size:17
Alignment explanation
Indices: 3077348--3077413 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
3077338 TAATTATACT
3077348 AATTATTTATATAAATA
1 AATTATTTATATAAATA
**
3077365 AATTA-TTATATAGCTA
1 AATTATTTATATAAATA
* *
3077381 TAATTATTTATTTATACTA
1 -AATTATTTATATA-AATA
3077400 AA-TATTTATA-AAAT
1 AATTATTTATATAAAT
3077414 CACATCCTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.05
16 10 0.25
17 17 0.43
18 8 0.20
19 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTATTTATATAAATA
Found at i:3103643 original size:1 final size:1
Alignment explanation
Indices: 3103637--3103666 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
3103627 ACCCAAAACA
*
3103637 TTTTTTTTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3103667 ACAGAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:3106418 original size:389 final size:388
Alignment explanation
Indices: 3105701--3106477 Score: 1527
Period size: 389 Copynumber: 2.0 Consensus size: 388
3105691 AAAATATTAC
3105701 TAATTTTATATCAAGTTATATTGTTAATATATTATAATAAATAATAAAATTCATGATAACTTTAT
1 TAATTTTATATCAAGTTATATTGTTAATATATTATAATAAATAATAAAATTCATGATAACTTTAT
3105766 TATGTTTTGATTAATTATTAGTTTAATTATGTTTTAATTAATAATAATTAATTGATTTGATATAA
66 TATGTTTTGATTAATTATTAGTTTAATTATGTTTTAATTAATAATAATTAATTGATTTGATATAA
3105831 AATAAATTATATGAATTTAATTGGAGTAATAATAAAATAATAAAAATATATTTAAATTTTTTTAA
131 AATAAATTATATGAATTTAATTGGAGTAATAATAAAATAATAAAAATATATTTAAATTTTTTTAA
3105896 ATAATTAAAAAAAACTTTACTGTTTAAACCAAGATTTATTTACTATTTAATTTTACTGCCATTAC
196 ATAATTAAAAAAAACTTTACTGTTTAAACCAAGATTTATTTACTATTTAATTTTACTGCCATTAC
3105961 TAGAGTAATATTGAGATTGAGAAATGAGTTAATGAGAAATTTTAGACTATTCCCGGTTGTATTAT
261 TAGAGTAATATTGAGATTGAGAAATGAGTTAATGAGAAATTTTAGACTATTCCCGGTTGTATTAT
3106026 TGTAAAACGATCTTCCGCAATCCATCAGGAGTTGGGACCATCACCATTTTTCATCGGAGCCAA
326 TGTAAAACGATCTTCCGCAATCCATCAGGAGTTGGGACCATCACCATTTTTCATCGGAGCCAA
* *
3106089 NTAATTTTATATCAAGTTATATTGTTAATATATTATAATAAATAGTGAAATTCATGATAACTTTA
1 -TAATTTTATATCAAGTTATATTGTTAATATATTATAATAAATAATAAAATTCATGATAACTTTA
3106154 TTATGTTTTGATTAATTATTAGTTTAATTATGTTTTAATTAATAATAATTAATTGATTTGATATA
65 TTATGTTTTGATTAATTATTAGTTTAATTATGTTTTAATTAATAATAATTAATTGATTTGATATA
3106219 AAATAAATTATATGAATTTAATTGGAGTAATAATAAAATAATAAAAATATATTTAAATTTTTTTA
130 AAATAAATTATATGAATTTAATTGGAGTAATAATAAAATAATAAAAATATATTTAAATTTTTTTA
3106284 AATAATTAAAAAAAACTTTACTGTTTAAACCAAGATTTATTTACTATTTAATTTTACTGCCATTA
195 AATAATTAAAAAAAACTTTACTGTTTAAACCAAGATTTATTTACTATTTAATTTTACTGCCATTA
3106349 CTAGAGTAATATTGAGATTGAGAAATGAGTTAATGAGAAATTTTAGACTATTCCCGGTTGTATTA
260 CTAGAGTAATATTGAGATTGAGAAATGAGTTAATGAGAAATTTTAGACTATTCCCGGTTGTATTA
3106414 TTGTAAAACGATCTTCCGCAATCCATCAGGAGTTGGGACCATCACCATTTTTCATCGGAGCCAA
325 TTGTAAAACGATCTTCCGCAATCCATCAGGAGTTGGGACCATCACCATTTTTCATCGGAGCCAA
3106478 GCACGTGTGG
Statistics
Matches: 386, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
389 386 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (388 bp):
TAATTTTATATCAAGTTATATTGTTAATATATTATAATAAATAATAAAATTCATGATAACTTTAT
TATGTTTTGATTAATTATTAGTTTAATTATGTTTTAATTAATAATAATTAATTGATTTGATATAA
AATAAATTATATGAATTTAATTGGAGTAATAATAAAATAATAAAAATATATTTAAATTTTTTTAA
ATAATTAAAAAAAACTTTACTGTTTAAACCAAGATTTATTTACTATTTAATTTTACTGCCATTAC
TAGAGTAATATTGAGATTGAGAAATGAGTTAATGAGAAATTTTAGACTATTCCCGGTTGTATTAT
TGTAAAACGATCTTCCGCAATCCATCAGGAGTTGGGACCATCACCATTTTTCATCGGAGCCAA
Found at i:3109166 original size:29 final size:29
Alignment explanation
Indices: 3109133--3109197 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
3109123 TCCGTGTATG
3109133 TGCAGTTGCTGATTACTTGGATAAAGACA
1 TGCAGTTGCTGATTACTTGGATAAAGACA
* * **
3109162 TGCAGTTGCTGGTTATTTGGATTTAGACA
1 TGCAGTTGCTGATTACTTGGATAAAGACA
3109191 TGCAGTT
1 TGCAGTT
3109198 ACTTGTAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (29 bp):
TGCAGTTGCTGATTACTTGGATAAAGACA
Found at i:3117182 original size:1 final size:1
Alignment explanation
Indices: 3117176--3117206 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
3117166 ATATATATAT
3117176 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3117207 TTCCATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3120894 original size:31 final size:30
Alignment explanation
Indices: 3120858--3120917 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
3120848 AAGTTAAAAA
3120858 TTTTATTCT-ATTCAAATAAATTTTTTATATT
1 TTTTATTCTAATT-AAAT-AATTTTTTATATT
*
3120889 TTTTATTTTAAATTAAATAATTTTTTATA
1 TTTTATTCT-AATTAAATAATTTTTTATA
3120918 ATTAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 19 0.73
32 4 0.15
33 3 0.12
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTATTCTAATTAAATAATTTTTTATATT
Found at i:3121060 original size:30 final size:30
Alignment explanation
Indices: 3121026--3121096 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 30
3121016 AATCATTAAT
3121026 TATAAAAATTTATTTAATTTAAA-ATAA-AAA
1 TATAAAAATTTATTT-A-TTAAATATAATAAA
3121056 TAT-AAAA-TT-TTTATTAAATATAATAAA
1 TATAAAAATTTATTTATTAAATATAATAAA
*
3121083 AATAAAAATTTATT
1 TATAAAAATTTATT
3121097 AAATAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 8 0.23
28 6 0.17
29 6 0.17
30 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATAAAAATTTATTTATTAAATATAATAAA
Found at i:3121062 original size:29 final size:27
Alignment explanation
Indices: 3121027--3121102 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
3121017 ATCATTAATT
*
3121027 ATAAAAATTTATTTAATTTAAAATAAAA
1 ATAAAAATTTATTTAA-ATAAAATAAAA
* *
3121055 ATATAAAATTTTTATTAAATATAATAAAA
1 ATA-AAAATTTAT-TTAAATAAAATAAAA
3121084 ATAAAAATTTA-TTAAATAA
1 ATAAAAATTTATTTAAATAA
3121103 TTTAAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 7 0.17
28 10 0.24
29 20 0.49
30 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAAAAATTTATTTAAATAAAATAAAA
Found at i:3134712 original size:18 final size:18
Alignment explanation
Indices: 3134689--3134741 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
3134679 ATAAATGTGT
*
3134689 CACGATAACACGTTTAAA
1 CACGATAACACGATTAAA
*
3134707 CACGATAACATGATTAAA
1 CACGATAACACGATTAAA
3134725 CACGATAACACGATTAA
1 CACGATAACACGATTAA
3134742 GTAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (18 bp):
CACGATAACACGATTAAA
Found at i:3141782 original size:66 final size:66
Alignment explanation
Indices: 3141700--3141832 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
3141690 CAAGGTCGTT
3141700 GAGGTATTGCTTTAAAATTTAAAATTATATATTTAGAATGATTGTAACTTCAATCCCTTCCTCCT
1 GAGGTATTGCTTTAAAATTTAAAATTATATATTTAGAATGATTGTAACTTCAATCCCTTCCTCCT
3141765 A
66 A
3141766 GAGGTATTGCTTTAAAATTTAAAATTATATATTTAGAATGATTGTAACTTCAATCCCTTCCTCCT
1 GAGGTATTGCTTTAAAATTTAAAATTATATATTTAGAATGATTGTAACTTCAATCCCTTCCTCCT
3141831 A
66 A
3141832 G
1 G
3141833 TACACTAACT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (66 bp):
GAGGTATTGCTTTAAAATTTAAAATTATATATTTAGAATGATTGTAACTTCAATCCCTTCCTCCT
A
Found at i:3154084 original size:2 final size:2
Alignment explanation
Indices: 3154077--3154119 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3154067 TGTATTGCTC
3154077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3154119 A
1 A
3154120 CATGTCCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3164445 original size:24 final size:24
Alignment explanation
Indices: 3164418--3164464 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3164408 AAAGCAACCA
3164418 CCACCGCCACCACCATAACCACCG
1 CCACCGCCACCACCATAACCACCG
*
3164442 CCACCGCCACCGCCATAACCACC
1 CCACCGCCACCACCATAACCACC
3164465 TCTCCTTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.60, G:0.09, T:0.04
Consensus pattern (24 bp):
CCACCGCCACCACCATAACCACCG
Found at i:3173049 original size:19 final size:19
Alignment explanation
Indices: 3173010--3173045 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3173000 CAAAATCACC
*
3173010 AAGAAAAAATTATTAAATA
1 AAGAAAAAATTATAAAATA
3173029 AAGAAAAAATTA-AAAAT
1 AAGAAAAAATTATAAAAT
3173046 TAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
AAGAAAAAATTATAAAATA
Found at i:3179552 original size:16 final size:16
Alignment explanation
Indices: 3179528--3179559 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3179518 TAGTTATTAT
*
3179528 GTGATAATAGAATAAA
1 GTGAAAATAGAATAAA
3179544 GTGAAAATAGAATAAA
1 GTGAAAATAGAATAAA
3179560 ATAGTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (16 bp):
GTGAAAATAGAATAAA
Found at i:3179797 original size:22 final size:23
Alignment explanation
Indices: 3179754--3179806 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
3179744 AATTTAATTA
3179754 AAATATTAATAATTAATCA-TTT
1 AAATATTAATAATTAATCATTTT
* * * *
3179776 GAATATTAATATTTATTTATTTT
1 AAATATTAATAATTAATCATTTT
3179799 AAATATTA
1 AAATATTA
3179807 TTATGATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATATTAATAATTAATCATTTT
Found at i:3188743 original size:13 final size:13
Alignment explanation
Indices: 3188725--3188749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3188715 TTTCTAATAT
3188725 GATGGTGTTCTGC
1 GATGGTGTTCTGC
3188738 GATGGTGTTCTG
1 GATGGTGTTCTG
3188750 TCAGCTTAAT
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:0.08, C:0.12, G:0.40, T:0.40
Consensus pattern (13 bp):
GATGGTGTTCTGC
Found at i:3199784 original size:30 final size:30
Alignment explanation
Indices: 3199750--3199820 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
3199740 AATAATTAGT
* **
3199750 TATAAATGTTTATTTGACTTAAAATAAAAG
1 TATAAAAGTTTATTTGACACAAAATAAAAG
**
3199780 TATAAAAACTTATTTGACACAAAATAAAAG
1 TATAAAAGTTTATTTGACACAAAATAAAAG
* *
3199810 TACAAAGGTTT
1 TATAAAAGTTT
3199821 GACTGACTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (30 bp):
TATAAAAGTTTATTTGACACAAAATAAAAG
Found at i:3200112 original size:87 final size:87
Alignment explanation
Indices: 3200011--3200183 Score: 269
Period size: 87 Copynumber: 2.0 Consensus size: 87
3200001 AAGTAATCTT
* *
3200011 TATCTACTTAAAACTAGCTAACAAAAGTTATTACATAACAGTTT-AAAATTTAAATGTT-AAAAT
1 TATCTACTTAAAACTAGCTAACAAAAGTTATTACATAAAAATTTCAAAA-TTAAATGTTAAAAAT
3200074 AGCAACAATTTTTAAATTTTAATA
65 -GCAACAATTTTTAAATTTTAATA
* *
3200098 TATCTACTTAAAACTAGCTAACAAGAGTTATTATATAAAAATTTCAAAATTAAATGTTAAAAATG
1 TATCTACTTAAAACTAGCTAACAAAAGTTATTACATAAAAATTTCAAAATTAAATGTTAAAAATG
*
3200163 CAATAATTTTTAAATTTTAAT
66 CAACAATTTTTAAATTTTAAT
3200184 GTAAATACAT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
87 70 0.89
88 9 0.11
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (87 bp):
TATCTACTTAAAACTAGCTAACAAAAGTTATTACATAAAAATTTCAAAATTAAATGTTAAAAATG
CAACAATTTTTAAATTTTAATA
Found at i:3203563 original size:22 final size:23
Alignment explanation
Indices: 3203526--3203568 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3203516 TGGTGGGTTA
* *
3203526 ATTTTTTTTGATTGATTGTTTTG
1 ATTTTTTTTGAGTGATCGTTTTG
3203549 ATTTTTTTTG-GTGATCGTTT
1 ATTTTTTTTGAGTGATCGTTT
3203569 ATTGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.12, C:0.02, G:0.19, T:0.67
Consensus pattern (23 bp):
ATTTTTTTTGAGTGATCGTTTTG
Found at i:3204009 original size:33 final size:33
Alignment explanation
Indices: 3203972--3204081 Score: 141
Period size: 33 Copynumber: 3.3 Consensus size: 33
3203962 AGGCTGTTGG
* * **
3203972 GGTTCCAAGTGAAGTTGAACCTCTGGAGGATGT
1 GGTTCCAAGTGAGGTTGGACCTAAGGAGGATGT
3204005 GGTT-CAGAGTGAGGTTGGACCTAAGGAGGATGT
1 GGTTCCA-AGTGAGGTTGGACCTAAGGAGGATGT
**
3204038 GGTTCGGAGTGAGGTTGGACCTAAGGAGGATGT
1 GGTTCCAAGTGAGGTTGGACCTAAGGAGGATGT
*
3204071 AGTTCCAAGTG
1 GGTTCCAAGTG
3204082 CTAAGGAGGA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.03
33 64 0.97
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.25
Consensus pattern (33 bp):
GGTTCCAAGTGAGGTTGGACCTAAGGAGGATGT
Found at i:3216843 original size:28 final size:28
Alignment explanation
Indices: 3216811--3216868 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
3216801 TAAACCTTGT
*
3216811 ATAGCTTTGAAGTGAATAAGA-ATGAACA
1 ATAGCTTTAAAGTGAATAA-ACATGAACA
3216839 ATAGCTTTAAAGTGAATAAACATGAACA
1 ATAGCTTTAAAGTGAATAAACATGAACA
3216867 AT
1 AT
3216869 CAGATGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (28 bp):
ATAGCTTTAAAGTGAATAAACATGAACA
Found at i:3219300 original size:2 final size:2
Alignment explanation
Indices: 3219295--3219323 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3219285 CTAAATCTTT
3219295 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
3219324 TTAATAAAAA
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:3219370 original size:2 final size:2
Alignment explanation
Indices: 3219363--3219389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3219353 TTACANTTAT
3219363 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
3219390 TTTAACTAAA
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:3224165 original size:17 final size:17
Alignment explanation
Indices: 3224128--3224168 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3224118 TACCATTTAT
*
3224128 TATT-TTTTTTAATGTA
1 TATTATTTTTTAATGAA
3224144 TATTATTTTTTAAT-AA
1 TATTATTTTTTAATGAA
3224160 TGATTATTT
1 T-ATTATTT
3224169 GAATTAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (17 bp):
TATTATTTTTTAATGAA
Found at i:3224167 original size:20 final size:18
Alignment explanation
Indices: 3224124--3224167 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3224114 TTATTACCAT
*
3224124 TTATTATTTTTTTTAATG
1 TTATTATTTTTTATAATG
3224142 TATATTATTTTTTAATAATG
1 T-TATTATTTTTT-ATAATG
3224162 ATTATT
1 -TTATT
3224168 TGAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 9 0.41
21 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTATTATTTTTTATAATG
Found at i:3229138 original size:20 final size:21
Alignment explanation
Indices: 3229086--3229138 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
3229076 TCTTGTATCT
3229086 TTCCTTGTCTTTCAATCCGATG
1 TTCCTTGTC-TTCAATCCGATG
*
3229108 TT-CTGGTTCTTC-ATCCGATG
1 TTCCTTG-TCTTCAATCCGATG
3229128 TTCCTTGTCTT
1 TTCCTTGTCTT
3229139 TCAAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 14 0.52
21 9 0.33
22 4 0.15
ACGTcount: A:0.09, C:0.26, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCCTTGTCTTCAATCCGATG
Found at i:3236717 original size:70 final size:69
Alignment explanation
Indices: 3236610--3236745 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 69
3236600 TATTAATTCC
* *
3236610 CAACTATTTATCCTATTTTCAATCAAGTAATAGTAATATATATTTAATGATCTTTAATACTTTTT
1 CAACTATTTATCCTATTTTCAATCAAGTAATAGTAATATATATCTAATGATCTCTAAT-CTTTTT
3236675 TTTCT
65 TTTCT
* *
3236680 CAACTATTT-TCTCTATTTTCAATCAATTAAT-GATAATATGTATCTAATGATCTCTAATCTTTT
1 CAACTATTTATC-CTATTTTCAATCAAGTAATAG-TAATATATATCTAATGATCTCTAATCTTTT
3236743 TTT
64 TTT
3236746 CATATATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
69 11 0.18
70 49 0.82
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (69 bp):
CAACTATTTATCCTATTTTCAATCAAGTAATAGTAATATATATCTAATGATCTCTAATCTTTTTT
TTCT
Found at i:3242679 original size:11 final size:11
Alignment explanation
Indices: 3242656--3242698 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
3242646 AAAAATTAAA
3242656 AAAT-AATAAT
1 AAATAAATAAT
3242666 AAATGAAA-AAT
1 AAAT-AAATAAT
3242677 AAATAAATAAT
1 AAATAAATAAT
3242688 -AATAAATAAT
1 AAATAAATAAT
3242698 A
1 A
3242699 TAATTGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 17 0.59
11 10 0.34
12 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:3242708 original size:28 final size:26
Alignment explanation
Indices: 3242646--3242713 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 26
3242636 TTTAATATTA
3242646 AAAAATTAAA-AAATAATAATAAATG
1 AAAAATTAAATAAATAATAATAAATG
3242671 AAAAA-TAAATAAATAATAATAAAT-
1 AAAAATTAAATAAATAATAATAAATG
3242695 AATATAATTGAAATAAATA
1 AA-A-AATT-AAATAAATA
3242714 TTTGAGTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.16
25 20 0.53
26 2 0.05
27 1 0.03
28 9 0.24
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (26 bp):
AAAAATTAAATAAATAATAATAAATG
Done.