Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 10 of 213
Found at i:2840319 original size:10 final size:9
Alignment explanation
Indices: 2840190--2840305 Score: 76
Period size: 9 Copynumber: 12.7 Consensus size: 9
2840180 TTTTTATGCA
2840190 TTTTATAATT
1 TTTTATAA-T
*
2840200 TTTTATCAT
1 TTTTATAAT
* *
2840209 TTTTAAAAAA
1 TTTT-ATAAT
2840219 TTTTAT-AT
1 TTTTATAAT
*
2840227 TTTTATATT
1 TTTTATAAT
*
2840236 TTTTCTAAT
1 TTTTATAAT
2840245 TTTTAT-AT
1 TTTTATAAT
2840253 TTTTAT-AT
1 TTTTATAAT
*
2840261 TTTTATTAAAA
1 TTTTA-T-AAT
* *
2840272 TTTAATATT
1 TTTTATAAT
*
2840281 TTTTATAAC
1 TTTTATAAT
*
2840290 TTTTATTTAT
1 TTTTA-TAAT
2840300 TTTTAT
1 TTTTAT
2840306 TTTTATAAAT
Statistics
Matches: 81, Mismatches: 19, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
8 22 0.27
9 33 0.41
10 21 0.26
11 5 0.06
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2849702 original size:39 final size:40
Alignment explanation
Indices: 2849648--2849725 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
2849638 CTTTATATTG
2849648 CCAAAAAGAAAAATAGAAATCCC-CCCAAATCCCTTTTTT
1 CCAAAAAGAAAAATAGAAATCCCTCCCAAATCCCTTTTTT
*
2849687 CCAAAAAGAAAAATAGAAATCCCTCCTAAATCCCTTTTT
1 CCAAAAAGAAAAATAGAAATCCCTCCCAAATCCCTTTTT
2849726 AACGTTTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 23 0.62
40 14 0.38
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (40 bp):
CCAAAAAGAAAAATAGAAATCCCTCCCAAATCCCTTTTTT
Found at i:2851500 original size:90 final size:90
Alignment explanation
Indices: 2851406--2851572 Score: 212
Period size: 90 Copynumber: 1.9 Consensus size: 90
2851396 TTAGTGGCTA
* * * * **
2851406 ATCCTATAAATTCGGTAG-GTTTATCAAGTCTATCTCAATAGGACCACCCAAACTCT-AGGCTGT
1 ATCCTATAAATTCGG-AGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTATGA-GCAAT
2851469 GAACTCATTAAGAGCTTCTAGTAGTTC
64 GAACTCATTAAGAGCTTCTAGTAGTTC
* * * *
2851496 ATCCTATAAATTTGGAGAATTCATCAAGTCCGTCTTAGTAGGACCACCCAAACTATGAGCAATGA
1 ATCCTATAAATTCGGAGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTATGAGCAATGA
2851561 ACTCATTAAGAG
66 ACTCATTAAGAG
2851573 TAACAAACTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 2 0.03
90 62 0.95
91 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (90 bp):
ATCCTATAAATTCGGAGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTATGAGCAATGA
ACTCATTAAGAGCTTCTAGTAGTTC
Found at i:2852015 original size:15 final size:15
Alignment explanation
Indices: 2851991--2852020 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2851981 ATTTTATGGT
2851991 GGAGCAAGCAACACA
1 GGAGCAAGCAACACA
*
2852006 GGAGCGAGCAACACA
1 GGAGCAAGCAACACA
2852021 CGTCTGTTTA
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:0.43, C:0.27, G:0.30, T:0.00
Consensus pattern (15 bp):
GGAGCAAGCAACACA
Found at i:2868041 original size:16 final size:15
Alignment explanation
Indices: 2868020--2868049 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2868010 ACACTATGCT
2868020 TTTTCTTTTTCTTTTC
1 TTTTCTTTTT-TTTTC
2868036 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
2868050 ATATCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:2868455 original size:33 final size:33
Alignment explanation
Indices: 2868413--2868477 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
2868403 TGAGATTGAA
*
2868413 TCATAAAAATTGTCTACTAATGGTGTATGTAGT
1 TCATAAAAATTGTCTACTAATGGTGTACGTAGT
2868446 TCATAAAAATTGTCTACTAATGGTGTACGTAG
1 TCATAAAAATTGTCTACTAATGGTGTACGTAG
2868478 ATAATAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (33 bp):
TCATAAAAATTGTCTACTAATGGTGTACGTAGT
Found at i:2873480 original size:18 final size:18
Alignment explanation
Indices: 2873459--2873497 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2873449 TCTAAATAAT
2873459 ATATAAATAAAATT-AAAA
1 ATATAAA-AAAATTCAAAA
2873477 ATATAAAAAAATTCAAAA
1 ATATAAAAAAATTCAAAA
2873495 ATA
1 ATA
2873498 ATAATTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATATAAAAAAATTCAAAA
Found at i:2873718 original size:15 final size:15
Alignment explanation
Indices: 2873698--2873733 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2873688 AAATAATTTC
2873698 ACTCGATTCAATTCA
1 ACTCGATTCAATTCA
* *
2873713 ATTCGATTCGATTCA
1 ACTCGATTCAATTCA
2873728 ACTCGA
1 ACTCGA
2873734 CTTGAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (15 bp):
ACTCGATTCAATTCA
Found at i:2877580 original size:15 final size:16
Alignment explanation
Indices: 2877553--2877582 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2877543 AAATATCATA
2877553 AGCCCGAGCCCGGCCT
1 AGCCCGAGCCCGGCCT
2877569 AGCCCG-GCCCGGCC
1 AGCCCGAGCCCGGCC
2877583 CGGCCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.53, G:0.33, T:0.03
Consensus pattern (16 bp):
AGCCCGAGCCCGGCCT
Found at i:2877649 original size:31 final size:30
Alignment explanation
Indices: 2877604--2877662 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
2877594 TAAAATAAAC
*
2877604 ATTTAAAAATTATTTTAAAAATAAAAAATTT
1 ATTTAAAAAGTA-TTTAAAAATAAAAAATTT
*
2877635 ATTTTAAAAGTATTTAAAAATAAAAAAT
1 ATTTAAAAAGTATTTAAAAATAAAAAAT
2877663 AAAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTAAAAAGTATTTAAAAATAAAAAATTT
Found at i:2877662 original size:7 final size:7
Alignment explanation
Indices: 2877650--2877685 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
2877640 AAAAGTATTT
2877650 AAAAATA
1 AAAAATA
2877657 AAAAATA
1 AAAAATA
*
2877664 AAAAAAA
1 AAAAATA
2877671 TAAAAATA
1 -AAAAATA
2877679 AAAAATA
1 AAAAATA
2877686 TATATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:2877668 original size:15 final size:15
Alignment explanation
Indices: 2877650--2877683 Score: 59
Period size: 15 Copynumber: 2.2 Consensus size: 15
2877640 AAAAGTATTT
2877650 AAAAATAAAAAATAAA
1 AAAAAT-AAAAATAAA
2877666 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
2877681 AAA
1 AAA
2877684 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:2883049 original size:12 final size:11
Alignment explanation
Indices: 2883032--2883064 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
2883022 TTAATACAAA
2883032 AAATATGATTTT
1 AAATAT-ATTTT
2883044 AAATATA-TTT
1 AAATATATTTT
2883054 AAATATATTTT
1 AAATATATTTT
2883065 TTTTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
AAATATATTTT
Found at i:2883860 original size:23 final size:24
Alignment explanation
Indices: 2883834--2883883 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
2883824 TAGTTGACTT
*
2883834 AAATTTTTAAA-CTCGAAAAATAA
1 AAATTATTAAATCTCGAAAAATAA
* *
2883857 AAA-TATTAAATTTCTAAAAATAA
1 AAATTATTAAATCTCGAAAAATAA
2883880 AAAT
1 AAAT
2883884 ATAAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTATTAAATCTCGAAAAATAA
Found at i:2883865 original size:22 final size:23
Alignment explanation
Indices: 2883840--2883885 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2883830 ACTTAAATTT
2883840 TTAAA-CTCGAAAAATAAAAATA
1 TTAAATCTCGAAAAATAAAAATA
* *
2883862 TTAAATTTCTAAAAATAAAAATA
1 TTAAATCTCGAAAAATAAAAATA
2883885 T
1 T
2883886 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAATCTCGAAAAATAAAAATA
Found at i:2892578 original size:6 final size:6
Alignment explanation
Indices: 2892569--2892602 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2892559 CACCGATCTT
*
2892569 CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCT
2892603 ATCCTTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCCTTC
Found at i:2895496 original size:20 final size:20
Alignment explanation
Indices: 2895471--2895512 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2895461 TTTCTGTTTA
2895471 ATATATAAATTTATTAATAT
1 ATATATAAATTTATTAATAT
2895491 ATATATAAATTTATTAATAT
1 ATATATAAATTTATTAATAT
2895511 AT
1 AT
2895513 GTAAAAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATAAATTTATTAATAT
Found at i:2895765 original size:21 final size:21
Alignment explanation
Indices: 2895740--2895781 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2895730 CCTTTCTCTT
2895740 TCAGTTATATGGAGGAGTGAG
1 TCAGTTATATGGAGGAGTGAG
2895761 TCAGTTATATGGAGGAGTGAG
1 TCAGTTATATGGAGGAGTGAG
2895782 AGCTTAGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.38, T:0.29
Consensus pattern (21 bp):
TCAGTTATATGGAGGAGTGAG
Found at i:2903005 original size:16 final size:15
Alignment explanation
Indices: 2902964--2903006 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2902954 TTTTTACAAT
*
2902964 TATTTTAATTTTATT
1 TATTTTAATTTTATA
2902979 TATTTTTAATTTTATCA
1 TA-TTTTAATTTTAT-A
*
2902996 TATTTAAATTT
1 TATTTTAATTT
2903007 CCTTTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTAATTTTATA
Found at i:2904579 original size:40 final size:39
Alignment explanation
Indices: 2904460--2904592 Score: 171
Period size: 40 Copynumber: 3.4 Consensus size: 39
2904450 GTTCGAGTTC
* * *
2904460 ATGAGACACTGGGTGTCAATCTATCACTTCAGATTTATTTG
1 ATGAGGCACTGGGTGTCAATTTAT-ACTTC-GATTTATCTG
* *
2904501 ATGAGGCACTGGGTGCCAA-TT-TACTTCGATTTAACTG
1 ATGAGGCACTGGGTGTCAATTTATACTTCGATTTATCTG
*
2904538 ATGAGGCACTGGGTGTCAATTTACTACTTCGAATTATCTG
1 ATGAGGCACTGGGTGTCAATTTA-TACTTCGATTTATCTG
2904578 ATGAGGCACTGGGTG
1 ATGAGGCACTGGGTG
2904593 CCAAATTGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
37 26 0.32
38 7 0.09
39 1 0.01
40 30 0.37
41 17 0.21
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
ATGAGGCACTGGGTGTCAATTTATACTTCGATTTATCTG
Found at i:2906065 original size:31 final size:32
Alignment explanation
Indices: 2906006--2906070 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
2905996 GGCAAATTAC
2906006 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
2906038 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
2906069 AA
1 AA
2906071 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:2911803 original size:98 final size:98
Alignment explanation
Indices: 2911634--2911824 Score: 328
Period size: 98 Copynumber: 1.9 Consensus size: 98
2911624 ATACAATAAA
*
2911634 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
2911699 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* * *
2911732 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTATGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
* *
2911797 CCTTTAGGATCTCAAACTCGGAATATTT
66 CCTTTAGAATCCCAAACTCGGAATATTT
2911825 TCTTCATGAT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:2912929 original size:19 final size:19
Alignment explanation
Indices: 2912896--2912987 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
2912886 AATCATATAT
*
2912896 TCTAAGATTGCATATCATA
1 TCTAATATTGCATATCATA
**
2912915 TCTAATATTATATATCATA
1 TCTAATATTGCATATCATA
2912934 TCTAATATTGCATATCATA
1 TCTAATATTGCATATCATA
**
2912953 TCTAGGATTGCATATCATA
1 TCTAATATTGCATATCATA
*
2912972 TCTAAGATTGCATATC
1 TCTAATATTGCATATC
2912988 CTCAAAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAATATTGCATATCATA
Found at i:2912944 original size:38 final size:38
Alignment explanation
Indices: 2912873--2912987 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 38
2912863 AAATTAAATC
*
2912873 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
* * *
2912915 TCTAATATTATATATCATATCTAATATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
2912953 TCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
2912988 CTCAAAAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 48 0.75
39 3 0.05
41 4 0.06
42 9 0.14
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:2913458 original size:132 final size:132
Alignment explanation
Indices: 2913216--2914530 Score: 2035
Period size: 132 Copynumber: 10.0 Consensus size: 132
2913206 CTGCAACTGC
* * * ** *
2913216 AGGGAGATAATA-CTTACAATCTTCAACCTATTCCACTGCTAACCAGGG-AGATAGAATTACTGA
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGG
** *
2913279 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTCGATCTACTCCACTACT
64 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
2913344 GCTT
129 GCTT
** * *
2913348 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
2913413 TTAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCAATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
2913478 TT
131 TT
* *
2913480 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCTAGGG-AGATAGAATTACTGAC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGC
* *
2913544 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTG
65 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
2913609 CTT
130 CTT
* ** * *
2913612 AGGGAGATAAGATCTGAAATCTTCAATCTATTTCACTATTGCCCAGGGAGGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
2913677 TCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCGCAATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
2913742 TT
131 TT
* * *
2913744 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCTAGGG-AGATAGAATTACTGAC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGC
* * * **
2913808 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACTATCTTTGATCTATTCCACTACTG
65 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
2913873 CTT
130 CTT
* ** * *
2913876 AGGGAGATAAGATCTGAAATCTTCAATTTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* *
2913941 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCAATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
2914006 TT
131 TT
2914008 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
2914073 TCAATGTACTCCACTATAACCACATGGAGGTAAAATCCGTCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
2914138 TT
131 TT
*
2914140 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * * * *
2914205 TCAATGTACTCTACTATAACTATAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
2914270 TT
131 TT
*
2914272 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* *
2914337 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
2914402 TT
131 TT
*
2914404 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
2914469 TCAATGTACTCCATTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCGACTAC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC
2914531 AAACGAGGAA
Statistics
Matches: 1084, Mismatches: 93, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
131 3 0.00
132 1073 0.99
133 8 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:2915789 original size:6 final size:6
Alignment explanation
Indices: 2915780--2915821 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
2915770 TCACTTTCAT
2915780 TTTTTG TTTTTG TTTTTG TTTTTTG TTTTTG TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG
2915822 AATTTGAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
7 6 0.18
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:2915795 original size:13 final size:13
Alignment explanation
Indices: 2915780--2915820 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2915770 TCACTTTCAT
2915780 TTTTTG-TTTTTG
1 TTTTTGTTTTTTG
2915792 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
2915805 TTTTTGTTTTTT-
1 TTTTTGTTTTTTG
2915817 TTTT
1 TTTT
2915821 GAATTTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:2915801 original size:19 final size:18
Alignment explanation
Indices: 2915779--2915820 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
2915769 TTCACTTTCA
2915779 TTTTTTGTTTTTGTTTTT
1 TTTTTTGTTTTTGTTTTT
2915797 GTTTTTTGTTTTTGTTTTT
1 -TTTTTTGTTTTTGTTTTT
2915816 TTTTT
1 TTTTT
2915821 GAATTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTTTTGTTTTTGTTTTT
Found at i:2920117 original size:37 final size:37
Alignment explanation
Indices: 2920076--2920215 Score: 235
Period size: 37 Copynumber: 3.8 Consensus size: 37
2920066 TTTGAGTACT
**
2920076 TCTGATCAAGAAACAAAGTGATAAGTGACTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
2920113 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
2920150 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
** *
2920187 TCTGATCAAGTGATAAAGTGATAAGTGGT
1 TCTGATCAAGAAACAAAGTGATAAGTGGT
2920216 AGCTTCAGCT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
Found at i:2920232 original size:46 final size:44
Alignment explanation
Indices: 2920179--2920299 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 44
2920169 GATAAGTGGT
*
2920179 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGC
1 TACACTTATCTGATCAAGTGA-AAAGTGATAAGTGGTAGCCT-AGC
*
2920225 TACACTTATCTGATCAAGTAGCAAAGTGATAAGTGGTAGCCTAGC
1 TACACTTATCTGATCAAGT-GAAAAGTGATAAGTGGTAGCCTAGC
*
2920270 TACA-TTATCTGATCAAG-GACAAGTGATAAG
1 TACACTTATCTGATCAAGTGAAAAGTGATAAG
2920300 AGGTCATATG
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
42 11 0.16
44 13 0.19
45 7 0.10
46 38 0.54
47 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (44 bp):
TACACTTATCTGATCAAGTGAAAAGTGATAAGTGGTAGCCTAGC
Found at i:2927771 original size:37 final size:37
Alignment explanation
Indices: 2927730--2927869 Score: 235
Period size: 37 Copynumber: 3.8 Consensus size: 37
2927720 TTTGAGTACT
**
2927730 TCTGATCAAGAAACAAAGTGATAAGTGACTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
2927767 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
2927804 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
** *
2927841 TCTGATCAAGTGATAAAGTGATAAGTGGT
1 TCTGATCAAGAAACAAAGTGATAAGTGGT
2927870 AGCTTCAGCT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
Found at i:2927886 original size:46 final size:44
Alignment explanation
Indices: 2927833--2927954 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 44
2927823 GATAAGTGGT
*
2927833 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGC
1 TACACTTATCTGATCAAGTGA-AAAGTGATAAGTGGTAGCCT-AGC
*
2927879 TACACTTATCTGATCAAGTAGCAAAGTGATAAGTGGTAGCCTAGC
1 TACACTTATCTGATCAAGT-GAAAAGTGATAAGTGGTAGCCTAGC
* *
2927924 TACATTTATCTGATCAAG-GACAAGTGATAAG
1 TACACTTATCTGATCAAGTGAAAAGTGATAAG
2927955 AGGTCATATG
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
43 11 0.16
45 20 0.29
46 38 0.54
47 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (44 bp):
TACACTTATCTGATCAAGTGAAAAGTGATAAGTGGTAGCCTAGC
Found at i:2929994 original size:98 final size:98
Alignment explanation
Indices: 2929825--2930019 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
2929815 ATACAATAAA
*
2929825 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
2929890 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
2929923 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
* *
2929988 CCTTTAGGATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
2930020 CATGATTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:2931108 original size:19 final size:19
Alignment explanation
Indices: 2931084--2931175 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
2931074 AATCATATAT
*
2931084 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
**
2931103 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
2931122 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2931141 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2931160 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2931176 CTCAAAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2931131 original size:38 final size:38
Alignment explanation
Indices: 2931061--2931175 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
2931051 AAATTAAATC
* *
2931061 TCTAAGATTACAAAATCATATATTCTAAGATTGTATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
2931103 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
2931141 TCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
2931176 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 50 0.75
39 3 0.04
41 4 0.06
42 10 0.15
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:2932503 original size:40 final size:40
Alignment explanation
Indices: 2932446--2932556 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
2932436 GTTTGGATAA
* * *
2932446 AAAATGCCACTAAAGATCGAGCATTAGCGGCGCTCTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTCTTTGG
* *
2932486 AAAACGCCGCTAAAGATCGAGTATTAGCAGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTCTTTGG
* *
2932526 AAAACGCCGCTAAA-AACAAGCATTAGCAGCG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCG
2932557 TTTTCCAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 14 0.22
40 49 0.78
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTCTTTGG
Found at i:2932691 original size:41 final size:41
Alignment explanation
Indices: 2932619--2933032 Score: 591
Period size: 41 Copynumber: 10.1 Consensus size: 41
2932609 CTTTGGGGGT
* *
2932619 TTTAGCGGCGTTTTTGAGAAAGCGACGCTAATGCTCAGGAC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
2932660 TTTAGCGGCGTTTTTGGGAAATCGCCACTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
2932701 TTTAGCGGCATTTTTGGGAAAGCGCCGCTTATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
2932742 TTTAGCGACATTTTTGTA-AAAGCGCTGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTG-AGAAAGCGCCGCTAATGCTCAGGGC
*
2932783 TTTAACGGCGTTTTTG-GTAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAG-AAAGCGCCGCTAATGCTCAGGGC
2932824 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
2932865 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
*
2932906 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
** *
2932947 TTTAGCGGCGTTTTTGTTAAAGCGCCGCGAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
2932988 TTTAGCGACATTTTCTAAG-AAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTT-TGAGAAAGCGCCGCTAATGCTCAGGGC
2933029 TTTA
1 TTTA
2933033 AAATAATTTA
Statistics
Matches: 336, Mismatches: 32, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
41 334 0.99
42 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:2933277 original size:7 final size:7
Alignment explanation
Indices: 2933250--2933368 Score: 55
Period size: 7 Copynumber: 16.4 Consensus size: 7
2933240 GGTTTATAAA
2933250 TTATGGGT
1 TTAT-GGT
* *
2933258 TTAGGGG
1 TTATGGT
2933265 TTATGGT
1 TTATGGT
2933272 TTATGGT
1 TTATGGT
*
2933279 TTATGAT
1 TTATGGT
* *
2933286 TTAAAGGC
1 TT-ATGGT
*
2933294 TTAAGGT
1 TTATGGT
*
2933301 TTA-GAGG
1 TTATG-GT
2933308 TTAT-GT
1 TTATGGT
*
2933314 GTTAAGAGT
1 -TTATG-GT
2933323 TTATGGTT
1 TTATGG-T
2933331 TTATGGTT
1 TTATGG-T
2933339 TTATGGT
1 TTATGGT
*
2933346 TTA-AGT
1 TTATGGT
*
2933352 TTGTGGT
1 TTATGGT
*
2933359 TTAGGGT
1 TTATGGT
2933366 TTA
1 TTA
2933369 GATTAACTAG
Statistics
Matches: 85, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
6 6 0.07
7 51 0.60
8 26 0.31
9 2 0.02
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (7 bp):
TTATGGT
Found at i:2933335 original size:8 final size:8
Alignment explanation
Indices: 2933322--2933347 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2933312 GTGTTAAGAG
2933322 TTTATGGT
1 TTTATGGT
2933330 TTTATGGT
1 TTTATGGT
2933338 TTTATGGT
1 TTTATGGT
2933346 TT
1 TT
2933348 AAGTTTGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (8 bp):
TTTATGGT
Found at i:2938369 original size:16 final size:16
Alignment explanation
Indices: 2938348--2938415 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
2938338 GATTTGCTAT
2938348 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2938364 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
2938380 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
*
2938396 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
2938412 TACA
1 TACA
2938416 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2942347 original size:43 final size:43
Alignment explanation
Indices: 2942286--2942372 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
2942276 CAATGATGTA
* * *
2942286 CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* *
2942329 CAAGATTTACTTGATTAAGAAAATGCATTTTATGTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
2942372 C
1 C
2942373 TTGCATATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:2942571 original size:24 final size:22
Alignment explanation
Indices: 2942544--2942595 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2942534 TAATATTTTT
* *
2942544 TATTTATTCTTAAAACATATATAA
1 TATTTA-TCATAAAA-ATAAATAA
*
2942568 TATTTATCATAAAAATAAATAT
1 TATTTATCATAAAAATAAATAA
2942590 TATTTA
1 TATTTA
2942596 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
23 7 0.28
24 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTATCATAAAAATAAATAA
Found at i:2942677 original size:43 final size:43
Alignment explanation
Indices: 2942630--2942852 Score: 383
Period size: 43 Copynumber: 5.2 Consensus size: 43
2942620 GTTTTTAGTA
2942630 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
* *
2942673 GCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
** * * *
2942716 GTATTTGTGGGAGAAGCGCCGCTAAAGGTCTTGTTCTATAGTG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
2942759 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
2942802 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
2942845 GCGTTTGT
1 GCGTTTGT
2942853 TTCTAAAAAC
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 170 1.00
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
Found at i:2954361 original size:9 final size:9
Alignment explanation
Indices: 2954347--2954371 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2954337 CTTGGGTCAG
2954347 AACCTCTTC
1 AACCTCTTC
2954356 AACCTCTTC
1 AACCTCTTC
2954365 AACCTCT
1 AACCTCT
2954372 AATTCCTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (9 bp):
AACCTCTTC
Found at i:2959816 original size:19 final size:20
Alignment explanation
Indices: 2959794--2959833 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2959784 TTTTTTAGAT
2959794 AATT-ACATTTATTTTTTTA
1 AATTAACATTTATTTTTTTA
*
2959813 AATTAAGATTTATTTTTTTA
1 AATTAACATTTATTTTTTTA
2959833 A
1 A
2959834 TTTCATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTAACATTTATTTTTTTA
Found at i:2960617 original size:20 final size:19
Alignment explanation
Indices: 2960588--2960625 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2960578 AAATATCTTG
*
2960588 ATATTTTTTAGTTAAAATT
1 ATATTTTTTAATTAAAATT
2960607 ATATATTTTTAATTAAAAT
1 ATAT-TTTTTAATTAAAAT
2960626 AATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAATTAAAATT
Found at i:2960635 original size:21 final size:20
Alignment explanation
Indices: 2960592--2960631 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2960582 ATCTTGATAT
* * *
2960592 TTTTTAGTTAAAATTATATA
1 TTTTTAATTAAAATAATAAA
2960612 TTTTTAATTAAAATAATAAA
1 TTTTTAATTAAAATAATAAA
2960632 ATTTACAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAATTAAAATAATAAA
Found at i:2960936 original size:42 final size:42
Alignment explanation
Indices: 2960890--2960969 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
2960880 AGCTAGACAC
* *
2960890 GCTTTCTGCATAGTTAGT-AGAAAAGCTCGTACAGCTGGGCAA
1 GCTTTCTGCATAATTA-TCAGAAAAGCTCATACAGCTGGGCAA
* * *
2960932 GCTTTTTGCATAATTATCAGGAAAGCTCATTCAGCTGG
1 GCTTTCTGCATAATTATCAGAAAAGCTCATACAGCTGG
2960970 ATGAGCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.03
42 31 0.97
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
GCTTTCTGCATAATTATCAGAAAAGCTCATACAGCTGGGCAA
Found at i:2961529 original size:3 final size:3
Alignment explanation
Indices: 2961521--2961563 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2961511 TATCAACCAC
2961521 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2961564 CACACTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2965155 original size:19 final size:19
Alignment explanation
Indices: 2965123--2965173 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
2965113 GAAGAGAATG
* *
2965123 GAAAAAAA-GAAAAAAAAA
1 GAAAAAAATTAAAAGAAAA
*
2965141 GAAAGAAAATTAAAAGAACA
1 GAAA-AAAATTAAAAGAAAA
*
2965161 TAAAAAAATTAAA
1 GAAAAAAATTAAA
2965174 TTGCTCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (19 bp):
GAAAAAAATTAAAAGAAAA
Found at i:2967804 original size:17 final size:17
Alignment explanation
Indices: 2967782--2967826 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2967772 ACTTGACAGA
* *
2967782 AGAGTTCGCCAAACCCT
1 AGAGTTTGCCAAAACCT
*
2967799 AGAGTTTGCCAAAACTT
1 AGAGTTTGCCAAAACCT
2967816 AGAGTTTGCCA
1 AGAGTTTGCCA
2967827 GACGACGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (17 bp):
AGAGTTTGCCAAAACCT
Found at i:2971835 original size:15 final size:15
Alignment explanation
Indices: 2971811--2971843 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2971801 AACATTGGGG
2971811 TAAT-ATTAAATATA
1 TAATAATTAAATATA
2971825 TAATAATTAAATATA
1 TAATAATTAAATATA
2971840 -AATA
1 TAATA
2971844 CAATGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATTAAATATA
Found at i:2978794 original size:38 final size:38
Alignment explanation
Indices: 2978752--2978829 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2978742 TGATCAAAGC
2978752 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
1 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
2978790 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
1 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
2978828 AA
1 AA
2978830 CTATACGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (38 bp):
AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
Found at i:2983911 original size:21 final size:21
Alignment explanation
Indices: 2983873--2983912 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2983863 TAATCTGTCC
*
2983873 ATTAAAGCTTATGTTGCTAAA
1 ATTAAAGATTATGTTGCTAAA
2983894 ATTAAAGATT-TGTGTGCTA
1 ATTAAAGATTATGT-TGCTA
2983913 TGTTAGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTAAAGATTATGTTGCTAAA
Found at i:2988486 original size:31 final size:31
Alignment explanation
Indices: 2988443--2988502 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2988433 CATATTCACT
2988443 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
* *
2988474 TATATCCACCTATGCGGAATGCATACATA
1 TATACCCACCTATGCCGAATGCATACATA
2988503 AACACACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (31 bp):
TATACCCACCTATGCCGAATGCATACATATA
Found at i:2988757 original size:41 final size:42
Alignment explanation
Indices: 2988707--2988888 Score: 230
Period size: 41 Copynumber: 4.4 Consensus size: 42
2988697 TGGCACGTCA
* * * * *
2988707 CCTGATAGGCTTATAGTCC-AATTCTGTTCATCGGCACTTAG
1 CCTGCTAGGCGTATAGTCCTGATTCAGTTCACCGGCACTTAG
*
2988748 CCTGCTAGGCCTATAG-CCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCGTATAGTCCTGATTCAGTTCACCGGCACTTAG
* *
2988789 CCTGCTAGGCTTGTAG-CCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCGTATAGTCCTGATTCAGTTCACCGGCACTTAG
*
2988830 CCTGCT-GGACGTATAGTCC-GATTCAATTCACCGGCACTTAG
1 CCTGCTAGG-CGTATAGTCCTGATTCAGTTCACCGGCACTTAG
*
2988871 CCTGCTAGACGTATAGTC
1 CCTGCTAGGCGTATAGTC
2988889 TGAACAATTT
Statistics
Matches: 126, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
40 4 0.03
41 119 0.94
42 3 0.02
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (42 bp):
CCTGCTAGGCGTATAGTCCTGATTCAGTTCACCGGCACTTAG
Found at i:2992650 original size:3 final size:3
Alignment explanation
Indices: 2992624--2992679 Score: 62
Period size: 3 Copynumber: 18.0 Consensus size: 3
2992614 ATTAGCAATT
2992624 TTA TTA TTTA GTTAA TTA TT- TTA TTA TTA TT- TTCA TTA TTA TTA TTA
1 TTA TTA -TTA -TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
2992671 TTA TTA TTA
1 TTA TTA TTA
2992680 GTTTTATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.09
3 33 0.70
4 9 0.19
5 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2992686 original size:15 final size:14
Alignment explanation
Indices: 2992621--2992687 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 14
2992611 GTTATTAGCA
2992621 ATTTTATTATTTAGTT
1 ATTTTATTA-TTA-TT
2992637 AATTATT-TTATTATT
1 -ATT-TTATTATTATT
2992652 ATTTTCATTATTATT
1 ATTTT-ATTATTATT
2992667 A--TTATTATTATT
1 ATTTTATTATTATT
2992679 AGTTTTATT
1 A-TTTTATT
2992688 TTCCTTTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
12 10 0.23
13 4 0.09
14 3 0.07
15 16 0.36
16 3 0.07
17 6 0.14
18 2 0.05
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:3001372 original size:51 final size:51
Alignment explanation
Indices: 3001310--3001418 Score: 209
Period size: 51 Copynumber: 2.1 Consensus size: 51
3001300 ATAGATATAG
*
3001310 ATAGTATGGTAGAAAGATTCATATTTTTTTTCTACCATACTATCGAGTTTT
1 ATAGGATGGTAGAAAGATTCATATTTTTTTTCTACCATACTATCGAGTTTT
3001361 ATAGGATGGTAGAAAGATTCATATTTTTTTTCTACCATACTATCGAGTTTT
1 ATAGGATGGTAGAAAGATTCATATTTTTTTTCTACCATACTATCGAGTTTT
3001412 ATAGGAT
1 ATAGGAT
3001419 ACTGCTGATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (51 bp):
ATAGGATGGTAGAAAGATTCATATTTTTTTTCTACCATACTATCGAGTTTT
Found at i:3004915 original size:6 final size:6
Alignment explanation
Indices: 3004913--3004957 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
3004903 GCATATACAT
3004913 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
3004958 GAGAGTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:3008949 original size:13 final size:13
Alignment explanation
Indices: 3008931--3008958 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3008921 TTAATAAATT
3008931 CATTTTTATTACA
1 CATTTTTATTACA
3008944 CATTTTTATTACA
1 CATTTTTATTACA
3008957 CA
1 CA
3008959 ATCAGTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (13 bp):
CATTTTTATTACA
Found at i:3013333 original size:5 final size:5
Alignment explanation
Indices: 3013292--3013332 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
3013282 GACCTGTCAT
* *
3013292 TCCAA TCCAA TCCAA TCCAA TCCAA TCCAA TTCAA TTCAA T
1 TCCAA TCCAA TCCAA TCCAA TCCAA TCCAA TCCAA TCCAA T
3013333 TAATCTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (5 bp):
TCCAA
Found at i:3013417 original size:5 final size:5
Alignment explanation
Indices: 3013407--3013436 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3013397 ACTTGACCTG
3013407 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT
1 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT
3013437 TGAATCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CCAAT
Found at i:3015017 original size:20 final size:20
Alignment explanation
Indices: 3014954--3015018 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
3014944 AGAGATGAAT
* *
3014954 TGATTATTATAAGAATCGGG
1 TGATTATTAAAAGAATCGAG
**
3014974 TGAGCAGTTATAAAGAGATC-AG
1 TGATTA-TTA-AAAGA-ATCGAG
*
3014996 TGATTATTACAAGAATCGAG
1 TGATTATTAAAAGAATCGAG
3015016 TGA
1 TGA
3015019 GTAGTTTACA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
21 6 0.18
22 9 0.26
23 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (20 bp):
TGATTATTAAAAGAATCGAG
Found at i:3015029 original size:22 final size:22
Alignment explanation
Indices: 3014964--3015030 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
3014954 TGATTATTAT
* *
3014964 AAGAATCGGGTGAGCAGTTATA-
1 AAGAATCGAGTGAGTAGTT-TAC
*
3014986 AAGAGATC-AGTGATTA--TTAC
1 AAGA-ATCGAGTGAGTAGTTTAC
3015006 AAGAATCGAGTGAGTAGTTTAC
1 AAGAATCGAGTGAGTAGTTTAC
3015028 AAG
1 AAG
3015031 GAGTAGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
19 5 0.14
20 12 0.33
22 16 0.44
23 3 0.08
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (22 bp):
AAGAATCGAGTGAGTAGTTTAC
Found at i:3017345 original size:17 final size:17
Alignment explanation
Indices: 3017323--3017357 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3017313 ATTCTTAGTC
*
3017323 CTATTATTAGTGCATGT
1 CTATTATTAGTCCATGT
3017340 CTATTATTAGTCCATGT
1 CTATTATTAGTCCATGT
3017357 C
1 C
3017358 ATTGAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (17 bp):
CTATTATTAGTCCATGT
Found at i:3017949 original size:6 final size:7
Alignment explanation
Indices: 3017921--3017948 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3017911 TTTTAATTAT
3017921 ATTAAAA
1 ATTAAAA
3017928 ATTAAAA
1 ATTAAAA
3017935 ATTAAAA
1 ATTAAAA
3017942 ATTAAAA
1 ATTAAAA
3017949 TAAGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATTAAAA
Found at i:3027470 original size:16 final size:16
Alignment explanation
Indices: 3027451--3027509 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
3027441 CCTTATTATA
3027451 ATAAAAT-TTAATTAGC
1 ATAAAATATTAA-TAGC
*
3027467 ATAAAATATTTATAGC
1 ATAAAATATTAATAGC
* **
3027483 ATAAATTA-TAATATA
1 ATAAAATATTAATAGC
3027498 ATAAAA-ATTAAT
1 ATAAAATATTAAT
3027510 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 1 0.03
15 13 0.37
16 18 0.51
17 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (16 bp):
ATAAAATATTAATAGC
Found at i:3039915 original size:27 final size:27
Alignment explanation
Indices: 3039885--3039947 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3039875 GGTAATCGAA
*
3039885 AGGCGGCACCAAAGGTGCCTTTC-CGAT
1 AGGCGGCACCAAAGGTACCTTTCTC-AT
* *
3039912 AGGCGGCACCGATGGTACCTTTCTCAT
1 AGGCGGCACCAAAGGTACCTTTCTCAT
*
3039939 AGGTGGCAC
1 AGGCGGCAC
3039948 AAGACTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.21
Consensus pattern (27 bp):
AGGCGGCACCAAAGGTACCTTTCTCAT
Found at i:3040492 original size:27 final size:27
Alignment explanation
Indices: 3040449--3040538 Score: 146
Period size: 27 Copynumber: 3.3 Consensus size: 27
3040439 TTTTAGTCTT
3040449 GTGCCGCCTAT-GAGAAAGGCACCATCG
1 GTGCCGCCTATCG-GAAAGGCACCATCG
3040476 GTGCCGCCTATCGGAAAGGCACCATCG
1 GTGCCGCCTATCGGAAAGGCACCATCG
* *
3040503 GTGCCGCCTATCGGAAAGGCACCTTTG
1 GTGCCGCCTATCGGAAAGGCACCATCG
3040530 GTGCCGCCT
1 GTGCCGCCT
3040539 TTCCATTACC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 59 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18
Consensus pattern (27 bp):
GTGCCGCCTATCGGAAAGGCACCATCG
Found at i:3040631 original size:27 final size:27
Alignment explanation
Indices: 3040559--3040638 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
3040549 CTCCTTCAGC
3040559 TTTTTTTTGTATTATTTTGGTAAATAA
1 TTTTTTTTGTATTATTTTGGTAAATAA
* * **
3040586 ATTTTTTTGTATATCATTTTGGT-ATTTT
1 TTTTTTTTGTAT-T-ATTTTGGTAAATAA
*
3040614 TTTTCTTTTGTATTATTTTAGTAAA
1 TTTT-TTTTGTATTATTTTGGTAAA
3040639 AATCCCGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
27 18 0.43
28 8 0.19
29 16 0.38
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (27 bp):
TTTTTTTTGTATTATTTTGGTAAATAA
Found at i:3045112 original size:22 final size:22
Alignment explanation
Indices: 3045084--3045129 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3045074 GTGAGAGTCG
*
3045084 ATAAGCTCTGATATCATATGAA
1 ATAAGCTCTGATACCATATGAA
3045106 ATAAGCTCTGATACCATATGAA
1 ATAAGCTCTGATACCATATGAA
3045128 AT
1 AT
3045130 CAAGGGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (22 bp):
ATAAGCTCTGATACCATATGAA
Found at i:3050436 original size:7 final size:7
Alignment explanation
Indices: 3050424--3050449 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3050414 AAAGTATTTT
3050424 AAAATTA
1 AAAATTA
3050431 AAAATTA
1 AAAATTA
3050438 AAAATTA
1 AAAATTA
3050445 AAAAT
1 AAAAT
3050450 ATATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:3050753 original size:27 final size:26
Alignment explanation
Indices: 3050723--3050782 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
3050713 GGCCAATCAC
* *
3050723 ATTGGCGGCACCAAAGGTGCCAAAGTG
1 ATTGGCGG-ACCAAAAGTGCCAAAGAG
* *
3050750 ATTGGCCTGACCAAAAGTGCTAAAGAG
1 ATTGG-CGGACCAAAAGTGCCAAAGAG
3050777 ATTGGC
1 ATTGGC
3050783 CTGACCGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.04
27 25 0.89
28 2 0.07
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (26 bp):
ATTGGCGGACCAAAAGTGCCAAAGAG
Found at i:3050783 original size:27 final size:27
Alignment explanation
Indices: 3050732--3050788 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3050722 CATTGGCGGC
* *
3050732 ACCAAAGGTGCCAAAGTGATTGGCCTG
1 ACCAAAAGTGCCAAAGAGATTGGCCTG
*
3050759 ACCAAAAGTGCTAAAGAGATTGGCCTG
1 ACCAAAAGTGCCAAAGAGATTGGCCTG
3050786 ACC
1 ACC
3050789 GGACTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (27 bp):
ACCAAAAGTGCCAAAGAGATTGGCCTG
Found at i:3051335 original size:27 final size:27
Alignment explanation
Indices: 3051296--3051355 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
3051286 GTCCGGTCAG
*
3051296 GCCAATCATTTTGGCACCTTTGGTGCC
1 GCCAATCACTTTGGCACCTTTGGTGCC
3051323 GCCAATCACTTTGGCACCTTTGGTGCC
1 GCCAATCACTTTGGCACCTTTGGTGCC
*
3051350 GTCAAT
1 GCCAAT
3051356 GTAATTGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.32
Consensus pattern (27 bp):
GCCAATCACTTTGGCACCTTTGGTGCC
Found at i:3051434 original size:27 final size:28
Alignment explanation
Indices: 3051404--3051458 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3051394 TGCAGGTTTT
* *
3051404 TTTTTGGT-ATATTTTTGTAAATAAAAA
1 TTTTTGATAATATTTTGGTAAATAAAAA
*
3051431 TTTTTTATAATATTTTGGTAAATAAAAA
1 TTTTTGATAATATTTTGGTAAATAAAAA
3051459 AAAAGATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (28 bp):
TTTTTGATAATATTTTGGTAAATAAAAA
Found at i:3054612 original size:31 final size:30
Alignment explanation
Indices: 3054573--3054635 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
3054563 ATAACATCGA
*
3054573 TTTTAATAGTCT-AGTGACTTAAATGAAAAT
1 TTTTAATAGT-TGAGTGACTTAAATAAAAAT
*
3054603 TTTTGAATAGTTGAGTGGCTTAAATAAAAAT
1 TTTT-AATAGTTGAGTGACTTAAATAAAAAT
3054634 TT
1 TT
3054636 ACCCATAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTTAATAGTTGAGTGACTTAAATAAAAAT
Found at i:3081407 original size:42 final size:43
Alignment explanation
Indices: 3081342--3081431 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
3081332 AGAATCCACC
* *
3081342 TTGAGAACTTAGTGGAAATTTCC-TTTTCTATTAAAATGATTT
1 TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
* *
3081384 TTGAAAACTTGGTGTAAAATTCCTTTTTCTATTAAAATGATTT
1 TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
3081427 TTGAA
1 TTGAA
3081432 CTAATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 19 0.44
43 24 0.56
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (43 bp):
TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
Found at i:3082150 original size:12 final size:12
Alignment explanation
Indices: 3082133--3082157 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3082123 GAATGAGAAG
3082133 AAAAAAGAAAAA
1 AAAAAAGAAAAA
3082145 AAAAAAGAAAAA
1 AAAAAAGAAAAA
3082157 A
1 A
3082158 GAGCGTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:3085854 original size:9 final size:9
Alignment explanation
Indices: 3085842--3085924 Score: 68
Period size: 9 Copynumber: 9.4 Consensus size: 9
3085832 TTTATTTTTT
3085842 AAAATTATA
1 AAAATTATA
3085851 AAAATT-TA
1 AAAATTATA
*
3085859 AAAAATATAA
1 AAAATTAT-A
*
3085869 AAAATTTTA
1 AAAATTATA
3085878 AAAA-T-TA
1 AAAATTATA
3085885 AAAATT-T-
1 AAAATTATA
* *
3085892 AAAATCATT
1 AAAATTATA
3085901 AAAATTATTAA
1 AAAATTA-T-A
3085912 AAAATTATA
1 AAAATTATA
3085921 AAAA
1 AAAA
3085925 CCAAAATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
7 11 0.18
8 11 0.18
9 23 0.38
10 9 0.15
11 7 0.11
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:3085867 original size:17 final size:17
Alignment explanation
Indices: 3085842--3085924 Score: 80
Period size: 18 Copynumber: 4.8 Consensus size: 17
3085832 TTTATTTTTT
*
3085842 AAAATTATAAAAATTTA
1 AAAAATATAAAAATTTA
*
3085859 AAAAATATAAAAAATTTT
1 AAAAATAT-AAAAATTTA
3085877 AAAAAT-TAAAAATTTA
1 AAAAATATAAAAATTTA
* *
3085893 AAATCAT-TAAAATTATTA
1 AAA-AATATAAAAAT-TTA
3085911 AAAAATTATAAAAA
1 AAAAA-TATAAAAA
3085925 CCAAAATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
16 11 0.20
17 17 0.31
18 21 0.39
19 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATATAAAAATTTA
Found at i:3087070 original size:12 final size:12
Alignment explanation
Indices: 3087050--3087081 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3087040 ACACCTCTTA
*
3087050 TGTTTAAATTGC
1 TGTTCAAATTGC
3087062 TGTTCAAATTGC
1 TGTTCAAATTGC
3087074 TGTTCAAA
1 TGTTCAAA
3087082 CTGGCACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (12 bp):
TGTTCAAATTGC
Found at i:3098535 original size:16 final size:16
Alignment explanation
Indices: 3098514--3098564 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
3098504 AAGAAAGAGC
3098514 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
3098530 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
3098546 AAACACGCTAGTAAAT
1 AAATACGCTAGTAAAT
3098562 AAA
1 AAA
3098565 ATACTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:3099504 original size:16 final size:17
Alignment explanation
Indices: 3099483--3099516 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3099473 AATTAGAGAA
3099483 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
3099499 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
3099516 T
1 T
3099517 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:3100209 original size:15 final size:15
Alignment explanation
Indices: 3100191--3100221 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3100181 ATAACTAAAG
3100191 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
3100206 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
3100221 A
1 A
3100222 GATGAGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:3105928 original size:23 final size:22
Alignment explanation
Indices: 3105902--3105946 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3105892 AATATTAAGA
3105902 ATATTAAGTA-ATTAATAATATTT
1 ATATT-AGTATATTAAT-ATATTT
*
3105925 ATATTATTATATTAATATATTT
1 ATATTAGTATATTAATATATTT
3105947 CGATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAGTATATTAATATATTT
Found at i:3105934 original size:8 final size:8
Alignment explanation
Indices: 3105923--3106077 Score: 50
Period size: 8 Copynumber: 19.9 Consensus size: 8
3105913 TTAATAATAT
3105923 TTATATTA
1 TTATATTA
3105931 TTATATTA
1 TTATATTA
*
3105939 ATATATTTCGA
1 TTATA-TT--A
*
3105950 TT-TATAAA
1 TTATAT-TA
3105958 TCTATATT-
1 T-TATATTA
3105966 TCTATATTA
1 T-TATATTA
3105975 TT-TATT-
1 TTATATTA
*
3105981 TTATTATTC
1 TTA-TATTA
*
3105990 TATCTATTA
1 T-TATATTA
3105999 TTATATTA
1 TTATATTA
*
3106007 -TCTATTA
1 TTATATTA
3106014 TTATATTA
1 TTATATTA
3106022 TCTAT-TTA
1 T-TATATTA
*
3106030 TAAT-TTA
1 TTATATTA
3106037 -TAT-TTA
1 TTATATTA
*
3106043 GT-TATTA
1 TTATATTA
3106050 TT-TAGTTA
1 TTATA-TTA
3106058 TTAT-TTA
1 TTATATTA
3106065 -TAT-TTA
1 TTATATTA
*
3106071 GTATATT
1 TTATATT
3106078 TAGAAATTTA
Statistics
Matches: 116, Mismatches: 12, Indels: 38
0.70 0.07 0.23
Matches are distributed among these distances:
6 14 0.12
7 28 0.24
8 51 0.44
9 15 0.13
10 6 0.05
11 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:3106037 original size:15 final size:15
Alignment explanation
Indices: 3105960--3106027 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
3105950 TTTATAAATC
3105960 TATATT-TCTA-TAT
1 TATATTATCTATTAT
3105973 TAT-TTAT-T-TTAT
1 TATATTATCTATTAT
3105985 TAT-TCTATCTATTAT
1 TATAT-TATCTATTAT
3106000 TATATTATCTATTAT
1 TATATTATCTATTAT
3106015 TATATTATCTATT
1 TATATTATCTATT
3106028 TATAATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
12 10 0.20
13 7 0.14
14 1 0.02
15 30 0.61
16 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTATCTATTAT
Found at i:3106037 original size:20 final size:20
Alignment explanation
Indices: 3105921--3106040 Score: 59
Period size: 20 Copynumber: 6.5 Consensus size: 20
3105911 AATTAATAAT
*
3105921 ATTTATATTAT-TATAT-TA
1 ATTTATATTATCTATTTATA
*
3105939 A--TATATT-TCGATTTATAA
1 ATTTATATTATCTATTTAT-A
* *
3105957 ATCTATATT-TCTATATTATTT
1 ATTTATATTATCTAT-TTA-TA
* *
3105978 ATTT-TATTATTCTATCTATT
1 ATTTATATTA-TCTATTTATA
3105998 A-TTATATTATCTA--T-T-
1 ATTTATATTATCTATTTATA
3106013 A-TTATATTATCTATTTATA
1 ATTTATATTATCTATTTATA
3106032 ATTTATATT
1 ATTTATATT
3106041 TAGTTATTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 28
0.70 0.05 0.24
Matches are distributed among these distances:
15 14 0.17
16 10 0.12
17 3 0.04
18 4 0.05
19 7 0.09
20 29 0.36
21 8 0.10
22 6 0.07
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTTATATTATCTATTTATA
Found at i:3106040 original size:28 final size:28
Alignment explanation
Indices: 3105922--3106012 Score: 51
Period size: 28 Copynumber: 3.1 Consensus size: 28
3105912 ATTAATAATA
* * *
3105922 TTTATATTATTATATTAATATATT-TCGA
1 TTTATAAT-TTATATTATTATATTATCTA
* *
3105950 TTTATAAATCTATATT-TCTATATTATTTA
1 TTTAT-AATTTATATTAT-TATATTATCTA
*
3105979 TTTTATTATTCTATCTATTATTATATTATCTA
1 -TTTATAATT-TA--TATTATTATATTATCTA
3106011 TT
1 TT
3106013 ATTATATTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
28 17 0.36
29 6 0.13
30 7 0.15
31 2 0.04
32 14 0.30
33 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTATAATTTATATTATTATATTATCTA
Found at i:3106048 original size:28 final size:29
Alignment explanation
Indices: 3106015--3106077 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
3106005 TATCTATTAT
*
3106015 TATATTATCTATTTATAATTTATATTTAG
1 TATATTATCTAGTTATAATTTATATTTAG
* *
3106044 T-TATTATTTAGTTATTATTTATATTTAG
1 TATATTATCTAGTTATAATTTATATTTAG
3106072 TATATT
1 TATATT
3106078 TAGAAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (29 bp):
TATATTATCTAGTTATAATTTATATTTAG
Found at i:3106053 original size:11 final size:11
Alignment explanation
Indices: 3106037--3106064 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3106027 TTATAATTTA
3106037 TATTTAGTTAT
1 TATTTAGTTAT
3106048 TATTTAGTTAT
1 TATTTAGTTAT
3106059 TATTTA
1 TATTTA
3106065 TATTTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (11 bp):
TATTTAGTTAT
Found at i:3106086 original size:17 final size:16
Alignment explanation
Indices: 3106066--3106103 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
3106056 TATTATTTAT
3106066 ATTTAGTATATTTAGAA
1 ATTTAGTATATTTAG-A
3106083 ATTTAGTATATTTAGA
1 ATTTAGTATATTTAGA
3106099 ATTTA
1 ATTTA
3106104 TTATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (16 bp):
ATTTAGTATATTTAGA
Found at i:3106153 original size:31 final size:33
Alignment explanation
Indices: 3106118--3106188 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
3106108 TTATTAAAAT
*
3106118 ATTTAATTTAAGT-TAAATAGAA-AAATTAATA
1 ATTTAATTTAAGTATAAATAAAATAAATTAATA
* *
3106149 ATTTAATTTAAGTATAATTAAAATAAATTATTA
1 ATTTAATTTAAGTATAAATAAAATAAATTAATA
3106182 ATTTAAT
1 ATTTAAT
3106189 AATTTTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 13 0.37
32 7 0.20
33 15 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (33 bp):
ATTTAATTTAAGTATAAATAAAATAAATTAATA
Found at i:3111085 original size:12 final size:12
Alignment explanation
Indices: 3111068--3111096 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3111058 TTAAATTATA
3111068 CAATTTCTAATT
1 CAATTTCTAATT
3111080 CAATTTCTAATT
1 CAATTTCTAATT
3111092 CAATT
1 CAATT
3111097 ATTATACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (12 bp):
CAATTTCTAATT
Found at i:3111892 original size:25 final size:25
Alignment explanation
Indices: 3111858--3111907 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3111848 ATCTAGTTTC
3111858 TTTTTATAATATCTATTTATTTCTA
1 TTTTTATAATATCTATTTATTTCTA
3111883 TTTTTATAATATCTATTTATTTCTA
1 TTTTTATAATATCTATTTATTTCTA
3111908 ATAAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTTATAATATCTATTTATTTCTA
Found at i:3111899 original size:15 final size:15
Alignment explanation
Indices: 3111858--3111900 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3111848 ATCTAGTTTC
3111858 TTTTTATAATATCTA
1 TTTTTATAATATCTA
3111873 --TTTAT--T-TCTA
1 TTTTTATAATATCTA
3111883 TTTTTATAATATCTA
1 TTTTTATAATATCTA
3111898 TTT
1 TTT
3111901 ATTTCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 4 0.17
11 1 0.04
12 5 0.22
13 5 0.22
14 1 0.04
15 7 0.30
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTATAATATCTA
Found at i:3111914 original size:21 final size:23
Alignment explanation
Indices: 3111862--3111915 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
3111852 AGTTTCTTTT
*
3111862 TATAATATCTATTTATTTCTATTTT
1 TATAATATCTATTTATTTCTA--TA
3111887 TATAATATCTATTTATTTCTA-A
1 TATAATATCTATTTATTTCTATA
3111909 TA-AATAT
1 TATAATAT
3111916 TTATATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 2 0.07
25 21 0.75
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
TATAATATCTATTTATTTCTATA
Found at i:3113677 original size:51 final size:51
Alignment explanation
Indices: 3113614--3113722 Score: 209
Period size: 51 Copynumber: 2.1 Consensus size: 51
3113604 AATCAGCAGT
3113614 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
1 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
3113665 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
1 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
*
3113716 ATACTAT
1 ATCCTAT
3113723 CTATATCTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (51 bp):
ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
Found at i:3128031 original size:29 final size:29
Alignment explanation
Indices: 3127989--3128046 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3127979 TAAATAAATT
3127989 CTTTTTTGGAACTACATAGATCTATGGAA
1 CTTTTTTGGAACTACATAGATCTATGGAA
3128018 CTTTTTTGGAACTACATAGATCTATGGAA
1 CTTTTTTGGAACTACATAGATCTATGGAA
3128047 TCGGTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (29 bp):
CTTTTTTGGAACTACATAGATCTATGGAA
Found at i:3129223 original size:14 final size:14
Alignment explanation
Indices: 3129204--3129231 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3129194 TATTTACCTT
3129204 CGATCAATATTATC
1 CGATCAATATTATC
3129218 CGATCAATATTATC
1 CGATCAATATTATC
3129232 TTTATCTTGA
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:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CGATCAATATTATC
Found at i:3129801 original size:23 final size:23
Alignment explanation
Indices: 3129775--3129820 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3129765 GGGATATTAG
3129775 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
3129798 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
3129821 TCAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
ATATTGACTAGTTATATACGAAC
Found at i:3134195 original size:21 final size:21
Alignment explanation
Indices: 3134155--3134211 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
3134145 TTTTGACTTT
3134155 TTTTCTCTT-GTTCGGTTTTTTC
1 TTTTCTCTTGGTT--GTTTTTTC
3134177 TTTTCTCTTGGTTGTTTTTTC
1 TTTTCTCTTGGTTGTTTTTTC
3134198 TTTTCTCTTGGTTG
1 TTTTCTCTTGGTTG
3134212 GAAAAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.65
22 9 0.26
23 3 0.09
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (21 bp):
TTTTCTCTTGGTTGTTTTTTC
Found at i:3135212 original size:11 final size:11
Alignment explanation
Indices: 3135196--3135220 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3135186 GCGATTATTG
3135196 TATTTATTGTA
1 TATTTATTGTA
3135207 TATTTATTGTA
1 TATTTATTGTA
3135218 TAT
1 TAT
3135221 AAATATAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTATTGTA
Found at i:3135852 original size:21 final size:21
Alignment explanation
Indices: 3135813--3135852 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3135803 TTTATTTAAA
*
3135813 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
3135834 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
3135853 TACTGATAAA
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:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:3135996 original size:14 final size:14
Alignment explanation
Indices: 3135977--3136005 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3135967 TAGATAAATA
3135977 ATAATCTATATAAC
1 ATAATCTATATAAC
3135991 ATAATCTATATAAC
1 ATAATCTATATAAC
3136005 A
1 A
3136006 AAGTAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATCTATATAAC
Found at i:3137710 original size:19 final size:19
Alignment explanation
Indices: 3137686--3137725 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3137676 ATTTTTTTTT
* *
3137686 ATTAGAATCGAAAAGTTTA
1 ATTAGAATAGAAAAGTATA
3137705 ATTAGAATAGAAAAGTATA
1 ATTAGAATAGAAAAGTATA
3137724 AT
1 AT
3137726 AAAAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (19 bp):
ATTAGAATAGAAAAGTATA
Found at i:3139238 original size:16 final size:16
Alignment explanation
Indices: 3139217--3139249 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3139207 TCTTATTCCT
*
3139217 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
3139233 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
3139249 T
1 T
3139250 AGAATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:3142559 original size:29 final size:29
Alignment explanation
Indices: 3142512--3142569 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3142502 GCAACCCATT
*
3142512 TTTAGTATCATATCGAAACGCTATTCCTA
1 TTTAGTATCATATCAAAACGCTATTCCTA
* *
3142541 TTTATTATCATATTAAAACGCTATTCCTA
1 TTTAGTATCATATCAAAACGCTATTCCTA
3142570 ATAGAAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTAGTATCATATCAAAACGCTATTCCTA
Found at i:3144953 original size:14 final size:14
Alignment explanation
Indices: 3144934--3144962 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3144924 ACAGATGGAT
3144934 TCGTATAATTCTTA
1 TCGTATAATTCTTA
3144948 TCGTATAATTCTTA
1 TCGTATAATTCTTA
3144962 T
1 T
3144963 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:3149191 original size:20 final size:21
Alignment explanation
Indices: 3149125--3149193 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
3149115 TCACTTCGTT
3149125 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
3149146 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
3149167 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
3149188 -CTTTTT
1 TCTTTTT
3149194 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:3151586 original size:18 final size:18
Alignment explanation
Indices: 3151553--3151646 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
3151543 AAGGTTTTCT
3151553 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
3151568 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
3151586 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
3151604 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
3151622 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
3151640 TATTGAT
1 TATTGAT
3151647 CGTGACCTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:3159916 original size:14 final size:14
Alignment explanation
Indices: 3159897--3159924 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3159887 TATATTAGTA
3159897 TTTTCTATTCTATT
1 TTTTCTATTCTATT
3159911 TTTTCTATTCTATT
1 TTTTCTATTCTATT
3159925 AGTATTAGAG
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:3159932 original size:6 final size:6
Alignment explanation
Indices: 3159921--3159994 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
3159911 TTTTCTATTC
*
3159921 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
3159968 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
3159995 TAGTGATCCC
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 4 0.07
5 23 0.39
6 26 0.44
8 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (6 bp):
TATTAG
Found at i:3159947 original size:11 final size:11
Alignment explanation
Indices: 3159922--3159998 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
3159912 TTTCTATTCT
3159922 ATTAGTATTAG
1 ATTAGTATTAG
3159933 ---AGTATTAG
1 ATTAGTATTAG
**
3159941 ATTAGTATTCT
1 ATTAGTATTAG
3159952 ATTAGTATTAG
1 ATTAGTATTAG
3159963 ATTAGTATTAG
1 ATTAGTATTAG
3159974 -TTAG-ATTAG
1 ATTAGTATTAG
3159983 ATTAGTATTAG
1 ATTAGTATTAG
3159994 -TTAGT
1 ATTAGT
3159999 GATCCCGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:3159952 original size:30 final size:30
Alignment explanation
Indices: 3159916--3159994 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
3159906 CTATTTTTTC
3159916 TATTCTATTAGTATTAG-AGTATTAGATTAG
1 TATTCTATTAGTATTAGTAGTATTAG-TTAG
3159946 TATTCTATTAGTATTAGATTAGTATTAGTTAG
1 TATTCTATTAGTATTAG--TAGTATTAGTTAG
**
3159978 -ATTAGATTAGTATTAGT
1 TATTCTATTAGTATTAGT
3159995 TAGTGATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 14 0.32
32 4 0.09
33 8 0.18
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (30 bp):
TATTCTATTAGTATTAGTAGTATTAGTTAG
Found at i:3159966 original size:5 final size:5
Alignment explanation
Indices: 3159936--3159997 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
3159926 GTATTAGAGT
**
3159936 ATTAG ATTAG TATTCT ATTAG TATTAG ATTAG TATTAG -TTAG ATTAG
1 ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG ATTAG
3159983 ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG
3159998 TGATCCCGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.47
Consensus pattern (5 bp):
ATTAG
Found at i:3159983 original size:20 final size:21
Alignment explanation
Indices: 3159922--3159998 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
3159912 TTTCTATTCT
3159922 ATTAGTATTAG--AGTATTAG
1 ATTAGTATTAGTTAGTATTAG
3159941 ATTAGTATTCTA-TTAGTATTAG
1 ATTAGTA-T-TAGTTAGTATTAG
3159963 ATTAGTATTAGTTAG-ATTAG
1 ATTAGTATTAGTTAGTATTAG
3159983 ATTAGTATTAGTTAGT
1 ATTAGTATTAGTTAGT
3159999 GATCCCGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.13
20 23 0.44
21 7 0.13
22 15 0.29
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (21 bp):
ATTAGTATTAGTTAGTATTAG
Found at i:3176083 original size:12 final size:12
Alignment explanation
Indices: 3176066--3176090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3176056 TGCTCATTCT
3176066 ACTTAATTTTAC
1 ACTTAATTTTAC
3176078 ACTTAATTTTAC
1 ACTTAATTTTAC
3176090 A
1 A
3176091 TATTTTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ACTTAATTTTAC
Done.