Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 132 of 207
Found at i:40340551 original size:17 final size:18
Alignment explanation
Indices: 40340520--40340553 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40340510 AATTTAATTT
40340520 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
40340538 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
40340554 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:40340793 original size:21 final size:21
Alignment explanation
Indices: 40340767--40340850 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
40340757 CCTTAAACCC
40340767 TAAGGTTTAGGGTTTGAGATT
1 TAAGGTTTAGGGTTTGAGATT
40340788 TAAGGTTTAGGGTTTGAGATT
1 TAAGGTTTAGGGTTTGAGATT
* *
40340809 TTAGGTTTAAGGTTTGAG-TT
1 TAAGGTTTAGGGTTTGAGATT
** *
40340829 T-AGGTTCGGGGTTTGAGGTT
1 TAAGGTTTAGGGTTTGAGATT
40340849 TA
1 TA
40340851 GGCTTTAAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 13 0.23
20 6 0.11
21 37 0.66
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.44
Consensus pattern (21 bp):
TAAGGTTTAGGGTTTGAGATT
Found at i:40340794 original size:14 final size:14
Alignment explanation
Indices: 40340769--40340859 Score: 64
Period size: 14 Copynumber: 6.6 Consensus size: 14
40340759 TTAAACCCTA
*
40340769 AGGTTTAGGGTTTG
1 AGGTTTAAGGTTTG
*
40340783 AGATTTAAGGTTT-
1 AGGTTTAAGGTTTG
* * *
40340796 AGGGTTTGAGATTTT
1 A-GGTTTAAGGTTTG
40340811 AGGTTTAAGGTTTG
1 AGGTTTAAGGTTTG
*
40340825 A-GTTT-AGGTTCG
1 AGGTTTAAGGTTTG
* *
40340837 GGGTTTGAGGTTT-
1 AGGTTTAAGGTTTG
40340850 AGGCTTTAAG
1 AGG-TTTAAG
40340860 TTTAAGATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
12 6 0.10
13 11 0.19
14 41 0.69
15 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (14 bp):
AGGTTTAAGGTTTG
Found at i:40340848 original size:7 final size:7
Alignment explanation
Indices: 40340777--40340849 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
40340767 TAAGGTTTAG
40340777 GGTTTGA
1 GGTTTGA
* *
40340784 GATTTAA
1 GGTTTGA
40340791 GGTTT-A
1 GGTTTGA
40340797 GGGTTTGA
1 -GGTTTGA
* *
40340805 GATTTTA
1 GGTTTGA
*
40340812 GGTTTAA
1 GGTTTGA
40340819 GGTTTGA
1 GGTTTGA
40340826 -GTTT-A
1 GGTTTGA
* *
40340831 GGTTCGG
1 GGTTTGA
40340838 GGTTTGA
1 GGTTTGA
40340845 GGTTT
1 GGTTT
40340850 AGGCTTTAAG
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
5 1 0.02
6 8 0.16
7 40 0.80
8 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.45
Consensus pattern (7 bp):
GGTTTGA
Found at i:40341364 original size:24 final size:22
Alignment explanation
Indices: 40341336--40341421 Score: 95
Period size: 24 Copynumber: 3.8 Consensus size: 22
40341326 TTTTTGTTAA
40341336 AATTTAATATAATAAATAAATTAT
1 AATTTAA-AT-ATAAATAAATTAT
40341360 AATTTAAATATAAATAATGATTAT
1 AATTTAAATATAAATAA--ATTAT
* *
40341384 TATTTAAATATAAAATAATTTA-
1 AATTTAAATAT-AAATAAATTAT
40341406 AATTTAAATA-AAATAA
1 AATTTAAATATAAATAA
40341422 TGAAATAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
20 6 0.11
22 17 0.30
23 5 0.09
24 22 0.39
25 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
AATTTAAATATAAATAAATTAT
Found at i:40341431 original size:22 final size:22
Alignment explanation
Indices: 40341358--40341438 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
40341348 TAAATAAATT
*
40341358 ATAATTTAAATATAAATAATGATT
1 ATAATTTAAATA-AAATAATGA-A
* *
40341382 ATTATTTAAATATAA-AAT-AA
1 ATAATTTAAATAAAATAATGAA
*
40341402 TTTAAATTTAAATAAAATAATGAA
1 -AT-AATTTAAATAAAATAATGAA
*
40341426 ATAATTTAGATAA
1 ATAATTTAAATAA
40341439 CAAAAATAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
21 2 0.04
22 24 0.53
23 6 0.13
24 13 0.29
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAATTTAAATAAAATAATGAA
Found at i:40341447 original size:46 final size:47
Alignment explanation
Indices: 40341336--40341443 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 47
40341326 TTTTTGTTAA
* *
40341336 AATTTAATATAATAAATAAATTATAATTTAAATATAAATAATGATTAT
1 AATTTAA-ATAAAAAATAAATTATAATTTAAATATAAATAATGATAAT
* * *
40341384 TATTTAAATATAAAATAATTTA-AATTTAAATA-AAATAATGA-AAT
1 AATTTAAATAAAAAATAAATTATAATTTAAATATAAATAATGATAAT
*
40341428 AATTTAGATAACAAAA
1 AATTTAAATAA-AAAA
40341444 ATAACTTTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 10 0.20
45 13 0.25
46 10 0.20
47 12 0.24
48 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (47 bp):
AATTTAAATAAAAAATAAATTATAATTTAAATATAAATAATGATAAT
Found at i:40344746 original size:72 final size:72
Alignment explanation
Indices: 40344666--40344809 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
40344656 CCGGTTAAGT
* * *
40344666 ATATAGAAATATCAAATAAATTTGAGTTGACATCTTTAATAATGTATGGTGTGCCTCATATTTTC
1 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAGGGTGTGCCTCATATTTTC
*
40344731 AGTTGAA
66 AGCTGAA
*
40344738 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTGGGGTGTGCCTCATATTTTC
1 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAGGGTGTGCCTCATATTTTC
40344803 AGCTGAA
66 AGCTGAA
40344810 TAGACAACGA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (72 bp):
ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAGGGTGTGCCTCATATTTTC
AGCTGAA
Found at i:40347946 original size:28 final size:28
Alignment explanation
Indices: 40347906--40347963 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
40347896 TTGTCTTCAC
40347906 ATCCATTTGATGTACCAACAAATTGTGA
1 ATCCATTTGATGTACCAACAAATTGTGA
*
40347934 ATCCATTTGATGTACCAGCAAATTGTGA
1 ATCCATTTGATGTACCAACAAATTGTGA
40347962 AT
1 AT
40347964 GAAATCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (28 bp):
ATCCATTTGATGTACCAACAAATTGTGA
Found at i:40351226 original size:22 final size:22
Alignment explanation
Indices: 40351178--40351219 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40351168 GTAGTAATAG
* * *
40351178 AAGGGTAAAATAGTAAATATGC
1 AAGGGCAAAAGAGTAAAAATGC
40351200 AAGGGCAAAAGAGTAAAAAT
1 AAGGGCAAAAGAGTAAAAAT
40351220 CATAGGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.17
Consensus pattern (22 bp):
AAGGGCAAAAGAGTAAAAATGC
Found at i:40352594 original size:27 final size:26
Alignment explanation
Indices: 40352556--40352627 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 26
40352546 AAAAATAAAA
40352556 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATATTATAA-TTTTTTT
40352583 ATTTACCAAAATATATATAATTTTTTT
1 ATTTACCAAAATAT-TATAATTTTTTT
*
40352610 ATTTACGAAAATA-TATAA
1 ATTTACCAAAATATTATAA
40352628 AAAAACTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 5 0.12
27 33 0.77
28 5 0.12
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (26 bp):
ATTTACCAAAATATTATAATTTTTTT
Found at i:40352713 original size:27 final size:26
Alignment explanation
Indices: 40352682--40352748 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
40352672 CACGCAAATG
40352682 GCATTGGCGGCACCAATGGTGCCAAT
1 GCATTGGCGGCACCAATGGTGCCAAT
40352708 GCCATTGGCGGCACCAATGGTGCCATATT
1 G-CATTGGCGGCACCAATGGTGCCA-A-T
40352737 G-ATTGGCGGCAC
1 GCATTGGCGGCAC
40352749 TATTCGTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 1 0.03
27 34 0.89
28 1 0.03
29 2 0.05
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (26 bp):
GCATTGGCGGCACCAATGGTGCCAAT
Found at i:40352921 original size:19 final size:21
Alignment explanation
Indices: 40352883--40352921 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40352873 AACTTTTGAT
*
40352883 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
40352904 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
40352922 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:40355273 original size:5 final size:5
Alignment explanation
Indices: 40355260--40355429 Score: 55
Period size: 5 Copynumber: 32.8 Consensus size: 5
40355250 ATAAAATTAC
* * ** * *
40355260 CTTTT -TTTT CTTTT -TTTT CCTTC CTTCC CTCTT CTTTT TTTTT CTCTTCT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CT-TT-T
* * * *
40355310 CCTCT CCTTTT CTTTC CTTCTTT CTTTCT TTTTT CTTTT CTTTT CCTTTT
1 CTTTT C-TTTT CTTTT CTT--TT CTTT-T CTTTT CTTTT CTTTT -CTTTT
* * *
40355360 CTTCTT CTTCTT -TCTTT CTTTT -TTTCT CTTCT CTTCTC CTTTC CTTTT
1 CTT-TT CTT-TT CT-TTT CTTTT CTTT-T CTTTT CTT-TT CTTTT CTTTT
* *
40355408 CTTTC CTTCT -TTTT C-TTT CTTT
1 CTTTT CTTTT CTTTT CTTTT CTTT
40355430 CCTCTCCTTT
Statistics
Matches: 122, Mismatches: 26, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
4 18 0.15
5 68 0.56
6 30 0.25
7 6 0.05
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (5 bp):
CTTTT
Found at i:40355294 original size:24 final size:25
Alignment explanation
Indices: 40355267--40355377 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 25
40355257 TACCTTTTTT
40355267 TTCTTTTTTTTCCTTCCTTC-CCTC
1 TTCTTTTTTTTCCTTCCTTCTCCTC
*
40355291 TTCTTTTTTTTTC-T-CTTCTCCTC
1 TTCTTTTTTTTCCTTCCTTCTCCTC
* * * *
40355314 TCCTTTTCTTTCCTTCTTTCT-TTC
1 TTCTTTTTTTTCCTTCCTTCTCCTC
* * *
40355338 TT-TTTTCTTTTCTTTTCCTTTTCTTC
1 TTCTTTT-TTTTC-CTTCCTTCTCCTC
40355364 TTCTTCTTTCTTTC
1 TTCTT-TTT-TTTC
40355378 TTTTTTTCTC
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
22 4 0.06
23 19 0.28
24 20 0.30
25 10 0.15
26 5 0.07
27 3 0.04
28 6 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (25 bp):
TTCTTTTTTTTCCTTCCTTCTCCTC
Found at i:40355297 original size:23 final size:25
Alignment explanation
Indices: 40355271--40355334 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 25
40355261 TTTTTTTTCT
*
40355271 TTTTTTTCCTTC-CTTC-CCTCTTC
1 TTTTTTTCCTTCTCTTCTCCTCTCC
40355294 TTTTTTT--TTCTCTTCTCCTCTCC
1 TTTTTTTCCTTCTCTTCTCCTCTCC
40355317 TTTTCTTTCCTTCT-TTCT
1 TTTT-TTTCCTTCTCTTCT
40355335 TTCTTTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 3 0.09
22 4 0.11
23 17 0.49
24 3 0.09
25 4 0.11
26 4 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTTTTCCTTCTCTTCTCCTCTCC
Found at i:40355334 original size:4 final size:4
Alignment explanation
Indices: 40355318--40355456 Score: 94
Period size: 4 Copynumber: 34.0 Consensus size: 4
40355308 CTCCTCTCCT
*
40355318 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTTTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC -TTT-C TTTC T-TTC
* *
40355364 -TTC -TTC TTTC TTTC TTTT TTTC TCTTC TCTTC -TCC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC T-TTC TTTC TTT-C -TTTC
* *
40355409 TTTC CTTC -TT- TTTC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC
40355457 CCTCCCCTTC
Statistics
Matches: 112, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
3 16 0.14
4 66 0.59
5 25 0.22
6 5 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:40355376 original size:18 final size:18
Alignment explanation
Indices: 40355289--40355447 Score: 84
Period size: 18 Copynumber: 8.8 Consensus size: 18
40355279 CTTCCTTCCC
40355289 TCTTCTT-TTT-TTTTC-
1 TCTTCTTCTTTCTTTTCT
* *
40355304 TCTTCTCCTCTCCTTTTCTT
1 TCTTCTTCT-TTCTTTTC-T
40355324 TCCTTCTTTCTTTCTTTT-T
1 T-CTTC-TTCTTTCTTTTCT
40355343 TCTT-TTCTTTTCCTTTTCT
1 TCTTCTTC-TTT-CTTTTCT
40355362 TCTTCTTCTTTC-TTTCT
1 TCTTCTTCTTTCTTTTCT
* *
40355379 T-TTTTTCTCTTCTCTTCT
1 TCTTCTTCT-TTCTTTTCT
* * *
40355397 CCTT-TCCTTTTCTTTCCT
1 TCTTCTTC-TTTCTTTTCT
* *
40355415 TCTTTTTCTTTC-TTTCC
1 TCTTCTTCTTTCTTTTCT
*
40355432 TCTCCTTTCTTTCTTT
1 TCTTC-TTCTTTCTTT
40355448 CTTTCTTTCC
Statistics
Matches: 110, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
15 6 0.05
16 10 0.09
17 19 0.17
18 41 0.37
19 17 0.15
20 4 0.04
21 10 0.09
22 3 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTCTTCTTTCTTTTCT
Found at i:40355398 original size:82 final size:75
Alignment explanation
Indices: 40355296--40355455 Score: 196
Period size: 82 Copynumber: 2.0 Consensus size: 75
40355286 CCCTCTTCTT
* * * *
40355296 TTTTTTTCTCTTCTCCTCTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTTTCTTTTCCTTTTC
1 TTTTTTTCTCTTCTCCTCTCC-TTTCCTT--TTCTTTCCTTC-TTTTTC-TTTC-TTTCCTCTCC
40355361 -TTCTTCTTCTTTCTTTC
60 TTTC-T-TTCTTTCTTTC
*
40355378 TTTTTTTCTCTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCTT
1 TTTTTTTCTCTTCTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCTT
40355443 TCTTTCTTTC
66 TCTTTCTTTC
40355453 TTT
1 TTT
40355456 CCCTCCCCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
75 14 0.19
76 9 0.12
77 7 0.10
78 6 0.08
79 10 0.14
81 6 0.08
82 20 0.28
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (75 bp):
TTTTTTTCTCTTCTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCTT
TCTTTCTTTC
Found at i:40355403 original size:48 final size:50
Alignment explanation
Indices: 40355314--40355430 Score: 152
Period size: 48 Copynumber: 2.4 Consensus size: 50
40355304 TCTTCTCCTC
* * * * *
40355314 TCCTT-TTCTTTCCTTCTTTCTTTCTTTTTTCTTTTCTTTTCCTTTTC-T
1 TCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCTTCTCCTTTCCTTTTCTT
*
40355362 T-CTTCTTCTTTCTTTCTTTTTTTCTCTTCTCTTCTCCTTTCCTTTTCTT
1 TCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCTTCTCCTTTCCTTTTCTT
40355411 TCCTTCTT-TTTCTTTCTTTC
1 TCCTTCTTCTTTCTTTCTTTC
40355431 CTCTCCTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
47 3 0.05
48 37 0.63
49 13 0.22
50 6 0.10
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (50 bp):
TCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCTTCTCCTTTCCTTTTCTT
Found at i:40355416 original size:26 final size:24
Alignment explanation
Indices: 40355318--40355457 Score: 82
Period size: 23 Copynumber: 5.8 Consensus size: 24
40355308 CTCCTCTCCT
40355318 TTTCTTTCCTTCTTTCTTT-CTT-T-
1 TTTCTTTCC-T-TTTCTTTCCTTCTC
* *
40355341 TTTCTTTTCTTTTCCTTTTCTTCT-
1 TTTCTTTCCTTTT-CTTTCCTTCTC
40355365 TCTTCTTTCTTTCTTTT-TTTCTCTTCTC
1 T-TTCTTTC---CTTTTCTTTC-CTTCTC
*
40355393 TTCTCCTTTCCTTTTCTTTCCTTCTT
1 TT-T-CTTTCCTTTTCTTTCCTTCTC
* *
40355419 TTTCTTT-CTTTCCTCTCCTT-TC
1 TTTCTTTCCTTTTCTTTCCTTCTC
40355441 TTTCTTT-C-TTTCTTTCC
1 TTTCTTTCCTTTTCTTTCC
40355458 CTCCCCTTCT
Statistics
Matches: 96, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
21 10 0.10
22 14 0.15
23 22 0.23
24 6 0.06
25 7 0.07
26 15 0.16
27 10 0.10
28 7 0.07
29 5 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTCTTTCCTTTTCTTTCCTTCTC
Found at i:40355467 original size:22 final size:24
Alignment explanation
Indices: 40355371--40355467 Score: 62
Period size: 23 Copynumber: 4.2 Consensus size: 24
40355361 TTCTTCTTCT
* *
40355371 TTCTTTCTTT-TTTTCTCTTCT-C
1 TTCTTTCTTTCTTTCCTCTCCTCC
* * * *
40355393 TTC-TCCTTTCCTTTTCTTTCCTTC
1 TTCTTTCTTT-CTTTCCTCTCCTCC
*
40355417 TT-TTTCTTTCTTTCCTCTCCTTTCT
1 TTCTTTCTTTCTTTCCTCTCC--TCC
40355442 TTCTTTCTTTCTTTCC-CTCC-CC
1 TTCTTTCTTTCTTTCCTCTCCTCC
40355464 TTCT
1 TTCT
40355468 GCCCCCCACC
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
21 5 0.08
22 8 0.14
23 18 0.31
24 8 0.14
25 7 0.12
26 13 0.22
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (24 bp):
TTCTTTCTTTCTTTCCTCTCCTCC
Found at i:40355467 original size:26 final size:25
Alignment explanation
Indices: 40355412--40355467 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
40355402 CCTTTTCTTT
40355412 CCTTC-TTTTTCTTTCTTTCCTCTC
1 CCTTCTTTTTTCTTTCTTTCCTCTC
*
40355436 CTTTCTTTCTTTCTTTCTTTCC-CTCC
1 CCTTCTTT-TTTCTTTCTTTCCTCT-C
40355462 CCTTCT
1 CCTTCT
40355468 GCCCCCCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 4 0.15
26 19 0.70
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (25 bp):
CCTTCTTTTTTCTTTCTTTCCTCTC
Found at i:40355639 original size:28 final size:28
Alignment explanation
Indices: 40355604--40355675 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
40355594 TTTGTTTTTT
40355604 TATATATTTTGGTAAATAAAAAAAATTA
1 TATATATTTTGGTAAATAAAAAAAATTA
40355632 TATATATTTTGGTAAATAAAAAAAATTA
1 TATATATTTTGGTAAATAAAAAAAATTA
*
40355660 TA-ATATTTTGATAAAT
1 TATATATTTTGGTAAAT
40355676 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 13 0.30
28 30 0.70
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAATTA
Found at i:40365417 original size:58 final size:58
Alignment explanation
Indices: 40365347--40365462 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
40365337 TGTGGCGTTA
40365347 GCTATACCTTTGGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
1 GCTATACCTTTGGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
* * * * *
40365405 GCTATACCTTTGGTTGCTTTCTTGTTAGATAGTGGGTCAAGGTTTATTTGCTGATTTC
1 GCTATACCTTTGGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
40365463 ATTTTTTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.45
Consensus pattern (58 bp):
GCTATACCTTTGGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
Found at i:40370831 original size:42 final size:41
Alignment explanation
Indices: 40370693--40370843 Score: 169
Period size: 41 Copynumber: 3.7 Consensus size: 41
40370683 TTAAATAGAT
* * * *
40370693 TCACCGGCACTTAGTCTGTTAGACTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAACCTGATTCAGA
* *
40370734 TCACCTGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAACCTGATTCAGA
* *
40370775 TCACCGACACTTAGCCTGCTAGGTTTTAAAACCTGATTCAG-
1 TCACCGGCACTTAGCCTGCTAGG-CTTAAAACCTGATTCAGA
** * *
40370816 TACACCGGCTTTTAGCCTACTAGACTTA
1 T-CACCGGCACTTAGCCTGCTAGGCTTA
40370844 TAGTCTGAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 60 0.65
42 32 0.35
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAACCTGATTCAGA
Found at i:40371390 original size:76 final size:75
Alignment explanation
Indices: 40371179--40371393 Score: 225
Period size: 77 Copynumber: 2.8 Consensus size: 75
40371169 TACATTTAAC
* * ** *
40371179 ATTCGAATCTCACATATACCTATATAATTTCATATCCCAT-TTCAATACAAGAACTTATACATGT
1 ATTCGAATCTAACATATACATATATAATTTCATA-CTTATATTCAATACAAGAA-TTATACATGC
* *
40371243 ACATATATACAT
64 ACACACATACAT
* * * * * *
40371255 ATTCGAATCTACATATATACATATATAATTTTATACTTACATTCAAAACAAGTATTTATACTTGC
1 ATTCGAATCTA-ACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACATGC
*
40371320 ATACACATACAT
64 ACACACATACAT
* * *
40371332 ATTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAATTATACAT
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACAT
40371394 ATGTATACAT
Statistics
Matches: 112, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
76 54 0.48
77 57 0.51
78 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (75 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAGAATTATACATGCAC
ACACATACAT
Found at i:40371411 original size:76 final size:74
Alignment explanation
Indices: 40371179--40371433 Score: 221
Period size: 76 Copynumber: 3.4 Consensus size: 74
40371169 TACATTTAAC
* * **
40371179 ATTCGAATCTCACATATACCTATATAATTTCATATCCCAT-TTCAATACAAGAACTTATACA-TG
1 ATTCGAATCTAACATATACATATATAATTTCATA-CTTATATTCAATACAAGAA-TTATACATTG
*
40371242 TACATATATACAT
64 T--ATACATACAT
* * * * *
40371255 ATTCGAATCTACATATATACATATATAATTTTATACTTACATTCAAAACAAGTATTTATAC-TTG
1 ATTCGAATCTA-ACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACATTG
*
40371319 CATACACATACAT
64 --TATACATACAT
* * *
40371332 ATTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAATTATACATATG
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACAT-TG
* *
40371397 TATACATGCTT
64 TATACATACAT
* *
40371408 ATTCG-ATCCAAACATATACAAATATA
1 ATTCGAAT-CTAACATATACATATATA
40371434 TTATACATAT
Statistics
Matches: 144, Mismatches: 26, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
75 2 0.01
76 81 0.56
77 57 0.40
78 3 0.02
79 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (74 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAGAATTATACATTGTA
TACATACAT
Found at i:40374045 original size:51 final size:51
Alignment explanation
Indices: 40373982--40374085 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
40373972 GCTCGATGCC
* *
40373982 TAGCAGGTTTAATGCCGGTGAATTATTTCAGACTTTATGTCTAGCAGGCTT
1 TAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGACTAGCAGGCTT
*
40374033 TAGCAGGCTTAATGCCGGTGAATTATTTTAGACTTTATGACTAGCAGGCTT
1 TAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGACTAGCAGGCTT
40374084 TA
1 TA
40374086 TGCCGGTGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (51 bp):
TAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGACTAGCAGGCTT
Found at i:40380547 original size:84 final size:83
Alignment explanation
Indices: 40380376--40380536 Score: 191
Period size: 83 Copynumber: 1.9 Consensus size: 83
40380366 GTGAATTGTC
* * * *
40380376 AAAAGAAAACCTAGAATTTTAAAGACAAAAAAATGTCTTCTTCTGCATTGATTCTTATATCAACC
1 AAAAGAAAACCTAGAATTTTAAAGACAAAAAAATCTCTTATTCTGAATTGATTCTTATATAAACC
**
40380441 ATGATTTTTGAGAACTGAA
66 ATGATTTTCCAGAAC-GAA
* *
40380460 AAAAGAAAACCT-GAAATTTTAAAGA-AAAAAAATCTCTTATTTTTAATTGATTCTTATATAAAA
1 AAAAGAAAACCTAG-AATTTTAAAGACAAAAAAATCTCTTATTCTGAATTGATTCTTATAT---A
40380523 AACCATGATTTTCC
62 AACCATGATTTTCC
40380537 CAGACCAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 30 0.46
84 23 0.35
86 12 0.18
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (83 bp):
AAAAGAAAACCTAGAATTTTAAAGACAAAAAAATCTCTTATTCTGAATTGATTCTTATATAAACC
ATGATTTTCCAGAACGAA
Found at i:40381356 original size:87 final size:88
Alignment explanation
Indices: 40381181--40381411 Score: 247
Period size: 87 Copynumber: 2.6 Consensus size: 88
40381171 AAAAACACAA
* * * * *
40381181 GTTTTTGAGAAAAGAATCAATGGAAAAGAAGACA-TTTTTTTGTCTTTAAAATTATGGGTTTTCT
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTTGTCTTTAAAAATCTAGGTTTTCT
40381245 CTTTTCAGTTCTCAAAAATCATG
66 CTTTTCAGTTCTCAAAAATCATG
* *
40381268 GTTTTTAAGAAAAGAATCAATTGAGAAGAAGGCATTTTTTTTGTCTTTAAAAATCTAGGTTTT-T
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTTGTCTTTAAAAATCTAGGTTTTCT
*****
40381332 -TTTTCAGTT-TACTGGGTTCAATG
66 CTTTTCAGTTCT-CAAAAATC-ATG
* * *
40381355 GTTTTTGAGATAAGAATCAATGGAGAATAAGG-TTTGAATTTTTTGTCTTTAAAAATC
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATT---TTTTTTGTCTTTAAAAATC
40381412 AGATGGAGGG
Statistics
Matches: 121, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
85 1 0.01
86 14 0.12
87 62 0.51
88 25 0.21
89 19 0.16
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (88 bp):
GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTTGTCTTTAAAAATCTAGGTTTTCT
CTTTTCAGTTCTCAAAAATCATG
Found at i:40399311 original size:7 final size:7
Alignment explanation
Indices: 40399299--40399329 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40399289 GTGAGCATTT
40399299 ATATGAG
1 ATATGAG
40399306 ATATGAG
1 ATATGAG
40399313 ATATGAG
1 ATATGAG
40399320 ATATGAG
1 ATATGAG
40399327 ATA
1 ATA
40399330 GAGGGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (7 bp):
ATATGAG
Found at i:40405956 original size:24 final size:24
Alignment explanation
Indices: 40405819--40405961 Score: 101
Period size: 25 Copynumber: 5.8 Consensus size: 24
40405809 CGTTATATGT
* *
40405819 CTCTCACGAGCTTCCCGATTAATGG
1 CTCTCATGAGCTTCCCGA-TATTGG
* * * *
40405844 TTCTCTTGAACTTTCC-ATATATGG
1 CTCTCATGAGCTTCCCGATAT-TGG
* *
40405868 CTCGTAATAAGCTTCCCGATAATTGG
1 CTC-TCATGAGCTTCCCGAT-ATTGG
* * *
40405894 CTCTCATAAGCTTCCTGATTAATGG
1 CTCTCATGAGCTTCCCGA-TATTGG
*
40405919 ATCTC-TGGAGCTTCCCGATATTGG
1 CTCTCAT-GAGCTTCCCGATATTGG
*
40405943 CTCACATGAGCTTCCCGAT
1 CTCTCATGAGCTTCCCGAT
40405962 TATGACCTCT
Statistics
Matches: 90, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
23 2 0.02
24 27 0.30
25 50 0.56
26 9 0.10
27 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.34
Consensus pattern (24 bp):
CTCTCATGAGCTTCCCGATATTGG
Found at i:40408781 original size:54 final size:54
Alignment explanation
Indices: 40408699--40408819 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
40408689 TCCCTCTCTT
* * *
40408699 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTGTTTGTGTTCTC
1 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
40408753 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
1 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
40408807 CTAATTCAACTAG
1 CTAATTCAACTAG
40408820 GGTTCCTCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (54 bp):
CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
Found at i:40408990 original size:2 final size:2
Alignment explanation
Indices: 40408983--40409023 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
40408973 AGTTTCTATA
*
40408983 AG AG AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
40409024 TTTACTTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:40415663 original size:20 final size:20
Alignment explanation
Indices: 40415640--40415702 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
40415630 TATTGAAGTA
*
40415640 CAATCAGGGGCACGTATGTG
1 CAATCAGGGGCACATATGTG
* * * *
40415660 CAATTAGGGGTACCA-AAGTA
1 CAATCAGGGGCA-CATATGTG
40415680 CAATCAGGGGCACATATGTG
1 CAATCAGGGGCACATATGTG
40415700 CAA
1 CAA
40415703 ACATTCAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.91
21 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (20 bp):
CAATCAGGGGCACATATGTG
Found at i:40419977 original size:37 final size:37
Alignment explanation
Indices: 40419927--40420005 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40419917 TTATTACGAA
* * * *
40419927 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCACCGG
*
40419964 GTCTTACCCGGACAAAATCCCCACACGTAGTCACCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCACCGG
40420001 GTCTT
1 GTCTT
40420006 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCACCGG
Found at i:40420398 original size:147 final size:142
Alignment explanation
Indices: 40420126--40420459 Score: 528
Period size: 147 Copynumber: 2.3 Consensus size: 142
40420116 CTTCGGGACT
* * * * * *
40420126 TATCACATT-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACACT
1 TATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACT
40420190 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
40420255 GCCATTAGGCCC
131 GCCATTAGGCCC
40420267 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAT
1 TATCACAT-TATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC----ATATAT
*
40420332 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACATTCATCA
61 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
40420397 CATCGGCCATTAGGCCT
126 CATCGGCCATTAGGCCC
*
40420414 TATCAC-GTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
40420460 TTACTATCAT
Statistics
Matches: 178, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
141 8 0.04
142 1 0.01
143 38 0.21
145 39 0.22
147 92 0.52
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (142 bp):
TATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCCATTAGGCCC
Found at i:40420460 original size:47 final size:47
Alignment explanation
Indices: 40420124--40420462 Score: 516
Period size: 47 Copynumber: 7.1 Consensus size: 47
40420114 CCCTTCGGGA
* * * * * *
40420124 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40420171 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40420218 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40420265 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40420314 CCTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40420365 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40420412 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40420459 CTTA
1 CTTA
40420463 CTATCATTTC
Statistics
Matches: 275, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
47 180 0.65
49 47 0.17
51 48 0.17
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40427635 original size:20 final size:19
Alignment explanation
Indices: 40427612--40427747 Score: 65
Period size: 20 Copynumber: 6.8 Consensus size: 19
40427602 GGGTATCGAA
40427612 GTACAAACAGGGGCACACAT
1 GTACAAACAGGGGCAC-CAT
* * *
40427632 GTACAAACAAGGGTACCGAA
1 GTACAAACAGGGGCACC-AT
* *
40427652 GAACAAACAGGGGCACTTAT
1 GTACAAACAGGGGCAC-CAT
* * * * * *
40427672 GTGCGAACAAGGGTACTGAA
1 GTACAAACAGGGGCAC-CAT
*
40427692 GTACAAACAGGGGCACGTAT
1 GTACAAACAGGGGCAC-CAT
* * * *
40427712 GTGCAATCAGGGGTACCGAA
1 GTACAAACAGGGGCACC-AT
*
40427732 GTACAATCAGGGGCAC
1 GTACAAACAGGGGCAC
40427748 ATATGTGCAA
Statistics
Matches: 84, Mismatches: 29, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
19 1 0.01
20 83 0.99
ACGTcount: A:0.37, C:0.21, G:0.29, T:0.13
Consensus pattern (19 bp):
GTACAAACAGGGGCACCAT
Found at i:40427652 original size:40 final size:40
Alignment explanation
Indices: 40427602--40427760 Score: 219
Period size: 40 Copynumber: 4.0 Consensus size: 40
40427592 ATGCGTTTAG
* * *
40427602 GGGTATCGAAGTACAAACAGGGGCACACATGTACAAACAA
1 GGGTACCGAAGTACAAACAGGGGCACATATGTGCAAACAA
* * *
40427642 GGGTACCGAAGAACAAACAGGGGCACTTATGTGCGAACAA
1 GGGTACCGAAGTACAAACAGGGGCACATATGTGCAAACAA
* * * *
40427682 GGGTACTGAAGTACAAACAGGGGCACGTATGTGCAATCAG
1 GGGTACCGAAGTACAAACAGGGGCACATATGTGCAAACAA
*
40427722 GGGTACCGAAGTACAATCAGGGGCACATATGTGCAAACA
1 GGGTACCGAAGTACAAACAGGGGCACATATGTGCAAACA
40427761 TTCAATAATT
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.14
Consensus pattern (40 bp):
GGGTACCGAAGTACAAACAGGGGCACATATGTGCAAACAA
Found at i:40436649 original size:40 final size:40
Alignment explanation
Indices: 40436560--40436668 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
40436550 CGTGATTCAG
* **
40436560 GTGGATCAGCTCTTATGATCTTCTG-TTGGCGTGTTTCTA
1 GTGGATCAGCTCTTATGAGCTTCTGTTTGGCGCATTTCTA
* *
40436599 GTGAACCAGCTCTTATGAGCTTCTGTTTGGCGCATTTCTA
1 GTGGATCAGCTCTTATGAGCTTCTGTTTGGCGCATTTCTA
* *
40436639 TTGGATCAGCTCTTATGAGCTTCTATTTGG
1 GTGGATCAGCTCTTATGAGCTTCTGTTTGG
40436669 TGTGTTCGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 22 0.37
40 38 0.63
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (40 bp):
GTGGATCAGCTCTTATGAGCTTCTGTTTGGCGCATTTCTA
Found at i:40437546 original size:103 final size:103
Alignment explanation
Indices: 40437367--40437576 Score: 402
Period size: 103 Copynumber: 2.0 Consensus size: 103
40437357 GTATAATGTT
*
40437367 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATAATGTTGATAGACTTACTCATTTATGA
1 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATAATGTTAATAGACTTACTCATTTATGA
40437432 GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
66 GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
*
40437470 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
1 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATAATGTTAATAGACTTACTCATTTATGA
40437535 GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
66 GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
40437573 TATA
1 TATA
40437577 GGTTTATATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (103 bp):
TATAAAATACTATTAAGTTAGGAATGAAAAATATATATAATGTTAATAGACTTACTCATTTATGA
GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
Found at i:40439402 original size:39 final size:39
Alignment explanation
Indices: 40439318--40439428 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
40439308 AGATACCAAT
** *
40439318 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
40439358 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
40439398 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
40439429 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:40443608 original size:25 final size:25
Alignment explanation
Indices: 40443580--40443640 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
40443570 TTGTACACTG
*
40443580 TACTGAGAACACTGTAGATAGTGTA
1 TACTGAAAACACTGTAGATAGTGTA
40443605 TACTGAAAACACTGTAGATAGTGTA
1 TACTGAAAACACTGTAGATAGTGTA
40443630 TACTGAAAACA
1 TACTGAAAACA
40443641 GTAGCGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (25 bp):
TACTGAAAACACTGTAGATAGTGTA
Found at i:40463467 original size:34 final size:34
Alignment explanation
Indices: 40463424--40463501 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
40463414 AAATTATCCG
* *
40463424 TGTAAATCATGTATTTTATGTAGCTTATAAACCA
1 TGTAAATCATGTATTTCATGTAACTTATAAACCA
* * *
40463458 TGTAAATCATGTATTTCATGTAATTTATAATCCT
1 TGTAAATCATGTATTTCATGTAACTTATAAACCA
40463492 TGTAAATCAT
1 TGTAAATCAT
40463502 ATAACTCTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (34 bp):
TGTAAATCATGTATTTCATGTAACTTATAAACCA
Found at i:40463732 original size:23 final size:23
Alignment explanation
Indices: 40463676--40463756 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
40463666 CTCTGCTGGT
* *
40463676 AAACGGTAAGCTCTATCGAGCT-
1 AAACGGTAAGCTCTGTAGAGCTA
*
40463698 GAACGGTAAGCTCTGTAGAGCTA
1 AAACGGTAAGCTCTGTAGAGCTA
* *
40463721 AAATGGTAAGCTCCGTAGAGCTA
1 AAACGGTAAGCTCTGTAGAGCTA
40463744 AAACGGTAAGCTC
1 AAACGGTAAGCTC
40463757 ATAAGAACTG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (23 bp):
AAACGGTAAGCTCTGTAGAGCTA
Found at i:40463774 original size:23 final size:23
Alignment explanation
Indices: 40463718--40463782 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
40463708 CTCTGTAGAG
* *
40463718 CTAAAATGGTAAGCTCCGT-AGAG
1 CTAAAATGGTAAGCT-CATAAGAA
*
40463741 CTAAAACGGTAAGCTCATAAGAA
1 CTAAAATGGTAAGCTCATAAGAA
*
40463764 CTGAAATGGTAAGCTCATA
1 CTAAAATGGTAAGCTCATA
40463783 CAAGGTGTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (23 bp):
CTAAAATGGTAAGCTCATAAGAA
Found at i:40466462 original size:12 final size:12
Alignment explanation
Indices: 40466445--40466470 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40466435 TCAGACATAC
40466445 CCTGATTCTATA
1 CCTGATTCTATA
40466457 CCTGATTCTATA
1 CCTGATTCTATA
40466469 CC
1 CC
40466471 ATACATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (12 bp):
CCTGATTCTATA
Found at i:40473273 original size:28 final size:28
Alignment explanation
Indices: 40473229--40473311 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
40473219 CAGTACAGTG
**
40473229 TGGGCC-TAGCCCGATACAGTAACAATA
1 TGGGCCTTAGCCTAATACAGTAACAATA
* * *
40473256 TGGGCCTTAGCCTAATACAGTAATAGTG
1 TGGGCCTTAGCCTAATACAGTAACAATA
*
40473284 T-GGCCTTAG-CTCAATATAGTAACAATA
1 TGGGCCTTAGCCT-AATACAGTAACAATA
40473311 T
1 T
40473312 AGTGCCATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
26 2 0.04
27 26 0.58
28 17 0.38
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (28 bp):
TGGGCCTTAGCCTAATACAGTAACAATA
Found at i:40473441 original size:26 final size:26
Alignment explanation
Indices: 40473412--40473466 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
40473402 AACACACCAA
* * *
40473412 TATCGCAGCAAAGTTTCCAATAATAG
1 TATCGCAGCAAAGCTGCCAATAACAG
40473438 TATCGCAGCAAAGCTGCCAATAACAG
1 TATCGCAGCAAAGCTGCCAATAACAG
40473464 TAT
1 TAT
40473467 ATGTGGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAATAACAG
Found at i:40473677 original size:27 final size:27
Alignment explanation
Indices: 40473647--40473734 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
40473637 TGATCTCCTA
*
40473647 GAGGTATAATAGTTATTTTACCCTATG
1 GAGGTATAATAGTCATTTTACCCTATG
** * *
40473674 GAGGTATTTTTGTCATTTTACCTTATG
1 GAGGTATAATAGTCATTTTACCCTATG
* * *
40473701 GAGGTAT-TTCGATCATTTTACCTTATG
1 GAGGTATAATAG-TCATTTTACCCTATG
*
40473728 GGGGTAT
1 GAGGTAT
40473735 TTTGGTCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
26 3 0.06
27 50 0.94
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (27 bp):
GAGGTATAATAGTCATTTTACCCTATG
Found at i:40473735 original size:27 final size:26
Alignment explanation
Indices: 40473661--40473736 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
40473651 TATAATAGTT
* *
40473661 ATTTTACCCTATGGAGGTATTTTTGTC
1 ATTTTACCTTATGGAGGTA-TTTCGTC
40473688 ATTTTACCTTATGGAGGTATTTCGATC
1 ATTTTACCTTATGGAGGTATTTCG-TC
*
40473715 ATTTTACCTTATGGGGGTATTT
1 ATTTTACCTTATGGAGGTATTT
40473737 TGGTCTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 4 0.09
27 41 0.91
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (26 bp):
ATTTTACCTTATGGAGGTATTTCGTC
Found at i:40480998 original size:27 final size:27
Alignment explanation
Indices: 40480968--40481080 Score: 79
Period size: 27 Copynumber: 4.2 Consensus size: 27
40480958 ATCTCCTAGA
*
40480968 GGTATAAT-AGTCATTTTACCCTATGTG
1 GGTAT-ATCAGTCATTTTACCCTATGGG
* *
40480995 GGTATTTCGGTCATTTTACCCTATGGG
1 GGTATATCAGTCATTTTACCCTATGGG
** * *
40481022 GGTAT-TTTGATAATTTTACCCTGTGGG
1 GGTATATCAG-TCATTTTACCCTATGGG
** * *
40481049 GGTAT-TTTGATAATTTTACCCTATGAG
1 GGTATATCAG-TCATTTTACCCTATGGG
40481076 GGTAT
1 GGTAT
40481081 TTTGGTCTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 3 0.04
27 72 0.96
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.42
Consensus pattern (27 bp):
GGTATATCAGTCATTTTACCCTATGGG
Found at i:40481081 original size:27 final size:27
Alignment explanation
Indices: 40480980--40481084 Score: 156
Period size: 27 Copynumber: 3.9 Consensus size: 27
40480970 TATAATAGTC
* * * *
40480980 ATTTTACCCTATGTGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTTGATA
40481007 ATTTTACCCTATGGGGGTATTTTGATA
1 ATTTTACCCTATGGGGGTATTTTGATA
*
40481034 ATTTTACCCTGTGGGGGTATTTTGATA
1 ATTTTACCCTATGGGGGTATTTTGATA
*
40481061 ATTTTACCCTATGAGGGTATTTTG
1 ATTTTACCCTATGGGGGTATTTTG
40481085 GTCTTTTAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTTGATA
Found at i:40492520 original size:7 final size:7
Alignment explanation
Indices: 40492494--40492564 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
40492484 TGAGAGCTAA
*
40492494 GAGAGTT
1 GAGAGAT
40492501 GAGAGA-
1 GAGAGAT
40492507 GAG-GAT
1 GAGAGAT
40492513 GAGAGAT
1 GAGAGAT
40492520 GAGAGGGAT
1 GAGA--GAT
*
40492529 GAGGGAT
1 GAGAGAT
*
40492536 GAGGGAT
1 GAGAGAT
*
40492543 GAGGGAT
1 GAGAGAT
40492550 GA-AG-T
1 GAGAGAT
*
40492555 GAGAAAT
1 GAGAGAT
40492562 GAG
1 GAG
40492565 CTCTTATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 5 0.09
6 8 0.15
7 35 0.65
9 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.14
Consensus pattern (7 bp):
GAGAGAT
Found at i:40492541 original size:14 final size:14
Alignment explanation
Indices: 40492522--40492551 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40492512 TGAGAGATGA
40492522 GAGGGATGAGGGAT
1 GAGGGATGAGGGAT
40492536 GAGGGATGAGGGAT
1 GAGGGATGAGGGAT
40492550 GA
1 GA
40492552 AGTGAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.57, T:0.13
Consensus pattern (14 bp):
GAGGGATGAGGGAT
Found at i:40499475 original size:22 final size:23
Alignment explanation
Indices: 40499447--40499491 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40499437 ATGCAATCTT
40499447 ATATATGA-TATGCAATATTAGA
1 ATATATGATTATGCAATATTAGA
* *
40499469 ATATATGATTTTGTAATATTAGA
1 ATATATGATTATGCAATATTAGA
40499492 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (23 bp):
ATATATGATTATGCAATATTAGA
Found at i:40500331 original size:27 final size:27
Alignment explanation
Indices: 40500293--40500356 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
40500283 TGATTCACTG
*
40500293 CAAAGGCATTTTCTTTCAGATTTAGCCA
1 CAAAGGC-TTTTCTTTCAGAGTTAGCCA
* *
40500321 CAAAGGCTTTTTTTTCATAGTTAGCCA
1 CAAAGGCTTTTCTTTCAGAGTTAGCCA
40500348 CAAAGGCTT
1 CAAAGGCTT
40500357 CTTTTCTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 26 0.79
28 7 0.21
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
CAAAGGCTTTTCTTTCAGAGTTAGCCA
Found at i:40502851 original size:61 final size:61
Alignment explanation
Indices: 40502784--40502918 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 61
40502774 TAAAGGATAG
* * *
40502784 CCTTTGTGGCAAAACCCTGGATAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGGCAA
1 CCTTTGTGGCAAAACCCTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAA
** * * *
40502845 CCTTTGTGGCAAAACTTTGAACAGGAAAGCCTTTGTGGCGAGTACTGGATGTAAATGACAA
1 CCTTTGTGGCAAAACCCTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAA
40502906 CCTTTGTGGCAAA
1 CCTTTGTGGCAAA
40502919 TCTCAGGAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (61 bp):
CCTTTGTGGCAAAACCCTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAA
Found at i:40502915 original size:32 final size:31
Alignment explanation
Indices: 40502811--40502915 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 31
40502801 TGGATAGGAA
* *
40502811 AACCTTTGTGGCGAGTACTGAAAGTAAATGGC
1 AACCTTTGTGGCGAGTACTG-ATGTAAATGAC
** * *
40502843 AACCTTTGTGGC-AAAACT-TTG-AACAGGA-
1 AACCTTTGTGGCGAGTACTGATGTAA-ATGAC
40502871 AAGCCTTTGTGGCGAGTACTGGATGTAAATGAC
1 AA-CCTTTGTGGCGAGTACT-GATGTAAATGAC
40502904 AACCTTTGTGGC
1 AACCTTTGTGGC
40502916 AAATCTCAGG
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
28 4 0.07
29 13 0.23
30 4 0.07
31 4 0.07
32 27 0.48
33 4 0.07
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (31 bp):
AACCTTTGTGGCGAGTACTGATGTAAATGAC
Found at i:40502936 original size:61 final size:61
Alignment explanation
Indices: 40502808--40502946 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 61
40502798 CCCTGGATAG
* * ** *
40502808 GAAAACCTTTGTGGCGAGTACTGAAAGTAAATGGCAACCTTTGTGGCAAAACTTTGAACAG
1 GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACTAGGAACAC
* * *
40502869 GAAAGCCTTTGTGGCGAGTACTGGATGTAAATGACAACCTTTGTGGCAAATCTCAGGAA-AC
1 GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACT-AGGAACAC
* **
40502930 GTAAGCCTAGGTGGCGA
1 GAAAGCCTTTGTGGCGA
40502947 ACCTCTACAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
61 63 0.95
62 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACTAGGAACAC
Found at i:40523434 original size:26 final size:27
Alignment explanation
Indices: 40523400--40523478 Score: 99
Period size: 26 Copynumber: 2.9 Consensus size: 27
40523390 ATATTTTACA
40523400 AATTTTACAGTTTTATCCCTATTTTTT
1 AATTTTACAGTTTTATCCCTATTTTTT
*
40523427 -ATTTTACAATTTTA-CTCCTATTTTTT
1 AATTTTACAGTTTTATC-CCTATTTTTT
* *
40523453 AGATTTTACAGTTTTGTTCCTATTTT
1 A-ATTTTACAGTTTTATCCCTATTTT
40523479 ACAAAAATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
25 1 0.02
26 23 0.52
28 20 0.45
ACGTcount: A:0.22, C:0.14, G:0.05, T:0.59
Consensus pattern (27 bp):
AATTTTACAGTTTTATCCCTATTTTTT
Found at i:40524340 original size:17 final size:17
Alignment explanation
Indices: 40524318--40524374 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
40524308 GTTTCATTTT
40524318 TTTATTCGGATTTATTG
1 TTTATTCGGATTTATTG
* *
40524335 TTTATT-AG-TTTCATTTT
1 TTTATTCGGATTT-A-TTG
40524352 TTTATTCGGATTTATTG
1 TTTATTCGGATTTATTG
40524369 TTTATT
1 TTTATT
40524375 TCTTTTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 22 0.69
18 2 0.06
19 3 0.09
ACGTcount: A:0.18, C:0.05, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTATTCGGATTTATTG
Found at i:40524349 original size:34 final size:34
Alignment explanation
Indices: 40524306--40524374 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40524296 TTTTCGAAGG
40524306 TAGTTTCATTTTTTTATTCGGATTTATTGTTTAT
1 TAGTTTCATTTTTTTATTCGGATTTATTGTTTAT
40524340 TAGTTTCATTTTTTTATTCGGATTTATTGTTTAT
1 TAGTTTCATTTTTTTATTCGGATTTATTGTTTAT
40524374 T
1 T
40524375 TCTTTTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.06, G:0.12, T:0.65
Consensus pattern (34 bp):
TAGTTTCATTTTTTTATTCGGATTTATTGTTTAT
Found at i:40525328 original size:3 final size:3
Alignment explanation
Indices: 40525320--40525357 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40525310 CTTGACTTTC
40525320 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40525358 ATGGTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40525374 original size:9 final size:8
Alignment explanation
Indices: 40525321--40525382 Score: 52
Period size: 9 Copynumber: 7.1 Consensus size: 8
40525311 TTGACTTTCA
40525321 TTATTATT
1 TTATTATT
40525329 ATTATTATT
1 -TTATTATT
40525338 ATTATTATT
1 -TTATTATT
40525347 ATTATTATT
1 -TTATTATT
* **
40525356 ATATGGTT
1 TTATTATT
40525364 TTCATTATT
1 TT-ATTATT
40525373 TTATTTATT
1 TTA-TTATT
40525382 T
1 T
40525383 ACATATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
8 7 0.16
9 38 0.84
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (8 bp):
TTATTATT
Found at i:40529921 original size:23 final size:23
Alignment explanation
Indices: 40529890--40529940 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
40529880 ACCTACTTTC
* * *
40529890 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGCAATTTTCGGGATA
40529913 TTACAGTAGCAATTTTCGGGATA
1 TTACAGTAGCAATTTTCGGGATA
40529936 TTACA
1 TTACA
40529941 CTTCACCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACAGTAGCAATTTTCGGGATA
Found at i:40537021 original size:23 final size:23
Alignment explanation
Indices: 40536994--40537040 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40536984 ACTATATTAG
* * *
40536994 TGAGAAATTCACTTATTGTGAAA
1 TGAGAAACTCACCTATTGAGAAA
*
40537017 TGAGATACTCACCTATTGAGAAA
1 TGAGAAACTCACCTATTGAGAAA
40537040 T
1 T
40537041 TATGTTGCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (23 bp):
TGAGAAACTCACCTATTGAGAAA
Found at i:40540222 original size:98 final size:98
Alignment explanation
Indices: 40540099--40540397 Score: 447
Period size: 98 Copynumber: 3.1 Consensus size: 98
40540089 GAATCTCATT
* * * *
40540099 TCCCTAGCGTTGTACTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAAGTT
1 TCCCTAGCGTTGCAGTGGAACAGATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTT
* *
40540164 ACAGTGGAGCAGATTAAAGCCACCAACCTTATT
66 ATAGTGGAGCAGATTAAAGCCACCAACCTTATC
*
40540197 TCCCTAGCGTTGCAGTGGAATAGATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTT
1 TCCCTAGCGTTGCAGTGGAACAGATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTT
* *
40540262 ATAGTGGAGCAGATTTAAGCCACCAACATTATC
66 ATAGTGGAGCAGATTAAAGCCACCAACCTTATC
* * *
40540295 TCCCT-GAAGTTGCAGTGGAACAAATTAAAGCTATAAATTATGGCGAATCTTATCTTCCTGAAGT
1 TCCCTAG-CGTTGCAGTGGAACAGATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGT
* * *
40540359 TGTAGTGGAGCAGATTGAAGCCACCATCCTTATC
65 TATAGTGGAGCAGATTAAAGCCACCAACCTTATC
40540393 TCCCT
1 TCCCT
40540398 GAAGATACAG
Statistics
Matches: 183, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
97 1 0.01
98 182 0.99
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (98 bp):
TCCCTAGCGTTGCAGTGGAACAGATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTT
ATAGTGGAGCAGATTAAAGCCACCAACCTTATC
Found at i:40540276 original size:54 final size:53
Alignment explanation
Indices: 40540218--40540379 Score: 153
Period size: 54 Copynumber: 3.2 Consensus size: 53
40540208 GCAGTGGAAT
*
40540218 AGATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTTATAGTGGAGC
1 AGATTAAAGCTATAAATTATGGC-GATCTTATCTTCCTGAAGTTGTAGTGGAGC
* * ** * * *
40540272 AGATTTAAGCCA-CCA--A---C-A--TTATCTCCCTGAAGTTGCAGTGGAAC
1 AGATTAAAGCTATAAATTATGGCGATCTTATCTTCCTGAAGTTGTAGTGGAGC
*
40540316 AAATTAAAGCTATAAATTATGGCGAATCTTATCTTCCTGAAGTTGTAGTGGAGC
1 AGATTAAAGCTATAAATTATGGCG-ATCTTATCTTCCTGAAGTTGTAGTGGAGC
*
40540370 AGATTGAAGC
1 AGATTAAAGC
40540380 CACCATCCTT
Statistics
Matches: 80, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
44 31 0.39
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
50 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
54 41 0.51
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (53 bp):
AGATTAAAGCTATAAATTATGGCGATCTTATCTTCCTGAAGTTGTAGTGGAGC
Found at i:40540464 original size:143 final size:143
Alignment explanation
Indices: 40540290--40540807 Score: 685
Period size: 143 Copynumber: 3.6 Consensus size: 143
40540280 GCCACCAACA
** *
40540290 TTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTATAAATTATGGCGAATCTTATCTTCCTG
1 TTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTG
* * * * *
40540355 AAGTTGTAGTGGAGCAGATTGAAGCCACCATCCTTATCTCCCTGAAGATACAGCGGAGCAGACTG
66 AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
*
40540420 AAGAAAATGAATC
131 AAGACAATGAATC
* *
40540433 TTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAGTTATGGCAAATCTTATCTTCCTG
1 TTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTG
* * * * *
40540498 AAGTTGCAGTGGAGCAGATTGAAGTCACCAGCCTTATCTCCTTGAAGTTGTATCAGAGTAGACTG
66 AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
*
40540563 AAGACTATGAATC
131 AAGACAATGAATC
* * * * * * * *
40540576 TTATTTCTCTGGCATTGTAGTGGAACAGATTAAAGCTACAAGTTATGGCGGATCTTATCCTCCTG
1 TTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTG
* * *
40540641 AAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCTCTGAAGTTGCAGCGGGGTAGACTG
66 AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
**
40540706 AAGACAGCGAATC
131 AAGACAATGAATC
* * * * * * *
40540719 TTATTTCCCTGGCGTTGTAGTAGAACAAATTAAAACTACAAATCATGGAGGATCTTATCTTCCTG
1 TTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTG
* *
40540784 AAGTTACAGTGGAGCAGATCGAAG
66 AAGTTGCAGTGGAGCAGATTGAAG
40540808 ACATAATTCT
Statistics
Matches: 327, Mismatches: 48, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
143 327 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (143 bp):
TTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTG
AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
AAGACAATGAATC
Found at i:40540693 original size:241 final size:237
Alignment explanation
Indices: 40540001--40540693 Score: 620
Period size: 241 Copynumber: 2.9 Consensus size: 237
40539991 TATTACGGTG
* *
40540001 AATCTTATCTTCCTGAAGTTATAGTGGGGCAGATTGAAGCTACCAGTCTTATCTCCCTGAAGTTG
1 AATCTTATCTTCCTGAAGTTATAGTGGAGCAGATTGAAGC-ACCAGCCTTATCTCCCTGAAGTTG
* * * * * * *
40540066 CAGCGGAGCAGACTGAAGAC-AGTGAATCTCATTTCCCTAGCGTTGTACTGGAACAGATTAAAGC
65 TAACAGAGTAGACTGAAGACTA-TGAATCTTATTT-CCT-GCATTGTAGTGGAACAGATTAAAGC
* * *
40540130 TACAAATTATGGCGGATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTAAAGCCACCAACCTTA
127 TAC-AATTATGGCGGATCTTATCCTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTA
* * * * *
40540195 TTTCCCT-AGCGTTGCAGTGGAATAGATTAAAGCTATAAATTATGGCG
191 TCTCCCTGA-CGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCA
* * * *
40540242 GATCTTATCTTCCTGAAGTTATAGTGGAGCAGATTTAAGCCACCAACATTATCTCCCTGAAGTTG
1 AATCTTATCTTCCTGAAGTTATAGTGGAGCAGATTGAAG-CACCAGCCTTATCTCCCTGAAGTT-
* * * * * * *
40540307 CAGTGGAACAAATTAAAGCT-ATAAATTATGGCGAATCTTATCTTCCTGAAGTTGTAGTGGAGCA
64 --GT--AACAGAGTAGA-CTGA-AGACTAT---GAATCTTAT-TTCCTGCA-TTGTAGTGGAACA
* ** * * * **
40540371 GATTGAAGC--C-ACCAT--C----CTTAT-CTCCCTGAAGATACAGCGGAGCAGACTGAAGAAA
118 GATTAAAGCTACAATTATGGCGGATCTTATCCT-CCTGAAGTTACAGTGGAGCAGATTGAAG-CC
** * * *
40540426 ATGAATCTTATCTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAAGTTATGGCA
181 ACCAACCTTATCTCCCTGACGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCA
** *
40540483 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACCAGCCTTATCTCCTTGAAGTTG
1 AATCTTATCTTCCTGAAGTTATAGTGGAGCAGATTGAAG-CACCAGCCTTATCTCCCTGAAGTTG
*
40540548 TATCAGAGTAGACTGAAGACTATGAATCTTATTTCTCTGGCATTGTAGTGGAACAGATTAAAGCT
65 TAACAGAGTAGACTGAAGACTATGAATCTTATTTC-CT-GCATTGTAGTGGAACAGATTAAAGCT
* * *
40540613 ACAAGTTATGGCGGATCTTATCCTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTAT
128 ACAA-TTATGGCGGATCTTATCCTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTAT
* *
40540678 CTCTCTGAAGTTGCAG
192 CTCCCTGACGTTGCAG
40540694 CGGGGTAGAC
Statistics
Matches: 347, Mismatches: 74, Indels: 62
0.72 0.15 0.13
Matches are distributed among these distances:
231 3 0.01
232 31 0.09
233 2 0.01
234 1 0.00
235 8 0.02
236 10 0.03
238 3 0.01
239 1 0.00
240 28 0.08
241 178 0.51
242 29 0.08
243 2 0.01
244 2 0.01
246 9 0.03
247 5 0.01
248 2 0.01
249 1 0.00
250 30 0.09
251 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (237 bp):
AATCTTATCTTCCTGAAGTTATAGTGGAGCAGATTGAAGCACCAGCCTTATCTCCCTGAAGTTGT
AACAGAGTAGACTGAAGACTATGAATCTTATTTCCTGCATTGTAGTGGAACAGATTAAAGCTACA
ATTATGGCGGATCTTATCCTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATCTCC
CTGACGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCA
Found at i:40543679 original size:86 final size:86
Alignment explanation
Indices: 40543563--40543887 Score: 352
Period size: 86 Copynumber: 3.8 Consensus size: 86
40543553 AACAAGTGGC
* * * * *
40543563 GGCTAGTCCACAAAACCCAGTAGCAATTTGTTTAATCTGCGAATATGTTATGCACCCACAATAAG
1 GGCTCGTCCACAAAACCCAGTGGCAATTTGTTTAATCTGTGAATATGTTGTGCACTCACAATAAG
*
40543628 TGACAGTAACTACAAACATGT
66 TGACAGTAACTACAAATATGT
* * * **
40543649 GGCTTGTCCACAAAACCTAGTGGCAGTTTGTTTAATCTGTGAATATAATGTGCACTCAC-ATCAA
1 GGCTCGTCCACAAAACCCAGTGGCAATTTGTTTAATCTGTGAATATGTTGTGCACTCACAAT-AA
40543713 GTGACAGTAACTACAAATATGT
65 GTGACAGTAACTACAAATATGT
* * * * *
40543735 GGCTCATCTACAAAACCCAGTGGCTAATTTGTTTAATCTATAAATATGTTGTGCACTCACAACAA
1 GGCTCGTCCACAAAACCCAGTGGC-AATTTGTTTAATCTGTGAATATGTTGTGCACTCACAATAA
**
40543800 GTGGTAGTAACTACAAATATGT
65 GTGACAGTAACTACAAATATGT
* * * ** * * *
40543822 GGCTCGTCC-CCAAACCTAGTGACTGTTTGTTTAAT-T-TACAACCATGTTGTGCACTCACAACA
1 GGCTCGTCCACAAAACCCAGTGGCAATTTGTTTAATCTGT-GAA-TATGTTGTGCACTCACAATA
40543884 AGTG
64 AGTG
40543888 GAAGTAATTG
Statistics
Matches: 203, Mismatches: 31, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
83 1 0.00
84 3 0.01
85 35 0.17
86 104 0.51
87 59 0.29
88 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (86 bp):
GGCTCGTCCACAAAACCCAGTGGCAATTTGTTTAATCTGTGAATATGTTGTGCACTCACAATAAG
TGACAGTAACTACAAATATGT
Found at i:40545295 original size:22 final size:26
Alignment explanation
Indices: 40545269--40545329 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 26
40545259 AGCTGAAGAA
40545269 CGGTAAGCTC-TAGAGAG-TGA-A-AT
1 CGGTAAGCTCATA-AGAGCTGATATAT
40545292 -GGTAAGCTCATAAGAGCTGATATAT
1 CGGTAAGCTCATAAGAGCTGATATAT
40545317 CGGTAAGCTCATA
1 CGGTAAGCTCATA
40545330 CGGGCTGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
22 13 0.39
23 5 0.15
24 1 0.03
25 2 0.06
26 12 0.36
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (26 bp):
CGGTAAGCTCATAAGAGCTGATATAT
Found at i:40547165 original size:25 final size:26
Alignment explanation
Indices: 40547118--40547167 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
40547108 AAGAATAAAT
40547118 AAATTAACTAAGTTTTCAAAAATAGA
1 AAATTAACTAAGTTTTCAAAAATAGA
40547144 AAATTAACTAAG-TTTCAAAAATAG
1 AAATTAACTAAGTTTTCAAAAATAG
40547168 TTATCATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (26 bp):
AAATTAACTAAGTTTTCAAAAATAGA
Found at i:40557735 original size:54 final size:54
Alignment explanation
Indices: 40557645--40557749 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
40557635 ATAGCATCTC
* *
40557645 ACACGGCTTGACAAATAGTCGTGTAACCTAAGTCAGAGAATTACACGATCTGGG
1 ACACGGCCTGACAAATAGTCGTGTAACCTAAATCAGAGAATTACACGATCTGGG
* * * *
40557699 ACACGGCCTGACACATATTCGTGTGA-CTCAAATCAGAGAGTTACACGATCT
1 ACACGGCCTGACAAATAGTCGTGTAACCT-AAATCAGAGAATTACACGATCT
40557750 AGACAGACGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (54 bp):
ACACGGCCTGACAAATAGTCGTGTAACCTAAATCAGAGAATTACACGATCTGGG
Found at i:40559556 original size:29 final size:29
Alignment explanation
Indices: 40559496--40559562 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
40559486 ATTAACTTGG
* *
40559496 GAAAGAAAAAATTATTTAAATACCACTTAT
1 GAAA-AAAAAAATATTTAAATACCACTCAT
*
40559526 GATAAAAAAAAATATTTAAGTACCAC-CAT
1 GA-AAAAAAAAATATTTAAATACCACTCAT
40559555 GAAAAAAA
1 GAAAAAAA
40559563 GTTTATGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.18
29 4 0.12
30 21 0.64
31 2 0.06
ACGTcount: A:0.58, C:0.10, G:0.07, T:0.24
Consensus pattern (29 bp):
GAAAAAAAAAATATTTAAATACCACTCAT
Found at i:40561765 original size:2 final size:2
Alignment explanation
Indices: 40561758--40561785 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40561748 TTCTGGTTTT
40561758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40561786 AATACTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40564398 original size:30 final size:30
Alignment explanation
Indices: 40564364--40564457 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
40564354 AAGTAGGATC
*
40564364 ACACGACCGTGTAACTCTCTGACTTGCCAT
1 ACACGGCCGTGTAACTCTCTGACTTGCCAT
* *
40564394 ACACGGCCGTATAACTCTCTGACTTACCAT
1 ACACGGCCGTGTAACTCTCTGACTTGCCAT
*
40564424 ACACGGCTGTGTAACTCTCTGACTTGCCAT
1 ACACGGCCGTGTAACTCTCTGACTTGCCAT
40564454 ACAC
1 ACAC
40564458 AGCGGTGTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (30 bp):
ACACGGCCGTGTAACTCTCTGACTTGCCAT
Found at i:40564491 original size:42 final size:42
Alignment explanation
Indices: 40564432--40564519 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
40564422 ATACACGGCT
* *
40564432 GTGTAACTCTCTGACTTGCCATACACAG-CGGTGTCGCAGGCC
1 GTGTAACTCTCTAACTTGCCACACACAGTC-GTGTCGCAGGCC
* *
40564474 GTGTAACTCTCTAACTTGCCACACACAGTCGTGTGGTAGGCC
1 GTGTAACTCTCTAACTTGCCACACACAGTCGTGTCGCAGGCC
40564516 GTGT
1 GTGT
40564520 GCTAGGCCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (42 bp):
GTGTAACTCTCTAACTTGCCACACACAGTCGTGTCGCAGGCC
Found at i:40567222 original size:37 final size:37
Alignment explanation
Indices: 40567164--40567234 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
40567154 ACTACATGTG
* *
40567164 AGCTGGGAACAGAAAGGTTGCGAACTGATGGAGTGCA
1 AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGTGCA
* * *
40567201 AGCTGCGAACAGAGAGCTTGCGCACTGGTGGAGT
1 AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGT
40567235 ACGAGTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.38, T:0.17
Consensus pattern (37 bp):
AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGTGCA
Found at i:40569000 original size:18 final size:18
Alignment explanation
Indices: 40568977--40569019 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40568967 ACCCAATCTA
**
40568977 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
40568995 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
40569013 AACCCAA
1 AACCCAA
40569020 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:40569143 original size:9 final size:9
Alignment explanation
Indices: 40569144--40569193 Score: 91
Period size: 9 Copynumber: 5.6 Consensus size: 9
40569134 TTAATTTGGT
40569144 TAATTCGGG
1 TAATTCGGG
*
40569153 TAATTCGGT
1 TAATTCGGG
40569162 TAATTCGGG
1 TAATTCGGG
40569171 TAATTCGGG
1 TAATTCGGG
40569180 TAATTCGGG
1 TAATTCGGG
40569189 TAATT
1 TAATT
40569194 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (9 bp):
TAATTCGGG
Found at i:40569156 original size:18 final size:18
Alignment explanation
Indices: 40569135--40569193 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
40569125 TCAATTTGGT
*
40569135 TAATTTGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
40569153 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
40569171 TAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGG
40569189 TAATT
1 TAATT
40569194 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:40569162 original size:27 final size:27
Alignment explanation
Indices: 40569127--40569194 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
40569117 GTAGTGATTC
* *
40569127 AATTTGGTTAATTTGGTTAATTCGGGT
1 AATTCGGTTAATTTGGGTAATTCGGGT
*
40569154 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTCGGTTAATTTGGGTAATTCGGGT
*
40569181 AATTCGGGTAATTT
1 AATTCGGTTAATTT
40569195 TTAACCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (27 bp):
AATTCGGTTAATTTGGGTAATTCGGGT
Found at i:40569774 original size:21 final size:22
Alignment explanation
Indices: 40569749--40569835 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 22
40569739 CTCTCTCAAA
40569749 AATTTC-ATTATATAATAAAAT
1 AATTTCAATTATATAATAAAAT
* * *
40569770 AATTT-TATTTTAAAATAAAAT
1 AATTTCAATTATATAATAAAAT
*
40569791 AATTTCAATTTCATATAAT-TAAT
1 AATTTCAA-TT-ATATAATAAAAT
*
40569814 AAGTTTACTATTATATAATAAA
1 AA-TTT-CAATTATATAATAAA
40569836 TTGTTAAACA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
21 23 0.45
22 1 0.02
23 14 0.27
24 11 0.22
25 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (22 bp):
AATTTCAATTATATAATAAAAT
Found at i:40569981 original size:24 final size:24
Alignment explanation
Indices: 40569935--40569982 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40569925 ACTTTTTATT
* * **
40569935 TTATTAATTTATATTTTTTTATAA
1 TTATTAAATTATAATTTAATATAA
40569959 TTATTAAATTATAATTTAATATAA
1 TTATTAAATTATAATTTAATATAA
40569983 ATATAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTAAATTATAATTTAATATAA
Found at i:40569999 original size:25 final size:26
Alignment explanation
Indices: 40569971--40570019 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
40569961 ATTAAATTAT
40569971 AATTTAATATAAATATA-ATTTTAAC
1 AATTTAATATAAATATACATTTTAAC
* * *
40569996 AATTTATTTTATATATACATTTTA
1 AATTTAATATAAATATACATTTTA
40570020 TTTAATGTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTTAATATAAATATACATTTTAAC
Found at i:40575935 original size:19 final size:18
Alignment explanation
Indices: 40575899--40575940 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
40575889 AGAAATCGGC
*
40575899 AGAAAAAGAGAAAAAAAT
1 AGAAAAACAGAAAAAAAT
40575917 AAGAAAAACA-AAAAGAAAT
1 -AGAAAAACAGAAAA-AAAT
40575936 AGAAA
1 AGAAA
40575941 TTTGTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (18 bp):
AGAAAAACAGAAAAAAAT
Found at i:40589840 original size:44 final size:44
Alignment explanation
Indices: 40589655--40589976 Score: 172
Period size: 44 Copynumber: 7.3 Consensus size: 44
40589645 CAGTAAGGAT
*
40589655 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * * ** * *
40589699 GGTAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAGGCC
1 AGCAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGAC
* * * * * * * * * * **
40589743 ACCAAACCTTGTCTCTCTGAGCAGCAGCGGAGTAGGTTAAAGGT
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
*
40589787 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * ** *
40589831 GGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCC
1 AGCAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGAC
* * ** * * * * * * *
40589875 ACCGAGGCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTC-AAGAT
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGAC
*
40589919 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
40589963 GGTAAATCTTATCT
1 AGCAAATCTTATCT
40589977 TTCCAGGATA
Statistics
Matches: 191, Mismatches: 73, Indels: 28
0.65 0.25 0.10
Matches are distributed among these distances:
42 8 0.04
43 14 0.07
44 151 0.79
45 14 0.07
46 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
Found at i:40589895 original size:132 final size:132
Alignment explanation
Indices: 40589649--40590044 Score: 684
Period size: 132 Copynumber: 3.0 Consensus size: 132
40589639 ACAGACCAGT
40589649 AAGGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTT
1 AAGG-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTT
* * * *
40589714 TCCAAGATAGTGGGAAGCAGATTTAGGCCACCAAACCTTGTCTCTCTGAGCAGCAGCGGAGTAGG
65 TCCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
40589779 TTA
130 TTA
*
40589782 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
1 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTT
*
40589847 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGGCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
*
40589912 TC
131 TA
*
40589914 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTT
1 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTT
* * *
40589979 CCAGGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGTGGACTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
40590044 T
131 T
40590045 GAAAATTACA
Statistics
Matches: 250, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
132 246 0.98
133 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (132 bp):
AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
TA
Found at i:40593918 original size:25 final size:25
Alignment explanation
Indices: 40593890--40593962 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
40593880 TTATTGATAC
* *
40593890 TCAGCTCATATAAGCTTACCGTTAT
1 TCAGCTCAGAGAAGCTTACCGTTAT
* *
40593915 TCAGCTCGGAGGAGCTTACCGTTAT
1 TCAGCTCAGAGAAGCTTACCGTTAT
* *
40593940 TCAGCTCGGAGGAGCTTACCGTT
1 TCAGCTCAGAGAAGCTTACCGTT
40593963 TATAGCTCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (25 bp):
TCAGCTCAGAGAAGCTTACCGTTAT
Found at i:40594163 original size:31 final size:31
Alignment explanation
Indices: 40594128--40594187 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
40594118 TATACATGAA
40594128 ATATATGGAAAT-GATGATACATGATATATTG
1 ATATATGGAAATGGATGATACATG-TATATTG
* * *
40594159 ATATATTGTAATGGATGATATATGTATAT
1 ATATATGGAAATGGATGATACATGTATAT
40594188 GATGAAACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (31 bp):
ATATATGGAAATGGATGATACATGTATATTG
Found at i:40596668 original size:40 final size:40
Alignment explanation
Indices: 40596584--40596729 Score: 140
Period size: 40 Copynumber: 3.6 Consensus size: 40
40596574 TCGAATGATG
* * * *
40596584 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
40596623 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
**
40596664 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA-
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTA-C-TAAT
* *
40596705 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGACTAAGTCCCGAAGGCATTTG
40596730 AATGAGTAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
39 1 0.01
40 77 0.84
41 11 0.12
42 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:40604656 original size:40 final size:39
Alignment explanation
Indices: 40604572--40604756 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
40604562 TCGAATGATG
* * * *
40604572 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
40604612 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40604652 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
40604691 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
40604732 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
40604757 AATGAGTAGC
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40604708 original size:79 final size:81
Alignment explanation
Indices: 40604572--40604754 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
40604562 TCGAATGATG
* *
40604572 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
40604636 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
40604651 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
40604713 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
40604731 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40604755 TGAATGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:40604778 original size:79 final size:79
Alignment explanation
Indices: 40604625--40604789 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
40604615 GGACTAAGAT
* **
40604625 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
40604690 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
40604704 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
40604767 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40604783 CCGAAGG
1 CCGAAGG
40604790 TACGTGATTG
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.66
80 23 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40614043 original size:5 final size:5
Alignment explanation
Indices: 40614033--40614084 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
40614023 GAACAAATAT
* *
40614033 ATTCG ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ATTCG ACTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG
40614084 A
1 A
40614085 GAAAACTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 33 0.80
6 6 0.15
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (5 bp):
ATTCG
Found at i:40618760 original size:15 final size:15
Alignment explanation
Indices: 40618740--40618783 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
40618730 AAAATCGTCG
*
40618740 AATAAAATTGAAAAA
1 AATAAAATAGAAAAA
*
40618755 AATAAAA-AAATAAAA
1 AATAAAATAGA-AAAA
40618770 AATAAAATAGAAAA
1 AATAAAATAGAAAA
40618784 TTCCCCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 21 0.88
16 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (15 bp):
AATAAAATAGAAAAA
Found at i:40619547 original size:44 final size:44
Alignment explanation
Indices: 40619498--40620019 Score: 126
Period size: 44 Copynumber: 11.2 Consensus size: 44
40619488 TAACTTCAAA
*
40619498 GAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATACTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
* * * * * **
40619542 GAGATAGGATTAC-TAGCTTCAATCTGCTCCGTTGTAATCTCAGG
1 GAGATAAGA-TACTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
* * * *
40619586 GAGATAAGAT--TTCTGGCTTCAATATGATGCGATTTACTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-G-TT---T-TAATCCG-----CTCCACTGTAATC-TCAGG
* *
40619640 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATACTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
* * * * * *
40619684 GAGATAGGATTAC-TAGCTTCAATCTGCT-TAGCTGTAATCTCAGG
1 GAGATAAGA-TACTTTGTTTTAATCCGCTCCA-CTGTAATCTCAGG
* * *
40619728 GAGATAAGAT--TTCTGGCTTCAATCTGGTGCGATCTACTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-GTTTTAATC-----CG--CT-C-C-ACTGTAATC-TCAGG
*
40619782 GAGATAAGAT-CATTTATTTTAATCC-CTCCACTGTAATCTCAGG
1 GAGATAAGATAC-TTTGTTTTAATCCGCTCCACTGTAATCTCAGG
* * * * *
40619825 GAGATAGGATTAC-TAGCTTCAATCTGCT-CAGCTGTAATCTCAGG
1 GAGATAAGA-TACTTTGTTTTAATCCGCTCCA-CTGTAATCTCAGG
* * *
40619869 GAGATAAGAT--TTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-G-TT---T-TAATCCG--CT-C-C-ACTGTAATC-TCAGG
* * *
40619923 GAGATAAGATCCTTTATTTTAAT-CGCTCCACTGTAATCTCAGT
1 GAGATAAGATACTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
* * * * * * *
40619966 GAGATAGGATTAC-TAGCTTCAATCTGCTCCGCTGTAATCTTAGG
1 GAGATAAGA-TACTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
40620010 GAGATAAGAT
1 GAGATAAGAT
40620020 TTCTGGCGTC
Statistics
Matches: 347, Mismatches: 69, Indels: 125
0.64 0.13 0.23
Matches are distributed among these distances:
42 3 0.01
43 58 0.17
44 159 0.46
45 10 0.03
46 4 0.01
48 4 0.01
49 16 0.05
50 2 0.01
51 4 0.01
53 7 0.02
54 69 0.20
55 5 0.01
56 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
GAGATAAGATACTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
Found at i:40619892 original size:141 final size:142
Alignment explanation
Indices: 40619459--40620118 Score: 1171
Period size: 141 Copynumber: 4.7 Consensus size: 142
40619449 TGCTGTTGTA
* *
40619459 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTGTTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
* *
40619524 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGTTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAG
40619589 ATAAGATTTCTG
131 ATAAGATTTCTG
* *
40619601 GCTTCAATATGATGCGATTTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
*
40619666 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAG
40619731 ATAAGATTTCTG
131 ATAAGATTTCTG
* *
40619743 GCTTCAATCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCC-
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
40619807 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAG
40619872 ATAAGATTTCTG
131 ATAAGATTTCTG
40619884 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT-CG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
* * *
40619948 CTCCACTGTAATCTCAGTGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTTAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAG
40620013 ATAAGATTTCTG
131 ATAAGATTTCTG
* * *
40620025 GCGTCAATCTGATGCGATCTACTGTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
40620090 CTCCACTGTAATCTCAGGGAGATAGGATT
66 CTCCACTGTAATCTCAGGGAGATAGGATT
40620119 TCTTCTATCT
Statistics
Matches: 495, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
140 1 0.00
141 269 0.54
142 225 0.45
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (142 bp):
GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAG
ATAAGATTTCTG
Found at i:40620032 original size:44 final size:44
Alignment explanation
Indices: 40619943--40620035 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
40619933 CCTTTATTTT
* * *
40619943 AATC-GCTCCACTGTAATCTCAGTGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCGTC
* * * *
40619986 AATCTGCTCCGCTGTAATCTTAGGGAGATAAGATTTCTGGCGTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCGTC
40620030 AATCTG
1 AATCTG
40620036 ATGCGATCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 4 0.10
44 38 0.90
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCGTC
Found at i:40637966 original size:20 final size:20
Alignment explanation
Indices: 40637941--40637980 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40637931 TTCACCTCAT
40637941 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
40637961 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
40637981 AAGACCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:40645019 original size:50 final size:50
Alignment explanation
Indices: 40644957--40645334 Score: 258
Period size: 50 Copynumber: 7.6 Consensus size: 50
40644947 TTGAAAAGTA
*
40644957 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
* * * * *** * * * * **
40645007 AATAGATTGAAGCTACGACAGCGGATCTGGTTTCCCT-GATATTGCAATTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTGG
* ** *
40645057 AAAAGATTAAAGCCACAACGGTAGATCTTACTTCCTTAGCAGTGCAGCGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
* * * * *** * * * **
40645107 AATAGATTGAAGCTACGACAGCGGATCTGGTTTCCTT-GATATTGCAATTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTGG
*
40645157 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGTAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
* * * *** ** * * * **
40645207 AACAGATTGAAGCTACGACGGCGGATCTGGTTTCC-CGGATACTGCAATTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTGG
* *
40645257 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGAAGTAG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
* * * *
40645307 AACAGATTGAAGCTACGACGGCAGATCT
1 AAAAGATTGAAGCCACAACGGCGGATCT
40645335 GGTTTCCCTG
Statistics
Matches: 230, Mismatches: 92, Indels: 12
0.69 0.28 0.04
Matches are distributed among these distances:
49 3 0.01
50 224 0.97
51 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (50 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
Found at i:40645128 original size:100 final size:100
Alignment explanation
Indices: 40644955--40645467 Score: 760
Period size: 100 Copynumber: 5.1 Consensus size: 100
40644945 GGTTGAAAAG
* *
40644955 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
*
40645020 TACGACAGCGGATCTGGTTTCCCTGATATTGCAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
* ** * *
40645055 TAAAAAGATTAAAGCCACAACGGTAGATCTTACTTCCTTAGCAGTGCAGCGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
* *
40645120 TACGACAGCGGATCTGGTTTCCTTGATATTGCAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
*
40645155 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGTAGTGGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
* *
40645220 TACGACGGCGGATCTGGTTTCCCGGATACTGCAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
* *
40645255 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGAAGTAGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
* *
40645320 TACGACGGCAGATCTGGTTTCCCTGATATAGCAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
* * * * *
40645355 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTGCCTGA-CGGTGCGGTAGAACAGATTGAAG
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTGGAACAGATTGAAG
* * * *
40645419 CTACGACGGCAGATCTGGTTTCCCCGACATTGCAGT
65 CTACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
40645455 TAAACAA-ATTGAA
1 TAAA-AAGATTGAA
40645468 AATTTCAGAT
Statistics
Matches: 382, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
100 376 0.98
101 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (100 bp):
TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
Found at i:40645364 original size:50 final size:49
Alignment explanation
Indices: 40645010--40645442 Score: 228
Period size: 50 Copynumber: 8.7 Consensus size: 49
40645000 GCAGCGGAAT
*
40645010 AGATTGAAGCTACGACAGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA-TGCAATTAAAA
* * * ** *** * * **** *
40645060 AGATTAAAGCCACAACGGTAGATCTTACTTCCTTAGCA-GTGCAGCGGAAT
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-ATATGCAATTAAAA
* *
40645110 AGATTGAAGCTACGACAGCGGATCTGGTTTCCTTGATATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA-TGCAATTAAAA
* * *** * * * * ** *
40645160 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCA-GTGTAGTGGAAC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-ATATGCAATTAAAA
*
40645210 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCGGATACTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA-TGCAATTAAAA
* * *** * * * *
40645260 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCA-GTG-AAGTAGAAC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCT-G-ATATGCAATTA-AAA
*
40645310 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATAGCAATTAAAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT-GCAATTAAAA
* * * *** * ** ** *
40645360 AGATTGAAGCCACAACGGCAGATCTTACTTGCCTGACGGTGC-GGTAGAAC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TATGCAATTA-AAA
*
40645410 AGATTGAAGCTACGACGGCAGATCTGGTTTCCC
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCC
40645443 CGACATTGCA
Statistics
Matches: 274, Mismatches: 93, Indels: 32
0.69 0.23 0.08
Matches are distributed among these distances:
48 3 0.01
49 10 0.04
50 250 0.91
51 8 0.03
52 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (49 bp):
AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATGCAATTAAAA
Found at i:40646780 original size:28 final size:27
Alignment explanation
Indices: 40646749--40646823 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
40646739 CATACATACG
*
40646749 TTTTATAATACATATACATTTTTTTTCA
1 TTTTATAATACATATACATTTTCTTT-A
*
40646777 TTTTATAATTC--ATACATTTTCTTTA
1 TTTTATAATACATATACATTTTCTTTA
* * *
40646802 TATTAT-ATACATACAGATTTTC
1 TTTTATAATACATATACATTTTC
40646824 ACACATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.08
25 6 0.15
26 20 0.51
28 10 0.26
ACGTcount: A:0.32, C:0.12, G:0.01, T:0.55
Consensus pattern (27 bp):
TTTTATAATACATATACATTTTCTTTA
Found at i:40660662 original size:85 final size:85
Alignment explanation
Indices: 40660519--40660688 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
40660509 TCACTTTTGG
*
40660519 GACTAAATTAGAAATTTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
1 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
40660584 AGAGCCAAAGTGAGATTTTA
66 AGAGCCAAAGTGAGATTTTA
*
40660604 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCTAGAAA
1 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
*
40660669 ATAGCCAAAGTGAGATTTTA
66 AGAGCCAAAGTGAGATTTTA
40660689 ATTACTCATA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (85 bp):
GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
AGAGCCAAAGTGAGATTTTA
Found at i:40666285 original size:16 final size:16
Alignment explanation
Indices: 40666246--40666285 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
40666236 TCTTCAACTG
*
40666246 AAGAAAGAATATGCCT
1 AAGAAAGAATACGCCT
*
40666262 AATAAAGAATACGCCT
1 AAGAAAGAATACGCCT
*
40666278 AAGGAAGA
1 AAGAAAGA
40666286 GTATGCCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (16 bp):
AAGAAAGAATACGCCT
Found at i:40667661 original size:25 final size:25
Alignment explanation
Indices: 40667618--40667671 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40667608 TTGTAGCGAG
* **
40667618 TTATTTGTAAGGCTTTTATGAAAAA
1 TTATTTGTAAAGCCCTTATGAAAAA
**
40667643 TTATTTGTAAAGCCCTTATGGCAAA
1 TTATTTGTAAAGCCCTTATGAAAAA
40667668 TTAT
1 TTAT
40667672 CTAAAAGGCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (25 bp):
TTATTTGTAAAGCCCTTATGAAAAA
Found at i:40671062 original size:23 final size:22
Alignment explanation
Indices: 40671019--40671062 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
40671009 TTCTAAGTTG
40671019 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
40671042 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
40671063 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:40671171 original size:45 final size:45
Alignment explanation
Indices: 40671107--40671195 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
40671097 AACAGATACT
* *
40671107 CAGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CAGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
40671152 CAGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CAGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
40671196 TCGGTTCACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (45 bp):
CAGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:40671268 original size:51 final size:51
Alignment explanation
Indices: 40671202--40671342 Score: 176
Period size: 51 Copynumber: 2.8 Consensus size: 51
40671192 ATGTTCGGTT
* *
40671202 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCAATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCAATA
* * * * **
40671253 CACGTAGTAGTCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCAATA
* *
40671304 CGCATAGTAGCCTGCAGATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
40671343 CACTTTCAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.03
51 71 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCAATA
Found at i:40674877 original size:39 final size:39
Alignment explanation
Indices: 40674823--40674903 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
40674813 GAAAATAAGA
40674823 CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
1 CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
* *
40674862 CGAATAACACGAGTAAGCTTTTATAAATCTTAGTAAGTT
1 CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
40674901 CGA
1 CGA
40674904 TGATTAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (39 bp):
CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
Found at i:40677058 original size:41 final size:41
Alignment explanation
Indices: 40676999--40677146 Score: 208
Period size: 41 Copynumber: 3.6 Consensus size: 41
40676989 TAAGGCCCAA
* * * *
40676999 ACTGATTCTATGATGGGCTATGGCCCTACTGCATATTTGAA
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* *
40677040 ATTGATTCTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* *
40677081 ACTGATACTGTGATGGGCTACGGCCCTACTACATATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
*
40677122 ACTG-TACTGAGATGGGCTAAGGCCC
1 ACTGATACTGTGATGGGCTAAGGCCC
40677147 AAACTGCTAC
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 19 0.20
41 78 0.80
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
Found at i:40677153 original size:82 final size:80
Alignment explanation
Indices: 40676999--40677165 Score: 210
Period size: 82 Copynumber: 2.1 Consensus size: 80
40676989 TAAGGCCCAA
* * * * * *
40676999 ACTGATTCTATGATGGGCTATGGCCCTACTGCATATTTGAAATTGATTCTGTGATGGGCTAAGGC
1 ACTGATACTATGATGGGCTACGGCCCTACTACATATTTGAAACTGATACTGAGATGGGCTAAGGC
* *
40677064 CCTACTGCATATTTGAT
66 CCAACTGC-TA-CTGAT
* *
40677081 ACTGATACTGTGATGGGCTACGGCCCTACTACATATTTGATACTG-TACTGAGATGGGCTAAGGC
1 ACTGATACTATGATGGGCTACGGCCCTACTACATATTTGAAACTGATACTGAGATGGGCTAAGGC
40677145 CCAAACTGCTACTGAT
66 CC-AACTGCTACTGAT
40677161 ACTGA
1 ACTGA
40677166 AATAGGGCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 9 0.12
81 21 0.28
82 44 0.59
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (80 bp):
ACTGATACTATGATGGGCTACGGCCCTACTACATATTTGAAACTGATACTGAGATGGGCTAAGGC
CCAACTGCTACTGAT
Found at i:40682271 original size:22 final size:22
Alignment explanation
Indices: 40682227--40682271 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40682217 TTAAGTGACT
* *
40682227 AAAATTGGTTTTTGGATGGTCG
1 AAAATAGGTTTTTGGATGCTCG
40682249 AAAATAGG-TTTTGGAGTGCTCG
1 AAAATAGGTTTTTGGA-TGCTCG
40682271 A
1 A
40682272 GGATCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.36
Consensus pattern (22 bp):
AAAATAGGTTTTTGGATGCTCG
Found at i:40683554 original size:40 final size:41
Alignment explanation
Indices: 40683462--40683649 Score: 236
Period size: 41 Copynumber: 4.6 Consensus size: 41
40683452 TAAGGCCCAA
* * *
40683462 ACTGATTCTGTAATGGGCTAAGGCCCTACTGCATATTTGAA
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* *
40683503 ACTGATCCTGTGATGGGCTAAGGCCCTA-TGGATATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* * *
40683543 ACTGATACTGTGATAGGTTAAGGCCCTACTGCAGATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* * * *
40683584 ACTGATGCTATGATGGGCTAAGACCCTACTACATATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* *
40683625 ACT-ATACTGAGATGGGCAAAGGCCC
1 ACTGATACTGTGATGGGCTAAGGCCC
40683650 AAATTGTTAC
Statistics
Matches: 125, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 52 0.42
41 73 0.58
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (41 bp):
ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
Found at i:40683647 original size:81 final size:81
Alignment explanation
Indices: 40683474--40683649 Score: 237
Period size: 81 Copynumber: 2.2 Consensus size: 81
40683464 TGATTCTGTA
* * * **
40683474 ATGGGCTAAGGCCCTACTGCATATTTGAAACTGATCCTGTGATGGGCTAAGGCCCTATGGATATT
1 ATGGGCTAAGGCCCTACTGCAGATTTGAAACTGATCCTATGATGGGCTAAGACCCTATACATATT
*
40683539 TGATACTGATACTGTG
66 TGATACTGATACTGAG
* * * *
40683555 ATAGGTTAAGGCCCTACTGCAGATTTGATACTGATGCTATGATGGGCTAAGACCCTACTACATAT
1 ATGGGCTAAGGCCCTACTGCAGATTTGAAACTGATCCTATGATGGGCTAAGACCCTA-TACATAT
40683620 TTGATACT-ATACTGAG
65 TTGATACTGATACTGAG
*
40683636 ATGGGCAAAGGCCC
1 ATGGGCTAAGGCCC
40683650 AAATTGTTAC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 68 0.84
82 13 0.16
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (81 bp):
ATGGGCTAAGGCCCTACTGCAGATTTGAAACTGATCCTATGATGGGCTAAGACCCTATACATATT
TGATACTGATACTGAG
Done.