Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 9 of 235
Found at i:2449339 original size:19 final size:20
Alignment explanation
Indices: 2449301--2449341 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2449291 CAGATCTTAT
2449301 TATATTATCAATCTTTAAAA
1 TATATTATCAATCTTTAAAA
2449321 TATATTATCCAA-C-TTAAAA
1 TATATTAT-CAATCTTTAAAA
2449340 TA
1 TA
2449342 AATCTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 9 0.45
21 3 0.15
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATTATCAATCTTTAAAA
Found at i:2451749 original size:80 final size:80
Alignment explanation
Indices: 2451616--2451777 Score: 279
Period size: 80 Copynumber: 2.0 Consensus size: 80
2451606 TTTAACAACA
* * *
2451616 AAAACTAGTGATGTTATCAATTTGGACGAGGTTAATTCCATTCAATTACTTTTTCATCCATTAAT
1 AAAACTAGTGATATTATCAATTTAGACGAGGTTAACTCCATTCAATTACTTTTTCATCCATTAAT
2451681 ACCTAATTCATGTTT
66 ACCTAATTCATGTTT
* *
2451696 AAAACTAGTGATATTATCAATTTAGACGAGGTTAACTCCATTCCATTACTTTTTTATCCATTAAT
1 AAAACTAGTGATATTATCAATTTAGACGAGGTTAACTCCATTCAATTACTTTTTCATCCATTAAT
2451761 ACCTAATTCATGTTT
66 ACCTAATTCATGTTT
2451776 AA
1 AA
2451778 TCACCATGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (80 bp):
AAAACTAGTGATATTATCAATTTAGACGAGGTTAACTCCATTCAATTACTTTTTCATCCATTAAT
ACCTAATTCATGTTT
Found at i:2457710 original size:30 final size:30
Alignment explanation
Indices: 2457674--2457742 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
2457664 TAGGTACAAG
*
2457674 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
2457704 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
2457734 TGGTGGTGG
1 TGGTGGTGG
2457743 CAAAGGCTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.14, C:0.04, G:0.52, T:0.29
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:2458621 original size:14 final size:14
Alignment explanation
Indices: 2458602--2458651 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 14
2458592 GAGTTGATTT
*
2458602 TTGAAAAGCATAAA
1 TTGAAAAGCAGAAA
2458616 TTGAAAAAGCAGAAA
1 TTG-AAAAGCAGAAA
* *
2458631 TTGAAAA-CGGAAT
1 TTGAAAAGCAGAAA
2458644 TTGAAAAG
1 TTGAAAAG
2458652 ACCTCGGCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 11 0.35
14 7 0.23
15 13 0.42
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:2458667 original size:103 final size:104
Alignment explanation
Indices: 2458464--2458713 Score: 315
Period size: 103 Copynumber: 2.4 Consensus size: 104
2458454 TGAGCCAAGG
* * *
2458464 CTCAACTCATCTCTCGCAATATGAGTTAATTTTTTTTTAAAACACATAAATTAAAAAACAGAAAC
1 CTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAACACATAAATTAAAAAACAGAAAC
* *
2458529 TAAAAATAGAATTTGAAAAGACATCGACATGTGGCCCGAGA
64 TAAAAACAGAATTTGAAAAGACATCGACATATGGCCCGAGA
* * *
2458570 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA-GCATAAATTGAAAAAGCAGAAATT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACACATAAATT-AAAAAACAGAAACT
* * * * *
2458633 GAAAACGGAATTTGAAAAGACCTCGGCGTATGGCCCGAGA
65 AAAAACAGAATTTGAAAAGACATCGACATATGGCCCGAGA
* *
2458673 CTCAACTCACTTCTCGCAATACGAGTTGAATTTTTTGAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTGAAAA
2458714 ATGGCAATTA
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
102 8 0.06
103 80 0.63
104 1 0.01
105 10 0.08
106 27 0.21
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (104 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACACATAAATTAAAAAACAGAAACTA
AAAACAGAATTTGAAAAGACATCGACATATGGCCCGAGA
Found at i:2458801 original size:14 final size:14
Alignment explanation
Indices: 2458782--2458816 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2458772 GTTGATTCTT
*
2458782 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
2458796 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
2458810 TTGAAAA
1 TTGAAAA
2458817 TACCTCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:2458860 original size:91 final size:84
Alignment explanation
Indices: 2458744--2459123 Score: 272
Period size: 86 Copynumber: 4.5 Consensus size: 84
2458734 AGCGTGTCCT
*
2458744 GAGGCTCAACTCACCTCTCGAAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGA-AAAGCAGA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAA--AGAAATTGACAAA-CAGA
2458808 AATTGAAAATACCTCAGCACGTGAGC-C
62 AATTGAAAATA-CT--GCA-GTG-GCTC
* * *
2458835 GAGGCTCAACTCATCTCTCGCAATATGAGTTGGA-TTTTTGAAAAATAAATTGACAAACGGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTTTGAAAAAGAAATTGACAAACAGAAAT
* * *
2458899 TGAAAATACTTCAGTGTCTT
65 TGAAAATACTGCAGTGGCTC
* * **
2458919 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-ACAA-ACA---A-AAATTGAAATT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAGAAATTGACAAACAGAAATT
*** *
2458977 -ACCTTA--GC-GTGTCCT-
66 GAAAATACTGCAGTG-GCTC
*******
2458992 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-ATTTTTTTTTGA-AAGACAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAAGAAATTGACAA-ACAGAAA
* * *
2459055 TTGAAAATACCTGAACGTGTCTT
64 TTGAAAATA-CTGCA-GTGGCTC
2459078 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAA
2459124 CAGAAATAAA
Statistics
Matches: 237, Mismatches: 33, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
73 36 0.15
74 3 0.01
75 7 0.03
76 3 0.01
77 9 0.04
78 1 0.00
79 3 0.01
80 7 0.03
81 5 0.02
82 3 0.01
83 9 0.04
84 34 0.14
85 4 0.02
86 44 0.19
87 3 0.01
88 22 0.09
89 3 0.01
90 9 0.04
91 30 0.13
92 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (84 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAGAAATTGACAAACAGAAATT
GAAAATACTGCAGTGGCTC
Found at i:2459056 original size:86 final size:86
Alignment explanation
Indices: 2458952--2459119 Score: 275
Period size: 86 Copynumber: 2.0 Consensus size: 86
2458942 TATGAGTTGA
* * *
2458952 TTTTTGACAAACAAAAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTTTTGACAAACAAAAATTGAAAATACCTGAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
2459017 TGAGTTGATTTTTTTGATTTT
66 TGAGTTGATTTTTTTGATTTT
* *
2459038 TTTTTGA-AAGACAGAAATTGAAAATACCTGAACGTGTCTTGAGGCTCAACTCACCTCTCGCAAT
1 TTTTTGACAA-ACAAAAATTGAAAATACCTGAACGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
2459102 ATGAGTTGATTTTTTTGA
65 ATGAGTTGATTTTTTTGA
2459120 AAAACAGAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 2 0.03
86 74 0.97
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (86 bp):
TTTTTGACAAACAAAAATTGAAAATACCTGAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTTTGATTTT
Found at i:2471455 original size:22 final size:22
Alignment explanation
Indices: 2471415--2471482 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 22
2471405 CGTTCTATTA
*
2471415 TTAGCACGTTAAGTGCTCTCTGT
1 TTAGCAC-TTTAGTGCTCTCTGT
2471438 TTAGCACATTT-GTGCTCTCTGT
1 TTAGCAC-TTTAGTGCTCTCTGT
*
2471460 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACTTTAGTGCTCTCTGT
2471482 T
1 T
2471483 CTTTTGTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.08
22 28 0.70
23 9 0.22
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (22 bp):
TTAGCACTTTAGTGCTCTCTGT
Found at i:2474157 original size:23 final size:25
Alignment explanation
Indices: 2474114--2474159 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2474104 GAATCAAACG
*
2474114 GAAACAAGAGAAAAAACAAGAAAGA
1 GAAACAAGAGAAAAAAAAAGAAAGA
2474139 GAAA-AAGA-AAAAAAAAAGAAA
1 GAAACAAGAGAAAAAAAAAGAAA
2474160 AACCCGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.00
Consensus pattern (25 bp):
GAAACAAGAGAAAAAAAAAGAAAGA
Found at i:2481782 original size:75 final size:75
Alignment explanation
Indices: 2481659--2481810 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 75
2481649 TAAATTTCAC
*
2481659 AAGTAGGATTAAAGGGTTAACGATTATCCTATAGAGATATATTAAATATTAAAAGAAATAAGTAT
1 AAGTAAGATTAAAGGGTTAACGATTATCCTATAGAGATATATTAAATATTAAAAGAAATAAGTAT
2481724 TTAGAAAAAA
66 TTAGAAAAAA
2481734 AAGTAAGATTAAAGGGTTAACGATTATCCTATAGAGATATATTAAATATTAAAAGAAATAAGTAT
1 AAGTAAGATTAAAGGGTTAACGATTATCCTATAGAGATATATTAAATATTAAAAGAAATAAGTAT
2481799 TTAGAAAAAA
66 TTAGAAAAAA
2481809 AA
1 AA
2481811 AAGTGTCAAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (75 bp):
AAGTAAGATTAAAGGGTTAACGATTATCCTATAGAGATATATTAAATATTAAAAGAAATAAGTAT
TTAGAAAAAA
Found at i:2485686 original size:32 final size:31
Alignment explanation
Indices: 2485640--2485707 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
2485630 AATAGTCTAT
* *
2485640 ATTTTTATAATTTTTAAAGAATTAAA-TAAA
1 ATTTTTATAATTTTTAAAAAATCAAAGTAAA
*
2485670 ATTTTTGATCAATTTTTAAAAAATCAAAGTATA
1 ATTTTT-AT-AATTTTTAAAAAATCAAAGTAAA
2485703 ATTTT
1 ATTTT
2485708 ATCATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 6 0.19
31 2 0.06
32 16 0.50
33 8 0.25
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAAAATCAAAGTAAA
Found at i:2487338 original size:16 final size:17
Alignment explanation
Indices: 2487308--2487340 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2487298 CATATAAATT
*
2487308 TTTTTAAATGTTTTAAC
1 TTTTTAAATGCTTTAAC
2487325 TTTTTAAA-GCTTTAAC
1 TTTTTAAATGCTTTAAC
2487341 CCACAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTTTAAATGCTTTAAC
Found at i:2488167 original size:6 final size:6
Alignment explanation
Indices: 2488156--2488180 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2488146 TTATGATGAT
2488156 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
2488181 CTGAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:2489289 original size:23 final size:24
Alignment explanation
Indices: 2489258--2489303 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
2489248 TTGCAGATGT
2489258 CACTCTGCATCGAAGTGCCACTAA
1 CACTCTGCATCGAAGTGCCACTAA
*
2489282 CACT-TGCATCGTAGTGCCACTA
1 CACTCTGCATCGAAGTGCCACTA
2489304 TCATTTGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (24 bp):
CACTCTGCATCGAAGTGCCACTAA
Found at i:2490327 original size:18 final size:21
Alignment explanation
Indices: 2490285--2490327 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
2490275 CAAACTGAAA
*
2490285 AAATGATATACTTTAAGAGCT
1 AAATGATATACTTTAAGACCT
2490306 AAATGAT-T-CTTTAAG-CCT
1 AAATGATATACTTTAAGACCT
2490324 AAAT
1 AAAT
2490328 AAAGCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 1 0.05
21 7 0.33
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATGATATACTTTAAGACCT
Found at i:2492484 original size:30 final size:27
Alignment explanation
Indices: 2492450--2492507 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 27
2492440 AAAATTATGG
2492450 AAGTACTATAAAATTAGATATATTTAATTT
1 AAGTACTATAAAATT---TATATTTAATTT
* *
2492480 AAGTAGTTTAAAATTTATATTTAATTT
1 AAGTACTATAAAATTTATATTTAATTT
2492507 A
1 A
2492508 TTTATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 13 0.50
30 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (27 bp):
AAGTACTATAAAATTTATATTTAATTT
Found at i:2498645 original size:16 final size:17
Alignment explanation
Indices: 2498619--2498658 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2498609 TATTTAGTGT
2498619 ATTATATTTT-AAGAAAA
1 ATTA-ATTTTAAAGAAAA
*
2498636 ATTAATTTTAAATAAAA
1 ATTAATTTTAAAGAAAA
2498653 ATTAAT
1 ATTAAT
2498659 CTAAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTAATTTTAAAGAAAA
Found at i:2505723 original size:21 final size:21
Alignment explanation
Indices: 2505669--2505723 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
2505659 TTGAAAAACA
2505669 TTTAAAAATA-TTATTATATT
1 TTTAAAAATATTTATTATATT
** * * *
2505689 AATAAGAATTTTTATTTTATT
1 TTTAAAAATATTTATTATATT
2505710 TTTAAAAATATTTA
1 TTTAAAAATATTTA
2505724 AAATTATTAA
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAAAAATATTTATTATATT
Found at i:2505850 original size:16 final size:16
Alignment explanation
Indices: 2505828--2505864 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2505818 CAATTTTATT
2505828 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
2505845 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
2505860 TAATA
1 TAATA
2505865 TTCATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:2505977 original size:34 final size:33
Alignment explanation
Indices: 2505897--2505982 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 33
2505887 ATTCAACATT
*
2505897 AATATTTTAATAATAAATATTTATTATTCACCA
1 AATATATTAATAATAAATATTTATTATTCACCA
2505930 AA-A-A-TAATAATAAATATTTATTACAATT-A-CA
1 AATATATTAATAATAAATATTTATT---ATTCACCA
2505961 AATATATTAATAATAAATATTT
1 AATATATTAATAATAAATATTT
2505983 TGTAGTATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
30 18 0.39
31 4 0.09
32 3 0.07
33 6 0.13
34 15 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATATTAATAATAAATATTTATTATTCACCA
Found at i:2518596 original size:24 final size:25
Alignment explanation
Indices: 2518569--2518617 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2518559 CTTTTTTTAT
*
2518569 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
2518593 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
2518618 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:2518610 original size:25 final size:23
Alignment explanation
Indices: 2518581--2518645 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
2518571 AATAAAAAAC
*
2518581 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
2518606 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
2518627 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
2518646 AATAATGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:2518644 original size:19 final size:20
Alignment explanation
Indices: 2518607--2518645 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2518597 TCAAATACAT
2518607 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
2518627 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
2518646 AATAATGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:2527524 original size:42 final size:42
Alignment explanation
Indices: 2527462--2527553 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
2527452 TAGATACCCG
*
2527462 CCACCACCAAATCAAGATCCATATCCACCTACGTCGTATCAA
1 CCACCACCAAATCAACATCCATATCCACCTACGTCGTATCAA
* * * *
2527504 CCGCCACCAAATCAACATCCATATCCATCTATGTTGTATCAA
1 CCACCACCAAATCAACATCCATATCCACCTACGTCGTATCAA
2527546 CCACCACC
1 CCACCACC
2527554 TCAATACGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.39, G:0.07, T:0.21
Consensus pattern (42 bp):
CCACCACCAAATCAACATCCATATCCACCTACGTCGTATCAA
Found at i:2532033 original size:24 final size:24
Alignment explanation
Indices: 2532006--2532067 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
2531996 TAGTTTGTAC
*
2532006 ATTATTCATATATTTTTAAAA-AAT
1 ATTATTCA-AGATTTTTAAAATAAT
*
2532030 ATTATTC-AGGTTTTTAAAATAAT
1 ATTATTCAAGATTTTTAAAATAAT
2532053 ATTATTCAAG-TTTTT
1 ATTATTCAAGATTTTT
2532068 CATTGCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 10 0.29
23 15 0.44
24 9 0.26
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (24 bp):
ATTATTCAAGATTTTTAAAATAAT
Found at i:2532053 original size:23 final size:22
Alignment explanation
Indices: 2532018--2532067 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
2532008 TATTCATATA
*
2532018 TTTTTAAAAAATATTATTCAGG
1 TTTTTAAAAAATATTATTCAAG
2532040 TTTTTAAAATAATATTATTCAAG
1 TTTTTAAAA-AATATTATTCAAG
2532063 TTTTT
1 TTTTT
2532068 CATTGCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (22 bp):
TTTTTAAAAAATATTATTCAAG
Found at i:2534393 original size:16 final size:16
Alignment explanation
Indices: 2534372--2534402 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2534362 ATATTTTAAC
2534372 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
2534388 AAAAAAATAGAAAAA
1 AAAAAAAAAGAAAAA
2534403 TCATACTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:2535016 original size:28 final size:28
Alignment explanation
Indices: 2534976--2535034 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
2534966 CTATTTCAGA
2534976 CAAATACGTGTAACAATTCATAAATATG
1 CAAATACGTGTAACAATTCATAAATATG
*
2535004 CAAATACTTGTAACAATTCATAAATATG
1 CAAATACGTGTAACAATTCATAAATATG
2535032 CAA
1 CAA
2535035 TTCACTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (28 bp):
CAAATACGTGTAACAATTCATAAATATG
Found at i:2535698 original size:31 final size:31
Alignment explanation
Indices: 2535663--2535732 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
2535653 CTTGTCATTT
2535663 GTAGCCGAAGCTACCACTATTCACTAATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
* * * * *
2535694 GTAGCCGGAGCTACCATTTTTCATTGATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
2535725 GTAGCCGA
1 GTAGCCGA
2535733 TGATCAGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAA
Found at i:2535738 original size:15 final size:15
Alignment explanation
Indices: 2535718--2535747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2535708 CATTTTTCAT
2535718 TGATCAAGTAGCCGA
1 TGATCAAGTAGCCGA
*
2535733 TGATCAGGTAGCCGA
1 TGATCAAGTAGCCGA
2535748 AGCTACCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (15 bp):
TGATCAAGTAGCCGA
Found at i:2535752 original size:46 final size:46
Alignment explanation
Indices: 2535689--2535778 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
2535679 CTATTCACTA
* * * *
2535689 ATCAAGTAGCCGGAGCTACCATTTTTCATTGATCAAGTAGCCGATG
1 ATCAAGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGATG
*
2535735 ATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGA
1 ATCAAGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGA
2535779 AGCTACCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (46 bp):
ATCAAGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGATG
Found at i:2535779 original size:31 final size:31
Alignment explanation
Indices: 2535733--2535791 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2535723 AAGTAGCCGA
* *
2535733 TGATCAGGTAGCCGAAGCTACCACTTTTCAC
1 TGATCAAGTAACCGAAGCTACCACTTTTCAC
*
2535764 TGATCAAGTAACCGAAGCTACCGCTTTT
1 TGATCAAGTAACCGAAGCTACCACTTTT
2535792 TACTTGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
TGATCAAGTAACCGAAGCTACCACTTTTCAC
Found at i:2535856 original size:50 final size:50
Alignment explanation
Indices: 2535793--2535947 Score: 265
Period size: 50 Copynumber: 3.1 Consensus size: 50
2535783 ACCGCTTTTT
2535793 ACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
1 ACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
*
2535844 ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATC
1 ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
* * *
2535894 ACTTTCACTTATCCTTGATCAGATAAGTGTAGCCAAAACTATCACTTATC
1 ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
2535944 ACTT
1 ACTT
2535948 GTTGCCATGG
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 95 0.96
51 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (50 bp):
ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
Found at i:2542093 original size:92 final size:92
Alignment explanation
Indices: 2541943--2542122 Score: 263
Period size: 92 Copynumber: 2.0 Consensus size: 92
2541933 AAGTATTTTT
* * * * *
2541943 AAGTTTCATAAGACCTCAAGAATGTACGGGAAAATAGCACCGTGCTAAATGTTTGGGACTTATGA
1 AAGTTGCATAAGACCTCAAGAATGTACGGGAAAATAACACCATACTAAATGTATGGGACTTATGA
2542008 AA-CATTCATTTACAAGCATATATTTGC
66 AATC-TTCATTTACAAGCATATATTTGC
* **
2542035 AAGTTGCATAAGACCTCAAGAATGTATGGGAAAATAACATTATACTAAATGTATGGGACTTATGA
1 AAGTTGCATAAGACCTCAAGAATGTACGGGAAAATAACACCATACTAAATGTATGGGACTTATGA
*
2542100 AATCTTCATTTACACGCATATAT
66 AATCTTCATTTACAAGCATATAT
2542123 AGAAGCAAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 77 0.99
93 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (92 bp):
AAGTTGCATAAGACCTCAAGAATGTACGGGAAAATAACACCATACTAAATGTATGGGACTTATGA
AATCTTCATTTACAAGCATATATTTGC
Found at i:2542324 original size:159 final size:159
Alignment explanation
Indices: 2542028--2542331 Score: 416
Period size: 159 Copynumber: 1.9 Consensus size: 159
2542018 TACAAGCATA
*
2542028 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAATAACATTATACTAAATGTATGGGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGA
* * * * * * * * * *
2542093 CTTATGAAATCTTCATTTACACGCATATATAGAAGCAAGCATGCATGCATGCATGTATACATACA
66 CCTATGAAACCTTCATTTACACACACACACAGAACCAAGCATGCAAGCATGCATGCATACACACA
2542158 TACATACATATGTATTTATGTATGTACAAG
131 TA-ATACATATGTATTTATGTATGTACAAG
*
2542188 TATTTGCAAGTTGCATAAGACCTCAAGAATGTAT-GGAAAACAACATTATACTAAATGTATTGGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGA
* * *
2542252 CCTATGAAGCCTTCATTTACATACACACACAGACATCCATA-CATGCAAGCATGCATGCATTCAC
66 CCTATGAAACCTTCATTTACACACACACACAGA-A-CCA-AGCATGCAAGCATGCATGCATACAC
2542316 ACAT-ATACATATGTAT
128 ACATAATACATATGTAT
2542332 GTACGTATAT
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
159 65 0.52
160 35 0.28
161 25 0.20
162 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (159 bp):
TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGA
CCTATGAAACCTTCATTTACACACACACACAGAACCAAGCATGCAAGCATGCATGCATACACACA
TAATACATATGTATTTATGTATGTACAAG
Found at i:2542495 original size:94 final size:94
Alignment explanation
Indices: 2542373--2542559 Score: 270
Period size: 94 Copynumber: 2.0 Consensus size: 94
2542363 TATCTAGAAG
* * *
2542373 TATTTGTAAGTTGCATAAGACCTCAAGAATGTATGGGAA-AACAGCATTATACTGAATGTATTG-
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTAT-GGAACAACAACATTATACTAAATGTA-TGA
*
2542436 GACCTATGAAACCTTCAATTACATACATACA
64 GACCTATGAAACCTGCAATTACATACATACA
*
2542467 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGAACAACAACATTATGCTAAATGTATGAGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGAACAACAACATTATACTAAATGTATGAGA
* * *
2542532 TCTATGGAACCTGCATTTACATACATAC
66 CCTATGAAACCTGCAATTACATACATAC
2542560 TTACATATGT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
93 6 0.07
94 77 0.93
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (94 bp):
TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGAACAACAACATTATACTAAATGTATGAGA
CCTATGAAACCTGCAATTACATACATACA
Found at i:2545125 original size:18 final size:18
Alignment explanation
Indices: 2545102--2545143 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2545092 AACTCAAAAT
2545102 AAAAAATAAAAAAAAAGA
1 AAAAAATAAAAAAAAAGA
* *
2545120 AAAAAATGAAGAAAAAGA
1 AAAAAATAAAAAAAAAGA
2545138 AAAAAA
1 AAAAAA
2545144 CCTAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAATAAAAAAAAAGA
Found at i:2546341 original size:19 final size:19
Alignment explanation
Indices: 2546317--2546354 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2546307 TTGAGATTGC
*
2546317 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
2546336 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
2546355 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:2552248 original size:25 final size:25
Alignment explanation
Indices: 2552201--2552248 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2552191 TAGTCCCTAA
*
2552201 ACTTGAGAATGATTCCCATATTAAG
1 ACTTGAGAATGATTCCCACATTAAG
* * *
2552226 ACTTGATAATTATTCTCACATTA
1 ACTTGAGAATGATTCCCACATTA
2552249 GAGCTAGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (25 bp):
ACTTGAGAATGATTCCCACATTAAG
Found at i:2555785 original size:19 final size:19
Alignment explanation
Indices: 2555740--2555791 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
2555730 GCAATCTCCA
*
2555740 TATATATAA-AAGT-GTTT
1 TATATATAATATGTAGTTT
2555757 TATATATAATATGTAGTTT
1 TATATATAATATGTAGTTT
2555776 TATATATAATATGTAG
1 TATATATAATATGTAG
2555792 CTGCAGTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 9 0.28
18 3 0.09
19 20 0.62
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (19 bp):
TATATATAATATGTAGTTT
Found at i:2560807 original size:33 final size:32
Alignment explanation
Indices: 2560764--2560828 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2560754 ACTAAATATC
* * *
2560764 TTCGACTTAAATTGAACTTCAAATTTTAAAATG
1 TTCGAATTAAATTG-ACTTCAAACTTCAAAATG
*
2560797 TTCGAATTAAATTGACTTTAAACTTCAAAATG
1 TTCGAATTAAATTGACTTCAAACTTCAAAATG
2560829 GTTTAATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (32 bp):
TTCGAATTAAATTGACTTCAAACTTCAAAATG
Found at i:2561488 original size:61 final size:61
Alignment explanation
Indices: 2561393--2561514 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
2561383 AGAGAAATAG
2561393 AGAGCAGAATCTGAATCTTTCAAATACAAGTAGATTTTCGATTAAATCAAAACGATTTTCC
1 AGAGCAGAATCTGAATCTTTCAAATACAAGTAGATTTTCGATTAAATCAAAACGATTTTCC
2561454 AGAGCAGAATCTGAATCTTTCAAATACAAGTAGATTTTCGATTAAATCAAAACGATTTTCC
1 AGAGCAGAATCTGAATCTTTCAAATACAAGTAGATTTTCGATTAAATCAAAACGATTTTCC
2561515 TTCTTTTCGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (61 bp):
AGAGCAGAATCTGAATCTTTCAAATACAAGTAGATTTTCGATTAAATCAAAACGATTTTCC
Found at i:2563565 original size:3 final size:3
Alignment explanation
Indices: 2563557--2563931 Score: 193
Period size: 3 Copynumber: 127.7 Consensus size: 3
2563547 TTTTAGCTAC
* * * * *
2563557 ATT ATT ATT A-A ATT AATT AATT -TT ACT ATC ATT ATT ATT CTT ACT
1 ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * *
2563602 ATT ATT ATT ATT ACT ACA ACT ATT ATT ATT ATG ATT A-T ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
2563648 TTT A-T ACTT ATT -TG CTT ATT ATT ACT ATT A-C ATT ATT A-T ATC
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
2563690 ATT AATT -TT A-T ATT ATT ACT ATT ATT ATT ATT ATT ATT ATA ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
2563734 ATT ACT ATT ATT A-T GTT GTT GTT TTT CTCT GTT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* * * * **
2563778 ATT ATT ATT ACT ATT ATT TTT ATT TTT ATT ACT ATT ACC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
2563826 ATT ACT ACT ATT ATT ATT ATT TTT ACT ATT ATT ATT TTT CCTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
* * * * * *
2563872 ATT ATA ATA ATT GTT ATT ACT ATT ATT -TT TTT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
2563919 GTC ATT -TT ATT AT
1 ATT ATT ATT ATT AT
2563932 ATTTTATATT
Statistics
Matches: 282, Mismatches: 71, Indels: 38
0.72 0.18 0.10
Matches are distributed among these distances:
2 24 0.09
3 242 0.86
4 16 0.06
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2563958 original size:12 final size:11
Alignment explanation
Indices: 2563943--2563985 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2563933 TTTTATATTT
2563943 TTTATTTACTTA
1 TTTATTT-CTTA
2563955 TTTATTTGCTTA
1 TTTATTT-CTTA
*
2563967 TTTCATTTTTTA
1 TTT-ATTTCTTA
2563979 TTTATTT
1 TTTATTT
2563986 GTTTAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 4 0.14
12 20 0.71
13 4 0.14
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTTCTTA
Found at i:2563990 original size:12 final size:12
Alignment explanation
Indices: 2563952--2563990 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2563942 TTTTATTTAC
*
2563952 TTATTTATTTGC
1 TTATTTATTTGT
2563964 TTATTTCATTT-T
1 TTATTT-ATTTGT
2563976 TTATTTATTTGT
1 TTATTTATTTGT
2563988 TTA
1 TTA
2563991 AACTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (12 bp):
TTATTTATTTGT
Found at i:2569703 original size:48 final size:48
Alignment explanation
Indices: 2569632--2569737 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
2569622 CAAGATAAAT
* * *
2569632 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
2569680 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
2569728 ATGTGTATAT
1 ATATGTATAT
2569738 ATTGTGGCTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:2569921 original size:37 final size:37
Alignment explanation
Indices: 2569871--2569942 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
2569861 GAAATATATT
*
2569871 CCGGGTAAGACCCGATGGCTACGTGTGGAGATTATGC
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
*
2569908 CCGGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
2569943 TCGAGCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
Found at i:2573537 original size:54 final size:54
Alignment explanation
Indices: 2573457--2573559 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
2573447 TACTTCACCT
* * *
2573457 AAAAAAGGGAGAGGCCAATGTGAAAACCCACAAAGGACGTTTTGAGACCTTCAA
1 AAAAAAGGGAAAGGCCAATGTAAAAACCCACAAAGGACGCTTTGAGACCTTCAA
* * *
2573511 AAAAAATGGAAAGGCCAA-GTCAAAAACCCGCAAAGGGCGCTTTGAGACC
1 AAAAAAGGGAAAGGCCAATGT-AAAAACCCACAAAGGACGCTTTGAGACC
2573560 AAAGGGGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 2 0.05
54 40 0.95
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (54 bp):
AAAAAAGGGAAAGGCCAATGTAAAAACCCACAAAGGACGCTTTGAGACCTTCAA
Found at i:2574363 original size:44 final size:43
Alignment explanation
Indices: 2574314--2574520 Score: 159
Period size: 44 Copynumber: 4.8 Consensus size: 43
2574304 TAAATTCACT
* *
2574314 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAAATTGTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATGAAAATTGTA
* * * *
2574358 GATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGAA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT-GAAAATTGTA
* * * ** *
2574402 AATCTTATCTTCCTAAGCATTAGTGGAGCAGAT-TTAA--GCCA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAATTG-TA
* * * * * *
2574443 CCATCCTATCTCCCTAAGCAGTAGTGAAGTAGGCTGAAGATTGTA
1 -GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATGAAAATTGTA
* **
2574488 GATCTTATCTCCCTGAGCAACAGTGGAGCAGAT
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
2574521 CGAAGACGAC
Statistics
Matches: 123, Mismatches: 33, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 25 0.20
43 6 0.05
44 88 0.72
45 1 0.01
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (43 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAATTGTA
Found at i:2574583 original size:44 final size:44
Alignment explanation
Indices: 2574535--2574679 Score: 202
Period size: 44 Copynumber: 3.3 Consensus size: 44
2574525 GACGACGAAT
* * **
2574535 CTTATATCCCT-ATGGTAGCAAGGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCCCTGA-GGTAGCAAGGGAGCAGACTGAAGCCACTAGC
* *
2574579 CTTATCTCCCTGAGGTAGCAAGGAAGCATACTGAAGCCACTAGC
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGCCACTAGC
*
2574623 CTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAGCCACTAGC
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGCCACTAGC
*
2574667 CTTGTCTCCCTGA
1 CTTATCTCCCTGA
2574680 ACAGTAGTGG
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 89 0.99
45 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (44 bp):
CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGCCACTAGC
Found at i:2575226 original size:138 final size:139
Alignment explanation
Indices: 2574975--2575228 Score: 293
Period size: 138 Copynumber: 1.8 Consensus size: 139
2574965 GGTTGAAGTT
* * *
2574975 CAAGTCTTATCTCCTTGAAATTGCAGTGGAGCAGACTGAAGACAACTAATCCTATCTCTCTGAAG
1 CAAGTCTTATCTCCCTGAAATTACAGTGGAGCAGACTGAAGACAACCAATCCTATCTCTCTGAAG
* * **
2575040 TTATAGTGCAGCAGATTAAAACGATAAGTCCTATACCTTTGAAATTGCAGTAGGTCGGATCAAAT
66 TTACAGCGCAGCAGATTAAAACGATAAGTCCTATACCCATGAAATTGCAGTAGGTCGGATCAAAT
2575105 CTACCATTA
131 CTACCATTA
* * *
2575114 CAAGTCTTATGTCCCTGAAGA-TACAGTGGAGCAGACTGAAGA-TACCAATCTTATCT-TCCTGA
1 CAAGTCTTATCTCCCTGAA-ATTACAGTGGAGCAGACTGAAGACAACCAATCCTATCTCT-CTGA
* * * * * *
2575176 AGTTGCAGCGGAGCAGATTGAAGCTACTAA-TCCTAT-CTCCATGAAGTTGCAGT
64 AGTTACAGCGCAGCAGATTAAAACGA-TAAGTCCTATAC-CCATGAAATTGCAGT
2575229 GGAGCAGATT
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
137 2 0.02
138 52 0.55
139 40 0.42
140 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (139 bp):
CAAGTCTTATCTCCCTGAAATTACAGTGGAGCAGACTGAAGACAACCAATCCTATCTCTCTGAAG
TTACAGCGCAGCAGATTAAAACGATAAGTCCTATACCCATGAAATTGCAGTAGGTCGGATCAAAT
CTACCATTA
Found at i:2575237 original size:44 final size:42
Alignment explanation
Indices: 2575127--2575272 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 42
2575117 GTCTTATGTC
* * * * *
2575127 CCTGAAGATACAGTGGAGCAGACTGAAGATACCAATCTTATCTT
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CAATCCTATC-T
*
2575171 CCTGAAGTTGCAGCGGAGCAGATTGAAGCTACTAATCCTATCT
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC-AATCCTATCT
* *
2575214 CCATGAAGTTGCAGTGGAGCAGATTAAAGCAACAAGTCCTATGC-
1 CC-TGAAGTTGCAGTGGAGCAGATTGAAGCTACAA-TCCTAT-CT
2575258 CTCTGAAGTTGCAGT
1 C-CTGAAGTTGCAGT
2575273 AGGTCGGATT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
43 6 0.07
44 80 0.91
45 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
CCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAATCCTATCT
Found at i:2576771 original size:3 final size:3
Alignment explanation
Indices: 2576763--2576975 Score: 64
Period size: 3 Copynumber: 71.3 Consensus size: 3
2576753 TTTTGCTATC
* ** * ** * *
2576763 ATT ATT ATT CTT GCT ATT ATT ATT ATT ACT ACA ACT ATT ATT ATT ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
2576811 ATT A-T ATT -TT CTT TTT A-T ACTT ATT -TG CTT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
2576853 A-C ATT ATT A-T ATC GTT AATT -TT A-T ATT ATT ACT ATT ATA ATA
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * ** * *
2576895 ATA ATA ATT ATT ATT ACA ATT ATT ATT ATGCT ATT TTT CTCT GATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT--T ATT ATT AT-T -A-TT
* *
2576942 ATT ACT ATT ATT ATT ATT ATT ATT ATC ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2576976 CTGTAACACC
Statistics
Matches: 156, Mismatches: 39, Indels: 30
0.69 0.17 0.13
Matches are distributed among these distances:
2 14 0.09
3 131 0.84
4 6 0.04
5 4 0.03
6 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:2576776 original size:18 final size:18
Alignment explanation
Indices: 2576755--2576789 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2576745 TTAATTAATT
2576755 TTGCTATCATTATTATTC
1 TTGCTATCATTATTATTC
*
2576773 TTGCTATTATTATTATT
1 TTGCTATCATTATTATT
2576790 ACTACAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (18 bp):
TTGCTATCATTATTATTC
Found at i:2583779 original size:12 final size:12
Alignment explanation
Indices: 2583762--2583792 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2583752 AGTGCTACCT
2583762 CGGCCTCGACCA
1 CGGCCTCGACCA
2583774 CGGCCTCGACCA
1 CGGCCTCGACCA
2583786 CGGCCTC
1 CGGCCTC
2583793 TTCCCTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.52, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:2586492 original size:21 final size:21
Alignment explanation
Indices: 2586468--2586526 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
2586458 TTTCAAATTA
*
2586468 ATTATTTTTATTATTATATTT
1 ATTATTATTATTATTATATTT
2586489 ATTATTATTATTATTATATTT
1 ATTATTATTATTATTATATTT
*
2586510 ACTATTATTATTATTAT
1 ATTATTATTATTATTAT
2586527 TAACGTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTATTATTATTATTATATTT
Found at i:2586539 original size:3 final size:3
Alignment explanation
Indices: 2586468--2586528 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
2586458 TTTCAAATTA
* *
2586468 ATT ATT TTT ATT ATT A-T ATTT ATT ATT ATT ATT ATT A-T ATTT ACT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT
2586513 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
2586529 ACGTATTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.08
3 42 0.84
4 4 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2586779 original size:3 final size:3
Alignment explanation
Indices: 2586773--2586851 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
2586763 TTACATCATC
*
2586773 ATT ATT ATT AATT -TGT ATT ATC ATT ATT ATT ATT ATT ATT ATT AATGT
1 ATT ATT ATT -ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT -AT-T
* *
2586821 ATT GTT ATT TTT ATT -TT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2586852 GTTTCATCCT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 5 0.08
3 49 0.78
4 8 0.13
5 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2587738 original size:15 final size:16
Alignment explanation
Indices: 2587715--2587748 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2587705 CTAAAATAAA
*
2587715 TTTATATATTATT-AT
1 TTTACATATTATTAAT
2587730 TTTACATATTATTAAT
1 TTTACATATTATTAAT
2587746 TTT
1 TTT
2587749 TGATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTACATATTATTAAT
Found at i:2589444 original size:11 final size:11
Alignment explanation
Indices: 2589430--2589458 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2589420 TATATCTATT
2589430 ATATATTTTAA
1 ATATATTTTAA
2589441 ATATATTTTAA
1 ATATATTTTAA
2589452 ATA-ATTT
1 ATATATTT
2589459 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATTTTAA
Found at i:2594705 original size:20 final size:20
Alignment explanation
Indices: 2594680--2594728 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2594670 ATTTTTTTCG
*
2594680 ATAAAAATAAATA-AAATTTT
1 ATAAAAATAAATACAAA-ATT
* *
2594700 ATAAAAGTACATACAAAATT
1 ATAAAAATAAATACAAAATT
2594720 ATAAAAATA
1 ATAAAAATA
2594729 TTTATAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAAAATAAATACAAAATT
Found at i:2596524 original size:19 final size:19
Alignment explanation
Indices: 2596502--2596556 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
2596492 TACCATCTCC
2596502 AAAAACCTTAGTTTTTAGG
1 AAAAACCTTAGTTTTTAGG
*
2596521 AAAAATCTTAGTTTTTAGG
1 AAAAACCTTAGTTTTTAGG
2596540 AAAAACCTTAGTTTTTA
1 AAAAACCTTAGTTTTTA
2596557 TCATGCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (19 bp):
AAAAACCTTAGTTTTTAGG
Found at i:2597750 original size:35 final size:35
Alignment explanation
Indices: 2597704--2597774 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2597694 CAAGGCCCGA
2597704 AAACCTAATAAAGAATCATGCAACACCAATTTAGC
1 AAACCTAATAAAGAATCATGCAACACCAATTTAGC
2597739 AAACCTAATAAAGAATCATGCAACACCAATTTAGC
1 AAACCTAATAAAGAATCATGCAACACCAATTTAGC
2597774 A
1 A
2597775 GTCTTATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.20
Consensus pattern (35 bp):
AAACCTAATAAAGAATCATGCAACACCAATTTAGC
Found at i:2600839 original size:15 final size:16
Alignment explanation
Indices: 2600819--2600858 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2600809 CTCCTCAGGC
2600819 CAAAAACAAAAC-AAA
1 CAAAAACAAAACTAAA
*
2600834 CAAAAATAAAACTAAA
1 CAAAAACAAAACTAAA
*
2600850 CCAAAACAA
1 CAAAAACAA
2600859 GAGAAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.75, C:0.20, G:0.00, T:0.05
Consensus pattern (16 bp):
CAAAAACAAAACTAAA
Found at i:2607002 original size:21 final size:22
Alignment explanation
Indices: 2606968--2607008 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2606958 CATGTACTTC
2606968 ATTTTGACATAATTTCATCCTT
1 ATTTTGACATAATTTCATCCTT
*
2606990 ATTTTGA-ATAATTTGATCC
1 ATTTTGACATAATTTCATCC
2607009 ATGTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTTGACATAATTTCATCCTT
Found at i:2608972 original size:33 final size:34
Alignment explanation
Indices: 2608933--2608998 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
2608923 TAAATTTAAT
* *
2608933 TTTTTATGAGAGCTAAAAT-ACAA-TTTATCATTG
1 TTTTTATAAGAACT-AAATCACAATTTTATCATTG
2608966 TTTTTATAAGAACTAAATCACAATTTTATCATT
1 TTTTTATAAGAACTAAATCACAATTTTATCATT
2608999 CTTGAGGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.14
33 16 0.55
34 9 0.31
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44
Consensus pattern (34 bp):
TTTTTATAAGAACTAAATCACAATTTTATCATTG
Found at i:2610848 original size:2 final size:2
Alignment explanation
Indices: 2610843--2610873 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2610833 AACAGAGCAA
*
2610843 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2610874 AGAAGAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2612731 original size:16 final size:16
Alignment explanation
Indices: 2612706--2612739 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2612696 ATAATTCATT
2612706 AATTAAAAAGG-ACAA
1 AATTAAAAAGGTACAA
2612721 AATTGAAAAAGGTACAA
1 AATT-AAAAAGGTACAA
2612738 AA
1 AA
2612740 CTTGCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 7 0.41
17 6 0.35
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (16 bp):
AATTAAAAAGGTACAA
Found at i:2613357 original size:21 final size:21
Alignment explanation
Indices: 2613331--2613480 Score: 113
Period size: 21 Copynumber: 7.1 Consensus size: 21
2613321 CGTGTTTACT
*
2613331 TTCTGTTTAGCTCTCACGAGC
1 TTCTGTTTAGCTCTTACGAGC
* * * *
2613352 TTCTGTTTAACCCTTATGAGT
1 TTCTGTTTAGCTCTTACGAGC
*
2613373 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTACGAGC
* * * *
2613394 TTCTGTTTAACCCTTATG-GG
1 TTCTGTTTAGCTCTTACGAGC
* *
2613414 TTCCTATTAAGCTCTTACGAGC
1 TT-CTGTTTAGCTCTTACGAGC
* * * * *
2613436 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTACGAGC
* *
2613457 TTCTGTTTAGCTTTTACAAGC
1 TTCTGTTTAGCTCTTACGAGC
2613478 TTC
1 TTC
2613481 CATTCAACCC
Statistics
Matches: 92, Mismatches: 35, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
20 3 0.03
21 86 0.93
22 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTACGAGC
Found at i:2613392 original size:42 final size:42
Alignment explanation
Indices: 2613330--2613507 Score: 257
Period size: 42 Copynumber: 4.2 Consensus size: 42
2613320 TCGTGTTTAC
* *
2613330 TTTCTGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
*
2613372 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
* * *
2613414 TTCCTATTAAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
* * ** *
2613456 TTTCTGTTTAGCTTTTACAAGCTTCCATTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
2613498 TTTCTGTTTA
1 TTTCTGTTTA
2613508 CCATTTATGT
Statistics
Matches: 122, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 122 1.00
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
Found at i:2615136 original size:18 final size:18
Alignment explanation
Indices: 2615104--2615155 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2615094 CTGAGACGAG
2615104 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
2615120 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
2615138 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
2615156 CACCTTGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:2617872 original size:15 final size:16
Alignment explanation
Indices: 2617847--2617880 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2617837 GAAATGTAAT
2617847 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
2617863 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
2617878 TTT
1 TTT
2617881 TTTTAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:2617966 original size:16 final size:15
Alignment explanation
Indices: 2617945--2617988 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2617935 TTCATATACT
2617945 AATTTAAAATTTTATA
1 AATTTAAAATTTTA-A
*
2617961 AATTTAAAAATGTTAA
1 AATTT-AAAATTTTAA
2617977 AATTT-AAATTTT
1 AATTTAAAATTTT
2617989 TTATTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATTTAAAATTTTAA
Found at i:2618793 original size:3 final size:3
Alignment explanation
Indices: 2618785--2618833 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
2618775 TATGCTGCCA
* * * * *
2618785 ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATC ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2618833 A
1 A
2618834 AATTTTCATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:2618899 original size:6 final size:6
Alignment explanation
Indices: 2618888--2618939 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
2618878 GTGAAAAATT
* *
2618888 GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GACACA GAAATA
1 GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA
2618936 GAAA
1 GAAA
2618940 ATGAAACGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.65, C:0.15, G:0.17, T:0.02
Consensus pattern (6 bp):
GAAACA
Found at i:2619370 original size:22 final size:22
Alignment explanation
Indices: 2619331--2619392 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
2619321 AGTAGGCACT
* * *
2619331 GAAGTGCTAAGCAATAGGAAAC
1 GAAGTGCAAATCAGTAGGAAAC
* *
2619353 GAAGTGCAAATCAGTAGGCACC
1 GAAGTGCAAATCAGTAGGAAAC
2619375 GTAA-TGCAAATCAGTAGG
1 G-AAGTGCAAATCAGTAGG
2619393 CATTGTACTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 32 0.94
23 2 0.06
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.16
Consensus pattern (22 bp):
GAAGTGCAAATCAGTAGGAAAC
Found at i:2620290 original size:3 final size:3
Alignment explanation
Indices: 2620282--2620309 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2620272 ATGTTTTAAC
2620282 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2620310 TTAACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2626058 original size:20 final size:20
Alignment explanation
Indices: 2626033--2626088 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2626023 CTTGAAGAAT
*
2626033 TAAAATGATTAAAATAAAAA
1 TAAAATGAATAAAATAAAAA
* *
2626053 TAAAAT-AATAAACTAAAAC
1 TAAAATGAATAAAATAAAAA
2626072 T-AAATAGAATAAAATAA
1 TAAAAT-GAATAAAATAA
2626089 GTAGAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 15 0.50
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (20 bp):
TAAAATGAATAAAATAAAAA
Found at i:2639153 original size:21 final size:21
Alignment explanation
Indices: 2639120--2639170 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
2639110 TAGGAATGAA
**
2639120 AAATATACGCATAAT-AATACT
1 AAATATATACATAATAAATA-T
*
2639141 AAATATATACATACTAAATAT
1 AAATATATACATAATAAATAT
*
2639162 ATATATATA
1 AAATATATA
2639171 GTATAAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATATATACATAATAAATAT
Found at i:2639156 original size:15 final size:15
Alignment explanation
Indices: 2639136--2639164 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2639126 ACGCATAATA
2639136 ATACTAAATATATAC
1 ATACTAAATATATAC
2639151 ATACTAAATATATA
1 ATACTAAATATATA
2639165 TATATAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACTAAATATATAC
Found at i:2639364 original size:24 final size:24
Alignment explanation
Indices: 2639337--2639383 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2639327 TACGAAAATA
2639337 ATAC-TATAAAAAAAGTATATATAT
1 ATACATATAAAAAAA-TATATATAT
*
2639361 ATACATATAATAAAATATATATA
1 ATACATATAAAAAAATATATATA
2639384 CTAAGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
ATACATATAAAAAAATATATATAT
Found at i:2640102 original size:14 final size:15
Alignment explanation
Indices: 2640085--2640124 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
2640075 AACTTAATAC
2640085 TATAT-TAAAACATA
1 TATATATAAAACATA
*
2640099 TATATATAATAATATA
1 TATATATAA-AACATA
2640115 TATATATAAA
1 TATATATAAA
2640125 GGTTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 14 0.61
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATATAAAACATA
Found at i:2640171 original size:66 final size:63
Alignment explanation
Indices: 2640041--2640170 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 63
2640031 ATAGAAGCTA
2640041 ATAATATATATATATATATAAAGTAAATAAAGATAACTTAATACTATATTAAAACATATATAT
1 ATAATATATATATATATATAAAGTAAATAAAGATAACTTAATACTATATTAAAACATATATAT
*
2640104 ATAATA-ATATATATATATAAAGGTTAAATAAAGATAACTTAATATTATATTAAAACATATATAT
1 ATAATATATATATATATATAAA-G-TAAATAAAGATAACTTAATACTATATTAAAACATATATAT
2640168 ATA
1 ATA
2640171 TGAATGTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
62 15 0.23
63 7 0.11
64 42 0.66
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (63 bp):
ATAATATATATATATATATAAAGTAAATAAAGATAACTTAATACTATATTAAAACATATATAT
Found at i:2640246 original size:14 final size:15
Alignment explanation
Indices: 2640219--2640253 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
2640209 TGATGACATT
2640219 AATAATAGATACTAA
1 AATAATAGATACTAA
2640234 AATAATA-ATACTAA
1 AATAATAGATACTAA
2640248 AATAAT
1 AATAAT
2640254 TAACTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (15 bp):
AATAATAGATACTAA
Found at i:2644880 original size:28 final size:28
Alignment explanation
Indices: 2644827--2644910 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
2644817 CACTTTGTGC
2644827 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
2644856 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* * *
2644884 GATACTTGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
2644911 CTGGTGTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.64
29 18 0.36
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.48
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:2644922 original size:23 final size:24
Alignment explanation
Indices: 2644831--2644924 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 24
2644821 TTGTGCTATT
2644831 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
2644858 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
*
2644888 CTTGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
2644911 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
2644925 TTGGACATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
23 16 0.28
24 1 0.02
25 2 0.04
28 17 0.30
29 14 0.25
30 5 0.09
31 2 0.04
ACGTcount: A:0.16, C:0.04, G:0.33, T:0.47
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:2645153 original size:23 final size:23
Alignment explanation
Indices: 2645115--2645221 Score: 111
Period size: 21 Copynumber: 5.0 Consensus size: 23
2645105 GCTATACTGA
* *
2645115 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTGTGTGTCGTATT
*
2645138 TTAGGCACCTTGTGTGTCGTA--
1 TCAGGCACCTTGTGTGTCGTATT
*
2645159 TCAGGCACCTCGTGTGTCG--TT
1 TCAGGCACCTTGTGTGTCGTATT
*
2645180 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTTGTGTGTCGTATT
*
2645202 T-AGGCA-CTTATGTGTCGTAT
1 TCAGGCACCTTGTGTGTCGTAT
2645222 ACTGATCAGG
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.14
21 42 0.58
22 3 0.04
23 18 0.25
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTTGTGTGTCGTATT
Found at i:2646461 original size:46 final size:48
Alignment explanation
Indices: 2646303--2646489 Score: 163
Period size: 46 Copynumber: 3.9 Consensus size: 48
2646293 TGGTTGGACC
2646303 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * * *
2646349 ATGGCATCAGAGATATGTGATTACGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
*
2646402 ATGGCATC--AGTGTGATATGTGATTCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
2646448 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
2646490 TTTTACTATG
Statistics
Matches: 114, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
45 1 0.01
46 33 0.29
47 8 0.07
48 18 0.16
49 13 0.11
50 1 0.01
51 7 0.06
52 5 0.04
53 27 0.24
54 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:2651745 original size:40 final size:40
Alignment explanation
Indices: 2651699--2651775 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
2651689 ACATACTATG
*
2651699 TGGGGATAGAATCGACCCACCCAACCCTACACACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
* *
2651739 TGGGGATATAATCAACCCATCCAACCCTACACACCAA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAA
2651776 AAGGTACCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.35, G:0.14, T:0.14
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:2653452 original size:20 final size:19
Alignment explanation
Indices: 2653425--2653472 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2653415 AGTTTCTTCT
2653425 TTTTTTCTTCATATTTTT-A
1 TTTTTTCTTC-TATTTTTCA
*
2653444 TTATTTTCTTCTTTTTTTCA
1 TT-TTTTCTTCTATTTTTCA
2653464 TTTTTTCTT
1 TTTTTTCTT
2653473 ATTAACCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCTTCTATTTTTCA
Found at i:2653463 original size:28 final size:27
Alignment explanation
Indices: 2653421--2653475 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2653411 CGATAGTTTC
2653421 TTCTTTTTTTCTTCATATTTTTATTATT
1 TTCTTTTTTTCTTCAT-TTTTTATTATT
*
2653449 TTCTTCTTTTT-TTCATTTTTTCTTATT
1 TTCTT-TTTTTCTTCATTTTTTATTATT
2653476 AACCGGAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 10 0.40
28 10 0.40
29 5 0.20
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (27 bp):
TTCTTTTTTTCTTCATTTTTTATTATT
Found at i:2656424 original size:20 final size:20
Alignment explanation
Indices: 2656379--2656417 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2656369 TTTCAATTAT
2656379 TTTAAAGTTTCATTTAAGTC
1 TTTAAAGTTTCATTTAAGTC
2656399 TTTAAAGTTTCATTTAAGT
1 TTTAAAGTTTCATTTAAGT
2656418 TATTAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTAAAGTTTCATTTAAGTC
Found at i:2659462 original size:23 final size:23
Alignment explanation
Indices: 2659432--2659518 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
2659422 GCTTTATCGA
* *
2659432 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
2659455 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
2659476 TCAGGCACCTCGTGTGTC--ATT
1 TCAGGCACCTCATGTGTCGTATT
* * *
2659497 TTAGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
2659519 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.02
21 32 0.60
23 20 0.38
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:2659479 original size:21 final size:22
Alignment explanation
Indices: 2659444--2659493 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
2659434 AGGCACTTTA
2659444 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
2659467 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
2659488 TGTGTC
1 TGTGTC
2659494 ATTTTAGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 18 0.67
23 9 0.33
ACGTcount: A:0.12, C:0.26, G:0.28, T:0.34
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:2660716 original size:11 final size:11
Alignment explanation
Indices: 2660700--2660724 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2660690 TACATGCCAT
2660700 AATTGAGTCGA
1 AATTGAGTCGA
2660711 AATTGAGTCGA
1 AATTGAGTCGA
2660722 AAT
1 AAT
2660725 CGGATGCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (11 bp):
AATTGAGTCGA
Found at i:2665748 original size:21 final size:21
Alignment explanation
Indices: 2665719--2665762 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2665709 TTAGTCCCAT
2665719 TAAGCATGGGTATAGAATTTA
1 TAAGCATGGGTATAGAATTTA
*
2665740 TAAGTATGGGTATAGAATTTA
1 TAAGCATGGGTATAGAATTTA
2665761 TA
1 TA
2665763 TTGGCAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (21 bp):
TAAGCATGGGTATAGAATTTA
Found at i:2671947 original size:30 final size:30
Alignment explanation
Indices: 2671889--2671945 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
2671879 ACCTCTAAAG
**
2671889 GGACCTTATAACAAATTTTATTAGTTTTGC
1 GGACCTTATAACAAATTTTACCAGTTTTGC
2671919 GGACCTTATAAC-AATTTTACCAGTTTT
1 GGACCTTATAACAAATTTTACCAGTTTT
2671946 TGGGGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (30 bp):
GGACCTTATAACAAATTTTACCAGTTTTGC
Found at i:2673915 original size:38 final size:38
Alignment explanation
Indices: 2673856--2673961 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
2673846 CATTTTTAAG
*
2673856 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
2673893 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
2673931 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
2673962 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:2674341 original size:20 final size:20
Alignment explanation
Indices: 2674316--2674377 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
2674306 AGTATATACA
*
2674316 ATATAATATTAGAAAAATAT
1 ATATAATAATAGAAAAATAT
* *
2674336 ATATAATAGT-GTAAAATAT
1 ATATAATAATAGAAAAATAT
2674355 A-ACTAATAATA-ATAAAATAT
1 ATA-TAATAATAGA-AAAATAT
2674375 ATA
1 ATA
2674378 CAATGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.03
19 15 0.44
20 17 0.50
21 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
ATATAATAATAGAAAAATAT
Found at i:2674353 original size:19 final size:21
Alignment explanation
Indices: 2674347--2674388 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2674337 TATAATAGTG
2674347 TAAAATATA-ACTAATAATAA
1 TAAAATATATACTAATAATAA
*
2674367 TAAAATATATAC-AATGATAA
1 TAAAATATATACTAATAATAA
2674387 TA
1 TA
2674389 TATATAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAATATATACTAATAATAA
Found at i:2674432 original size:15 final size:14
Alignment explanation
Indices: 2674332--2674442 Score: 72
Period size: 15 Copynumber: 7.9 Consensus size: 14
2674322 TATTAGAAAA
2674332 ATAT-ATATAATAGT
1 ATATAATATAATA-T
* *
2674346 GTAAAATATAACTA-
1 ATATAATATAA-TAT
*
2674360 ATAATAATAAAATAT
1 AT-ATAATATAATAT
*
2674375 ATACAATGATAATAT
1 ATATAAT-ATAATAT
2674390 ATATAA-A-AGATAT
1 ATATAATATA-ATAT
*
2674403 ATGTATATATAAT-T
1 ATATA-ATATAATAT
2674417 ATATAATATAATAT
1 ATATAATATAATAT
*
2674431 -TAAAATATAATA
1 ATATAATATAATA
2674443 ATACGACATA
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
12 1 0.01
13 27 0.36
14 16 0.21
15 29 0.38
16 3 0.04
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (14 bp):
ATATAATATAATAT
Found at i:2674783 original size:3 final size:3
Alignment explanation
Indices: 2674768--2674819 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
2674758 ATACACGTAC
* * *
2674768 ATA ATA CATA ATA ATA ATA CTA ATA CTA ATA ATA CTA ATA AT- ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
2674813 AAA ATA A
1 ATA ATA A
2674820 CAAGGATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2674799 original size:15 final size:15
Alignment explanation
Indices: 2674779--2674807 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2674769 TAATACATAA
2674779 TAATAATACTAATAC
1 TAATAATACTAATAC
2674794 TAATAATACTAATA
1 TAATAATACTAATA
2674808 ATATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATAATACTAATAC
Found at i:2674800 original size:9 final size:9
Alignment explanation
Indices: 2674768--2674810 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
2674758 ATACACGTAC
2674768 ATAATACATA
1 ATAATAC-TA
*
2674778 ATAATAATA
1 ATAATACTA
*
2674787 CTAATACTA
1 ATAATACTA
2674796 ATAATACTA
1 ATAATACTA
2674805 ATAATA
1 ATAATA
2674811 TAAAAATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 23 0.79
10 6 0.21
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAATACTA
Found at i:2675300 original size:11 final size:12
Alignment explanation
Indices: 2675284--2675319 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
2675274 AGAAAAAAAA
2675284 GAAGAGAG-AGG
1 GAAGAGAGAAGG
2675295 GAAGAGAGAAGG
1 GAAGAGAGAAGG
2675307 G-AGAGAGAAGG
1 GAAGAGAGAAGG
2675318 GA
1 GA
2675320 GGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:2675446 original size:8 final size:8
Alignment explanation
Indices: 2675428--2675494 Score: 57
Period size: 8 Copynumber: 8.2 Consensus size: 8
2675418 GTAAAAAAAA
2675428 TATTTTTT
1 TATTTTTT
*
2675436 T-TTTATT
1 TATTTTTT
2675443 T-TTTTTT
1 TATTTTTT
2675450 TATTTTTT
1 TATTTTTT
2675458 TATGTTTATAT
1 TAT-TTT-T-T
* *
2675469 TATATTGT
1 TATTTTTT
*
2675477 TATTTTTA
1 TATTTTTT
2675485 TATTTTTT
1 TATTTTTT
2675493 TA
1 TA
2675495 GTATATATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 12 0.26
8 25 0.53
9 3 0.06
10 3 0.06
11 4 0.09
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (8 bp):
TATTTTTT
Found at i:2675447 original size:12 final size:11
Alignment explanation
Indices: 2675428--2675458 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2675418 GTAAAAAAAA
2675428 TATTTTTTTTT
1 TATTTTTTTTT
2675439 TATTTTTTTTT
1 TATTTTTTTTT
2675450 TATTTTTTT
1 TATTTTTTT
2675459 ATGTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TATTTTTTTTT
Found at i:2675457 original size:19 final size:19
Alignment explanation
Indices: 2675427--2675493 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
2675417 GGTAAAAAAA
2675427 ATATTTTTTTTTTATTTTT
1 ATATTTTTTTTTTATTTTT
* *
2675446 -TTTTTATTTTTTTATGTTT
1 ATATTT-TTTTTTTATTTTT
* * *
2675465 ATATTATATTGTTATTTTT
1 ATATTTTTTTTTTATTTTT
2675484 ATATTTTTTT
1 ATATTTTTTT
2675494 AGTATATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 4 0.11
19 30 0.81
20 3 0.08
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (19 bp):
ATATTTTTTTTTTATTTTT
Found at i:2675493 original size:11 final size:11
Alignment explanation
Indices: 2675427--2675493 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
2675417 GGTAAAAAAA
2675427 ATATTTTTTTT
1 ATATTTTTTTT
*
2675438 TTATTTTTTTT
1 ATATTTTTTTT
*
2675449 TTA-TTTTTTT
1 ATATTTTTTTT
* * *
2675459 ATGTTTATATT
1 ATATTTTTTTT
2675470 ATATTGTTATTTTT
1 ATA-T-TT-TTTTT
2675484 ATATTTTTTT
1 ATATTTTTTT
2675494 AGTATATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
10 8 0.18
11 24 0.55
12 3 0.07
13 3 0.07
14 6 0.14
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
ATATTTTTTTT
Found at i:2675499 original size:27 final size:27
Alignment explanation
Indices: 2675449--2675500 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2675439 TATTTTTTTT
* *
2675449 TTATTTTTTTATGTTTATATTATATTG
1 TTATTTTTATATGTTTATAGTATATTG
* *
2675476 TTATTTTTATATTTTTTTAGTATAT
1 TTATTTTTATATGTTTATAGTATAT
2675501 ATATATATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (27 bp):
TTATTTTTATATGTTTATAGTATATTG
Found at i:2677005 original size:25 final size:26
Alignment explanation
Indices: 2676977--2677032 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2676967 TTTACAAATT
*
2676977 ATATTTAAATTA-AATAAT-AAAATAA
1 ATATATAAATTATAATAATGAAAA-AA
* *
2677002 ATATATAACTTATAATTATGAAAAAA
1 ATATATAAATTATAATAATGAAAAAA
2677028 ATATA
1 ATATA
2677033 AATAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 10 0.38
26 12 0.46
27 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
ATATATAAATTATAATAATGAAAAAA
Found at i:2677552 original size:24 final size:23
Alignment explanation
Indices: 2677504--2677552 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
2677494 AAACATTCAT
* *
2677504 TTGAGTTTTTTTTTATTATTTAA
1 TTGAGTTTTTTTATATTATTAAA
2677527 TTGAGTTTATTTTATATCTA-TAAA
1 TTGAGTTT-TTTTATAT-TATTAAA
2677551 TT
1 TT
2677553 TATATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 12 0.55
25 2 0.09
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (23 bp):
TTGAGTTTTTTTATATTATTAAA
Found at i:2677842 original size:15 final size:15
Alignment explanation
Indices: 2677822--2677873 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
2677812 ACTACAAAAC
2677822 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
2677837 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
2677856 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
2677871 ATT
1 ATT
2677874 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:2677968 original size:22 final size:22
Alignment explanation
Indices: 2677943--2677988 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2677933 TAAAATTAAA
2677943 ATATTAAATA-ATTAAATAAATT
1 ATATTAAATATATT-AATAAATT
* *
2677965 ATATTAATTATATTAATAATTT
1 ATATTAAATATATTAATAAATT
2677987 AT
1 AT
2677989 TATATGACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTAAATATATTAATAAATT
Found at i:2678069 original size:10 final size:10
Alignment explanation
Indices: 2678056--2678086 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2678046 ATTTTATATT
2678056 AATATTTTTA
1 AATATTTTTA
2678066 AATA-TTTTA
1 AATATTTTTA
2678075 AATATTTTTA
1 AATATTTTTA
2678085 AA
1 AA
2678087 AATAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATATTTTTA
Found at i:2678371 original size:16 final size:13
Alignment explanation
Indices: 2678341--2678378 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2678331 TTTCGAAGAA
2678341 TATTATTTAAATT
1 TATTATTTAAATT
2678354 TATTATTTAAACTT
1 TATTATTTAAA-TT
*
2678368 T-TTATTAAAAT
1 TATTATTTAAAT
2678379 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 19 0.83
14 3 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTTAAATT
Found at i:2678626 original size:19 final size:19
Alignment explanation
Indices: 2678582--2678627 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
2678572 TTTTATAGGG
2678582 AAAA-AAATTATTTTTCAT
1 AAAACAAATTATTTTTCAT
* *
2678600 TAACCAAATTATTTTTCAT
1 AAAACAAATTATTTTTCAT
2678619 AAAACAAAT
1 AAAACAAAT
2678628 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAACAAATTATTTTTCAT
Found at i:2685964 original size:42 final size:42
Alignment explanation
Indices: 2685905--2685988 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
2685895 AGTAGTGTTA
2685905 ATGTTTCCTCTTTTTCTTCTTTAGACTCTGACGCTGAATTAT
1 ATGTTTCCTCTTTTTCTTCTTTAGACTCTGACGCTGAATTAT
*
2685947 ATGTTTCCTCTTTTTCTTCTTTAGACTCTGACGTTGAATTAT
1 ATGTTTCCTCTTTTTCTTCTTTAGACTCTGACGCTGAATTAT
2685989 CTACTTGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (42 bp):
ATGTTTCCTCTTTTTCTTCTTTAGACTCTGACGCTGAATTAT
Found at i:2692100 original size:47 final size:49
Alignment explanation
Indices: 2691984--2692163 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 49
2691974 TGTAACCCGC
* * * *
2691984 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGG--G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
* *
2692030 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* * *
2692080 -C-TCA-CGAACTCGGACTCAACTCAATGAGTTCGGA---CATTCTCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
2692123 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC
2692164 CAAACATCCT
Statistics
Matches: 109, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.55
47 28 0.26
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Done.