Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 48 of 113
Found at i:12866521 original size:2 final size:2
Alignment explanation
Indices: 12866516--12866540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12866506 GTTAAATGTG
12866516 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12866541 TAGTAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12869408 original size:49 final size:49
Alignment explanation
Indices: 12869355--12869454 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
12869345 GTGAGAGTCA
* * *
12869355 CATAGTTTGTAAGTAAAATTTTAGATTTTTAATTTTAAAAATCAGAGTT
1 CATAGTTTGTAAGTAAAATATTAGATTTTTAATTTCAAAAATCAAAGTT
** * *
12869404 CATAGTTTGTTGGTAAAATATTATATTTTTAATTTCAATAATCAAAGTT
1 CATAGTTTGTAAGTAAAATATTAGATTTTTAATTTCAAAAATCAAAGTT
12869453 CA
1 CA
12869455 AATTCTGGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (49 bp):
CATAGTTTGTAAGTAAAATATTAGATTTTTAATTTCAAAAATCAAAGTT
Found at i:12876218 original size:2 final size:2
Alignment explanation
Indices: 12876213--12876245 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12876203 ATTTCTTACT
12876213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12876246 GCACACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12879426 original size:29 final size:29
Alignment explanation
Indices: 12879377--12879458 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
12879367 CTTTAAATTA
*
12879377 TTTAATTTCATTGAAATAAATTCATATATT
1 TTTAATTT-ATTCAAATAAATTCATATATT
** *
12879407 TTTAATTTATTCAAATAAATTTTTATCTT
1 TTTAATTTATTCAAATAAATTCATATATT
* *
12879436 TTTACTTCTATTCATATAAATTC
1 TTTAATT-TATTCAAATAAATTC
12879459 TTATTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTAATTTATTCAAATAAATTCATATATT
Found at i:12879455 original size:30 final size:29
Alignment explanation
Indices: 12879377--12879462 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
12879367 CTTTAAATTA
* * *
12879377 TTTAATTTCATTGAAATAAATTCATATATT
1 TTTAATTT-ATTCAAATAAATTCTTATCTT
*
12879407 TTTAATTTATTCAAATAAATTTTTATCTT
1 TTTAATTTATTCAAATAAATTCTTATCTT
* *
12879436 TTTACTTCTATTCATATAAATTCTTAT
1 TTTAATT-TATTCAAATAAATTCTTAT
12879463 TTCAAATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTAATTTATTCAAATAAATTCTTATCTT
Found at i:12880018 original size:13 final size:13
Alignment explanation
Indices: 12880000--12880027 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12879990 CTCTTACTTT
12880000 TTATATTTTAAAA
1 TTATATTTTAAAA
12880013 TTATATTTTAAAA
1 TTATATTTTAAAA
12880026 TT
1 TT
12880028 TTTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATTTTAAAA
Found at i:12881594 original size:33 final size:34
Alignment explanation
Indices: 12881542--12881605 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
12881532 AACTTATCGT
*
12881542 AAATAGATATTCGAGAAGTTTAAAGATTTCTCAA
1 AAATAGATATTCGAGAAGTTGAAAGATTTCTCAA
* * *
12881576 AAATGGAT-TTCGATAAGTTGAAAGGTTTCT
1 AAATAGATATTCGAGAAGTTGAAAGATTTCT
12881606 TAAACATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 19 0.73
34 7 0.27
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (34 bp):
AAATAGATATTCGAGAAGTTGAAAGATTTCTCAA
Found at i:12882232 original size:16 final size:16
Alignment explanation
Indices: 12882211--12882241 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12882201 AAAATAATGT
*
12882211 TTTTTTTAATAAATTA
1 TTTTTTAAATAAATTA
12882227 TTTTTTAAATAAATT
1 TTTTTTAAATAAATT
12882242 GATAATTGTG
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTAAATAAATTA
Found at i:12885494 original size:2 final size:2
Alignment explanation
Indices: 12885477--12885528 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
12885467 CTGTGCATGA
* *
12885477 AG AG AA AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12885519 AG AG AG AG AG
1 AG AG AG AG AG
12885529 CAATTTAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12891949 original size:15 final size:16
Alignment explanation
Indices: 12891919--12891951 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12891909 ATCATTTTCA
12891919 AAAACAAAATGAAAAG
1 AAAACAAAATGAAAAG
*
12891935 AAAAGAAAA-GAAAAG
1 AAAACAAAATGAAAAG
12891950 AA
1 AA
12891952 GGAAAAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAACAAAATGAAAAG
Found at i:12892368 original size:29 final size:29
Alignment explanation
Indices: 12892330--12892412 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
12892320 TAATTAAATT
* * *
12892330 AAAATGTTTAATATTATATTTAAATTTTA
1 AAAATTTTTAATATAATATTTAAATTATA
12892359 AAAATTTTTAATATAATATTTAAATTATA
1 AAAATTTTTAATATAATATTTAAATTATA
* *
12892388 AATATATTAATTAATATGATATTTA
1 AA-A-ATT-TTTAATATAATATTTA
12892413 TAAAATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 28 0.61
30 1 0.02
31 3 0.07
32 14 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
AAAATTTTTAATATAATATTTAAATTATA
Found at i:12892456 original size:20 final size:20
Alignment explanation
Indices: 12892431--12892472 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12892421 TTTATTTATT
12892431 ATATATAATTAT-TTAAATAA
1 ATATATAATTATATTAAA-AA
12892451 ATATATAATTATATTAAAAA
1 ATATATAATTATATTAAAAA
12892471 AT
1 AT
12892473 GAGTACCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATAATTATATTAAAAA
Found at i:12893362 original size:24 final size:25
Alignment explanation
Indices: 12893316--12893373 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
12893306 TTAACATAAC
**
12893316 TATTAAAATAATCAAAATTATTTGT
1 TATTAAAATAATCAAAATTATTTAA
**
12893341 TATTAAAAT-ATTGAAATTATTTAA
1 TATTAAAATAATCAAAATTATTTAA
12893365 TATTAAAAT
1 TATTAAAAT
12893374 TATTATACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (25 bp):
TATTAAAATAATCAAAATTATTTAA
Found at i:12893366 original size:16 final size:16
Alignment explanation
Indices: 12893347--12893377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12893337 TTGTTATTAA
*
12893347 AATATTGAAATTATTT
1 AATATTAAAATTATTT
12893363 AATATTAAAATTATT
1 AATATTAAAATTATT
12893378 ATACATTTAA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AATATTAAAATTATTT
Found at i:12893751 original size:20 final size:19
Alignment explanation
Indices: 12893712--12893761 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
12893702 ATTGCCATAT
*
12893712 TATTAAAATAATATACTTA
1 TATTAAAATAATATAATTA
*
12893731 TATTTAAATAATATTAA-T-
1 TATTAAAATAATA-TAATTA
12893749 TATTAAAATAATA
1 TATTAAAATAATA
12893762 AAAAATTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.44
19 13 0.48
20 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTAAAATAATATAATTA
Found at i:12900919 original size:10 final size:9
Alignment explanation
Indices: 12900902--12900981 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
12900892 AAAAGAAATT
12900902 TTTTAAAAA
1 TTTTAAAAA
12900911 TTCTTAAAAAA
1 TT-TT-AAAAA
*
12900922 TTTTTTAAAA
1 -TTTTAAAAA
* *
12900932 TTTGAAATA
1 TTTTAAAAA
12900941 TTTTAAAAA
1 TTTTAAAAA
**
12900950 TTAAAAAAA
1 TTTTAAAAA
12900959 CTATTTAAAAA
1 -T-TTTAAAAA
*
12900970 ATTTAAAAA
1 TTTTAAAAA
12900979 TTT
1 TTT
12900982 GTGAAAACTT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
9 32 0.59
10 7 0.13
11 13 0.24
12 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:12900931 original size:11 final size:11
Alignment explanation
Indices: 12900897--12900931 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12900887 ACATTAAAAG
12900897 AAATTTTTTAA
1 AAATTTTTTAA
* *
12900908 AAATTCTTAAA
1 AAATTTTTTAA
12900919 AAATTTTTTAA
1 AAATTTTTTAA
12900930 AA
1 AA
12900932 TTTGAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTTTTAA
Found at i:12900969 original size:21 final size:21
Alignment explanation
Indices: 12900939--12900978 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12900929 AAATTTGAAA
*
12900939 TATTTTAAAAATTAAAAAAAC
1 TATTTAAAAAATTAAAAAAAC
*
12900960 TATTTAAAAAATTTAAAAA
1 TATTTAAAAAATTAAAAAA
12900979 TTTGTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
TATTTAAAAAATTAAAAAAAC
Found at i:12901180 original size:22 final size:21
Alignment explanation
Indices: 12901135--12901181 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12901125 AAATCTAAAA
*
12901135 TTTTTTAAAAATTTTGCAAAT
1 TTTTTTAAAAATTATGCAAAT
*
12901156 TTTTTTAAAAAATTATG-AAAC
1 TTTTTT-AAAAATTATGCAAAT
12901177 TTTTT
1 TTTTT
12901182 CATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTTTAAAAATTATGCAAAT
Found at i:12901279 original size:10 final size:10
Alignment explanation
Indices: 12901266--12901301 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
12901256 TTTTTATTTT
12901266 ATTTTTAAAA
1 ATTTTTAAAA
12901276 ATTTTTAAAA
1 ATTTTTAAAA
*
12901286 TTTTTTAAAA
1 ATTTTTAAAA
12901296 ATTTTT
1 ATTTTT
12901302 TAGCATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTTTAAAA
Found at i:12901281 original size:11 final size:11
Alignment explanation
Indices: 12901267--12901303 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12901257 TTTTATTTTA
12901267 TTTTTAAAAA-
1 TTTTTAAAAAT
12901277 TTTTT-AAAAT
1 TTTTTAAAAAT
12901287 TTTTTAAAAAT
1 TTTTTAAAAAT
12901298 TTTTTA
1 TTTTTA
12901304 GCATATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAAAAT
Found at i:12901386 original size:19 final size:19
Alignment explanation
Indices: 12901364--12901428 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
12901354 TTTATAAATT
12901364 TTTAGATTTTTTAAAATAA
1 TTTAGATTTTTTAAAATAA
*
12901383 TTTAGATTTTTT-TAAT--
1 TTTAGATTTTTTAAAATAA
* *
12901399 TTTTGAATTTTTTAAAAAAA
1 TTTAG-ATTTTTTAAAATAA
12901419 TTTAGATTTT
1 TTTAGATTTT
12901429 CTTATTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 7 0.19
18 5 0.14
19 17 0.46
20 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTAGATTTTTTAAAATAA
Found at i:12901436 original size:35 final size:36
Alignment explanation
Indices: 12901360--12901436 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
12901350 AAAATTTATA
* *
12901360 AATTTTTAGATTTTTTAAAATAATTTAGATTTTTTT
1 AATTTTTAGATTTTTTAAAAAAATTTAGATTTTCTT
12901396 AATTTTT-GAATTTTTTAAAAAAATTTAGATTTTCTT
1 AATTTTTAG-ATTTTTTAAAAAAATTTAGATTTTCTT
12901432 -ATTTT
1 AATTTT
12901437 CAATTTTCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 6 0.16
36 32 0.84
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (36 bp):
AATTTTTAGATTTTTTAAAAAAATTTAGATTTTCTT
Found at i:12901488 original size:17 final size:17
Alignment explanation
Indices: 12901462--12901506 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
12901452 TTGTAATTTT
*
12901462 TTTTAATTTTAAGAAAA
1 TTTTATTTTTAAGAAAA
**
12901479 TTTTATTTTTATTAAAA
1 TTTTATTTTTAAGAAAA
12901496 TTTTCATTTTT
1 TTTT-ATTTTT
12901507 TGGATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTATTTTTAAGAAAA
Found at i:12901569 original size:19 final size:20
Alignment explanation
Indices: 12901540--12901590 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12901530 AGTTTTTAAG
12901540 TTTTAATAATTTTTAAAA-AA
1 TTTT-ATAATTTTTAAAAGAA
* *
12901560 TTTTATAATTTCTAAAAGTA
1 TTTTATAATTTTTAAAAGAA
12901580 TTTTAT-ATTTT
1 TTTTATAATTTT
12901591 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTATAATTTTTAAAAGAA
Found at i:12901784 original size:20 final size:20
Alignment explanation
Indices: 12901761--12901802 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12901751 AAATTTTAAA
12901761 TTAAATGACGAAATTAA-AAT
1 TTAAAT-ACGAAATTAATAAT
* *
12901781 TTAAGTACTAAATTAATAAT
1 TTAAATACGAAATTAATAAT
12901801 TT
1 TT
12901803 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
TTAAATACGAAATTAATAAT
Found at i:12903692 original size:3 final size:3
Alignment explanation
Indices: 12903684--12903712 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12903674 TTTAGTTACT
12903684 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12903713 GAATTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12906152 original size:27 final size:27
Alignment explanation
Indices: 12906113--12906175 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
12906103 TTTTATTAAA
* *
12906113 AAAAATACTATATGAA-ATTAAAATGTTT
1 AAAAATA-TATAT-AACAATAAAATATTT
12906141 AAAAATATATATAACAATAAAATATTT
1 AAAAATATATATAACAATAAAATATTT
12906168 -AAAATATA
1 AAAAATATA
12906176 AGAATAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.31
27 15 0.47
28 7 0.22
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (27 bp):
AAAAATATATATAACAATAAAATATTT
Found at i:12906838 original size:14 final size:14
Alignment explanation
Indices: 12906810--12906853 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12906800 ATATTTTATT
*
12906810 ATAAAAATAATATTA
1 ATAAAAATTA-ATTA
* *
12906825 ATCATAATTAATTA
1 ATAAAAATTAATTA
12906839 ATAAAAATTAATTA
1 ATAAAAATTAATTA
12906853 A
1 A
12906854 CTCCATTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAAAATTAATTA
Found at i:12906852 original size:28 final size:27
Alignment explanation
Indices: 12906790--12906853 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
12906780 ACCTTTATAT
* * *
12906790 TAAATTAATTATATTTTATTATAAAAA
1 TAAATTAATCATAATTAATTATAAAAA
12906817 TAATATTAATCATAATTAATTAATAAAAA
1 TAA-ATTAATCATAATTAATT-ATAAAAA
*
12906846 TTAATTAA
1 TAAATTAA
12906854 CTCCATTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 19 0.61
29 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTAATCATAATTAATTATAAAAA
Found at i:12907070 original size:9 final size:9
Alignment explanation
Indices: 12907058--12907147 Score: 50
Period size: 9 Copynumber: 10.2 Consensus size: 9
12907048 AATTTAAATA
12907058 ATAATTAAT
1 ATAATTAAT
12907067 ATAATTTAAT
1 ATAA-TTAAT
12907077 -TAATTAA-
1 ATAATTAAT
*
12907084 ATTAAATAAT
1 A-TAATTAAT
12907094 ATAA--AAT
1 ATAATTAAT
*
12907101 AATAATAAATT
1 -ATAATTAA-T
12907112 ATAATTAAT
1 ATAATTAAT
*
12907121 CTAA-TAA-
1 ATAATTAAT
12907128 AGTAATTAAT
1 A-TAATTAAT
*
12907138 -TAATTTAT
1 ATAATTAAT
12907146 AT
1 AT
12907148 TACTTAATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
7 3 0.05
8 21 0.33
9 24 0.38
10 15 0.23
11 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAATTAAT
Found at i:12907186 original size:60 final size:59
Alignment explanation
Indices: 12907113--12907265 Score: 155
Period size: 60 Copynumber: 2.5 Consensus size: 59
12907103 TAATAAATTA
* * * * * *
12907113 TAATTAATCTAATAAAGTAATTAATTAAT-TTATATTACTTAATTAAGTTGATATTAATAT
1 TAATTAATTTAATAAA-TAATTAATTAATATTAT-TTAATGAATGAAATTAATATTAATAT
** *
12907173 TAATTAATTTAATACTTATATTATTTAATATTATTTAATGAATGAAATTAATATTAATAT
1 TAATTAATTTAATAAATA-ATTAATTAATATTATTTAATGAATGAAATTAATATTAATAT
*
12907233 TATTTAATATTAATTAAATAATTAATTTAATAT
1 TAATTAAT-TTAA-TAAATAATTAA-TTAATAT
12907266 CATAATAAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
59 2 0.03
60 50 0.67
61 12 0.16
62 11 0.15
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (59 bp):
TAATTAATTTAATAAATAATTAATTAATATTATTTAATGAATGAAATTAATATTAATAT
Found at i:12907193 original size:21 final size:19
Alignment explanation
Indices: 12907132--12907261 Score: 81
Period size: 21 Copynumber: 6.7 Consensus size: 19
12907122 TAATAAAGTA
12907132 ATTAATTAATTTATATTA-
1 ATTAATTAATTTATATTAT
* *
12907150 CTTAATTAAGTTGATATTAAT
1 ATTAATTAA-TTTATATT-AT
12907171 ATTAATTAATTTAATACTTAT
1 ATTAATTAATTT-ATA-TTAT
*
12907192 ATTATTTAATATTAT-TTA-
1 ATTAATTAAT-TTATATTAT
* * *
12907210 ATGAATGAAATTAATATTAAT
1 ATTAAT-TAATTTATATT-AT
*
12907231 ATTATTTAATATTA-ATTA-
1 ATTAATTAAT-TTATATTAT
*
12907249 AATAATTAATTTA
1 ATTAATTAATTTA
12907262 ATATCATAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
17 3 0.03
18 23 0.27
19 16 0.19
20 10 0.12
21 30 0.35
22 4 0.05
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTAATTAATTTATATTAT
Found at i:12907236 original size:29 final size:27
Alignment explanation
Indices: 12907135--12907241 Score: 85
Period size: 29 Copynumber: 3.9 Consensus size: 27
12907125 TAAAGTAATT
*
12907135 AATTAATTT-ATATTACTTAATTAAGTTGA
1 AATTAATTTAATATTATTTAA-TAA--TGA
* * * *
12907164 TATTAATATTAAT-TAATTTAATACTTA
1 AATTAAT-TTAATATTATTTAATAATGA
*
12907191 TATT-ATTTAATATTATTTAATGAATGA
1 AATTAATTTAATATTATTTAAT-AATGA
12907218 AATTAATATTAATATTATTTAATA
1 AATTAAT-TTAATATTATTTAATA
12907242 TTAATTAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
25 5 0.08
26 10 0.16
27 12 0.19
28 3 0.05
29 23 0.37
30 8 0.13
31 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (27 bp):
AATTAATTTAATATTATTTAATAATGA
Found at i:12907263 original size:39 final size:37
Alignment explanation
Indices: 12907164--12907265 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 37
12907154 ATTAAGTTGA
12907164 TATTAATATTAATTAATTTAATACTTATATTATTTAATAT
1 TATTAA-A-TAATTAATTTAATA-TTATATTATTTAATAT
* * *
12907204 TATTTAATGAATGAAATTAATATTAATATTATTTAATAT
1 TATTAAAT-AATTAATTTAATATT-ATATTATTTAATAT
12907243 TAATTAAATAATTAATTTAATAT
1 T-ATTAAATAATTAATTTAATAT
12907266 CATAATAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.06
39 39 0.74
40 11 0.21
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (37 bp):
TATTAAATAATTAATTTAATATTATATTATTTAATAT
Found at i:12907306 original size:4 final size:4
Alignment explanation
Indices: 12907046--12907288 Score: 63
Period size: 4 Copynumber: 61.0 Consensus size: 4
12907036 AAAATGATAT
* *
12907046 TTAA TTTAA ATAA -TAA TTAA TATAA TTTAA TTAA TTAAA TTAA ATAA
1 TTAA -TTAA TTAA TTAA TTAA T-TAA -TTAA TTAA TT-AA TTAA TTAA
* * * *
12907093 TATAAA ATAA -TAA TAAA TT-A -TAA TTAA TCTAA TAAA GTAA TTAA TTAA
1 T-T-AA TTAA TTAA TTAA TTAA TTAA TTAA T-TAA TTAA TTAA TTAA TTAA
* *
12907141 TTTATA TTAC TTAA TTAA GTTGATA TTAA -T-A TTAA TTAA TTTAA -TAC
1 -TTA-A TTAA TTAA TTAA -TT-A-A TTAA TTAA TTAA TTAA -TTAA TTAA
* * * *
12907188 TTATA TTAT TTAA -T-A TTAT TTAA TGAA TGAAA TTAA -T-A TTAA -T-A
1 TTA-A TTAA TTAA TTAA TTAA TTAA TTAA T-TAA TTAA TTAA TTAA TTAA
* * * *
12907232 TTAT TTAA -T-A TTAA TTAA ATAA TTAA TTTAA TATCA -TAA TAAA TT-A
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA -TTAA T-TAA TTAA TTAA TTAA
12907278 -TAA TTAA TTAA
1 TTAA TTAA TTAA
12907289 AATATGTTAT
Statistics
Matches: 175, Mismatches: 29, Indels: 69
0.64 0.11 0.25
Matches are distributed among these distances:
2 7 0.04
3 24 0.14
4 91 0.52
5 45 0.26
6 7 0.04
7 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (4 bp):
TTAA
Found at i:12907313 original size:13 final size:13
Alignment explanation
Indices: 12907295--12907357 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
12907285 TTAAAATATG
12907295 TTATTTAATTAAA
1 TTATTTAATTAAA
12907308 TTATTTAA--ACAA
1 TTATTTAATTA-AA
12907320 -TATTATAATTAAA
1 TTATT-TAATTAAA
*
12907333 -TATTAGAATTAAA
1 TTATT-TAATTAAA
*
12907346 TTCTTTAATTAA
1 TTATTTAATTAA
12907358 TAAAGTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 5 0.12
12 5 0.12
13 28 0.67
14 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (13 bp):
TTATTTAATTAAA
Found at i:12907325 original size:27 final size:25
Alignment explanation
Indices: 12907273--12907333 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 25
12907263 TATCATAATA
*
12907273 AATTATAATTAATTAAAATATGTTATTT
1 AATTA-AATTAATTAAAATATATTA--T
*
12907301 AATTAAATTATTTAAACA-ATATTAT
1 AATTAAATTAATTAAA-ATATATTAT
12907326 AATTAAAT
1 AATTAAAT
12907334 ATTAGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 9 0.30
27 15 0.50
28 6 0.20
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
AATTAAATTAATTAAAATATATTAT
Found at i:12908004 original size:82 final size:82
Alignment explanation
Indices: 12907863--12908026 Score: 247
Period size: 82 Copynumber: 2.0 Consensus size: 82
12907853 GTATTAGTTC
* * * * *
12907863 TTATTGGTAAAACCTTCCATTTTTAGGAAAAATTACAAGGAAATAGATGGTAATGTTTAATATTT
1 TTATTGATAAAACCATCCATTTGTAGGAAAAATTACAAGGAAATAGATGGTAATATTTAATATTC
*
12907928 TGGTTATCTCATGCATG
66 TGATTATCTCATGCATG
* * *
12907945 TTATTGATAAAACCATCCATTTGTAGGAAAAATTATAAGGAAGTGGATGGTAATATTTAATATTC
1 TTATTGATAAAACCATCCATTTGTAGGAAAAATTACAAGGAAATAGATGGTAATATTTAATATTC
12908010 TGATTATCTCATGCATG
66 TGATTATCTCATGCATG
12908027 CGGTTAGATT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (82 bp):
TTATTGATAAAACCATCCATTTGTAGGAAAAATTACAAGGAAATAGATGGTAATATTTAATATTC
TGATTATCTCATGCATG
Found at i:12908481 original size:14 final size:14
Alignment explanation
Indices: 12908454--12908503 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
12908444 AATTATCATT
12908454 TAAATA-TA-AATA
1 TAAATATTATAATA
12908466 TAAATATTATAATA
1 TAAATATTATAATA
*
12908480 TAAATATTATTATA
1 TAAATATTATAATA
12908494 -AAATTATTAT
1 TAAA-TATTAT
12908504 TTTGGATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
14 23 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATATTATAATA
Found at i:12908483 original size:26 final size:25
Alignment explanation
Indices: 12908444--12908500 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
12908434 ATTATTATTG
* *
12908444 AATTATCATTTAAATATAAATATAA
1 AATTATAATATAAATATAAATATAA
* *
12908469 ATATTATAATATAAATATTATTATAA
1 A-ATTATAATATAAATATAAATATAA
12908495 AATTAT
1 AATTAT
12908501 TATTTTGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTATAATATAAATATAAATATAA
Found at i:12908501 original size:11 final size:12
Alignment explanation
Indices: 12908454--12908503 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
12908444 AATTATCATT
* *
12908454 TAAATATAAATA
1 TAAATATTATTA
12908466 TAAATATTATAATA
1 TAAATATTAT--TA
12908480 TAAATATTATTA
1 TAAATATTATTA
12908492 TAAA-ATTATTA
1 TAAATATTATTA
12908503 T
1 T
12908504 TTTGGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 8 0.24
12 14 0.41
14 12 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATATTATTA
Found at i:12909365 original size:10 final size:10
Alignment explanation
Indices: 12909350--12909379 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12909340 ATCGATGTTT
12909350 TATATTTTAA
1 TATATTTTAA
12909360 TATATTTTAA
1 TATATTTTAA
12909370 T-TATTTTAA
1 TATATTTTAA
12909379 T
1 T
12909380 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:12909376 original size:9 final size:9
Alignment explanation
Indices: 12909352--12909381 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
12909342 CGATGTTTTA
12909352 TATTTTAAT
1 TATTTTAAT
12909361 ATATTTTAAT
1 -TATTTTAAT
12909371 TATTTTAAT
1 TATTTTAAT
12909380 TA
1 TA
12909382 ATAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:12914991 original size:14 final size:15
Alignment explanation
Indices: 12914972--12915009 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12914962 CATCAAAAAT
*
12914972 AAATTAAA-GTATGA
1 AAATTAAACGTATAA
12914986 AAATTAAATCGTATAA
1 AAATTAAA-CGTATAA
12915002 AAATTAAA
1 AAATTAAA
12915010 ATAAGCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
16 13 0.62
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (15 bp):
AAATTAAACGTATAA
Found at i:12915020 original size:17 final size:16
Alignment explanation
Indices: 12915000--12915045 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
12914990 TAAATCGTAT
12915000 AAAAATTAAAATAAGCA
1 AAAAATTAAAATAA-CA
* *
12915017 AAAAATTTAAACAACA
1 AAAAATTAAAATAACA
12915033 AGAAAATTAAAAT
1 A-AAAATTAAAAT
12915046 GCATGAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (16 bp):
AAAAATTAAAATAACA
Found at i:12916492 original size:124 final size:126
Alignment explanation
Indices: 12916203--12916511 Score: 382
Period size: 124 Copynumber: 2.4 Consensus size: 126
12916193 TTAATATATG
* * * * * *
12916203 TTAT-TTAACATTTAATATGTAATTTAATAAGGGATTATAGTAAATTTTAAATGAAATTCCATAT
1 TTATGTTAAGATTTAATATATAATTTAATAAGGTATTATAGT-AATTTTAAATAAAAGTCCACA-
12916267 GTCAAATTTATATAAAGCAATGGTAAGAGTATTTTAGTAATTTAATATGTAATTAATTTTATA
64 GTCAAATTTATATAAAGCAATGGTAAGAGTATTTTAGTAATTTAATATGTAATTAATTTTATA
*
12916330 TTATGTTAAGATTTCATATATAATTTAATATAGGTATTATAGTAATTTTAAATAAACAGT-CACA
1 TTATGTTAAGATTTAATATATAATTTAATA-AGGTATTATAGTAATTTTAAATAAA-AGTCCACA
* *
12916394 -TCAAAGTTT-TATAAAGTAATGGTAATGA-TATTTTAGTAATTT-A-ATGTGATTAATTTTATA
64 GTCAAA-TTTATATAAAGCAATGGTAA-GAGTATTTTAGTAATTTAATATGTAATTAATTTTATA
* *
12916454 TTATGTTAA-AGTTTAATATATAATTTAATAGAAGTATTATAATAATTTTGAAATAAAA
1 TTATGTTAAGA-TTTAATATATAATTTAATA-AGGTATTATAGTAATTTT-AAATAAAA
12916512 TATTACATTT
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
123 1 0.01
124 60 0.37
125 8 0.05
126 34 0.21
127 9 0.06
128 37 0.23
129 13 0.08
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (126 bp):
TTATGTTAAGATTTAATATATAATTTAATAAGGTATTATAGTAATTTTAAATAAAAGTCCACAGT
CAAATTTATATAAAGCAATGGTAAGAGTATTTTAGTAATTTAATATGTAATTAATTTTATA
Found at i:12917301 original size:172 final size:179
Alignment explanation
Indices: 12917040--12917381 Score: 454
Period size: 172 Copynumber: 1.9 Consensus size: 179
12917030 AAATTTTGAT
* * *
12917040 TAATTATAAAATGAGAGATATTTTTGTAATTATGATATGATATGATATGTTATAGTAAATAATTA
1 TAATTATAAAAGGAGAGATATTTTCGTAATTATGATATGATATGATA-GTTATAATAAATAATTA
* * *
12917105 TAAAAAAAAAGGTATTTTCATAATTATGGTAT-AAGAATATCATAATAAATTT-ATATAT-ATGT
65 TAAAAAAAAAGGTACTTCCATAATTATGGTATGAA-AATATAATAATAAATTTGA-AT-TCATGT
12917167 CAAATTCTTAT-AAAATATGAA-AG-GGTATTATAATAATTTACTTAGGGATC
127 CAAATTCTTATCAAAATATGAAGAGAGGTATTATAATAATTTACTTAGGGATC
* *
12917217 TAATTAT-AAAGGAGAGATATTTTCGTAATTTTGATATGA-A-GGTA-TTATAATAAATAATTAT
1 TAATTATAAAAGGAGAGATATTTTCGTAATTATGATATGATATGATAGTTATAATAAATAATTAT
* * *
12917278 AAGAAGAAAA-GTACTTCCATAATTATGGTATGAAAATATAATAGTAAATTTGAATTCATGTGAA
66 AA-AAAAAAAGGTACTTCCATAATTATGGTATGAAAATATAATAATAAATTTGAATTCATGTCAA
*
12917342 ATTCTTATCAAAATATGAAGAGAGGTATTATAGTAATTTA
130 ATTCTTATCAAAATATGAAGAGAGGTATTATAATAATTTA
12917382 TTTTAAGATA
Statistics
Matches: 146, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
171 1 0.01
172 68 0.47
173 19 0.13
174 5 0.03
175 17 0.12
176 29 0.20
177 7 0.05
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (179 bp):
TAATTATAAAAGGAGAGATATTTTCGTAATTATGATATGATATGATAGTTATAATAAATAATTAT
AAAAAAAAAGGTACTTCCATAATTATGGTATGAAAATATAATAATAAATTTGAATTCATGTCAAA
TTCTTATCAAAATATGAAGAGAGGTATTATAATAATTTACTTAGGGATC
Found at i:12917453 original size:6 final size:6
Alignment explanation
Indices: 12917442--12917474 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12917432 AGATAATGTA
*
12917442 ATAATT ATAATT ATAATT ATAATT TTAATT ATA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATA
12917475 TAGTATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATAATT
Found at i:12917857 original size:28 final size:28
Alignment explanation
Indices: 12917783--12917863 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
12917773 TATTTAATGC
*
12917783 AATATTTAAATTTAAAAAATTTTTAATTT
1 AATATTT-AATTTAAAAATTTTTTAATTT
* * *
12917812 AGTATTTAACTTATAAATTTTTTAA-TT
1 AATATTTAATTTAAAAATTTTTTAATTT
*
12917839 AATATTATATTTTAAAAATTATTTT
1 AATATT-TAATTTAAAAATT-TTTT
12917864 TTATCATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 7 0.17
28 25 0.60
29 10 0.24
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
AATATTTAATTTAAAAATTTTTTAATTT
Found at i:12917953 original size:28 final size:29
Alignment explanation
Indices: 12917911--12917965 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
12917901 ATATATATTA
12917911 TATTAATTAATAAATTTAT-AATTTTATG
1 TATTAATTAATAAATTTATAAATTTTATG
*
12917939 TATTACATTAA-AAATTTTTAAATTTTA
1 TATTA-ATTAATAAATTTATAAATTTTA
12917966 AATATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
TATTAATTAATAAATTTATAAATTTTATG
Found at i:12917971 original size:29 final size:28
Alignment explanation
Indices: 12917910--12917972 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
12917900 CATATATATT
*
12917910 ATATTAATTAATAAATTTATAATTTTAT
1 ATATTAATTAATAAATTTATAATTTTAA
* *
12917938 GTATTACATTAA-AAATTTTTAAATTTTAA
1 ATATTA-ATTAATAAATTTAT-AATTTTAA
12917967 ATATTA
1 ATATTA
12917973 TATCAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
ATATTAATTAATAAATTTATAATTTTAA
Found at i:12917984 original size:29 final size:30
Alignment explanation
Indices: 12917925--12917995 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
12917915 AATTAATAAA
** *
12917925 TTTATAATTTTATGTATTACATTAAAAATT
1 TTTATAATTTTAAATATTACATCAAAAATT
* *
12917955 TTTA-AATTTTAAATATTATATCAAATATTT
1 TTTATAATTTTAAATATTACATCAAA-AATT
12917985 TATTATAATTT
1 T-TTATAATTT
12917996 AAAAAGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 17 0.52
30 8 0.24
31 3 0.09
32 5 0.15
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTATAATTTTAAATATTACATCAAAAATT
Found at i:12923699 original size:10 final size:10
Alignment explanation
Indices: 12923676--12923711 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
12923666 TGAATCATCA
*
12923676 TTTTTCTTTGT
1 TTTTTC-TTAT
12923687 TTTTTCTTAT
1 TTTTTCTTAT
12923697 TTTTTCTTAT
1 TTTTTCTTAT
12923707 TTTTT
1 TTTTT
12923712 TCAAGCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.06, C:0.08, G:0.03, T:0.83
Consensus pattern (10 bp):
TTTTTCTTAT
Found at i:12934281 original size:59 final size:56
Alignment explanation
Indices: 12934206--12934387 Score: 174
Period size: 59 Copynumber: 3.1 Consensus size: 56
12934196 GCTTTTGTAC
* * * *
12934206 AAAGAAAATTGATACTTTCAACTTTTTCT-TAAATTTTTTTCTTGATAATTTTTATTTTT
1 AAAGAAAATTGATACTTTCAACTTTTCCTCAAAATTATTTT-TT--TAA-TTTTAATTTT
*
12934265 AAAGAAAATT-AGTACTTCCAACTTTTCCTCAAAATTATTTTTTTAATTTTAATTTT
1 AAAGAAAATTGA-TACTTTCAACTTTTCCTCAAAATTATTTTTTTAATTTTAATTTT
* * *
12934321 -AAGAAAAATTGATACTTTCAACTTTCCCTTAAAAATATATTTTTTTGAAACTTTAATTTT
1 AAAG-AAAATTGATACTTTCAACTTTTCC-TCAAAAT-TATTTTTTT--AATTTTAATTTT
12934381 -AAGAAAA
1 AAAGAAAA
12934388 ATAAAAAAAT
Statistics
Matches: 106, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
55 3 0.03
56 29 0.27
57 10 0.09
58 10 0.09
59 31 0.29
60 23 0.22
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (56 bp):
AAAGAAAATTGATACTTTCAACTTTTCCTCAAAATTATTTTTTTAATTTTAATTTT
Found at i:12934337 original size:56 final size:55
Alignment explanation
Indices: 12934210--12934389 Score: 175
Period size: 56 Copynumber: 3.1 Consensus size: 55
12934200 TTGTACAAAG
* * * *
12934210 AAAATTGATACTTTCAACTTTTTCTTAAATTTTTTTCTTGATAATTTTTATTTTTAA-A
1 AAAATTGATACTTTCAACTTTTCCTAAAATTATTTT-TT--TAA-TTTTAATTTTAAGA
*
12934268 GAAAATT-AGTACTTCCAACTTTTCCTCAAAATTATTTTTTTAATTTTAATTTTAAGA
1 -AAAATTGA-TACTTTCAACTTTTCCT-AAAATTATTTTTTTAATTTTAATTTTAAGA
* *
12934325 AAAATTGATACTTTCAACTTTCCCTTAAAAATATATTTTTTTGAAACTTTAATTTTAAGA
1 AAAATTGATACTTTCAACTTTTCC-T-AAAAT-TATTTTTTT--AATTTTAATTTTAAGA
12934385 AAAAT
1 AAAAT
12934390 AAAAAAATAT
Statistics
Matches: 104, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
56 31 0.30
57 11 0.11
58 10 0.10
59 23 0.22
60 29 0.28
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (55 bp):
AAAATTGATACTTTCAACTTTTCCTAAAATTATTTTTTTAATTTTAATTTTAAGA
Found at i:12935265 original size:3 final size:3
Alignment explanation
Indices: 12935257--12935318 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
12935247 AGATAAAATC
*
12935257 AAT AAT AAT AAT AAT AAT -AT AAT AGCA- AAT AAT AAA AAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT -AAT AAT
12935302 AAT AAAT AAT AA- AAT AA
1 AAT -AAT AAT AAT AAT AA
12935319 AAACAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
2 7 0.14
3 34 0.69
4 7 0.14
5 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:12935287 original size:21 final size:19
Alignment explanation
Indices: 12935257--12935318 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
12935247 AGATAAAATC
12935257 AATAATAATAATAATAATAT
1 AATAA-AATAATAATAATAT
*
12935277 AATAGCAAATAATAAAAATA-
1 AATA--AAATAATAATAATAT
*
12935297 AATAAAATAAATAATAAAAT
1 AATAAAAT-AATAATAATAT
12935317 AA
1 AA
12935319 AAACAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.11
19 8 0.23
20 10 0.29
21 12 0.34
22 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAAATAATAATAATAT
Found at i:12935319 original size:21 final size:22
Alignment explanation
Indices: 12935260--12935319 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
12935250 TAAAATCAAT
*
12935260 AATAATAATAATAATATAATAGCA
1 AATAATAA-AATAA-ATAATAACA
*
12935284 AATAATAAAAATAAATAA-AATA
1 AATAAT-AAAATAAATAATAACA
12935306 AATAATAAAATAAA
1 AATAATAAAATAAA
12935320 AACAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 8 0.24
22 8 0.24
23 4 0.12
24 11 0.33
25 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAATAAAATAAATAATAACA
Found at i:12935330 original size:19 final size:22
Alignment explanation
Indices: 12935260--12935329 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
12935250 TAAAATCAAT
* **
12935260 AATAATAATAATAATATAATAGCA
1 AATAATAAAAATAA-ATAA-AATA
12935284 AATAATAAAAATAAATAAAATA
1 AATAATAAAAATAAATAAAATA
* *
12935306 AATAATAAAATAAAAACAAAATA
1 AATAATAAAA-ATAAATAAAATA
12935329 A
1 A
12935330 TTGAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 12 0.30
23 15 0.38
24 13 0.32
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (22 bp):
AATAATAAAAATAAATAAAATA
Found at i:12936079 original size:4 final size:4
Alignment explanation
Indices: 12936072--12936107 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
12936062 GTGAGTGATG
*
12936072 AGAA AGAA AG-A AGAA AGAA AGAA GGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
12936108 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:12936088 original size:11 final size:11
Alignment explanation
Indices: 12936072--12936106 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
12936062 GTGAGTGATG
12936072 AGAAAGAAAGA
1 AGAAAGAAAGA
12936083 AGAAAGAAAGA
1 AGAAAGAAAGA
12936094 AGGAAAGAAAGA
1 A-GAAAGAAAGA
12936106 A
1 A
12936107 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAGA
Found at i:12937203 original size:21 final size:21
Alignment explanation
Indices: 12937178--12937223 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12937168 CTAAATATAT
12937178 ATTTT-ATTATTAT-AATAATTA
1 ATTTTAATT-TTATCAA-AATTA
12937199 ATTTTAATTTTATCAAAATTA
1 ATTTTAATTTTATCAAAATTA
12937220 ATTT
1 ATTT
12937224 AACCAATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTAATTTTATCAAAATTA
Found at i:12939320 original size:57 final size:57
Alignment explanation
Indices: 12939198--12939442 Score: 226
Period size: 60 Copynumber: 4.1 Consensus size: 57
12939188 TTGTATAAAA
* * * *
12939198 AAAAATTGATACTTTCAACTTTTTTTTAAAATGT-TTTTCTTGATAATTTTTATTTTTAA-
1 AAAAATTGATACTTTCAACTTTTTCTAAAAATATATTTT-TT-A-AA-TTTTAATTTTAAG
* * *
12939257 AGAAAATT-AGTACTTCCAACTTTTTCTCAAAATATATTTTTTTAATTTTAATTTTAAG
1 A-AAAATTGA-TACTTTCAACTTTTTCTAAAAATATATTTTTTAAATTTTAATTTTAAG
* *
12939315 AAAAATTGATACTTTCAATTTTTTTCTAAAAATATATTTTTTAAATTTTTTTATTTTCAAG
1 AAAAATTGATACTTTCAA-CTTTTTCTAAAAATATATTTTTTAAA--TTTTAATTTT-AAG
* * * *
12939376 AGAAATTGATACTTTCAACTTTTCCAATAAAAATATATATTTTTGAAACTTTAGTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTC--TAAAAATATAT-TTTTT-AAATTTTAATTTTAAG
12939437 AAAAAT
1 AAAAAT
12939443 AAAAAAATAT
Statistics
Matches: 155, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
57 25 0.16
58 27 0.17
59 2 0.01
60 43 0.28
61 32 0.21
62 18 0.12
63 5 0.03
64 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTTCTAAAAATATATTTTTTAAATTTTAATTTTAAG
Found at i:12939389 original size:118 final size:120
Alignment explanation
Indices: 12939198--12939442 Score: 290
Period size: 117 Copynumber: 2.0 Consensus size: 120
12939188 TTGTATAAAA
*
12939198 AAAAATTGATACTTTCAACTTTTTTTTAAAATGTTTTTCTTGATAATTTTTATTTTTAAAGAAAA
1 AAAAATTGATACTTTCAACTTTTTTTTAAAATATTTTTCTTGATAATTTTTATTTTTAAAGAAAA
* * * *
12939263 TTAGTACTTCCAACTTTTTC-TCAAAATATAT-TTTTT-TAATTTTAATTTTAAG
66 TTAGTACTTCCAACTTTTCCATAAAAATATATATTTTTGAAACTTTAATTTTAAG
* *
12939315 AAAAATTGATACTTTCAA-TTTTTTTCTAAAAATATATTTT-TT-A-AATTTTTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTTTT-T-AAAATAT-TTTTCTTGATAATTTTTAT-TTTTAAAG
* *
12939376 AGAAATT-GATACTTTCAACTTTTCCAATAAAAATATATATTTTTGAAACTTTAGTTTTAAG
62 A-AAATTAG-TACTTCCAACTTTTCC-ATAAAAATATATATTTTTGAAACTTTAATTTTAAG
12939437 AAAAAT
1 AAAAAT
12939443 AAAAAAATAT
Statistics
Matches: 109, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
116 15 0.14
117 29 0.27
118 27 0.25
119 4 0.04
120 10 0.09
121 5 0.05
122 19 0.17
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (120 bp):
AAAAATTGATACTTTCAACTTTTTTTTAAAATATTTTTCTTGATAATTTTTATTTTTAAAGAAAA
TTAGTACTTCCAACTTTTCCATAAAAATATATATTTTTGAAACTTTAATTTTAAG
Found at i:12940318 original size:3 final size:3
Alignment explanation
Indices: 12940310--12940371 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
12940300 AGATAAAATC
*
12940310 AAT AAT AAT AAT AAT AAT -AT AAT AGCA- AAT AAT AAA AAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT -AAT AAT
12940355 AAT AAAT AAT AA- AAT AA
1 AAT -AAT AAT AAT AAT AA
12940372 AAACAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
2 7 0.14
3 34 0.69
4 7 0.14
5 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:12940370 original size:21 final size:22
Alignment explanation
Indices: 12940313--12940372 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
12940303 TAAAATCAAT
*
12940313 AATAATAATAATAATATAATAGCA
1 AATAATAA-AATAA-ATAATAACA
*
12940337 AATAATAAAAATAAATAA-AATA
1 AATAAT-AAAATAAATAATAACA
12940359 AATAATAAAATAAA
1 AATAATAAAATAAA
12940373 AACAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 8 0.24
22 8 0.24
23 4 0.12
24 11 0.33
25 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAATAAAATAAATAATAACA
Found at i:12940383 original size:19 final size:22
Alignment explanation
Indices: 12940313--12940382 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
12940303 TAAAATCAAT
* **
12940313 AATAATAATAATAATATAATAGCA
1 AATAATAAAAATAA-ATAA-AATA
12940337 AATAATAAAAATAAATAAAATA
1 AATAATAAAAATAAATAAAATA
* *
12940359 AATAATAAAATAAAAACAAAATA
1 AATAATAAAA-ATAAATAAAATA
12940382 A
1 A
12940383 TTGAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 12 0.30
23 15 0.38
24 13 0.32
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (22 bp):
AATAATAAAAATAAATAAAATA
Found at i:12941136 original size:4 final size:4
Alignment explanation
Indices: 12941129--12941164 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
12941119 GTGAGTGATG
*
12941129 AGAA AGAA AG-A AGAA AGAA AGAA GGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
12941165 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:12941145 original size:11 final size:11
Alignment explanation
Indices: 12941129--12941163 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
12941119 GTGAGTGATG
12941129 AGAAAGAAAGA
1 AGAAAGAAAGA
12941140 AGAAAGAAAGA
1 AGAAAGAAAGA
12941151 AGGAAAGAAAGA
1 A-GAAAGAAAGA
12941163 A
1 A
12941164 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAGA
Found at i:12942267 original size:21 final size:21
Alignment explanation
Indices: 12942242--12942287 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12942232 CTAAATATAT
12942242 ATTTT-ATTATTAT-AATAATTA
1 ATTTTAATT-TTATCAA-AATTA
12942263 ATTTTAATTTTATCAAAATTA
1 ATTTTAATTTTATCAAAATTA
12942284 ATTT
1 ATTT
12942288 AACCAATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTAATTTTATCAAAATTA
Found at i:12943109 original size:19 final size:19
Alignment explanation
Indices: 12943085--12943123 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12943075 TAATTCAATT
12943085 TTATATT-AAATTTGTATAA
1 TTATATTCAAATTTGT-TAA
*
12943104 TTATATTCTAATTTGTTAA
1 TTATATTCAAATTTGTTAA
12943123 T
1 T
12943124 CAATTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATATTCAAATTTGTTAA
Found at i:12946992 original size:25 final size:25
Alignment explanation
Indices: 12946940--12946992 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
12946930 AAAATCAATT
** *
12946940 TTATGAAAATTTTTTATTAAGAATA
1 TTATGAAAATTTTAAATTAAGAAAA
12946965 TTATGAAAATCTTTAAATTAA-AAAA
1 TTATGAAAAT-TTTAAATTAAGAAAA
12946990 TTA
1 TTA
12946993 CTTTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (25 bp):
TTATGAAAATTTTAAATTAAGAAAA
Found at i:12955478 original size:20 final size:21
Alignment explanation
Indices: 12955453--12955500 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 21
12955443 AACATATTTC
12955453 ATCAT-TTATGTAGTATATTA
1 ATCATATTATGTAGTATATTA
12955473 ATCATTACTTATGTAGTATATTA
1 ATCA-TA-TTATGTAGTATATTA
12955496 ATCAT
1 ATCAT
12955501 GTTTAGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.16
21 1 0.04
22 1 0.04
23 19 0.76
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (21 bp):
ATCATATTATGTAGTATATTA
Found at i:12957886 original size:24 final size:25
Alignment explanation
Indices: 12957833--12957886 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
12957823 TTGACTAAGA
12957833 TTAAA-AAAAAATCACAATTAAAAT
1 TTAAATAAAAAATCACAATTAAAAT
** *
12957857 AAAAATAAAAATTCAC-ATTAAAAT
1 TTAAATAAAAAATCACAATTAAAAT
12957881 TTAAAT
1 TTAAAT
12957887 TGTCAGCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (25 bp):
TTAAATAAAAAATCACAATTAAAAT
Found at i:12958360 original size:18 final size:18
Alignment explanation
Indices: 12958337--12958386 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
12958327 AAATTTTAAT
12958337 ATTCATAAAGGTTTCAAG
1 ATTCATAAAGGTTTCAAG
*
12958355 ATTCATATAAAAGTTTCAAG
1 ATTC--ATAAAGGTTTCAAG
*
12958375 ATT-GTAAAGGTT
1 ATTCATAAAGGTT
12958387 AAAAAATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 7 0.26
18 4 0.15
20 16 0.59
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (18 bp):
ATTCATAAAGGTTTCAAG
Found at i:12958431 original size:18 final size:18
Alignment explanation
Indices: 12958389--12958431 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12958379 TAAAGGTTAA
* *
12958389 AAAATGTGTAACAATTTT
1 AAAATTTGTAAAAATTTT
12958407 AAAATTTGTAAAAATTTT
1 AAAATTTGTAAAAATTTT
*
12958425 AAGATTT
1 AAAATTT
12958432 ACAAAGAATT
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:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (18 bp):
AAAATTTGTAAAAATTTT
Found at i:12964349 original size:59 final size:58
Alignment explanation
Indices: 12964280--12964417 Score: 138
Period size: 59 Copynumber: 2.3 Consensus size: 58
12964270 TTTTATCCTC
* *
12964280 ATTTTAAATTAATTATATTTTATTA-TAAAAA-TAATATA-AATCATAATCAATTAATAAAA
1 ATTTTAAATT-ATTA-A-TTAATTAGAAAAAATTAAT-TAGAATCATAATCAATTAATAAAA
* *
12964339 ATTTTTAATTATTAATTAATTAGAAAAAATTAATTAGTAATCATAATTAATTAATAAAAA
1 ATTTTAAATTATTAATTAATTAGAAAAAATTAATTAG-AATCATAATCAATTAAT-AAAA
* * *
12964399 AGTTTCAATAATTAATTAA
1 ATTTTAAATTATTAATTAA
12964418 CAAAAATAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
56 6 0.09
57 8 0.12
58 8 0.12
59 25 0.37
60 20 0.30
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (58 bp):
ATTTTAAATTATTAATTAATTAGAAAAAATTAATTAGAATCATAATCAATTAATAAAA
Found at i:12964569 original size:23 final size:23
Alignment explanation
Indices: 12964514--12964579 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
12964504 AATTATATTC
*
12964514 AATTTAAATTATTAT--TTAAAT
1 AATTTAAATAATTATAATTAAAT
* *
12964535 CATTTAATTAATTA-AATTAAAT
1 AATTTAAATAATTATAATTAAAT
12964557 AATATTAAATAATTATAA-TAAAT
1 AAT-TTAAATAATTATAATTAAAT
12964580 TATGATTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 11 0.31
22 8 0.22
23 15 0.42
24 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAAATAATTATAATTAAAT
Found at i:12964582 original size:10 final size:9
Alignment explanation
Indices: 12964540--12964581 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
12964530 TAAATCATTT
*
12964540 AATTAATTA
1 AATTAAATA
12964549 AATTAAATA
1 AATTAAATA
12964558 ATATTAAAT-
1 A-ATTAAATA
12964567 AATTATAATA
1 AATTA-AATA
12964577 AATTA
1 AATTA
12964582 TGATTAGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 4 0.14
9 13 0.45
10 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATA
Found at i:12964659 original size:21 final size:20
Alignment explanation
Indices: 12964604--12964698 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 20
12964594 TAAATAAATA
*
12964604 AATTTAATTATATTACTTAATT
1 AATTTAATT-TAATA-TTAATT
*
12964626 AATTTGATATTAATATTAATT
1 AATTTAAT-TTAATATTAATT
* *
12964647 AATTTAAATTTAAAATTATTT
1 AATTT-AATTTAATATTAATT
* *
12964668 AATGAATTAAGTTAATATCAATT
1 AAT---TTAATTTAATATTAATT
12964691 AATTTAAT
1 AATTTAAT
12964699 AAACTAGTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.07
21 24 0.41
22 13 0.22
23 15 0.26
24 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (20 bp):
AATTTAATTTAATATTAATT
Found at i:12964707 original size:27 final size:27
Alignment explanation
Indices: 12964660--12964725 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
12964650 TTAAATTTAA
* *
12964660 AATT-ATTTAATGAATTAAGTTAATA-T
1 AATTAATTTAATAAACTAAGTTAA-AGT
12964686 CAATTAATTTAATAAACT-AGTTAAAGT
1 -AATTAATTTAATAAACTAAGTTAAAGT
12964713 AATTATATTTAAT
1 AATTA-ATTTAAT
12964726 TAAAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.18
27 18 0.53
28 10 0.29
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (27 bp):
AATTAATTTAATAAACTAAGTTAAAGT
Found at i:12964787 original size:16 final size:16
Alignment explanation
Indices: 12964766--12964797 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12964756 ATATTAATTT
12964766 CATATAAAGACTATTC
1 CATATAAAGACTATTC
12964782 CATATAAAGACTATTC
1 CATATAAAGACTATTC
12964798 TTTACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
CATATAAAGACTATTC
Found at i:12965530 original size:2 final size:2
Alignment explanation
Indices: 12965523--12965566 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12965513 TATCCTTTAT
* * *
12965523 TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12965565 TA
1 TA
12965567 GTTTACATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12967716 original size:17 final size:17
Alignment explanation
Indices: 12967694--12967729 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12967684 AGTTCCCTCA
12967694 CAGACCTAAGCATTCAC
1 CAGACCTAAGCATTCAC
*
12967711 CAGACCTATGCATTCAC
1 CAGACCTAAGCATTCAC
12967728 CA
1 CA
12967730 ACCCCAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.36, G:0.11, T:0.19
Consensus pattern (17 bp):
CAGACCTAAGCATTCAC
Found at i:12969304 original size:3 final size:3
Alignment explanation
Indices: 12969296--12969412 Score: 102
Period size: 3 Copynumber: 39.3 Consensus size: 3
12969286 TTTTCAAAAT
12969296 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
12969343 ATGA ATA ATA TATA TTT TTA A-A ATA A-A ATTA A-A AGTT AGA ATA A-A
1 AT-A ATA ATA -ATA ATA ATA ATA ATA ATA A-TA ATA A-TA ATA ATA ATA
12969388 ATA A-A GATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA A
12969413 AAGGGAGAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
2 11 0.12
3 75 0.79
4 9 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12972476 original size:13 final size:11
Alignment explanation
Indices: 12972445--12972496 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
12972435 TTCTGTTTTG
*
12972445 ATTTTATT-TG
1 ATTTTATTATT
12972455 ATTTTATTATT
1 ATTTTATTATT
12972466 ATTTTTAATTATT
1 A-TTTT-ATTATT
12972479 ATTTTATTCATT
1 ATTTTATT-ATT
12972491 ATTTTA
1 ATTTTA
12972497 ATTAAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 8 0.22
11 5 0.14
12 17 0.46
13 7 0.19
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:12972483 original size:12 final size:12
Alignment explanation
Indices: 12972455--12972520 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
12972445 ATTTTATTTG
12972455 ATTTT-ATTATT
1 ATTTTAATTATT
12972466 ATTTTTAATTATT
1 A-TTTTAATTATT
12972479 ATTTT-ATTCATT
1 ATTTTAATT-ATT
**
12972491 ATTTTAATTAAA
1 ATTTTAATTATT
*
12972503 AATTTAATTATTT
1 ATTTTAATTA-TT
12972516 ATTTT
1 ATTTT
12972521 TTAAAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
11 4 0.09
12 26 0.59
13 14 0.32
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTAATTATT
Found at i:12972483 original size:24 final size:24
Alignment explanation
Indices: 12972455--12972500 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
12972445 ATTTTATTTG
12972455 ATTTTATT-ATTATTTTTAATTATT
1 ATTTTATTCATTA-TTTTAATTATT
12972479 ATTTTATTCATTATTTTAATTA
1 ATTTTATTCATTATTTTAATTA
12972501 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTATTCATTATTTTAATTATT
Found at i:12972507 original size:25 final size:24
Alignment explanation
Indices: 12972455--12972533 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
12972445 ATTTTATTTG
**
12972455 ATTTTATTATTATTTTTAATT-ATT
1 ATTTTATTATTA-TTTTAATTAAAA
12972479 ATTTTATTCATTATTTTAATTAAAA
1 ATTTTATT-ATTATTTTAATTAAAA
*
12972504 ATTTAATTATTTATTTT--TTAAAA
1 ATTTTATTA-TTATTTTAATTAAAA
12972527 ATATTTA
1 AT-TTTA
12972534 CGAATTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
23 8 0.17
24 20 0.43
25 19 0.40
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATTATTATTTTAATTAAAA
Found at i:12972653 original size:48 final size:44
Alignment explanation
Indices: 12972586--12972686 Score: 134
Period size: 48 Copynumber: 2.2 Consensus size: 44
12972576 AAAAAAATTC
*
12972586 AAATAAA--TTTACGAATTTTATCAAATTATTAGAAGATTTTTCAT
1 AAATAAATTTTTACGAATTTTATCAAATTATTAG-AGA-ATTTCAT
*
12972630 AAATTTAAATTTTTATGAATTTTATCAAATTATTAGAGAATTTCAT
1 AAA--TAAATTTTTACGAATTTTATCAAATTATTAGAGAATTTCAT
12972676 AAATAAATTTT
1 AAATAAATTTT
12972687 CAAAAGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
44 11 0.22
46 13 0.25
47 3 0.06
48 24 0.47
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (44 bp):
AAATAAATTTTTACGAATTTTATCAAATTATTAGAGAATTTCAT
Found at i:12972794 original size:26 final size:25
Alignment explanation
Indices: 12972765--12972817 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
12972755 CTATTAGAAG
12972765 ATTTAATAAAT-TTTCTTAAAAATAAA
1 ATTTAATAAATATTT-TT-AAAATAAA
* *
12972791 ATTTTATAAATATTTTTACAATAAA
1 ATTTAATAAATATTTTTAAAATAAA
12972816 AT
1 AT
12972818 CTCATCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 12 0.50
27 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAATAAATATTTTTAAAATAAA
Found at i:12973703 original size:19 final size:18
Alignment explanation
Indices: 12973657--12973712 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
12973647 AAAAGAATCT
*
12973657 AATT-ATTAATTTAATTTG
1 AATTAATTAATTTAA-TTA
*
12973675 AATTAGTTAATTTAATTA
1 AATTAATTAATTTAATTA
12973693 AATATAATTAA-TTAATTA
1 AAT-TAATTAATTTAATTA
12973711 AA
1 AA
12973713 AATTAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
AATTAATTAATTTAATTA
Found at i:12973719 original size:19 final size:20
Alignment explanation
Indices: 12973657--12973719 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 20
12973647 AAAAGAATCT
**
12973657 AATT-ATTAATTTAATT-TG
1 AATTAATTAATTTAATTAAA
*
12973675 AATTAGTTAATTTAATTAAA
1 AATTAATTAATTTAATTAAA
*
12973695 TA-TAATTAA-TTAATTAAA
1 AATTAATTAATTTAATTAAA
12973713 AATTAAT
1 AATTAAT
12973720 ATTCTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
18 14 0.39
19 21 0.58
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
AATTAATTAATTTAATTAAA
Found at i:12974038 original size:1 final size:1
Alignment explanation
Indices: 12974034--12974058 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12974024 GGTTTTTTAC
12974034 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12974059 CTTGATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12975289 original size:25 final size:24
Alignment explanation
Indices: 12975229--12975290 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
12975219 TTATTTACAA
*
12975229 AATAATGTCATACAAAAATAGTATC
1 AATAATATCATA-AAAAATAGTATC
12975254 AA-AATATCATAAAAAATA-TCATGC
1 AATAATATCATAAAAAATAGT-AT-C
12975278 AATAATATCATAA
1 AATAATATCATAA
12975291 TTAAAACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 9 0.27
24 11 0.33
25 12 0.36
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (24 bp):
AATAATATCATAAAAAATAGTATC
Found at i:12975468 original size:22 final size:23
Alignment explanation
Indices: 12975443--12975488 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12975433 ACAAATATAT
* *
12975443 AATAT-ATAATTATTCATGCAAA
1 AATATCATAATAAATCATGCAAA
12975465 AATATCATAATAAATCATGCAAA
1 AATATCATAATAAATCATGCAAA
12975488 A
1 A
12975489 TCATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (23 bp):
AATATCATAATAAATCATGCAAA
Found at i:12975878 original size:19 final size:19
Alignment explanation
Indices: 12975854--12975893 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12975844 CTAAATAAAC
12975854 AAACAAAATAA-AAAAATAA
1 AAAC-AAATAATAAAAATAA
*
12975873 AAACAAATAATAATAATAA
1 AAACAAATAATAAAAATAA
12975892 AA
1 AA
12975894 GCTAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (19 bp):
AAACAAATAATAAAAATAA
Found at i:12975919 original size:20 final size:19
Alignment explanation
Indices: 12975877--12975930 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
12975867 AAATAAAAAC
12975877 AAATAATAATAATAAAAGCTA
1 AAATAA-AATAA-AAAAGCTA
12975898 AAATAGAAACTAAAAAAG-TA
1 AAATA-AAA-TAAAAAAGCTA
12975918 AAATAAAATAAAA
1 AAATAAAATAAAA
12975931 TAATAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.16
19 3 0.10
20 7 0.23
21 12 0.39
22 4 0.13
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (19 bp):
AAATAAAATAAAAAAGCTA
Found at i:12976741 original size:32 final size:31
Alignment explanation
Indices: 12976635--12976741 Score: 94
Period size: 32 Copynumber: 3.4 Consensus size: 31
12976625 AATGAATACT
** *
12976635 TACAATACA-ATGAATGAATACGATGAATGAAA
1 TACAATACATAT-AA-GAATATAATGAATGTAA
* *
12976667 CACAATACATATAATGAATATAATGTACT-TAA
1 TACAATACATATAA-GAATATAATG-AATGTAA
12976699 TACAATACATATAA-AATATAATGAATGTAA
1 TACAATACATATAAGAATATAATGAATGTAA
12976729 TACATATAACATA
1 TACA-AT-ACATA
12976742 ATACATATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
29 2 0.03
30 16 0.25
31 2 0.03
32 39 0.62
33 4 0.06
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
TACAATACATATAAGAATATAATGAATGTAA
Found at i:12977516 original size:19 final size:20
Alignment explanation
Indices: 12977485--12977522 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12977475 ATTTATTAAT
12977485 TTATTATATTATAATAAAAA
1 TTATTATATTATAATAAAAA
*
12977505 TTATTA-ATTATATTAAAA
1 TTATTATATTATAATAAAA
12977523 GAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTATATTATAATAAAAA
Found at i:12980230 original size:3 final size:3
Alignment explanation
Indices: 12980222--12980259 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12980212 CTATTAAAGT
12980222 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12980260 TCATTCCTTC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12981366 original size:19 final size:19
Alignment explanation
Indices: 12981329--12981376 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
12981319 GAGAAGTTTC
* *
12981329 ATAAATAAGTTTTTTAAAAA
1 ATAAATAA-ATTTTGAAAAA
12981349 ATAAATAAATTTTGAAAAA
1 ATAAATAAATTTTGAAAAA
12981368 ATAAA-AAAT
1 ATAAATAAAT
12981377 AATTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
ATAAATAAATTTTGAAAAA
Found at i:12982332 original size:59 final size:59
Alignment explanation
Indices: 12982233--12982350 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 59
12982223 TTGTAGATTG
* * * *
12982233 TTTGGAATATTAATAATCAAGTGCCTCACATAATCGCAATTTCAGGTCCTATGACATAT
1 TTTGAAATATTAACAATCAAATGCCTCACATAATCGCAATTTCAAGTCCTATGACATAT
* * *
12982292 TTTGAAATATTGACAATCAAATGCCTCACATAGCA-C-CAATTTCAAGTCTTATGATATAT
1 TTTGAAATATTAACAATCAAATGCCTCACATA--ATCGCAATTTCAAGTCCTATGACATAT
12982351 ATTTCTTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 48 0.96
60 1 0.02
61 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (59 bp):
TTTGAAATATTAACAATCAAATGCCTCACATAATCGCAATTTCAAGTCCTATGACATAT
Found at i:12991054 original size:19 final size:21
Alignment explanation
Indices: 12991013--12991062 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
12991003 TAATAAATAT
12991013 ATAAATTT-TATTTTAATTCA
1 ATAAATTTATATTTTAATTCA
*
12991033 ATAAATTTATA-TTTGATT-A
1 ATAAATTTATATTTTAATTCA
12991052 ATAAATATTAT
1 ATAAAT-TTAT
12991063 TTCAGTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 7 0.26
20 18 0.67
21 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATAAATTTATATTTTAATTCA
Found at i:12991979 original size:17 final size:16
Alignment explanation
Indices: 12991949--12991982 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12991939 TCTATTTTTA
*
12991949 ATTTTTTTAAAAATTT
1 ATTTTTTAAAAAATTT
12991965 ATTTTTTAAATAAATTT
1 ATTTTTTAAA-AAATTT
12991982 A
1 A
12991983 AAAAATTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTTAAAAAATTT
Found at i:12993256 original size:13 final size:13
Alignment explanation
Indices: 12993235--12993264 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12993225 GATTTAGATC
*
12993235 AAATTTATATATT
1 AAATATATATATT
12993248 AAATATATATATT
1 AAATATATATATT
12993261 AAAT
1 AAAT
12993265 TTAGATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATATATATATT
Found at i:12993346 original size:19 final size:19
Alignment explanation
Indices: 12993322--12993363 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
12993312 AATCTAATTA
12993322 TATATATATTTTTAATTTT
1 TATATATATTTTTAATTTT
12993341 TATATATATTTTTAATTTT
1 TATATATATTTTTAATTTT
12993360 TATA
1 TATA
12993364 AAATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATATATTTTTAATTTT
Found at i:12993392 original size:13 final size:13
Alignment explanation
Indices: 12993376--12993439 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
12993366 ATAAAATAAT
12993376 AATTTTATATTAA
1 AATTTTATATTAA
12993389 AATTTTAT-TT-A
1 AATTTTATATTAA
12993400 AA---TATATTAA
1 AATTTTATATTAA
*
12993410 AATTTTATGTTAA
1 AATTTTATATTAA
** *
12993423 AATAATATATAAA
1 AATTTTATATTAA
12993436 AATT
1 AATT
12993440 AAAAATTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 3 0.08
11 3 0.08
12 2 0.05
13 27 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
AATTTTATATTAA
Found at i:12993396 original size:34 final size:34
Alignment explanation
Indices: 12993357--12993425 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
12993347 TATTTTTAAT
12993357 TTTTA-TAAAATAAAATAATAATTTTATATTAAAA
1 TTTTATTAAAATAAAATAA-AATTTTATATTAAAA
* * * *
12993391 TTTTATTTAAATATATTAAAATTTTATGTTAAAA
1 TTTTATTAAAATAAAATAAAATTTTATATTAAAA
12993425 T
1 T
12993426 AATATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 20 0.67
35 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
TTTTATTAAAATAAAATAAAATTTTATATTAAAA
Found at i:12993407 original size:21 final size:22
Alignment explanation
Indices: 12993381--12993423 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
12993371 ATAATAATTT
12993381 TATATTAAAATTTTAT-TTAAA
1 TATATTAAAATTTTATGTTAAA
12993402 TATATTAAAATTTTATGTTAAA
1 TATATTAAAATTTTATGTTAAA
12993424 ATAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTAAAATTTTATGTTAAA
Found at i:12994881 original size:17 final size:16
Alignment explanation
Indices: 12994838--12994893 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
12994828 CTTTTCCTAC
*
12994838 ATTTTT-TATTAGTTT
1 ATTTTTATATTAATTT
* *
12994853 AGTATTATTATTAAATTT
1 ATTTTTA-TATT-AATTT
*
12994871 ATTTTTATATTATTTT
1 ATTTTTATATTAATTT
12994887 ATTTTTA
1 ATTTTTA
12994894 AAGTTTATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 4 0.12
16 11 0.34
17 8 0.25
18 9 0.28
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
ATTTTTATATTAATTT
Found at i:12995625 original size:16 final size:14
Alignment explanation
Indices: 12995599--12995646 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
12995589 GGCCAAAATT
*
12995599 TTTTTTTTTTTGTG
1 TTTTTTGTTTTGTG
12995613 TTTTTCTAGTTTTGT-
1 TTTTT-T-GTTTTGTG
*
12995628 TTTTTTGTTGTGTG
1 TTTTTTGTTTTGTG
12995642 TTTTT
1 TTTTT
12995647 GTAGGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 6 0.21
16 6 0.21
ACGTcount: A:0.02, C:0.02, G:0.17, T:0.79
Consensus pattern (14 bp):
TTTTTTGTTTTGTG
Found at i:12995659 original size:29 final size:29
Alignment explanation
Indices: 12995598--12995659 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
12995588 TGGCCAAAAT
* * * * *
12995598 TTTTTTTTTTTTGTGTTTTTCTAGTTTTG
1 TTTTTTTGTTGTGTGTTTTTCTAGGTATA
*
12995627 TTTTTTTGTTGTGTGTTTTTGTAGGTATA
1 TTTTTTTGTTGTGTGTTTTTCTAGGTATA
12995656 TTTT
1 TTTT
12995660 GGCACTGGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.06, C:0.02, G:0.18, T:0.74
Consensus pattern (29 bp):
TTTTTTTGTTGTGTGTTTTTCTAGGTATA
Found at i:12996098 original size:27 final size:28
Alignment explanation
Indices: 12996051--12996103 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
12996041 AAGGAAACAA
*
12996051 AAAGAAGAAGAAAAACGTAAA-AAATGG
1 AAAGAAGAAGAAAAAAGTAAATAAATGG
*
12996078 AAAGAA-AGAGAAAAAATTAAATAAAT
1 AAAGAAGA-AGAAAAAAGTAAATAAAT
12996104 AATAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 1 0.05
27 17 0.77
28 4 0.18
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (28 bp):
AAAGAAGAAGAAAAAAGTAAATAAATGG
Found at i:12996109 original size:3 final size:3
Alignment explanation
Indices: 12996101--12996141 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12996091 AAATTAAATA
12996101 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12996142 AAATGGTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12996432 original size:51 final size:50
Alignment explanation
Indices: 12996370--12996554 Score: 255
Period size: 51 Copynumber: 3.6 Consensus size: 50
12996360 TAAAAGTTCT
*
12996370 TCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCATGAAAATGGCTCC
1 TCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCTTGAAAA-GGCTCC
* * *
12996421 TCTCAATAGAGGCTCAACAACTTTAAAAT-TCTTATCTTGAAAAAGCTCC
1 TCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCTTGAAAAGGCTCC
* **
12996470 TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGAAAAGGGCTTA
1 TCTCAACAGAGGCTCAACAACTTT-AAAATCTCATATCTTGAAAA-GGCTCC
*
12996522 TCTCAACAGAGGCTCAACAACATTAAAAATCTC
1 TCTCAACAGAGGCTCAACAAC-TTTAAAATCTC
12996555 CTCTCAGCAG
Statistics
Matches: 118, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
49 27 0.23
50 17 0.14
51 41 0.35
52 31 0.26
53 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (50 bp):
TCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCTTGAAAAGGCTCC
Found at i:12996541 original size:101 final size:100
Alignment explanation
Indices: 12996361--12996549 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 100
12996351 TTTTTTGTGT
* * * *
12996361 AAAAGTTCTTCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCATGAAAATGGCTCCTCTCA
1 AAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCATGAAAAGGGCTCATCTCA
* *
12996426 ATAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
66 ACAGAGGCTCAACAACATTAAAATTCTTATCTTGA
* * *
12996461 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGAAAAGGGCTTATCTC
1 AAAAGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAATCTCATATCATGAAAAGGGCTCATCTC
12996526 AACAGAGGCTCAACAACATTAAAA
65 AACAGAGGCTCAACAACATTAAAA
12996550 ATCTCCTCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 30 0.38
101 49 0.62
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (100 bp):
AAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATCTCATATCATGAAAAGGGCTCATCTCA
ACAGAGGCTCAACAACATTAAAATTCTTATCTTGA
Found at i:12996671 original size:47 final size:47
Alignment explanation
Indices: 12996546--12996659 Score: 149
Period size: 49 Copynumber: 2.4 Consensus size: 47
12996536 CAACAACATT
* *
12996546 AAAAATCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC-T-TCTTG
* *
12996595 AAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATC-TCTTGG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTCTT-G
*
12996642 AAAAGGCTCCTCTCAGCA
1 AAAAAGCTCCTCTCAGCA
12996660 AAAACTCAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 4 0.07
47 16 0.28
49 37 0.65
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (47 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTCTTG
Found at i:12996681 original size:24 final size:24
Alignment explanation
Indices: 12996649--12996695 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12996639 TGGAAAAGGC
12996649 TCCTCTCAGCAAAAACTCAACAAT
1 TCCTCTCAGCAAAAACTCAACAAT
**
12996673 TCCTCTCAGCAAAGGCTCAACAA
1 TCCTCTCAGCAAAAACTCAACAA
12996696 CTTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.19
Consensus pattern (24 bp):
TCCTCTCAGCAAAAACTCAACAAT
Done.