Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 102 of 126
Found at i:20084391 original size:16 final size:16
Alignment explanation
Indices: 20084347--20084408 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
20084337 ATAATTGAAG
20084347 ATAAAAATAAAAAATAAA
1 ATAAAAAT--AAAATAAA
* *
20084365 A-AAAATCTAAAATGAA
1 ATAAAA-ATAAAATAAA
*
20084381 ATGAAAATAAAATAAA
1 ATAAAAATAAAATAAA
*
20084397 ATAAAAACAAAA
1 ATAAAAATAAAA
20084409 ATTAGAATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
16 26 0.74
17 7 0.20
18 2 0.06
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
ATAAAAATAAAATAAA
Found at i:20084403 original size:34 final size:34
Alignment explanation
Indices: 20084350--20084421 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
20084340 ATTGAAGATA
*
20084350 AAAATAAAAAATAAAAAAAATCTAAAATGA-AATG
1 AAAATAAAAAATAAAAAAAA-CAAAAATGAGAATG
* *
20084384 AAAATAAAATAA-AATAAAAACAAAAATTAGAATG
1 AAAATAAAA-AATAAAAAAAACAAAAATGAGAATG
20084418 AAAA
1 AAAA
20084422 AAAGAAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 7 0.21
34 24 0.73
35 2 0.06
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.17
Consensus pattern (34 bp):
AAAATAAAAAATAAAAAAAACAAAAATGAGAATG
Found at i:20085791 original size:17 final size:17
Alignment explanation
Indices: 20085766--20085799 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20085756 TCCTTCATTT
*
20085766 AGAAGGAAAAAAAAAAG
1 AGAAAGAAAAAAAAAAG
*
20085783 AGAAAGAAAAGAAAAAG
1 AGAAAGAAAAAAAAAAG
20085800 CGTAAATCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAAAAG
Found at i:20090402 original size:119 final size:121
Alignment explanation
Indices: 20090179--20090421 Score: 393
Period size: 119 Copynumber: 2.0 Consensus size: 121
20090169 TATTATTAAT
* *
20090179 AATAAGGTAAGTTTAAAAAAATAATATGATTATTTTGGATGTTTTTATCCAATAATTTTTTTCTT
1 AATAAGGTAAATTTAAAAAAATAATATGATAATTTTGGATGTTTTTATCCAATAA-TTTTTTCTT
* *
20090244 TATATAAAATCAAATACAGTGATTTAATATCACCAATAATTTATAATATTACGTCAA
65 TATATAAAATCAAATACAGTGATTTAATATCACCAATAATTCATAATATTACATCAA
*
20090301 AATAAGGTAAATTTAAAAAAAATAATATGGTAATTTTGGAT-TTTTTATCCAATAA-TTTTT-TT
1 AATAAGGTAAATTT-AAAAAAATAATATGATAATTTTGGATGTTTTTATCCAATAATTTTTTCTT
*
20090363 TATATAAAATCAAATTCAGTGATTTAATATCACCAATAATTCATAATATTACATCAA
65 TATATAAAATCAAATACAGTGATTTAATATCACCAATAATTCATAATATTACATCAA
20090420 AA
1 AA
20090422 CCAGTAAGTT
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
119 58 0.51
120 5 0.04
122 27 0.24
123 24 0.21
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (121 bp):
AATAAGGTAAATTTAAAAAAATAATATGATAATTTTGGATGTTTTTATCCAATAATTTTTTCTTT
ATATAAAATCAAATACAGTGATTTAATATCACCAATAATTCATAATATTACATCAA
Found at i:20091519 original size:11 final size:11
Alignment explanation
Indices: 20091484--20091508 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20091474 TTCAACTCAA
20091484 TTTTTTTCCTT
1 TTTTTTTCCTT
20091495 TTTTTTTCCTT
1 TTTTTTTCCTT
20091506 TTT
1 TTT
20091509 CCTTTTATTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCCTT
Found at i:20092364 original size:17 final size:17
Alignment explanation
Indices: 20092342--20092378 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20092332 GACTTCACTC
*
20092342 TTTTTCATTTTTTTTAT
1 TTTTTCATTTTTTCTAT
20092359 TTTTTCATTTTTTCTAT
1 TTTTTCATTTTTTCTAT
20092376 TTT
1 TTT
20092379 CTTGTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTCATTTTTTCTAT
Found at i:20092906 original size:3 final size:3
Alignment explanation
Indices: 20092859--20092893 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20092849 TTTTAAATCT
*
20092859 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20092894 TCAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20099018 original size:14 final size:13
Alignment explanation
Indices: 20099001--20099033 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
20098991 TTTTGCCTAG
20099001 GCTTTTTTTGTTTT
1 GCTTTTTTT-TTTT
20099015 GCTTTTTTTTTTT
1 GCTTTTTTTTTTT
20099028 G-TTTTT
1 GCTTTTT
20099034 AATTATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 5 0.26
14 9 0.47
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (13 bp):
GCTTTTTTTTTTT
Found at i:20099384 original size:12 final size:13
Alignment explanation
Indices: 20099355--20099404 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
20099345 TATAAAAAAA
20099355 TATATTTTATTAT
1 TATATTTTATTAT
20099368 T-TATTTTATT-T
1 TATATTTTATTAT
* *
20099379 TATATTTATATAAA
1 TATATTT-TATTAT
*
20099393 TATATTATATTA
1 TATATTTTATTA
20099405 ATAAAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.07
12 14 0.47
13 8 0.27
14 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTTATTAT
Found at i:20099423 original size:29 final size:29
Alignment explanation
Indices: 20099384--20099455 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
20099374 TATTTTATAT
*
20099384 TTATATAAATATATT-ATATTAATAAAACTA
1 TTATATTAATATATTAAT-TTAATAAAA-TA
* *
20099414 TTAT-TTAATATTTTAATTTATTAAAATA
1 TTATATTAATATATTAATTTAATAAAATA
*
20099442 TTATATTTATATAT
1 TTATATTAATATAT
20099456 AGTTAAGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.17
29 23 0.66
30 6 0.17
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATATTAATATATTAATTTAATAAAATA
Found at i:20100072 original size:20 final size:21
Alignment explanation
Indices: 20100049--20100104 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
20100039 GTTTAAACAC
20100049 AAATAATCAAATTTAAAAT-T
1 AAATAATCAAATTTAAAATCT
* *
20100069 AAATAA-AAAAATT-AAATCT
1 AAATAATCAAATTTAAAATCT
*
20100088 AATTAATCAAATTTAAA
1 AAATAATCAAATTTAAA
20100105 TAGCTCATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 11 0.39
21 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAATCAAATTTAAAATCT
Found at i:20100105 original size:20 final size:19
Alignment explanation
Indices: 20100049--20100105 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
20100039 GTTTAAACAC
20100049 AAATAATCAAATTTAAAATT
1 AAATAATCAAATTT-AAATT
* *
20100069 AAATAA-AAAAATTAAATCT
1 AAATAATCAAATTTAAAT-T
*
20100088 AATTAATCAAATTTAAAT
1 AAATAATCAAATTTAAAT
20100106 AGCTCATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 15 0.50
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATCAAATTTAAATT
Found at i:20105523 original size:3 final size:3
Alignment explanation
Indices: 20105515--20105539 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20105505 AAGCTCTACG
20105515 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
20105540 TTTAAATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20107214 original size:16 final size:16
Alignment explanation
Indices: 20107190--20107224 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20107180 AGAACATGTA
20107190 ATTACTATATAAAAGC
1 ATTACTATATAAAAGC
*
20107206 ATTATTATATAAAAGC
1 ATTACTATATAAAAGC
20107222 ATT
1 ATT
20107225 TTGCAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (16 bp):
ATTACTATATAAAAGC
Found at i:20108249 original size:15 final size:15
Alignment explanation
Indices: 20108229--20108277 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
20108219 GCATTTTTGT
20108229 TGTTGCTTTGTTCAG
1 TGTTGCTTTGTTCAG
20108244 TGTTGCTTTGTTCAGTG
1 TGTTGCTTTGTTCA--G
*
20108261 TGTTGCTTTGTTTAG
1 TGTTGCTTTGTTCAG
20108276 TG
1 TG
20108278 AGAGCTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 17 0.55
17 14 0.45
ACGTcount: A:0.06, C:0.10, G:0.29, T:0.55
Consensus pattern (15 bp):
TGTTGCTTTGTTCAG
Found at i:20108265 original size:17 final size:17
Alignment explanation
Indices: 20108229--20108277 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
20108219 GCATTTTTGT
20108229 TGTTGCTTTGTTCA--G
1 TGTTGCTTTGTTCAGTG
20108244 TGTTGCTTTGTTCAGTG
1 TGTTGCTTTGTTCAGTG
*
20108261 TGTTGCTTTGTTTAGTG
1 TGTTGCTTTGTTCAGTG
20108278 AGAGCTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 14 0.45
17 17 0.55
ACGTcount: A:0.06, C:0.10, G:0.29, T:0.55
Consensus pattern (17 bp):
TGTTGCTTTGTTCAGTG
Found at i:20110765 original size:47 final size:49
Alignment explanation
Indices: 20110696--20110803 Score: 175
Period size: 47 Copynumber: 2.2 Consensus size: 49
20110686 GGAGGTCAAT
*
20110696 ATAAAATAAGATGAATTGATAAAAAGCTAATAAAGAGAATTAATGTTAA
1 ATAAAATAATATGAATTGATAAAAAGCTAATAAAGAGAATTAATGTTAA
* *
20110745 ATAAAATAATA-G-ATTGATAAAGAGCTAATAAAGAGGATTAATGTTAA
1 ATAAAATAATATGAATTGATAAAAAGCTAATAAAGAGAATTAATGTTAA
20110792 ATAAAATAATAT
1 ATAAAATAATAT
20110804 TGTAATTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 44 0.80
48 1 0.02
49 10 0.18
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (49 bp):
ATAAAATAATATGAATTGATAAAAAGCTAATAAAGAGAATTAATGTTAA
Found at i:20116479 original size:21 final size:21
Alignment explanation
Indices: 20116453--20116500 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
20116443 ATAGAGATAT
20116453 AATTAATTATTATAATAATAA
1 AATTAATTATTATAATAATAA
20116474 AATTAATTATTATAATAATAA
1 AATTAATTATTATAATAATAA
20116495 AATTAA
1 AATTAA
20116501 AATAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAATTATTATAATAATAA
Found at i:20116488 original size:18 final size:17
Alignment explanation
Indices: 20116457--20116491 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20116447 AGATATAATT
20116457 AATTATTATAATAATAA
1 AATTATTATAATAATAA
*
20116474 AATTAATTATTATAATAA
1 AATT-ATTATAATAATAA
20116492 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTATTATAATAATAA
Found at i:20117476 original size:23 final size:22
Alignment explanation
Indices: 20117424--20117476 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
20117414 TTAATATACT
20117424 ATTTTAATCTAAAAAAATTTTTG
1 ATTTT-ATCTAAAAAAATTTTTG
*
20117447 CTATTTAT-TAAATAAAATTTTTAG
1 AT-TTTATCTAAA-AAAATTTTT-G
20117471 ATTTTA
1 ATTTTA
20117477 AATGTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTTATCTAAAAAAATTTTTG
Found at i:20117665 original size:14 final size:15
Alignment explanation
Indices: 20117636--20117668 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20117626 CATCTAAAAT
*
20117636 TTTTTAAATTTATAA
1 TTTTTAAATATATAA
20117651 TTTTTAAATAT-TAA
1 TTTTTAAATATATAA
20117665 TTTT
1 TTTT
20117669 AATGAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTAAATATATAA
Found at i:20124686 original size:11 final size:11
Alignment explanation
Indices: 20124670--20124697 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20124660 TCTTTATTTG
20124670 TATTATTTTTA
1 TATTATTTTTA
20124681 TATTATTTTTA
1 TATTATTTTTA
20124692 TATTAT
1 TATTAT
20124698 GTCAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:20127485 original size:25 final size:25
Alignment explanation
Indices: 20127434--20127486 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
20127424 AATAAAAAGC
20127434 AAAATAAATTATAACTAAAATAGTA
1 AAAATAAATTATAACTAAAATAGTA
20127459 AAAATTAAATTATAA-TGAAAATA-TA
1 AAAA-TAAATTATAACT-AAAATAGTA
20127484 AAA
1 AAA
20127487 CTGGGGCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAATAAATTATAACTAAAATAGTA
Found at i:20129234 original size:20 final size:17
Alignment explanation
Indices: 20129209--20129249 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 17
20129199 CGAATTGAAG
20129209 TATATATTTTTATTAATTTT
1 TATATA-TTTTA--AATTTT
20129229 TATATATTTTAAATTTT
1 TATATATTTTAAATTTT
20129246 TATA
1 TATA
20129250 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
19 5 0.24
20 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATATTTTAAATTTT
Found at i:20129390 original size:20 final size:19
Alignment explanation
Indices: 20129365--20129412 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
20129355 TTAAATTGAA
20129365 TCGAATTATTAAAATTTAAT
1 TCGAATTA-TAAAATTTAAT
20129385 TCGAATTGATAAAATTTAAT
1 TCGAATT-ATAAAATTTAAT
*
20129405 TTGAATTA
1 TCGAATTA
20129413 AATCGATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (19 bp):
TCGAATTATAAAATTTAAT
Found at i:20131322 original size:7 final size:7
Alignment explanation
Indices: 20131285--20131335 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
20131275 TAATATCGAC
20131285 AAAATATT
1 AAAAT-TT
20131293 AAAATTT
1 AAAATTT
* *
20131300 TAATTTT
1 AAAATTT
20131307 AATAA-TT
1 AA-AATTT
20131314 AAAATTT
1 AAAATTT
20131321 AAAATTT
1 AAAATTT
20131328 GAAAATTT
1 -AAAATTT
20131336 CAAGTAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 2 0.06
7 21 0.58
8 13 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
AAAATTT
Found at i:20131334 original size:21 final size:21
Alignment explanation
Indices: 20131290--20131334 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20131280 TCGACAAAAT
* *
20131290 ATTAAAATTTTAATTTTAATA
1 ATTAAAATTTAAATTTGAATA
20131311 ATTAAAATTTAAAATTTGAA-A
1 ATTAAAATTT-AAATTTGAATA
20131332 ATT
1 ATT
20131335 TCAAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAAAATTTAAATTTGAATA
Found at i:20132452 original size:30 final size:31
Alignment explanation
Indices: 20132408--20132476 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
20132398 CATTTTTCTT
*
20132408 AAAATCAAATCATTTTGAATTTTGAA-CTTTG
1 AAAATCAAACCATTTT-AATTTTGAATCTTTG
* *
20132439 AAAAT-AAACCATTTTATTTTTGAATTTTTG
1 AAAATCAAACCATTTTAATTTTGAATCTTTG
20132469 AAAA-CAAA
1 AAAATCAAA
20132477 TCTAATTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 8 0.24
30 20 0.61
31 5 0.15
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (31 bp):
AAAATCAAACCATTTTAATTTTGAATCTTTG
Found at i:20133047 original size:63 final size:63
Alignment explanation
Indices: 20132980--20133190 Score: 246
Period size: 63 Copynumber: 3.3 Consensus size: 63
20132970 CAATTCATAG
* * * *
20132980 TTGTAGGATTCTAAATTCACAATTAGAGGTC-TCTGCATTCATATCAGATTCAATGATTCATAA
1 TTGTAGGACTCTAAATTCACAACTAGAGGTCTTC-GAATTCATATCAGATTCAATGATTCACAA
* ** * * * *
20133043 TTGTAGGACTTTGGATTCACAACTAAAGGTCTTCGTATTC-TCATTAAATTCAATGATTCACAA
1 TTGTAGGACTCTAAATTCACAACTAGAGGTCTTCGAATTCAT-ATCAGATTCAATGATTCACAA
* *
20133106 TTGTAGGACTCTAAATTCACAACTAGAGGTCTTCGAATCCACATCAGATTCAATGATTCACAA
1 TTGTAGGACTCTAAATTCACAACTAGAGGTCTTCGAATTCATATCAGATTCAATGATTCACAA
* * *
20133169 TTGGAGGACTATAGATTCACAA
1 TTGTAGGACTCTAAATTCACAA
20133191 TAAGAGTAAA
Statistics
Matches: 123, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
62 1 0.01
63 120 0.98
64 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (63 bp):
TTGTAGGACTCTAAATTCACAACTAGAGGTCTTCGAATTCATATCAGATTCAATGATTCACAA
Found at i:20133427 original size:42 final size:42
Alignment explanation
Indices: 20133364--20133489 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 42
20133354 CTTGATTGGC
* * * *
20133364 ACTAGA-TTAATGATTCTTAGTTATAGGACTCTAGATTCATA
1 ACTAGAGTTAACGATTCATAGTTGTAGGACTCTAGATTCACA
20133405 ACTAGAG-TAGACGATTCATAGTTGTAGGACTCTAGATTCACA
1 ACTAGAGTTA-ACGATTCATAGTTGTAGGACTCTAGATTCACA
* * *
20133447 ACTAGAGTTAATGATTCATAATTGTAGGACTTTAGATTCACA
1 ACTAGAGTTAACGATTCATAGTTGTAGGACTCTAGATTCACA
20133489 A
1 A
20133490 AAAAGGTTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
41 8 0.11
42 65 0.87
43 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (42 bp):
ACTAGAGTTAACGATTCATAGTTGTAGGACTCTAGATTCACA
Found at i:20133692 original size:17 final size:17
Alignment explanation
Indices: 20133621--20133700 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
20133611 CAAAAGTTCT
20133621 AAGATTCACAAGAGTTCA
1 AAGATTCACAAGAG-TCA
* *
20133639 AAGATTCATAAGAGTTA
1 AAGATTCACAAGAGTCA
* ***
20133656 TAGATTCACAATTTTCA
1 AAGATTCACAAGAGTCA
*
20133673 AAGATTCACAAGAGTAA
1 AAGATTCACAAGAGTCA
20133690 AAGATTCACAA
1 AAGATTCACAA
20133701 ATTCCAAATA
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
17 36 0.73
18 13 0.27
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (17 bp):
AAGATTCACAAGAGTCA
Found at i:20133750 original size:34 final size:33
Alignment explanation
Indices: 20133593--20133756 Score: 114
Period size: 34 Copynumber: 4.8 Consensus size: 33
20133583 TTTCAAGGTT
* * * *
20133593 ACAAAATTCCAAGAATTGCAAAAGTTCTAAGATTC
1 ACAAATTTCAAAG-ATTGCAAGAGTT-AAAGATTC
* *
20133628 ACAAGAGTTCAAAGATT-CATAAGAGTTATAGATTC
1 ACAA-ATTTCAAAGATTGC--AAGAGTTAAAGATTC
* * *
20133663 ACAATTTTCAAAGATTCACAAGAGTAAAAGATTC
1 ACAAATTTCAAAGATT-GCAAGAGTTAAAGATTC
* * *
20133697 ACAAATTCCAAATATTTGCAAGAGTTAAAGATTT
1 ACAAATTTCAAAGA-TTGCAAGAGTTAAAGATTC
** *
20133731 ATTAATTTCAAAGACTTGCAAAAGTT
1 ACAAATTTCAAAGA-TTGCAAGAGTT
20133757 CAAAAACTCA
Statistics
Matches: 102, Mismatches: 21, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
34 69 0.68
35 19 0.19
36 14 0.14
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (33 bp):
ACAAATTTCAAAGATTGCAAGAGTTAAAGATTC
Found at i:20133921 original size:36 final size:36
Alignment explanation
Indices: 20133881--20133959 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
20133871 ATATGTTTAT
* * *
20133881 AGATTTGTAAGAATTCAAAAATTTATACGAGTTCAC
1 AGATTTGTAAGAATTCAAAAATTTACAAGAGTTCAA
* ** *
20133917 AGATTCGTAAGTGTTCAAAAATTTGCAAGAGTTCAA
1 AGATTTGTAAGAATTCAAAAATTTACAAGAGTTCAA
20133953 AGATTTG
1 AGATTTG
20133960 CAAGTTTCAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (36 bp):
AGATTTGTAAGAATTCAAAAATTTACAAGAGTTCAA
Found at i:20133973 original size:17 final size:18
Alignment explanation
Indices: 20133853--20133981 Score: 82
Period size: 18 Copynumber: 7.2 Consensus size: 18
20133843 AGAGATTCGA
20133853 AAGAGTTCAAAGATTTGC
1 AAGAGTTCAAAGATTTGC
* * * *
20133871 ATA-TGTTTATAGATTTGT
1 A-AGAGTTCAAAGATTTGC
* * **
20133889 AAGAATTCAAAAATTTAT
1 AAGAGTTCAAAGATTTGC
* * * *
20133907 ACGAGTTCACAGATTCGT
1 AAGAGTTCAAAGATTTGC
* *
20133925 AAGTGTTCAAAAATTTGC
1 AAGAGTTCAAAGATTTGC
20133943 AAGAGTTCAAAGATTTGC
1 AAGAGTTCAAAGATTTGC
* * *
20133961 AAG-TTTCAGAGATTTGT
1 AAGAGTTCAAAGATTTGC
20133978 AAGA
1 AAGA
20133982 ATTTAAAAAT
Statistics
Matches: 81, Mismatches: 27, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
17 15 0.19
18 65 0.80
19 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (18 bp):
AAGAGTTCAAAGATTTGC
Found at i:20136103 original size:20 final size:20
Alignment explanation
Indices: 20136050--20136102 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
20136040 CTAAATTGAA
*
20136050 TCGAATTATTAAAATTTAAT
1 TCGAATTAATAAAATTTAAT
*
20136070 TCGAATTGATAAAATTTAAT
1 TCGAATTAATAAAATTTAAT
20136090 TCGAATTAA-AAAA
1 TCGAATTAATAAAA
20136103 AAATTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (20 bp):
TCGAATTAATAAAATTTAAT
Found at i:20136123 original size:23 final size:22
Alignment explanation
Indices: 20136080--20136123 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20136070 TCGAATTGAT
*
20136080 AAAATTTAATTCGAATTAAAAA
1 AAAATTTAATTCAAATTAAAAA
*
20136102 AAAATTTATATTTAAATTAAAA
1 AAAATTTA-ATTCAAATTAAAA
20136124 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATTTAATTCAAATTAAAAA
Found at i:20137988 original size:7 final size:7
Alignment explanation
Indices: 20137951--20138001 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
20137941 TAATATCGAC
20137951 AAAATATT
1 AAAAT-TT
20137959 AAAATTT
1 AAAATTT
* *
20137966 TAATTTT
1 AAAATTT
20137973 AATAA-TT
1 AA-AATTT
20137980 AAAATTT
1 AAAATTT
20137987 AAAATTT
1 AAAATTT
20137994 GAAAATTT
1 -AAAATTT
20138002 CAAGTAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 2 0.06
7 21 0.58
8 13 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
AAAATTT
Found at i:20138000 original size:21 final size:21
Alignment explanation
Indices: 20137956--20138000 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20137946 TCGACAAAAT
* *
20137956 ATTAAAATTTTAATTTTAATA
1 ATTAAAATTTAAATTTGAATA
20137977 ATTAAAATTTAAAATTTGAA-A
1 ATTAAAATTT-AAATTTGAATA
20137998 ATT
1 ATT
20138001 TCAAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAAAATTTAAATTTGAATA
Found at i:20139118 original size:30 final size:31
Alignment explanation
Indices: 20139074--20139142 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
20139064 CATTTTTCTT
*
20139074 AAAATCAAATCATTTTGAATTTTGAA-CTTTG
1 AAAATCAAACCATTTT-AATTTTGAATCTTTG
* *
20139105 AAAAT-AAACCATTTTATTTTTGAATTTTTG
1 AAAATCAAACCATTTTAATTTTGAATCTTTG
20139135 AAAA-CAAA
1 AAAATCAAA
20139143 TCTAATTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 8 0.24
30 20 0.61
31 5 0.15
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (31 bp):
AAAATCAAACCATTTTAATTTTGAATCTTTG
Found at i:20139711 original size:63 final size:63
Alignment explanation
Indices: 20139644--20139853 Score: 260
Period size: 63 Copynumber: 3.3 Consensus size: 63
20139634 CAATTCATAG
* * * *
20139644 TTGTAGGATTCTAAATTCACAACTAGAGGTCTCTGCATTCATATCAGATTCAATGATTCATAA
1 TTGTAGGACTCTAAATTCACAACTAGAGGTCTCTGAATTCACATCAGATTCAATGATTCACAA
* ** * * *
20139707 TTGTAGGACTTTGGATTCACAACTAAAGGTCTCTGTATTCACATTAGATTCAATGATTCACAA
1 TTGTAGGACTCTAAATTCACAACTAGAGGTCTCTGAATTCACATCAGATTCAATGATTCACAA
* * * *
20139770 TTGTAGGACTCTAAATTCATAACTAGAAGTCTTTGAATCCACATCAGATTCAATGA-TCACAA
1 TTGTAGGACTCTAAATTCACAACTAGAGGTCTCTGAATTCACATCAGATTCAATGATTCACAA
* * *
20139832 TTGGAGGACTATAGATTCACAA
1 TTGTAGGACTCTAAATTCACAA
20139854 TAAGAGTAAA
Statistics
Matches: 124, Mismatches: 23, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
62 24 0.19
63 100 0.81
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (63 bp):
TTGTAGGACTCTAAATTCACAACTAGAGGTCTCTGAATTCACATCAGATTCAATGATTCACAA
Found at i:20140089 original size:22 final size:22
Alignment explanation
Indices: 20140061--20140132 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
20140051 TAGATTTAAT
20140061 GATTCATAGTTATAGGACTCTA
1 GATTCATAGTTATAGGACTCTA
* * * **
20140083 GATTCATAATTAGAGTA-GAT-
1 GATTCATAGTTATAGGACTCTA
*
20140103 GATTCATAGTTGTAGGACTCTA
1 GATTCATAGTTATAGGACTCTA
20140125 GATTCATA
1 GATTCATA
20140133 ACTAGAGTTA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 13 0.35
21 2 0.05
22 22 0.59
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (22 bp):
GATTCATAGTTATAGGACTCTA
Found at i:20140119 original size:42 final size:42
Alignment explanation
Indices: 20140049--20140174 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 42
20140039 CTTAATTGGC
* *
20140049 ACTAGATTTAATGATTCATAGTTATAGGACTCTAGATTCATA
1 ACTAGAGTTAATGATTCATAGTTGTAGGACTCTAGATTCATA
*
20140091 ATTAGAG-TAGATGATTCATAGTTGTAGGACTCTAGATTCATA
1 ACTAGAGTTA-ATGATTCATAGTTGTAGGACTCTAGATTCATA
* * *
20140133 ACTAGAGTTAATGATTCACAATTGTAGGACTTTAGATTCATA
1 ACTAGAGTTAATGATTCATAGTTGTAGGACTCTAGATTCATA
20140175 GCAAAGGTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 71 0.95
43 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (42 bp):
ACTAGAGTTAATGATTCATAGTTGTAGGACTCTAGATTCATA
Found at i:20140571 original size:18 final size:18
Alignment explanation
Indices: 20140550--20140616 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
20140540 ATGTTTATAG
*
20140550 ATTTGTAAGAATTCAAAA
1 ATTTGTAAGAGTTCAAAA
* * * *
20140568 ATTTATATGAGTTCACAG
1 ATTTGTAAGAGTTCAAAA
* *
20140586 ATTCGTAAGTGTTCAAAA
1 ATTTGTAAGAGTTCAAAA
*
20140604 ATTTGCAAGAGTT
1 ATTTGTAAGAGTT
20140617 TAAAGATTTA
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (18 bp):
ATTTGTAAGAGTTCAAAA
Found at i:20140624 original size:36 final size:36
Alignment explanation
Indices: 20140512--20140624 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 36
20140502 AAGCATTCAG
* * *
20140512 AGATTCAG-AAGAATTCAAAGATTTGCATA-TGTTTAT
1 AGATTC-GTAAGAATTCAAAAATTTGCA-AGAGTTTAA
* ** * * *
20140548 AGATTTGTAAGAATTCAAAAATTTATATGAGTTCAC
1 AGATTCGTAAGAATTCAAAAATTTGCAAGAGTTTAA
**
20140584 AGATTCGTAAGTGTTCAAAAATTTGCAAGAGTTTAA
1 AGATTCGTAAGAATTCAAAAATTTGCAAGAGTTTAA
20140620 AGATT
1 AGATT
20140625 TACAAGTTTC
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
35 1 0.02
36 58 0.98
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (36 bp):
AGATTCGTAAGAATTCAAAAATTTGCAAGAGTTTAA
Found at i:20142012 original size:110 final size:110
Alignment explanation
Indices: 20141818--20142038 Score: 336
Period size: 110 Copynumber: 2.0 Consensus size: 110
20141808 CTTTTTTTAT
* * * * * *
20141818 CCTCCAAATGTGGTATTTTGATAGATGTCAAAACTAGCTGTAAAAAGGCTTAAAATTTTGGAAGA
1 CCTCCAAATGTGGCATTTCGATAGATGCCAAAACCAACTATAAAAAGGCTTAAAATTTTGGAAGA
* *
20141883 TTATTTAGGAATGAGAGAAATAGACTTAAATTTTCAAAATCAATG
66 TTATTTAGAAATGAGAGAAATAGACTCAAATTTTCAAAATCAATG
* *
20141928 CCTCCAAATGTGGCATTTCGATAGATGCCAAAACCAATTATAAAAAGGCTTAAGATTTTGGAAGA
1 CCTCCAAATGTGGCATTTCGATAGATGCCAAAACCAACTATAAAAAGGCTTAAAATTTTGGAAGA
20141993 TTATTTAGAAATG-GAAGAAATAGACTCAAATTTTCAAAATCAATG
66 TTATTTAGAAATGAG-AGAAATAGACTCAAATTTTCAAAATCAATG
20142038 C
1 C
20142039 TTTTAATGAA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 99 0.99
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (110 bp):
CCTCCAAATGTGGCATTTCGATAGATGCCAAAACCAACTATAAAAAGGCTTAAAATTTTGGAAGA
TTATTTAGAAATGAGAGAAATAGACTCAAATTTTCAAAATCAATG
Found at i:20143222 original size:28 final size:28
Alignment explanation
Indices: 20143181--20143234 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
20143171 CACACACAGC
* * *
20143181 AGCCTATATGTGAGGCCTATTACATGCA
1 AGCCCATATATGAGGCCCATTACATGCA
20143209 AGCCCATATATGAGGCCCATTACATG
1 AGCCCATATATGAGGCCCATTACATG
20143235 TAAAAACCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (28 bp):
AGCCCATATATGAGGCCCATTACATGCA
Found at i:20143853 original size:6 final size:7
Alignment explanation
Indices: 20143836--20143861 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20143826 ATGTCTTCAA
20143836 AAAAAAT
1 AAAAAAT
20143843 AAAAAAT
1 AAAAAAT
20143850 AAAAAAT
1 AAAAAAT
20143857 AAAAA
1 AAAAA
20143862 GAGAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:20144554 original size:24 final size:24
Alignment explanation
Indices: 20144527--20144572 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20144517 CAATGACATT
20144527 TTTTGTATTTTTT-TCATTTTTTCC
1 TTTTG-ATTTTTTATCATTTTTTCC
*
20144551 TTTTGATTTTTTATTATTTTTT
1 TTTTGATTTTTTATCATTTTTT
20144573 GTGTTGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTGATTTTTTATCATTTTTTCC
Found at i:20146974 original size:239 final size:243
Alignment explanation
Indices: 20146516--20147002 Score: 617
Period size: 244 Copynumber: 2.0 Consensus size: 243
20146506 TATCTTGGTA
* * ** *
20146516 CAAAAGAATTTTTATTTTTTTGTTATGCAATAATAAATTCTTAAATTTTATTCAATACATTATCT
1 CAAAAAAATTTTTATTTTTTTATTAAACAATAAAAAATTCTTAAATTTTATTCAATACATTATCT
* * * * ** *
20146581 TTTTTAGTTTGTTTAAAAATTTTATATATTTTTGAATTAACGAATTTATAAAAAAAATTATATTC
66 TTCTGAGTCTGTTCAAAAAAGTTATATACTTTTGAATTAACGAATTTAT-AAAAAAATTATATTC
*
20146646 TCATAATCTCTTGACAAATTTAAATCCAAACAACAACAAAAATTTTAATTCACCTTTAAGCTGTG
130 TCATAATCTCTTGACAAATTTAAATCCAAACAACAACAAAAATTTTAATTCACCTTTAAGCTATG
*
20146711 GTCTGCCGATGTAGGTGCATGGGATCCCATTCTTGCTAATAATCCGAAG
195 GTCTGCCGACGTAGGTGCATGGGATCCCATTCTTGCTAATAATCCGAAG
* * * * * *
20146760 CAAAAAAATTTTTATTTTTTTATTAAACAATAAAAAATTCTTGAGTTTTGTTTAATAGATTCTCT
1 CAAAAAAATTTTTATTTTTTTATTAAACAATAAAAAATTCTTAAATTTTATTCAATACATTATCT
* * * ** *
20146825 TTCTGAGTCTGTTCAAAAAAGTTGTCTACTTTT-AATTTAACGGATTTAT-AAAAGTTTATATTT
66 TTCTGAGTCTGTTCAAAAAAGTTATATACTTTTGAA-TTAACGAATTTATAAAAAAATTATATTC
* * * * *
20146888 TCATAATCT-TTGAACAAATTTGAATCCCAATAA-AA-AAAAA-TTTATTTCACCTTTGAGCTAT
130 TCATAATCTCTTG-ACAAATTTAAATCCAAACAACAACAAAAATTTTAATTCACCTTTAAGCTAT
*
20146949 TGTCTGCCGACGTAGGTGCATGGGATCCCATTCTTGCTAATAATCCGAAG
194 GGTCTGCCGACGTAGGTGCATGGGATCCCATTCTTGCTAATAATCCGAAG
20146999 CAAA
1 CAAA
20147003 TTTTCGGAAG
Statistics
Matches: 209, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
239 70 0.33
240 5 0.02
241 5 0.02
242 37 0.18
243 2 0.01
244 90 0.43
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (243 bp):
CAAAAAAATTTTTATTTTTTTATTAAACAATAAAAAATTCTTAAATTTTATTCAATACATTATCT
TTCTGAGTCTGTTCAAAAAAGTTATATACTTTTGAATTAACGAATTTATAAAAAAATTATATTCT
CATAATCTCTTGACAAATTTAAATCCAAACAACAACAAAAATTTTAATTCACCTTTAAGCTATGG
TCTGCCGACGTAGGTGCATGGGATCCCATTCTTGCTAATAATCCGAAG
Found at i:20147759 original size:22 final size:22
Alignment explanation
Indices: 20147728--20147772 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
20147718 GGTATCGTAA
20147728 GCCAAGAAAAGAAAGAG-G-AAAG
1 GCCAA-AAAA-AAAGAGAGAAAAG
20147750 GCCAAAAAAAAAGAGAGAAAAG
1 GCCAAAAAAAAAGAGAGAAAAG
20147772 G
1 G
20147773 GAGAATGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.62, C:0.09, G:0.29, T:0.00
Consensus pattern (22 bp):
GCCAAAAAAAAAGAGAGAAAAG
Found at i:20147762 original size:20 final size:23
Alignment explanation
Indices: 20147728--20147769 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
20147718 GGTATCGTAA
20147728 GCCAAGAAAAGAAAGAG-GAAAG
1 GCCAAGAAAAGAAAGAGAGAAAG
20147750 GCCAA-AAAA-AAAGAGAGAAA
1 GCCAAGAAAAGAAAGAGAGAAA
20147770 AGGGAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.64, C:0.10, G:0.26, T:0.00
Consensus pattern (23 bp):
GCCAAGAAAAGAAAGAGAGAAAG
Found at i:20153300 original size:1 final size:1
Alignment explanation
Indices: 20153294--20153341 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
20153284 TTAAGATTTC
* * * * *
20153294 AAAAAAAAAAATAAAAAAAAATAAAAAAAAGAAAAAAGAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20153342 GTTTTCTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.04
Consensus pattern (1 bp):
A
Found at i:20153311 original size:9 final size:9
Alignment explanation
Indices: 20153294--20153342 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
20153284 TTAAGATTTC
20153294 AAAAA-AAA
1 AAAAAGAAA
*
20153302 AAATA-AAA
1 AAAAAGAAA
*
20153310 AAAAATAAA
1 AAAAAGAAA
20153319 AAAAAGAAA
1 AAAAAGAAA
*
20153328 AAAGAGAAA
1 AAAAAGAAA
20153337 AAAAAG
1 AAAAAG
20153343 TTTTCTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
8 11 0.31
9 24 0.69
ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:20154268 original size:19 final size:20
Alignment explanation
Indices: 20154226--20154271 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20154216 AGTGAGCAAG
20154226 GATTCAATTGGAATCTCAAA
1 GATTCAATTGGAATCTCAAA
20154246 GATTCAATTGGAATCTC-AA
1 GATTCAATTGGAATCTCAAA
20154265 GATTCAA
1 GATTCAA
20154272 GAAAGTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
GATTCAATTGGAATCTCAAA
Found at i:20156223 original size:109 final size:108
Alignment explanation
Indices: 20156078--20156399 Score: 362
Period size: 109 Copynumber: 3.0 Consensus size: 108
20156068 TAAGACTTTC
** * * *
20156078 GAGCATAAATTTGATTCGCGGTATTATCCCGATCGATTCATTATTTTTTAACCTACGGTGTTGTC
1 GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
* * *
20156143 CAGTCGATTCTGTATGACCTCCGAACATGATTTTTAAGACCTTCA
66 C-GTCGATTCTGTAAGACCTCCGAGCATGATTCTTAAGACC-TCA
* * * * * * * *
20156188 G-GCATAAGTTCGATTTGTGGTGTTATCTCGATCGATTCATTA-TTTTCGACTTGCGGTGTTATC
1 GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGT-
* *
20156251 CCGTCGATTCTGTAAGACCTCC-AGGTATGATTCTTAAGACCTCC
65 CCGTCGATTCTGTAAGACCTCCGA-GCATGATTCTTAAGACCTCA
* * *
20156295 GAGCATAAATTCAATTCGCGGTGTTATCCCGATTGATTCATTATTTTTTGACTTATGTTGTTGTC
1 GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
* * *
20156360 TCGTCGATTTTGTAAGATCTCTGAGCATGATTCTTAAGAC
66 -CGTCGATTCTGTAAGACCTCCGAGCATGATTCTTAAGAC
20156400 TTCTGGGCAT
Statistics
Matches: 175, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
107 4 0.02
108 84 0.48
109 85 0.49
110 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (108 bp):
GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
CGTCGATTCTGTAAGACCTCCGAGCATGATTCTTAAGACCTCA
Found at i:20156288 original size:108 final size:109
Alignment explanation
Indices: 20156078--20156399 Score: 371
Period size: 108 Copynumber: 3.0 Consensus size: 109
20156068 TAAGACTTTC
** * * *
20156078 GAGCATAAATTTGATTCGCGGTATTATCCCGATCGATTCATTATTTTTTAACCTACGGTGTTGTC
1 GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
* * * *
20156143 CAGTCGATTCTGTATGACCTCCGAACATGATTTTTAAGACCTTCA
66 CCGTCGATTCTGTAAGACCTCCGAGCATGATTCTTAAGACC-TCA
* * * * * * * *
20156188 G-GCATAAGTTCGATTTGTGGTGTTATCTCGATCGATTCATTA-TTTTCGACTTGCGGTGTTATC
1 GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
* *
20156251 CCGTCGATTCTGTAAGACCTCC-AGGTATGATTCTTAAGACCTCC
66 CCGTCGATTCTGTAAGACCTCCGA-GCATGATTCTTAAGACCTCA
* * *
20156295 GAGCATAAATTCAATTCGCGGTGTTATCCCGATTGATTCATTATTTTTTGACTTATGTTGTTGTC
1 GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
* * * *
20156360 TCGTCGATTTTGTAAGATCTCTGAGCATGATTCTTAAGAC
66 CCGTCGATTCTGTAAGACCTCCGAGCATGATTCTTAAGAC
20156400 TTCTGGGCAT
Statistics
Matches: 175, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
107 4 0.02
108 85 0.49
109 84 0.48
110 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (109 bp):
GAGCATAAATTCAATTCGCGGTGTTATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTC
CCGTCGATTCTGTAAGACCTCCGAGCATGATTCTTAAGACCTCA
Found at i:20156397 original size:22 final size:22
Alignment explanation
Indices: 20156372--20156424 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
20156362 GTCGATTTTG
20156372 TAAGATCTCTGAGCATGA-TTC
1 TAAGATCTCTGAGCATGATTTC
*
20156393 TTAAGA-CTTCTGGGCATGATTTC
1 -TAAGATC-TCTGAGCATGATTTC
20156416 TAAGATCTC
1 TAAGATCTC
20156425 CGGACATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 1 0.04
22 22 0.81
23 4 0.15
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (22 bp):
TAAGATCTCTGAGCATGATTTC
Found at i:20156540 original size:131 final size:131
Alignment explanation
Indices: 20156256--20156540 Score: 317
Period size: 131 Copynumber: 2.2 Consensus size: 131
20156246 TTATCCCGTC
* *
20156256 GATTCTGTAAGACCTCCAGGTATGATTCTTAAGACCTCCGAGCATAAATTCAATTCGCGGTGTTA
1 GATTCT-TAAGACCTCCAGGCATGATTCTTAAGACCTCCGAGCATAAATTCAATTCGCAGTGTTA
* * * * * * *
20156321 TCCCGATTGATTCATTATTTTTTGACTTATGTTGTTGTCTCGTCGATTTTGTAAGATCTCTGAGC
65 TCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTCTCGTCGATTCTATAAGACCTCCGAGC
20156386 AT
130 AT
* ** * * *
20156388 GATTCTTAAGACTTCTGGGCATGATT-TCTAAGATCTCCG-GACATAAATTCGATTTGCAGTGTT
1 GATTCTTAAGACCTCCAGGCATGATTCT-TAAGACCTCCGAG-CATAAATTCAATTCGCAGTGTT
* * * *
20156451 ATTCTGATCGATTTATTATTTTTTGACTTACGGTGTTGTC-CAGTCGATTCTATAAGACCTCCGG
64 ATCCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTCTC-GTCGATTCTATAAGACCTCCGA
*
20156515 GTAT
128 GCAT
20156519 GATT-TCTAAGACCTCCAGGCAT
1 GATTCT-TAAGACCTCCAGGCAT
20156541 AAATTCAATT
Statistics
Matches: 126, Mismatches: 23, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
130 4 0.03
131 116 0.92
132 6 0.05
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (131 bp):
GATTCTTAAGACCTCCAGGCATGATTCTTAAGACCTCCGAGCATAAATTCAATTCGCAGTGTTAT
CCCGATCGATTCATTATTTTTTGACTTACGGTGTTGTCTCGTCGATTCTATAAGACCTCCGAGCA
T
Found at i:20156559 original size:109 final size:110
Alignment explanation
Indices: 20156388--20156854 Score: 501
Period size: 110 Copynumber: 4.3 Consensus size: 110
20156378 CTCTGAGCAT
* * * *
20156388 GATTCT-TAAGACTTCTGGGCATGATTTCTAAGATCTCCGGACATAAATTCGATTTGCAGTGTTA
1 GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTTA
* * * * * *
20156452 TTCTGATCGATTTATTATTTTTTGACTTACGGTGTTGT-CCAGTC
66 TCCTAATCGATTTCTTATTTTTTGACTTACGATGTTATCCCAATC
* * **
20156496 GATTCTATAAGACCTCCGGGTATGATTTCTAAGACCTCCAGG-CATAAATTCAATTCGTGGTGTT
1 GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCC-GGACATAAATTCGATTCGCAGTGTT
* *
20156560 ATCCTAATCGATTCCTTATTTTTT-ACTTGCGATGTTATCCCAATC
65 ATCCTAATCGATTTCTTATTTTTTGACTTACGATGTTATCCCAATC
* ** * * * * * * *
20156605 GATTCTGTAAGACCTTTGGGCATGATTTTCTAAAACTTTCGGGCATAATTTTGATTCGCGGTGTT
1 GATTCTATAAGACCTCCGGGCATGA-TTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTT
* * * *
20156670 ATCCTGATCGATTTTTTATTTTTTGACTTGCGATGTTATCCCAGTC
65 ATCCTAATCGATTTCTTATTTTTTGACTTACGATGTTATCCCAATC
* * * * * *
20156716 GATTCTGTAAGATCTCCTGGCATGATTTCTAAGACCTCTGGACATAATTTCGATTCGCAATGTTA
1 GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTTA
* * * *
20156781 TCCTAATTGATTTCTTATTTTTTGACTTATGGTGTTATTCCAATC
66 TCCTAATCGATTTCTTATTTTTTGACTTACGATGTTATCCCAATC
* * *
20156826 GATTCTATAAGACCTTCGGACATAATTTC
1 GATTCTATAAGACCTCCGGGCATGATTTC
20156855 GATTCACGGT
Statistics
Matches: 296, Mismatches: 57, Indels: 10
0.82 0.16 0.03
Matches are distributed among these distances:
108 17 0.06
109 94 0.32
110 144 0.49
111 41 0.14
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (110 bp):
GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTTA
TCCTAATCGATTTCTTATTTTTTGACTTACGATGTTATCCCAATC
Found at i:20156616 original size:240 final size:239
Alignment explanation
Indices: 20156168--20156631 Score: 587
Period size: 240 Copynumber: 1.9 Consensus size: 239
20156158 GACCTCCGAA
* * **
20156168 CATGATTTTTAAGACCTTCAGGCATAAGTTCGATTTGTGGTGTTATCTCGATCGATTCATTATTT
1 CATGATTTCTAAGACCTTCAGGCATAAATTCGATTTGCAGTGTTATCTCGATCGATTCATTATTT
* * *
20156233 TCGACTTGCGGTGTTATCCCGTCGATTCTGTAAGACCTCCAGGTATGATTCTTAAGACCTCCGAG
66 TCGACTTACGGTGTTATCCAGTCGATTCTATAAGACCTCCAGGTATGATTCTTAAGACCTCCGAG
* * * * * * *
20156298 CATAAATTCAATTCGCGGTGTTATCCCGATTGATTCATTATTTTTTGACTTATGTTGTTGTCTCG
131 CATAAATTCAATTCGCGGTGTTATCCCAATCGATTCATTATTTTTTGACTTACGATGTTATCCCA
* *
20156363 TCGATTTTGTAAGATCTCTGAGCATGATTCTTAAGACTTCTGGG
196 TCGATTCTGTAAGACCTCTGAGCATGATTCTTAAGACTTCTGGG
* * *
20156407 CATGATTTCTAAGATC-TCCGGACATAAATTCGATTTGCAGTGTTAT-TCTGATCGATTTATTAT
1 CATGATTTCTAAGACCTTCAGG-CATAAATTCGATTTGCAGTGTTATCTC-GATCGATTCATTA-
* * *
20156470 TTTTTGACTTACGGTGTTGTCCAGTCGATTCTATAAGACCTCCGGGTATGATT-TCTAAGACCTC
63 TTTTCGACTTACGGTGTTATCCAGTCGATTCTATAAGACCTCCAGGTATGATTCT-TAAGACCTC
* * * *
20156534 C-AGGCATAAATTCAATTCGTGGTGTTATCCTAATCGATTCCTTATTTTTT-ACTTGCGATGTTA
127 CGA-GCATAAATTCAATTCGCGGTGTTATCCCAATCGATTCATTATTTTTTGACTTACGATGTTA
* *
20156597 TCCCAATCGATTCTGTAAGACCTTTGGGCATGATT
191 TCCC-ATCGATTCTGTAAGACCTCTGAGCATGATT
20156632 TTCTAAAACT
Statistics
Matches: 191, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
238 6 0.03
239 61 0.32
240 124 0.65
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (239 bp):
CATGATTTCTAAGACCTTCAGGCATAAATTCGATTTGCAGTGTTATCTCGATCGATTCATTATTT
TCGACTTACGGTGTTATCCAGTCGATTCTATAAGACCTCCAGGTATGATTCTTAAGACCTCCGAG
CATAAATTCAATTCGCGGTGTTATCCCAATCGATTCATTATTTTTTGACTTACGATGTTATCCCA
TCGATTCTGTAAGACCTCTGAGCATGATTCTTAAGACTTCTGGG
Found at i:20156748 original size:22 final size:22
Alignment explanation
Indices: 20156723--20156766 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20156713 GTCGATTCTG
* *
20156723 TAAGATCTCCTGG-CATGATTTC
1 TAAGACCT-CTGGACATAATTTC
20156745 TAAGACCTCTGGACATAATTTC
1 TAAGACCTCTGGACATAATTTC
20156767 GATTCGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (22 bp):
TAAGACCTCTGGACATAATTTC
Found at i:20156800 original size:220 final size:219
Alignment explanation
Indices: 20156388--20156842 Score: 569
Period size: 220 Copynumber: 2.1 Consensus size: 219
20156378 CTCTGAGCAT
* *
20156388 GATTCTTAAGA-CTTCTGGGCATGATTTCTAAGATCTCCGGACATAAATTCGATTTGCAGTGTTA
1 GATTCTTAAGACCTTCTGGGCATGATTTCTAAAATCTCCGGACATAAATTCGATTCGCAGTGTTA
* * * *
20156452 TTCTGATCGATTTATTATTTTTTGACTTACGGTGTTGTCCAGTCGATTCTATAAGACCTCCGGGT
66 TCCTGATCGATTTATTATTTTTTGACTTACGATGTTATCCAGTCGATTCTATAAGACCTCCGGGC
***
20156517 ATGATTTCTAAGACCTCCAGGCATAAATTCAATTCGTGGTGTTATCCTAATCGATTCCTTATTTT
131 ATGATTTCTAAGACCTCCAGGCATAAATTCAATTCGCAATGTTATCCTAATCGATTCCTTATTTT
*
20156582 TT-ACTTGCGATGTTATCCCAATC
196 TTGACTTACGATGTTATCCCAATC
* * * * *
20156605 GATTCTGTAAGACCTT-TGGGCATGATTTTCTAAAA-CTTTCGGGCATAATTTTGATTCGCGGTG
1 GATTCT-TAAGACCTTCTGGGCATGA-TTTCTAAAATC-TCCGGACATAAATTCGATTCGCAGTG
* * * *
20156668 TTATCCTGATCGATTTTTTATTTTTTGACTTGCGATGTTATCCCAGTCGATTCTGTAAGATCTCC
63 TTATCCTGATCGATTTATTATTTTTTGACTTACGATGTTAT-CCAGTCGATTCTATAAGACCTCC
* * * * * *
20156733 TGGCATGATTTCTAAGACCT-CTGGACATAATTTCGATTCGCAATGTTATCCTAATTGATTTCTT
127 GGGCATGATTTCTAAGACCTCCAGG-CATAAATTCAATTCGCAATGTTATCCTAATCGATTCCTT
* * *
20156797 ATTTTTTGACTTATGGTGTTATTCCAATC
191 ATTTTTTGACTTACGATGTTATCCCAATC
20156826 GATTCTATAAGACCTTC
1 GATTCT-TAAGACCTTC
20156843 GGACATAATT
Statistics
Matches: 201, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
217 6 0.03
218 15 0.07
219 70 0.35
220 78 0.39
221 32 0.16
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (219 bp):
GATTCTTAAGACCTTCTGGGCATGATTTCTAAAATCTCCGGACATAAATTCGATTCGCAGTGTTA
TCCTGATCGATTTATTATTTTTTGACTTACGATGTTATCCAGTCGATTCTATAAGACCTCCGGGC
ATGATTTCTAAGACCTCCAGGCATAAATTCAATTCGCAATGTTATCCTAATCGATTCCTTATTTT
TTGACTTACGATGTTATCCCAATC
Found at i:20156856 original size:88 final size:88
Alignment explanation
Indices: 20156745--20156941 Score: 270
Period size: 88 Copynumber: 2.2 Consensus size: 88
20156735 GCATGATTTC
* * *
20156745 TAAGACCTCTGGACATAATTTCGATTCGCAATGTTATCCTAATTGATTTCTTATTTTTTGACTTA
1 TAAGACCTCTGGACATAATTTCGATTCACAATGTTATCCCAATCGATTTCTTATTTTTTGACTTA
*
20156810 TGGTGTTATTCCAATCGATTCTA
66 TGGTGTTATACCAATCGATTCTA
** *
20156833 TAAGACCT-TCGGACATAATTTCGATTCACGGTGTTATCCCGATCGATTTCTTATTTTTTGACTT
1 TAAGACCTCT-GGACATAATTTCGATTCACAATGTTATCCCAATCGATTTCTTATTTTTTGACTT
* * * *
20156897 GTGGTGTTATACCAGTTGATTCTG
65 ATGGTGTTATACCAATCGATTCTA
*
20156921 TAAGACCTCTAGACATAATTT
1 TAAGACCTCTGGACATAATTT
20156942 TTAAGACCTC
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
87 1 0.01
88 93 0.98
89 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (88 bp):
TAAGACCTCTGGACATAATTTCGATTCACAATGTTATCCCAATCGATTTCTTATTTTTTGACTTA
TGGTGTTATACCAATCGATTCTA
Found at i:20156949 original size:22 final size:22
Alignment explanation
Indices: 20156921--20156986 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
20156911 GTTGATTCTG
*
20156921 TAAGACCTCTAGACATAATTTT
1 TAAGACCTCCAGACATAATTTT
*
20156943 TAAGACCTCCA-AGCATAATCTT
1 TAAGACCTCCAGA-CATAATTTT
*
20156965 TAAGACTTCCAGACATAATTTT
1 TAAGACCTCCAGACATAATTTT
20156987 GATTCGTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (22 bp):
TAAGACCTCCAGACATAATTTT
Found at i:20157208 original size:3 final size:3
Alignment explanation
Indices: 20157200--20157251 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
20157190 TGGGTCTTTT
20157200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ACTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
20157248 ATA A
1 ATA A
20157252 ATATTTTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:20157312 original size:11 final size:11
Alignment explanation
Indices: 20157283--20157319 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
20157273 ATTAATTATT
*
20157283 AAAAAAAAGAG
1 AAAAAAAATAG
20157294 AGAAAAAAATAG
1 A-AAAAAAATAG
20157306 AAAAAAAATAG
1 AAAAAAAATAG
20157317 AAA
1 AAA
20157320 GTAGGGTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAAAAAATAG
Found at i:20157592 original size:22 final size:22
Alignment explanation
Indices: 20157566--20157614 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
20157556 TTCCCTTCAA
* *
20157566 CAACCCCAAACAGAACCCACAT
1 CAACCCCAAACAAAACCCACAC
20157588 CAACCCCAAACAAAACCCACAC
1 CAACCCCAAACAAAACCCACAC
20157610 CAACC
1 CAACC
20157615 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.49, G:0.02, T:0.02
Consensus pattern (22 bp):
CAACCCCAAACAAAACCCACAC
Found at i:20157624 original size:22 final size:22
Alignment explanation
Indices: 20157579--20157624 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20157569 CCCCAAACAG
* * *
20157579 AACCCACATCAACCCCAAACAA
1 AACCCACACCAACCACAAAAAA
*
20157601 AACCCACACCAACCATAAAAAA
1 AACCCACACCAACCACAAAAAA
20157623 AA
1 AA
20157625 AAACAAATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.39, G:0.00, T:0.04
Consensus pattern (22 bp):
AACCCACACCAACCACAAAAAA
Found at i:20158313 original size:17 final size:16
Alignment explanation
Indices: 20158291--20158342 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
20158281 AATTTTTTTT
20158291 TTATTTTTTATATATTA
1 TTATTTTTTATAT-TTA
20158308 TTATTTTTGT-TATTTTGA
1 TTATTTTT-TATA-TTT-A
*
20158326 GTATTTTTTATATTTA
1 TTATTTTTTATATTTA
20158342 T
1 T
20158343 GCATGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.03
17 16 0.55
18 12 0.41
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATTTTTTATATTTA
Found at i:20158726 original size:14 final size:14
Alignment explanation
Indices: 20158709--20158780 Score: 63
Period size: 15 Copynumber: 5.0 Consensus size: 14
20158699 CACTAATTCT
20158709 TAAATCCAAACCCC
1 TAAATCCAAACCCC
* *
20158723 TAAAATCCAAAACCT
1 T-AAATCCAAACCCC
* **
20158738 TAAAATCCTAACCTT
1 T-AAATCCAAACCCC
20158753 TAAATCCAAACCCC
1 TAAATCCAAACCCC
* *
20158767 AAAATCAAAACCCC
1 TAAATCCAAACCCC
20158781 AAACCTCAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
14 23 0.49
15 24 0.51
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAATCCAAACCCC
Found at i:20158730 original size:15 final size:15
Alignment explanation
Indices: 20158710--20158780 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 15
20158700 ACTAATTCTT
20158710 AAATCCAAACCCCTA
1 AAATCCAAACCCCTA
* *
20158725 AAATCCAAAACCTTA
1 AAATCCAAACCCCTA
* * *
20158740 AAATCCTAA-CCTTT
1 AAATCCAAACCCCTA
20158754 AAATCCAAACCCC-A
1 AAATCCAAACCCCTA
*
20158768 AAATCAAAACCCC
1 AAATCCAAACCCC
20158781 AAACCTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 24 0.51
15 23 0.49
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:20158813 original size:14 final size:14
Alignment explanation
Indices: 20158796--20158901 Score: 63
Period size: 14 Copynumber: 7.3 Consensus size: 14
20158786 TCAAATTTTA
20158796 AAAATCAAAACCCT
1 AAAATCAAAACCCT
* * *
20158810 AAAAACGAAACTCT
1 AAAATCAAAACCCT
20158824 AAAATTTTC-AAACCCT
1 AAAA---TCAAAACCCT
* *
20158840 AAAAT-TAAACCTT
1 AAAATCAAAACCCT
** *
20158853 AAAACTTTTAAACCTT
1 AAAA--TCAAAACCCT
*
20158869 CAAATCCAAAACCCT
1 AAAAT-CAAAACCCT
20158884 AAAATCAAAACCCT
1 AAAATCAAAACCCT
20158898 AAAA
1 AAAA
20158902 ACGAAACTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.15
14 29 0.40
15 11 0.15
16 21 0.29
17 1 0.01
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.22
Consensus pattern (14 bp):
AAAATCAAAACCCT
Found at i:20158908 original size:14 final size:14
Alignment explanation
Indices: 20158875--20158914 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20158865 CCTTCAAATC
*
20158875 CAAAACCCTAAAAT
1 CAAAACCCTAAAAA
20158889 CAAAACCCTAAAAA
1 CAAAACCCTAAAAA
* *
20158903 CGAAACTCTAAA
1 CAAAACCCTAAA
20158915 TTTCTCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.28, G:0.03, T:0.12
Consensus pattern (14 bp):
CAAAACCCTAAAAA
Found at i:20158925 original size:44 final size:45
Alignment explanation
Indices: 20158796--20158932 Score: 137
Period size: 44 Copynumber: 3.1 Consensus size: 45
20158786 TCAAATTTTA
20158796 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTT-TCAAACCCT
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTCTCAAACCCT
* * * *
20158840 AAAAT-TAAA-CCTTAAAACTTTTAAAC-CTTCAAA--TC-CAAAACCCT
1 AAAATCAAAACCCTAAAAAC---GAAACTC-TAAAATTTCTC-AAACCCT
20158884 AAAATCAAAACCCTAAAAACGAAACTCT-AAATTTCTCAAACCCT
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTCTCAAACCCT
20158928 AAAAT
1 AAAAT
20158933 TAAACATTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
42 11 0.15
43 10 0.14
44 33 0.45
45 12 0.16
46 8 0.11
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.23
Consensus pattern (45 bp):
AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTCTCAAACCCT
Found at i:20158989 original size:88 final size:87
Alignment explanation
Indices: 20158796--20158972 Score: 252
Period size: 88 Copynumber: 2.0 Consensus size: 87
20158786 TCAAATTTTA
* **
20158796 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTTCAAACCCTAAAATTAAACCTTAAAACTTT
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTTCAAACCCTAAAATTAAACATTAAAACTCC
*
20158861 TAAACCTTCAAATCCAAAACCCT
66 TAAACCTTAAAAT-CAAAACCCT
*
20158884 AAAATCAAAACCCTAAAAACGAAACTCT-AAATTTCTCAAACCCTAAAATTAAACATTAAACCTC
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTT-TCAAACCCTAAAATTAAACATTAAAACTC
*
20158948 CT-AACCTTAAAAAT-GAAACCCT
65 CTAAACCTT-AAAATCAAAACCCT
20158970 AAA
1 AAA
20158973 CCTTTCAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
86 10 0.12
87 12 0.15
88 59 0.73
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (87 bp):
AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTTCAAACCCTAAAATTAAACATTAAAACTCC
TAAACCTTAAAATCAAAACCCT
Found at i:20159074 original size:29 final size:29
Alignment explanation
Indices: 20158803--20159160 Score: 116
Period size: 29 Copynumber: 12.3 Consensus size: 29
20158793 TTAAAAATCA
* * * *
20158803 AAACCCTAAAAACGAAACTCTAAAATTTTC
1 AAACCCTAAAATCAAAACTC-CAAACTTTC
* * ** *
20158833 AAACCCTAAAATTAAACCTTAAAACTTTT
1 AAACCCTAAAATCAAAACTCCAAACTTTC
* * *
20158862 AAACCTTCAAATCCAAAAC-CCTAAA--ATC
1 AAACCCTAAAAT-CAAAACTCC-AAACTTTC
* * * *
20158890 AAAACCCTAAAAACGAAACTCTAAATTTCTC
1 -AAACCCTAAAATCAAAACTCCAAACTT-TC
* * * *
20158921 AAACCCTAAAAT-TAAACAT-TAAACCTCC
1 AAACCCTAAAATCAAAAC-TCCAAACTTTC
* * *
20158949 TAACCTTAAAAAT-GAAAC-CCTAAACCTTTC
1 AAACCCT-AAAATCAAAACTCC-AAA-CTTTC
* * * *
20158979 AAACCCTAAAATTAAAACCTTC-ACCTTCC
1 AAACCCTAAAATCAAAA-CTCCAAACTTTC
* * *
20159008 AAACCCTACAATCAAAACACCAAAC-CTC
1 AAACCCTAAAATCAAAACTCCAAACTTTC
* *
20159036 TAAGCTCTAAAATCAAAACTCCAAACTTTC
1 -AAACCCTAAAATCAAAACTCCAAACTTTC
* * * *
20159066 AAACCCTAAAAT-TAAAC-CATAAATCCTCC
1 AAACCCTAAAATCAAAACTC-CAAA-CTTTC
* * *
20159095 AAATCCTAAAACCAAAACTTCAAA-TCTT-
1 AAACCCTAAAATCAAAACTCCAAACT-TTC
*
20159123 AAACCCTAAAATCAAAAC-CCTAAA-TCTC
1 AAACCCTAAAATCAAAACTCC-AAACTTTC
20159151 AAACCCTAAA
1 AAACCCTAAA
20159161 TAAAAAACCT
Statistics
Matches: 236, Mismatches: 67, Indels: 52
0.66 0.19 0.15
Matches are distributed among these distances:
27 3 0.01
28 55 0.23
29 119 0.50
30 55 0.23
31 3 0.01
32 1 0.00
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (29 bp):
AAACCCTAAAATCAAAACTCCAAACTTTC
Found at i:20159096 original size:87 final size:86
Alignment explanation
Indices: 20158963--20159175 Score: 229
Period size: 87 Copynumber: 2.5 Consensus size: 86
20158953 CTTAAAAATG
** * *
20158963 AAACCCTAAACCTTTCAAACCCTAAAATTAAAACCTTCACCTTCCAAACCCTACAATCAAAACAC
1 AAACCCTAAA-CTTTCAAACCCTAAAATTAAAACCTAAACCTTCCAAACCCTAAAACCAAAACAC
* *
20159028 CAAACCTCTAAGCTCTAAAATCA
65 CAAACCT-TAAACCCTAAAATCA
*
20159051 AAACTCC-AAACTTTCAAACCCTAAAATT-AAACCATAAATCC-TCCAAATCCTAAAACCAAAAC
1 AAAC-CCTAAACTTTCAAACCCTAAAATTAAAACC-TAAA-CCTTCCAAACCCTAAAACCAAAAC
** *
20159113 TTCAAATCTTAAACCCTAAAATCA
63 ACCAAACCTTAAACCCTAAAATCA
* *
20159137 AAACCCTAAA-TCTCAAACCCT-AAATAAAAAACCTAAACC
1 AAACCCTAAACTTTCAAACCCTAAAAT-TAAAACCTAAACC
20159176 CAAAAATCTG
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
84 6 0.06
85 16 0.15
86 30 0.28
87 44 0.41
88 9 0.08
89 2 0.02
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (86 bp):
AAACCCTAAACTTTCAAACCCTAAAATTAAAACCTAAACCTTCCAAACCCTAAAACCAAAACACC
AAACCTTAAACCCTAAAATCA
Found at i:20159104 original size:58 final size:56
Alignment explanation
Indices: 20159042--20159160 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 56
20159032 CCTCTAAGCT
* * *
20159042 CTAAAATCAAAACTCCAAA-CTTTCAAACCCTAAAAT-TAAACCATAAATCCTCCAAATC
1 CTAAAACCAAAACTCCAAATC-TT-AAACCCTAAAATCAAAACCATAAAT-CT-CAAACC
* *
20159100 CTAAAACCAAAACTTCAAATCTTAAACCCTAAAATCAAAACCCTAAATCTCAAACC
1 CTAAAACCAAAACTCCAAATCTTAAACCCTAAAATCAAAACCATAAATCTCAAACC
20159156 CTAAA
1 CTAAA
20159161 TAAAAAACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
56 10 0.19
57 14 0.26
58 29 0.54
59 1 0.02
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (56 bp):
CTAAAACCAAAACTCCAAATCTTAAACCCTAAAATCAAAACCATAAATCTCAAACC
Found at i:20159140 original size:14 final size:13
Alignment explanation
Indices: 20159123--20159173 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
20159113 TTCAAATCTT
20159123 AAACCCTAAAATCA
1 AAACCCT-AAATCA
*
20159137 AAACCCTAAATCTC
1 AAACCCTAAATC-A
*
20159151 AAACCCTAAATAA
1 AAACCCTAAATCA
*
20159164 AAAACCTAAA
1 AAACCCTAAA
20159174 CCCAAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 14 0.44
14 18 0.56
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (13 bp):
AAACCCTAAATCA
Found at i:20159231 original size:22 final size:21
Alignment explanation
Indices: 20159197--20159239 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
20159187 AACTTGAAAC
*
20159197 CCTAATCCTAAAATCCAAAAT
1 CCTAAACCTAAAATCCAAAAT
20159218 CCTAAACCTTAAAATCCAAAAT
1 CCTAAACC-TAAAATCCAAAAT
20159240 TTTGAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTAAACCTAAAATCCAAAAT
Found at i:20163607 original size:18 final size:18
Alignment explanation
Indices: 20163584--20163619 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20163574 AACAATTCAA
*
20163584 TAGTTTATCACTAACAAT
1 TAGTTTATCACAAACAAT
*
20163602 TAGTTTATTACAAACAAT
1 TAGTTTATCACAAACAAT
20163620 ACAATCGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (18 bp):
TAGTTTATCACAAACAAT
Found at i:20163770 original size:15 final size:17
Alignment explanation
Indices: 20163740--20163772 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
20163730 TGAAAAATTA
20163740 AATATAATATTAAATAC
1 AATATAATATTAAATAC
20163757 AATA-AATATT-AATAC
1 AATATAATATTAAATAC
20163772 A
1 A
20163773 GTTATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATAATATTAAATAC
Found at i:20166064 original size:2 final size:2
Alignment explanation
Indices: 20166059--20166091 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20166049 ACTAAAAAAA
20166059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20166092 GAGTACCATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20167577 original size:29 final size:29
Alignment explanation
Indices: 20167552--20167633 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
20167542 ACTTTAATTG
20167552 TAAACTAGTAAATATCAACCAATTAAAAA
1 TAAACTAGTAAATATCAACCAATTAAAAA
20167581 TAAACTAGTAAATATCAACCAATTAAAAA
1 TAAACTAGTAAATATCAACCAATTAAAAA
*
20167610 TAAACTAGTAAATATACAAACAAT
1 TAAACTAGTAAATAT-CAACCAAT
20167634 CCTATGTAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 44 0.86
30 7 0.14
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (29 bp):
TAAACTAGTAAATATCAACCAATTAAAAA
Found at i:20171363 original size:49 final size:49
Alignment explanation
Indices: 20171305--20171412 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 49
20171295 CTATTACGAT
*
20171305 TTTTTTAAAATGGTCACTAAAGTATTAAAATTT-AATATAATAACTAATA
1 TTTTTTAAAATAGTCACTAAA-TATTAAAATTTCAATATAATAACTAATA
* * *
20171354 TTTTTTAAAATAGTCACTAAATATTAAAATTTCAATGTAGTAACTAATG
1 TTTTTTAAAATAGTCACTAAATATTAAAATTTCAATATAATAACTAATA
*
20171403 TTTTTAAAAA
1 TTTTTTAAAA
20171413 GTGCTTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
48 11 0.21
49 42 0.79
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (49 bp):
TTTTTTAAAATAGTCACTAAATATTAAAATTTCAATATAATAACTAATA
Found at i:20177489 original size:2 final size:2
Alignment explanation
Indices: 20177482--20177521 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20177472 ATATCAATAA
20177482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20177522 CATTCGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20181118 original size:22 final size:22
Alignment explanation
Indices: 20181079--20181130 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20181069 GATAGAAATT
20181079 TATGTACATAATATTTTACGA-A
1 TATGTACATAATATTTTA-GAGA
*
20181101 TATGTACATAGTGA-TTTAGAGA
1 TATGTACATAAT-ATTTTAGAGA
20181123 TATGTACA
1 TATGTACA
20181131 GTTGATGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (22 bp):
TATGTACATAATATTTTAGAGA
Found at i:20184060 original size:17 final size:17
Alignment explanation
Indices: 20184038--20184072 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20184028 TAAGGGTTAA
* *
20184038 GTTTAGGGTTTGAGTAG
1 GTTTAGGGCTTGACTAG
20184055 GTTTAGGGCTTGACTAG
1 GTTTAGGGCTTGACTAG
20184072 G
1 G
20184073 GTTTGGAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.40, T:0.37
Consensus pattern (17 bp):
GTTTAGGGCTTGACTAG
Found at i:20184092 original size:6 final size:6
Alignment explanation
Indices: 20184081--20184115 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
20184071 GGGTTTGGAG
*
20184081 TTAGGT TTAGGT TTAGGGT TTAGGA TTAGGT TTAG
1 TTAGGT TTAGGT TTA-GGT TTAGGT TTAGGT TTAG
20184116 TAAGGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (6 bp):
TTAGGT
Found at i:20184100 original size:13 final size:12
Alignment explanation
Indices: 20184072--20184115 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
20184062 GCTTGACTAG
20184072 GGTTT-GGAGTTA
1 GGTTTAGGA-TTA
*
20184084 GGTTTAGGTTTA
1 GGTTTAGGATTA
20184096 GGGTTTAGGATTA
1 -GGTTTAGGATTA
20184109 GGTTTAG
1 GGTTTAG
20184116 TAAGGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 15 0.54
13 13 0.46
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (12 bp):
GGTTTAGGATTA
Found at i:20186196 original size:14 final size:14
Alignment explanation
Indices: 20186147--20186632 Score: 110
Period size: 14 Copynumber: 33.5 Consensus size: 14
20186137 TAAACTAAAC
20186147 CCCTAAAATCCAAA
1 CCCTAAAATCCAAA
*
20186161 CTCTTAAAATCCAAAA
1 C-CCTAAAATCC-AAA
*
20186177 CCCTAAAATCCAAT
1 CCCTAAAATCCAAA
20186191 CCCTAAAATCCAGAA
1 CCCTAAAATCCA-AA
* * *
20186206 CCTTTAACATCTAAA
1 CC-CTAAAATCCAAA
*
20186221 CCCTTAAAT-CAAA
1 CCCTAAAATCCAAA
* * *
20186234 ACCTCAAACTTCAAA
1 CCCT-AAAATCCAAA
*** *
20186249 TTTTAAAAATCAAAA
1 CCCT-AAAATCCAAA
* *
20186264 CCCTAAAAACGAAA
1 CCCTAAAATCCAAA
* *
20186278 CTCTAAATTTTCCAAA
1 CCCTAAA--ATCCAAA
** *
20186294 CAATAAAAT-TAAA
1 CCCTAAAATCCAAA
*
20186307 CCTTAAAACTTCCAAA
1 CCCTAAAA--TCCAAA
*
20186323 CCCTTAAATCCAAAA
1 CCCTAAAATCC-AAA
*
20186338 CCTTAAAATCCAAA
1 CCCTAAAATCCAAA
* *
20186352 CGCTAAAAAT-GAAA
1 CCCT-AAAATCCAAA
* *
20186366 CTCTAAATTTCTCAAA
1 CCCTAAA-ATC-CAAA
*
20186382 CCCTAAAAT-TAAA
1 CCCTAAAATCCAAA
* * *
20186395 CCTTAAACCTCCTAA
1 CCCTAAA-ATCCAAA
* *
20186410 CCTTAAAAAT-GAAA
1 CCCT-AAAATCCAAA
*
20186424 CCCTAAACCTTCCAAA
1 CCCTAAA--ATCCAAA
**
20186440 CCCTAAAATTAAAA
1 CCCTAAAATCCAAA
* ***
20186454 CCTTCACCTTCCAAA
1 CCCT-AAAATCCAAA
* *
20186469 CCCTACAATCAAAA
1 CCCTAAAATCCAAA
* * *
20186483 CCCCAAACCTCCAAG
1 CCCTAAA-ATCCAAA
* **
20186498 CTCTAAAATTGAAA
1 CCCTAAAATCCAAA
* *
20186512 CTCC-AAACCTTCAAA
1 C-CCTAAA-ATCCAAA
*
20186527 CCCTAAAAT-TAAA
1 CCCTAAAATCCAAA
* *
20186540 TCGT-AAATCCTCTAAA
1 CCCTAAAAT-C-C-AAA
20186556 CCCTAAAA-CCAAA
1 CCCTAAAATCCAAA
* * *
20186569 ACTTCAAATCTCAAA
1 CCCTAAAATC-CAAA
* *
20186584 CCTTAAAATCAAAA
1 CCCTAAAATCCAAA
*
20186598 CCC-CAAATCCCAAA
1 CCCTAAAAT-CCAAA
*
20186612 CCCTAAAATCAAAA
1 CCCTAAAATCCAAA
*
20186626 ACCTAAA
1 CCCTAAA
20186633 CCATAAAATC
Statistics
Matches: 330, Mismatches: 106, Indels: 72
0.65 0.21 0.14
Matches are distributed among these distances:
12 4 0.01
13 47 0.14
14 111 0.34
15 109 0.33
16 56 0.17
17 3 0.01
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (14 bp):
CCCTAAAATCCAAA
Found at i:20186331 original size:29 final size:28
Alignment explanation
Indices: 20186287--20186563 Score: 157
Period size: 29 Copynumber: 9.5 Consensus size: 28
20186277 ACTCTAAATT
**
20186287 TTCCAAACAATAAAATTAAACCTTAAAAC
1 TTCCAAACCCTAAAATTAAACCTT-AAAC
* *
20186316 TTCCAAACCCTTAAATCCAAAACCTTAAA-
1 TTCCAAACCCTAAAAT--TAAACCTTAAAC
* * * *
20186345 ATCCAAACGCTAAAAATGAAA-CTCTAAAT
1 TTCCAAACCCT-AAAATTAAACCT-TAAAC
20186374 TTCTCAAACCCTAAAATTAAACCTTAAAC
1 TTC-CAAACCCTAAAATTAAACCTTAAAC
* * * * *
20186403 CTCCTAACCTTAAAAATGAAACCCTAAACC
1 TTCCAAACCCT-AAAATTAAACCTTAAA-C
* *
20186433 TTCCAAACCCTAAAATTAAAACCTTCACC
1 TTCCAAACCCTAAAATT-AAACCTTAAAC
* * **
20186462 TTCCAAACCCTACAATCAAAACCCCAAAC
1 TTCCAAACCCTAAAAT-TAAACCTTAAAC
* * * *
20186491 CTCCAAGCTCTAAAATTGAAA-CTCCAAACC
1 TTCCAAACCCTAAAATT-AAACCT-TAAA-C
* *
20186521 TT-CAAACCCTAAAATTAAATCGTAAATC
1 TTCCAAACCCTAAAATTAAACCTTAAA-C
* *
20186549 CTCTAAACCCTAAAA
1 TTCCAAACCCTAAAA
20186564 CCAAAACTTC
Statistics
Matches: 188, Mismatches: 44, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
27 2 0.01
28 22 0.12
29 123 0.65
30 34 0.18
31 7 0.04
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (28 bp):
TTCCAAACCCTAAAATTAAACCTTAAAC
Found at i:20186438 original size:88 final size:88
Alignment explanation
Indices: 20186254--20186447 Score: 223
Period size: 88 Copynumber: 2.2 Consensus size: 88
20186244 TCAAATTTTA
* *
20186254 AAAATCAAAACCCTAAAAACGAAACTCTAAATTTTCCAAACAATAAAATTAAACCTTAAAACTTC
1 AAAATCCAAACCCTAAAAACGAAACTCTAAATTTTCCAAACAATAAAATTAAACCTTAAAACCTC
** *
20186319 CAAACCCTTAAATCCAAAACCTT
66 CAAACCCTTAAAAACAAAACCCT
* * **
20186342 AAAATCCAAACGCTAAAAATGAAACTCTAAA-TTTCTCAAACCCTAAAATTAAACCTT-AAACCT
1 AAAATCCAAACCCTAAAAACGAAACTCTAAATTTTC-CAAACAATAAAATTAAACCTTAAAACCT
* **
20186405 CCTAA-CCTTAAAAATGAAACCCT
65 CCAAACCCTTAAAAACAAAACCCT
*
20186428 AAACCTTCCAAACCCTAAAA
1 AAA--ATCCAAACCCTAAAA
20186448 TTAAAACCTT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
86 16 0.18
87 13 0.15
88 60 0.67
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.22
Consensus pattern (88 bp):
AAAATCCAAACCCTAAAAACGAAACTCTAAATTTTCCAAACAATAAAATTAAACCTTAAAACCTC
CAAACCCTTAAAAACAAAACCCT
Found at i:20186491 original size:59 final size:57
Alignment explanation
Indices: 20186312--20186620 Score: 175
Period size: 58 Copynumber: 5.4 Consensus size: 57
20186302 TTAAACCTTA
* * * * * * * *
20186312 AAACTTCCAAACCCTTAAATCCAAAACCTTAAA-ATCCAAACGCTAAAAATGAAACTCT
1 AAACCTCCAAACCCTAAAAT--TAAACCTTAAACCTCCAAACCCTAAAAATAAAACCCC
** * * * *
20186370 AAATTTCTCAAACCCTAAAATTAAACCTTAAACCTCCTAACCTTAAAAATGAAACCCT
1 AAACCTC-CAAACCCTAAAATTAAACCTTAAACCTCCAAACCCTAAAAATAAAACCCC
* *
20186428 AAACCTTCCAAACCCTAAAATTAAAACCTT-CACCTTCCAAACCCT-ACAATCAAAACCCC
1 AAACC-TCCAAACCCTAAAATT-AAACCTTAAACC-TCCAAACCCTAAAAAT-AAAACCCC
* * * * * * **
20186487 AAACCTCCAAGCTCTAAAATTGAAA-CTCCAAACCTTCAAACCCT-AAAATTAAATCGT
1 AAACCTCCAAACCCTAAAATT-AAACCT-TAAACCTCCAAACCCTAAAAATAAAACCCC
* ** * * *
20186544 AAATCCTCTAAACCCTAAAACCAAAACTTCAAATCT-CAAA-CCTTAAAATCAAAACCCC
1 AAA-CCTCCAAACCCTAAAATTAAACCTT-AAACCTCCAAACCCTAAAAAT-AAAACCCC
*
20186602 AAATC-CCAAACCCTAAAAT
1 AAACCTCCAAACCCTAAAAT
20186621 CAAAAACCTA
Statistics
Matches: 197, Mismatches: 41, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
56 15 0.08
57 32 0.16
58 107 0.54
59 43 0.22
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.21
Consensus pattern (57 bp):
AAACCTCCAAACCCTAAAATTAAACCTTAAACCTCCAAACCCTAAAAATAAAACCCC
Found at i:20186557 original size:87 final size:88
Alignment explanation
Indices: 20186346--20186634 Score: 220
Period size: 87 Copynumber: 3.3 Consensus size: 88
20186336 AACCTTAAAA
* * * * ** **
20186346 TCCAAACGCTAAAAATGAAACTCTAAA-TTTCTCAAACCCTAAAA-TTAAACCTTAAACCTCCTA
1 TCCAAACCCTAAAATTAAAAC-CTAAACCTTC-CAAACCCTAAAACCAAAACCCCAAACCTCCTA
20186409 ACCTTAAAAATGAAACCCTAAACCT
64 ACCTTAAAAATGAAACCCTAAACCT
** * * *
20186434 TCCAAACCCTAAAATTAAAACCTTCACCTTCCAAACCCTACAATCAAAACCCCAAACCTCC-AAG
1 TCCAAACCCTAAAATTAAAACCTAAACCTTCCAAACCCTAAAACCAAAACCCCAAACCTCCTAAC
*
20186498 CTCTAAAATTGAAACTCC-AAACCT
66 CT-TAAAAATGAAAC-CCTAAACCT
* * * ** * *
20186522 T-CAAACCCTAAAATTAAATCGTAAATCC-TCTAAACCCTAAAACCAAAACTTCAAATCT-CAAA
1 TCCAAACCCTAAAATTAAAACCTAAA-CCTTCCAAACCCTAAAACCAAAACCCCAAACCTCCTAA
* *
20186584 CCTT-AAAATCAAAACCCCAAA--T
65 CCTTAAAAAT-GAAACCCTAAACCT
* *
20186606 CCCAAACCCTAAAATCAAAAACCTAAACC
1 TCCAAACCCTAAAAT-TAAAACCTAAACC
20186635 ATAAAATCTG
Statistics
Matches: 161, Mismatches: 30, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
84 1 0.01
85 21 0.13
86 17 0.11
87 66 0.41
88 54 0.34
89 2 0.01
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.20
Consensus pattern (88 bp):
TCCAAACCCTAAAATTAAAACCTAAACCTTCCAAACCCTAAAACCAAAACCCCAAACCTCCTAAC
CTTAAAAATGAAACCCTAAACCT
Found at i:20186590 original size:28 final size:28
Alignment explanation
Indices: 20186465--20186625 Score: 126
Period size: 28 Copynumber: 5.6 Consensus size: 28
20186455 CTTCACCTTC
* *
20186465 CAAACCCTACAATCAAAACCCCAAACCT
1 CAAACCCTAAAATCAAAACCCCAAATCT
* * ** * *
20186493 CCAAGCTCTAAAATTGAAACTCCAAACCTT
1 -CAAACCCTAAAATCAAAACCCCAAATC-T
* * **
20186523 CAAACCCTAAAAT-TAAATCGTAAATCCT
1 CAAACCCTAAAATCAAAACCCCAAAT-CT
* **
20186551 CTAAACCCTAAAACCAAAACTTCAAATCT
1 C-AAACCCTAAAATCAAAACCCCAAATCT
* *
20186580 CAAACCTTAAAATCAAAACCCCAAATCC
1 CAAACCCTAAAATCAAAACCCCAAATCT
20186608 CAAACCCTAAAATCAAAA
1 CAAACCCTAAAATCAAAA
20186626 ACCTAAACCA
Statistics
Matches: 102, Mismatches: 26, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
28 47 0.46
29 47 0.46
30 8 0.08
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (28 bp):
CAAACCCTAAAATCAAAACCCCAAATCT
Found at i:20186633 original size:21 final size:22
Alignment explanation
Indices: 20186609--20186660 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
20186599 CCCAAATCCC
20186609 AAACCCTAAAATCAAAAACCT-
1 AAACCCTAAAATCAAAAACCTG
* ** *
20186630 AAACCATAAAATCTGAAACTTG
1 AAACCCTAAAATCAAAAACCTG
20186652 AAACCCTAA
1 AAACCCTAA
20186661 CCCTAAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.54, C:0.25, G:0.04, T:0.17
Consensus pattern (22 bp):
AAACCCTAAAATCAAAAACCTG
Found at i:20187068 original size:13 final size:13
Alignment explanation
Indices: 20187035--20187060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20187025 TTTAATAATC
20187035 CAATTTCAAATTT
1 CAATTTCAAATTT
20187048 CAATTTCAAATTT
1 CAATTTCAAATTT
20187061 GCATTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
CAATTTCAAATTT
Found at i:20192739 original size:22 final size:21
Alignment explanation
Indices: 20192697--20192739 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20192687 TTTCAAGATT
* *
20192697 TCAAAAAAAAAATAAATAAAA
1 TCAAAAAAAAAAAAAAGAAAA
20192718 TCAAAAAAAAAAAAAGAGAAAA
1 TCAAAAAAAAAAAAA-AGAAAA
20192740 AGAAGTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.09
Consensus pattern (21 bp):
TCAAAAAAAAAAAAAAGAAAA
Found at i:20193638 original size:19 final size:19
Alignment explanation
Indices: 20193614--20193658 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
20193604 AGTGAGCAAG
20193614 GATTCAATTGGAATCTCAA
1 GATTCAATTGGAATCTCAA
20193633 GATTCAATTGGAATCTCAA
1 GATTCAATTGGAATCTCAA
20193652 GATTCAA
1 GATTCAA
20193659 GAAAGTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
GATTCAATTGGAATCTCAA
Found at i:20195882 original size:108 final size:109
Alignment explanation
Indices: 20195725--20196188 Score: 461
Period size: 109 Copynumber: 4.3 Consensus size: 109
20195715 ACCTAAGCAT
* * * *
20195725 GATTCT-TAAGACTTCTGGGCATGATTTCTAAGATCTCCGGACATAAATTCGATTTGCAGTGTTA
1 GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTTA
* * * * *
20195789 TTCTGATCGATTTATTATTTTTTGACTTACGGTGTTGT-CCAGTC
66 TCCTAATCGATTTCTTA-TTTTTGACTTACGGTGTTATCCCAATC
* * **
20195833 GATTCTATAA-ACCTCCGGGTATGATTTCTAAGACCTCCAGG-CATAAATTCAATTCGTGGTGTT
1 GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCC-GGACATAAATTCGATTCGCAGTGTT
* * *
20195896 ATCCTAATCGATTCCTTATTTTT-ACTTGCGATGTTATCCCAATC
65 ATCCTAATCGATTTCTTATTTTTGACTTACGGTGTTATCCCAATC
* ** * * * * * * *
20195940 GATTCTGTAAGACCTTTGGGCATGATTTTCTAAAACTTTCGGGCATAATTTTGATTCGCGGTGTT
1 GATTCTATAAGACCTCCGGGCATGA-TTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTT
* * * * * *
20196005 ATCCTAATCGATTTTTTATTTTTTAACTTGCAGTGTTATCCCAGTT
65 ATCCTAATCGATTTCTTA-TTTTTGACTTACGGTGTTATCCCAATC
* * * * * * *
20196051 GATTTTGTAAGACCTCCAGGCATAATTTCTAAGACCTCTGGACATAATTTCGATTCGCAATGTTA
1 GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTTA
* *
20196116 TCCTAATTGATTTCTTATTTTTGACTTACGGTGTTATTCCAATC
66 TCCTAATCGATTTCTTATTTTTGACTTACGGTGTTATCCCAATC
* * *
20196160 GATTCTATAAGACCTTCGGACATAATTTC
1 GATTCTATAAGACCTCCGGGCATGATTTC
20196189 GATTCACGGT
Statistics
Matches: 289, Mismatches: 59, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
106 11 0.04
107 19 0.07
108 75 0.26
109 95 0.33
110 52 0.18
111 37 0.13
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (109 bp):
GATTCTATAAGACCTCCGGGCATGATTTCTAAGACCTCCGGACATAAATTCGATTCGCAGTGTTA
TCCTAATCGATTTCTTATTTTTGACTTACGGTGTTATCCCAATC
Found at i:20196083 original size:22 final size:22
Alignment explanation
Indices: 20196058--20196101 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20196048 GTTGATTTTG
20196058 TAAGACCTCCAGG-CATAATTTC
1 TAAGACCT-CAGGACATAATTTC
*
20196080 TAAGACCTCTGGACATAATTTC
1 TAAGACCTCAGGACATAATTTC
20196102 GATTCGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (22 bp):
TAAGACCTCAGGACATAATTTC
Found at i:20196272 original size:88 final size:87
Alignment explanation
Indices: 20196080--20196275 Score: 250
Period size: 88 Copynumber: 2.2 Consensus size: 87
20196070 GCATAATTTC
* * *
20196080 TAAGACCTCTGGACATAATTTCGATTCGCAATGTTATCCTAATTGATTTCTTATTTTTGACTTAC
1 TAAGACCTCTGGACATAATTTCGATTCACAATGTTATCCCAATCGATTTCTTATTTTTGACTTAC
*
20196145 GGTGTTATTCCAATCGATTCTA
66 GGTGTTATACCAATCGATTCTA
** *
20196167 TAAGACCT-TCGGACATAATTTCGATTCACGGTGTTATCCCGATCGATTTCTTATTTTTTGACTT
1 TAAGACCTCT-GGACATAATTTCGATTCACAATGTTATCCCAATCGATTTCTTA-TTTTTGACTT
** * * *
20196231 GTGGTGTTATACCAGTTGATTCTG
64 ACGGTGTTATACCAATCGATTCTA
*
20196255 TAAGACCTCTAGACATAATTT
1 TAAGACCTCTGGACATAATTT
20196276 TTAAGACCTC
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
86 1 0.01
87 45 0.48
88 46 0.49
89 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (87 bp):
TAAGACCTCTGGACATAATTTCGATTCACAATGTTATCCCAATCGATTTCTTATTTTTGACTTAC
GGTGTTATACCAATCGATTCTA
Found at i:20196283 original size:22 final size:22
Alignment explanation
Indices: 20196255--20196320 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
20196245 GTTGATTCTG
*
20196255 TAAGACCTCTAGACATAATTTT
1 TAAGACCTCCAGACATAATTTT
*
20196277 TAAGACCTCCA-AGCATAATCTT
1 TAAGACCTCCAGA-CATAATTTT
*
20196299 TAAGACTTCCAGACATAATTTT
1 TAAGACCTCCAGACATAATTTT
20196321 GATTCGTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (22 bp):
TAAGACCTCCAGACATAATTTT
Found at i:20196932 original size:13 final size:14
Alignment explanation
Indices: 20196911--20196945 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20196901 CACACCAACC
*
20196911 ACAAAAAAAAACAA
1 ACAAAAAAATACAA
*
20196925 ACAAAAAAATAGAA
1 ACAAAAAAATACAA
20196939 ACAAAAA
1 ACAAAAA
20196946 GACAAACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.03
Consensus pattern (14 bp):
ACAAAAAAATACAA
Found at i:20198008 original size:14 final size:14
Alignment explanation
Indices: 20197991--20198062 Score: 63
Period size: 15 Copynumber: 5.0 Consensus size: 14
20197981 CACTAATTCT
20197991 TAAATCCAAACCCC
1 TAAATCCAAACCCC
* *
20198005 TAAAATCCAAAACCT
1 T-AAATCCAAACCCC
* **
20198020 TAAAATCCTAACCTT
1 T-AAATCCAAACCCC
20198035 TAAATCCAAACCCC
1 TAAATCCAAACCCC
* *
20198049 AAAATCAAAACCCC
1 TAAATCCAAACCCC
20198063 AAACCTCAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
14 23 0.49
15 24 0.51
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAATCCAAACCCC
Found at i:20198012 original size:15 final size:15
Alignment explanation
Indices: 20197992--20198062 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 15
20197982 ACTAATTCTT
20197992 AAATCCAAACCCCTA
1 AAATCCAAACCCCTA
* *
20198007 AAATCCAAAACCTTA
1 AAATCCAAACCCCTA
* * *
20198022 AAATCCTAA-CCTTT
1 AAATCCAAACCCCTA
20198036 AAATCCAAACCCC-A
1 AAATCCAAACCCCTA
*
20198050 AAATCAAAACCCC
1 AAATCCAAACCCC
20198063 AAACCTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 24 0.51
15 23 0.49
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:20198095 original size:14 final size:14
Alignment explanation
Indices: 20198078--20198183 Score: 63
Period size: 14 Copynumber: 7.3 Consensus size: 14
20198068 TCAAATTTTA
20198078 AAAATCAAAACCCT
1 AAAATCAAAACCCT
* * *
20198092 AAAAACGAAACTCT
1 AAAATCAAAACCCT
20198106 AAAATTTTC-AAACCCT
1 AAAA---TCAAAACCCT
* *
20198122 AAAAT-TAAACCTT
1 AAAATCAAAACCCT
** *
20198135 AAAACTTTTAAACCTT
1 AAAA--TCAAAACCCT
*
20198151 CAAATCCAAAACCCT
1 AAAAT-CAAAACCCT
20198166 AAAATCAAAACCCT
1 AAAATCAAAACCCT
20198180 AAAA
1 AAAA
20198184 ACGAAACTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.15
14 29 0.40
15 11 0.15
16 21 0.29
17 1 0.01
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.22
Consensus pattern (14 bp):
AAAATCAAAACCCT
Found at i:20198190 original size:14 final size:14
Alignment explanation
Indices: 20198157--20198196 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20198147 CCTTCAAATC
*
20198157 CAAAACCCTAAAAT
1 CAAAACCCTAAAAA
20198171 CAAAACCCTAAAAA
1 CAAAACCCTAAAAA
* *
20198185 CGAAACTCTAAA
1 CAAAACCCTAAA
20198197 TTTCTCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.28, G:0.03, T:0.12
Consensus pattern (14 bp):
CAAAACCCTAAAAA
Found at i:20198207 original size:44 final size:45
Alignment explanation
Indices: 20198078--20198214 Score: 137
Period size: 44 Copynumber: 3.1 Consensus size: 45
20198068 TCAAATTTTA
20198078 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTT-TCAAACCCT
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTCTCAAACCCT
* * * *
20198122 AAAAT-TAAA-CCTTAAAACTTTTAAAC-CTTCAAA--TC-CAAAACCCT
1 AAAATCAAAACCCTAAAAAC---GAAACTC-TAAAATTTCTC-AAACCCT
20198166 AAAATCAAAACCCTAAAAACGAAACTCT-AAATTTCTCAAACCCT
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTCTCAAACCCT
20198210 AAAAT
1 AAAAT
20198215 TAAACATTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
42 11 0.15
43 10 0.14
44 33 0.45
45 12 0.16
46 8 0.11
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.23
Consensus pattern (45 bp):
AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTCTCAAACCCT
Found at i:20198271 original size:88 final size:87
Alignment explanation
Indices: 20198078--20198254 Score: 252
Period size: 88 Copynumber: 2.0 Consensus size: 87
20198068 TCAAATTTTA
* **
20198078 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTTCAAACCCTAAAATTAAACCTTAAAACTTT
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTTCAAACCCTAAAATTAAACATTAAAACTCC
*
20198143 TAAACCTTCAAATCCAAAACCCT
66 TAAACCTTAAAAT-CAAAACCCT
*
20198166 AAAATCAAAACCCTAAAAACGAAACTCT-AAATTTCTCAAACCCTAAAATTAAACATTAAACCTC
1 AAAATCAAAACCCTAAAAACGAAACTCTAAAATTT-TCAAACCCTAAAATTAAACATTAAAACTC
*
20198230 CT-AACCTTAAAAAT-GAAACCCT
65 CTAAACCTT-AAAATCAAAACCCT
20198252 AAA
1 AAA
20198255 CCTTTCAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
86 10 0.12
87 12 0.15
88 59 0.73
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (87 bp):
AAAATCAAAACCCTAAAAACGAAACTCTAAAATTTTCAAACCCTAAAATTAAACATTAAAACTCC
TAAACCTTAAAATCAAAACCCT
Found at i:20198356 original size:29 final size:29
Alignment explanation
Indices: 20198085--20198449 Score: 121
Period size: 29 Copynumber: 12.6 Consensus size: 29
20198075 TTAAAAATCA
* * * *
20198085 AAACCCTAAAAACGAAACTCTAAAATTTTC
1 AAACCCTAAAATCAAAACTC-CAAACTTTC
* * ** *
20198115 AAACCCTAAAATTAAACCTTAAAACTTTT
1 AAACCCTAAAATCAAAACTCCAAACTTTC
* * *
20198144 AAACCTTCAAATCCAAAAC-CCTAAA--ATC
1 AAACCCTAAAAT-CAAAACTCC-AAACTTTC
* * * *
20198172 AAAACCCTAAAAACGAAACTCTAAATTTCTC
1 -AAACCCTAAAATCAAAACTCCAAACTT-TC
* * * *
20198203 AAACCCTAAAAT-TAAACAT-TAAACCTCC
1 AAACCCTAAAATCAAAAC-TCCAAACTTTC
* * *
20198231 TAACCTTAAAAAT-GAAAC-CCTAAACCTTTC
1 AAACCCT-AAAATCAAAACTCC-AAA-CTTTC
* * * *
20198261 AAACCCTAAAATTAAAACCTTC-ACCTTCC
1 AAACCCTAAAATCAAAA-CTCCAAACTTTC
* * *
20198290 AAACCCTACAATCAAAACACCAAAC-CTC
1 AAACCCTAAAATCAAAACTCCAAACTTTC
* *
20198318 TAAGCTCTAAAATCAAAACTCCAAACTTTC
1 -AAACCCTAAAATCAAAACTCCAAACTTTC
* * * *
20198348 AAACCCTAAAAT-TAAAC-CATAAATCCTCC
1 AAACCCTAAAATCAAAACTC-CAAA-CTTTC
* * *
20198377 AAATCCTAAAACCAAAACTTCAAA-TCTT-
1 AAACCCTAAAATCAAAACTCCAAACT-TTC
*
20198405 AAACCCTAAAATCAAAAC-CCTAAA-TCTC
1 AAACCCTAAAATCAAAACTCC-AAACTTTC
*
20198433 AAACCCTAAAATAAAAA
1 AAACCCTAAAATCAAAA
20198450 ACCTAAACCC
Statistics
Matches: 242, Mismatches: 68, Indels: 52
0.67 0.19 0.14
Matches are distributed among these distances:
27 3 0.01
28 61 0.25
29 119 0.49
30 55 0.23
31 3 0.01
32 1 0.00
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.22
Consensus pattern (29 bp):
AAACCCTAAAATCAAAACTCCAAACTTTC
Found at i:20198386 original size:58 final size:56
Alignment explanation
Indices: 20198324--20198449 Score: 148
Period size: 58 Copynumber: 2.2 Consensus size: 56
20198314 CCTCTAAGCT
* *
20198324 CTAAAATCAAAACTCCAAA-CTTTCAAACCCTAAAAT-TAAACCATAAATCCTCCAAATC
1 CTAAAATCAAAACTCCAAATC-TT-AAACCCTAAAATCAAAACCATAAAT-CT-CAAACC
* * *
20198382 CTAAAACCAAAACTTCAAATCTTAAACCCTAAAATCAAAACCCTAAATCTCAAACC
1 CTAAAATCAAAACTCCAAATCTTAAACCCTAAAATCAAAACCATAAATCTCAAACC
*
20198438 CTAAAATAAAAA
1 CTAAAATCAAAA
20198450 ACCTAAACCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 15 0.25
57 14 0.24
58 29 0.49
59 1 0.02
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (56 bp):
CTAAAATCAAAACTCCAAATCTTAAACCCTAAAATCAAAACCATAAATCTCAAACC
Found at i:20198422 original size:14 final size:14
Alignment explanation
Indices: 20198405--20198456 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
20198395 TTCAAATCTT
20198405 AAACCCTAAAATCA
1 AAACCCTAAAATCA
*
20198419 AAACCCT-AAATCTC
1 AAACCCTAAAATC-A
*
20198433 AAACCCTAAAATAA
1 AAACCCTAAAATCA
*
20198447 AAAACCTAAA
1 AAACCCTAAA
20198457 CCCAAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.16
14 23 0.72
15 4 0.12
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:20198514 original size:22 final size:21
Alignment explanation
Indices: 20198480--20198522 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
20198470 AACTTGAAAC
*
20198480 CCTAATCCTAAAATCCAAAAT
1 CCTAAACCTAAAATCCAAAAT
20198501 CCTAAACCTTAAAATCCAAAAT
1 CCTAAACC-TAAAATCCAAAAT
20198523 TTTGAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTAAACCTAAAATCCAAAAT
Found at i:20203827 original size:18 final size:18
Alignment explanation
Indices: 20203804--20203839 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20203794 AACAATTCAA
*
20203804 TAGTTTATCACTAACAAT
1 TAGTTTATCACAAACAAT
*
20203822 TAGTTTATTACAAACAAT
1 TAGTTTATCACAAACAAT
20203840 ACAATCGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (18 bp):
TAGTTTATCACAAACAAT
Found at i:20205444 original size:18 final size:18
Alignment explanation
Indices: 20205364--20205447 Score: 53
Period size: 18 Copynumber: 4.4 Consensus size: 18
20205354 TGTTATATTC
*
20205364 ATAAATTATTATTTTAAA
1 ATAAATTAATATTTTAAA
* * *
20205382 AGAAATTATATCTTAGTTATAT
1 ATAAATTA-ATATT--TTA-AA
* *
20205404 ATAAATATAGTATTTT-TA
1 ATAAAT-TAATATTTTAAA
*
20205422 TTAAATTAATATTTTAAA
1 ATAAATTAATATTTTAAA
20205440 ATAAATTA
1 ATAAATTA
20205448 TTAAATAATA
Statistics
Matches: 47, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
17 8 0.17
18 20 0.43
19 3 0.06
20 2 0.04
21 3 0.06
22 9 0.19
23 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (18 bp):
ATAAATTAATATTTTAAA
Found at i:20205466 original size:16 final size:18
Alignment explanation
Indices: 20205445--20205477 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
20205435 TTAAAATAAA
20205445 TTATTAA-ATA-ATAATT
1 TTATTAATATATATAATT
20205461 TTATTAATATATATAAT
1 TTATTAATATATATAAT
20205478 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATTAATATATATAATT
Found at i:20206566 original size:14 final size:14
Alignment explanation
Indices: 20206547--20206587 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
20206537 AAAAGAACAT
20206547 AAAAT-GAAAAGTAA
1 AAAATGGAAAA-TAA
20206561 AAAATGGAAAATAA
1 AAAATGGAAAATAA
*
20206575 AAAAAGGAAAATA
1 AAAATGGAAAATA
20206588 TTTTTGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAATGGAAAATAA
Found at i:20207822 original size:17 final size:17
Alignment explanation
Indices: 20207800--20207834 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20207790 TTAGGGTTAA
* *
20207800 GTTTAGGGTTTGAGTAG
1 GTTTAGGGCTTGACTAG
20207817 GTTTAGGGCTTGACTAG
1 GTTTAGGGCTTGACTAG
20207834 G
1 G
20207835 GTTTGGAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.40, T:0.37
Consensus pattern (17 bp):
GTTTAGGGCTTGACTAG
Done.