Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 6 of 17
Found at i:491500 original size:15 final size:16
Alignment explanation
Indices: 491426--491482 Score: 80
Period size: 17 Copynumber: 3.6 Consensus size: 16
491416 AGAAAGAAAG
491426 AAAGAAAAAGGAAAAA
1 AAAGAAAAAGGAAAAA
*
491442 AAAGAGAAAGGAGAAAA
1 AAAGAAAAAGGA-AAAA
*
491459 GAAGAAAAAGG-AAAA
1 AAAGAAAAAGGAAAAA
491474 AAAGAAAAA
1 AAAGAAAAA
491483 AAAGAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 12 0.33
16 11 0.31
17 13 0.36
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGGAAAAA
Found at i:492065 original size:22 final size:22
Alignment explanation
Indices: 491986--492068 Score: 64
Period size: 22 Copynumber: 3.7 Consensus size: 22
491976 ATATATTCGT
* **
491986 ATTTATATTTTTATTTAAAAT-
1 ATTTATATTTTTATTTTATTTC
*
492007 ATTATATTTTTTTATTTT-TTTAC
1 ATT-TATATTTTTATTTTATTT-C
*
492030 ATATTA-ATAATTTATTTTATTTC
1 AT-TTATAT-TTTTATTTTATTTC
492053 ATTTATATTTTTATTT
1 ATTTATATTTTTATTT
492069 ATACGTGTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
21 4 0.08
22 23 0.48
23 17 0.35
24 4 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATATTTTTATTTTATTTC
Found at i:492291 original size:22 final size:21
Alignment explanation
Indices: 492266--492324 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
492256 TGTTTTAATT
492266 TTTTATATATGTTAAGT-TTATA
1 TTTTATATA-GTTAA-TATTATA
* * *
492288 TTTTATCTAAATTCATATTATA
1 TTTTATAT-AGTTAATATTATA
492310 TTTTATATAGTTAAT
1 TTTTATATAGTTAAT
492325 CACCGTGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 6 0.21
22 22 0.76
23 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTTATATAGTTAATATTATA
Found at i:492556 original size:27 final size:28
Alignment explanation
Indices: 492512--492572 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
492502 ATAATTAGTA
492512 TTATATATATTTTGATATGT-TTATTTAT-
1 TTATATATATTTTGATAT-TATT-TTTATG
492540 TTATATCATA-TTT-ATATTATTTTTATG
1 TTATAT-ATATTTTGATATTATTTTTATG
492567 TTATAT
1 TTATAT
492573 TTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 6 0.20
27 12 0.40
28 9 0.30
29 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (28 bp):
TTATATATATTTTGATATTATTTTTATG
Found at i:492914 original size:8 final size:8
Alignment explanation
Indices: 492895--492957 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
492885 ATACATAATT
492895 TTTTTTTC
1 TTTTTTTC
492903 TTTTTCTT-
1 TTTTT-TTC
492911 TTTTTTTCC
1 TTTTTTT-C
*
492920 TTTCTTTC
1 TTTTTTTC
*
492928 TTTCTTTCTT
1 TTT-TTT-TC
492938 TTTTCTTTC
1 TTTT-TTTC
492947 TTTTTTTC
1 TTTTTTTC
492955 TTT
1 TTT
492958 CTCAACTGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
7 2 0.04
8 21 0.47
9 16 0.36
10 6 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:492914 original size:15 final size:15
Alignment explanation
Indices: 492894--492951 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
492884 AATACATAAT
*
492894 TTTTTTTTCTTTTTC
1 TTTTCTTTCTTTTTC
492909 TTTT-TTT-TTCCTTTC
1 TTTTCTTTCTT--TTTC
492924 -TTTCTTTCTTTCTT-
1 TTTTCTTTCTTT-TTC
492938 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
492952 TTCTTTCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 24 0.65
16 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:492926 original size:4 final size:4
Alignment explanation
Indices: 492905--492959 Score: 71
Period size: 4 Copynumber: 14.2 Consensus size: 4
492895 TTTTTTTCTT
*
492905 TTTC TTT- TTT- TTTCC TTTC TTTC TTTC TTTC TTT- TTTC TTTC TTTT
1 TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
492951 TTTC TTTC T
1 TTTC TTTC T
492960 CAACTGCCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 9 0.20
4 34 0.74
5 3 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:492938 original size:27 final size:27
Alignment explanation
Indices: 492905--492959 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
492895 TTTTTTTCTT
492905 TTTCTTTTTT-TTTCCTTTCTTTCTTTC
1 TTTCTTTTTTCTTT-CTTTCTTTCTTTC
*
492932 TTTCTTTTTTCTTTCTTTTTTTCTTTC
1 TTTCTTTTTTCTTTCTTTCTTTCTTTC
492959 T
1 T
492960 CAACTGCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTCTTTTTTCTTTCTTTCTTTCTTTC
Found at i:492939 original size:23 final size:23
Alignment explanation
Indices: 492905--492959 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
492895 TTTTTTTCTT
*
492905 TTTCTTTTTTTTTCCTTTCTTTC
1 TTTCTTTCTTTTTCCTTTCTTTC
* *
492928 TTTCTTTCTTTTTTCTTTCTTTT
1 TTTCTTTCTTTTTCCTTTCTTTC
492951 TTTCTTTCT
1 TTTCTTTCT
492960 CAACTGCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTCTTTTTCCTTTCTTTC
Found at i:492957 original size:19 final size:18
Alignment explanation
Indices: 492893--492953 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
492883 GAATACATAA
*
492893 TTTTTTTTTCTT-TTTCT
1 TTTTTTTTTTTTCTTTCT
*
492910 TTTTTTTTCCTTTCTTTCT
1 TTTTTTTT-TTTTCTTTCT
*
492929 TTCTTTCTTTTTTCTTTCT
1 TT-TTTTTTTTTTCTTTCT
492948 TTTTTT
1 TTTTTT
492954 CTTTCTCAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 8 0.22
18 5 0.14
19 18 0.50
20 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTTCTTTCT
Found at i:493358 original size:36 final size:37
Alignment explanation
Indices: 493318--493399 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
493308 ATTTAAGTTA
493318 TTTTTTCATATTTAA-AATATTA-TATATTTTATATAT
1 TTTTTTCATATTTAATAAT-TTATTATATTTTATATAT
* *
493354 TTTTTACATA-TTAATAATTTATTTTATTTTATATAT
1 TTTTTTCATATTTAATAATTTATTATATTTTATATAT
*
493390 ATTTTT-ATAT
1 TTTTTTCATAT
493400 GTACGTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 10 0.26
36 29 0.74
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (37 bp):
TTTTTTCATATTTAATAATTTATTATATTTTATATAT
Found at i:493381 original size:27 final size:27
Alignment explanation
Indices: 493334--493392 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
493324 CATATTTAAA
* *
493334 ATATTATATATTTTATATATTTTTTAC
1 ATATTATATAATTTATATATTTTATAC
* *
493361 ATATTA-ATAATTTATTTTATTTTATAT
1 ATATTATATAATTTA-TATATTTTATAC
493388 ATATT
1 ATATT
493393 TTTATATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATTATATAATTTATATATTTTATAC
Found at i:493841 original size:15 final size:16
Alignment explanation
Indices: 493821--493850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
493811 TTTTTAAATA
493821 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
493836 AATTTTATTTAATTA
1 AATTTTATTTAATTA
493851 AAAATTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:496899 original size:2 final size:2
Alignment explanation
Indices: 496892--496927 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
496882 AACATAGGTG
496892 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
496928 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:499019 original size:156 final size:156
Alignment explanation
Indices: 498735--499289 Score: 903
Period size: 156 Copynumber: 3.6 Consensus size: 156
498725 ACTATTAGCA
* *
498735 GTAGTTCATCCATTTGTGGAGCATCCACCTGCAATGGTGCTCCCTGCCAGAGGCCAGTTAAGGGA
1 GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTGCTCCCTGCCAGAGGACAGTTAAGGGA
* * *
498800 AATGGAAGATGTTTCGAGCACTCAAACAATGGTGGCAGCAGCATTAGTATTCCTAGCTCTTTTAG
66 AATGGAAGATGTTTCCAGCACTCAAACAATGGTGGCAGCAGCATTAGTATTCGTAGCTATTTTAG
*
498865 TCCACAGCATTCAAATTATGACGGGG
131 TCCACAGCATTCAAATTATGACGGCG
498891 GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTGCTCCCTGCCAGAGGACAGTTAAGGGA
1 GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTGCTCCCTGCCAGAGGACAGTTAAGGGA
* *
498956 AATGGAAGATGTTTCCAGCACTCAAACAATGGTGGCAGCAGCATTAGTATTAGTAGCTGTTTTAG
66 AATGGAAGATGTTTCCAGCACTCAAACAATGGTGGCAGCAGCATTAGTATTCGTAGCTATTTTAG
499021 TCCACAGCATTCAAATTATGACGGCG
131 TCCACAGCATTCAAATTATGACGGCG
*
499047 GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTACTCCCTGCCAGAGGACAGTTAAGGGA
1 GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTGCTCCCTGCCAGAGGACAGTTAAGGGA
* * ** * *
499112 AATGGAAGATGTTTCCAGCACTCAAACACTGGTAGCAGCAGCACCAGTATCCGTAGTTATTTTAG
66 AATGGAAGATGTTTCCAGCACTCAAACAATGGTGGCAGCAGCATTAGTATTCGTAGCTATTTTAG
* * *
499177 TCCACAGTATTCAATTTATGGCGGCG
131 TCCACAGCATTCAAATTATGACGGCG
* * *
499203 GTAGTTCATCCATTTGTGGAGCACCCACCAGAAATGGTGCTCCCTGCCAGAGGACAGTTAGGGGA
1 GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTGCTCCCTGCCAGAGGACAGTTAAGGGA
**
499268 AATGGAAGATGTTGGCAGCACT
66 AATGGAAGATGTTTCCAGCACT
499290 AATTGGTCAA
Statistics
Matches: 374, Mismatches: 25, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
156 374 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (156 bp):
GTAGTTCATCCATTTGTGGAGCACCCACCTGCAATGGTGCTCCCTGCCAGAGGACAGTTAAGGGA
AATGGAAGATGTTTCCAGCACTCAAACAATGGTGGCAGCAGCATTAGTATTCGTAGCTATTTTAG
TCCACAGCATTCAAATTATGACGGCG
Found at i:499438 original size:2 final size:2
Alignment explanation
Indices: 499433--499468 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
499423 TATATATATA
499433 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
499469 TTGCATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:500295 original size:25 final size:24
Alignment explanation
Indices: 500259--500323 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 24
500249 TAATTATGAT
500259 TAATATTATATATATTTTATAAATTTAA
1 TAAT-TTATATATA-TTTAT--ATTTAA
500287 TAATTTATATTATATTTATATTTATA
1 TAATTTATA-TATATTTATATTTA-A
*
500313 TAATTAATATA
1 TAATTTATATA
500324 ATACATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
25 7 0.21
26 9 0.26
27 10 0.29
28 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTTATATATATTTATATTTAA
Found at i:501168 original size:3 final size:3
Alignment explanation
Indices: 501162--501186 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
501152 AATTGATGGC
501162 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
501187 ATTATGTCTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:502846 original size:3 final size:3
Alignment explanation
Indices: 502840--502869 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
502830 TATATTATTT
502840 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
502870 TTGTATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:505594 original size:15 final size:14
Alignment explanation
Indices: 505575--505618 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
505565 TATGATCATC
505575 AAAATTTATATATA
1 AAAATTTATATATA
505589 ACAAATTATTATAATATA
1 A-AAA-T-TTAT-ATATA
505607 AAAATTTATATA
1 AAAATTTATATA
505619 AATATGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.15
15 7 0.27
16 2 0.08
17 7 0.27
18 6 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTTATATATA
Found at i:505623 original size:18 final size:18
Alignment explanation
Indices: 505580--505612 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
505570 TCATCAAAAT
505580 TTAT-ATATAACAAATTA
1 TTATAATATAACAAATTA
505597 TTATAATATAA-AAATT
1 TTATAATATAACAAATT
505613 TATATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAATATAACAAATTA
Found at i:505915 original size:22 final size:22
Alignment explanation
Indices: 505890--505933 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
505880 CAAAATAACC
*
505890 AAAACCACGAATTAAAAGTTTT
1 AAAACAACGAATTAAAAGTTTT
505912 AAAACAACGAATTAAAAGTTTT
1 AAAACAACGAATTAAAAGTTTT
505934 TTTTAAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (22 bp):
AAAACAACGAATTAAAAGTTTT
Found at i:506092 original size:2 final size:2
Alignment explanation
Indices: 506085--506113 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
506075 CTCCTTCCCA
506085 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
506114 AGTTTCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:507083 original size:5 final size:5
Alignment explanation
Indices: 507046--507136 Score: 55
Period size: 5 Copynumber: 18.2 Consensus size: 5
507036 TAAAATATTT
* * *
507046 TTATA TTTATA TAATA TT-T- TT-TA TTATT TTATA TTATA TCATA TTTATA
1 TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA
* * * *
507095 TTATA TT-TAA TTATT TTTTA TTATA TTCATA TGATA TAATA T
1 TTATA TTAT-A TTATA TTATA TTATA TT-ATA TTATA TTATA T
507137 CAAATTTAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
3 3 0.04
4 4 0.06
5 46 0.69
6 14 0.21
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:507091 original size:38 final size:39
Alignment explanation
Indices: 507048--507136 Score: 114
Period size: 36 Copynumber: 2.4 Consensus size: 39
507038 AAATATTTTT
* *
507048 ATATTTATATAATATTTTTTATTATTTTATATTATA-TC
1 ATATTTATATAATATATTTAATTATTTTATATTATATTC
*
507086 ATATTTATAT--TATATTTAATTATTTTTTATTATATTC
1 ATATTTATATAATATATTTAATTATTTTATATTATATTC
*
507123 ATA-TGATATAATAT
1 ATATTTATATAATAT
507137 CAAATTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
36 26 0.59
37 5 0.11
38 13 0.30
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (39 bp):
ATATTTATATAATATATTTAATTATTTTATATTATATTC
Found at i:507558 original size:16 final size:17
Alignment explanation
Indices: 507539--507576 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
507529 TCGGCTTCGA
507539 ACTTATTT-AGGTTCAG
1 ACTTATTTGAGGTTCAG
*
507555 ACTTATTTGAGTTTCAG
1 ACTTATTTGAGGTTCAG
507572 -CTTAT
1 ACTTAT
507577 ACGTGTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (17 bp):
ACTTATTTGAGGTTCAG
Found at i:507590 original size:16 final size:15
Alignment explanation
Indices: 507571--507619 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
507561 TTGAGTTTCA
507571 GCTTATACGTGTTCGG
1 GCTTATACG-GTTCGG
*
507587 GCTTATACAGGTTCGA
1 GCTTATAC-GGTTCGG
507603 GCTTATACGAGTTCGG
1 GCTTATACG-GTTCGG
507619 G
1 G
507620 TTTTTCGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (15 bp):
GCTTATACGGTTCGG
Found at i:507656 original size:17 final size:18
Alignment explanation
Indices: 507623--507659 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
507613 GTTCGGGTTT
507623 TTCGGGTTCGAGTTCAAG
1 TTCGGGTTCGAGTTCAAG
*
507641 TTCGGG-TCGGGTTCAAG
1 TTCGGGTTCGAGTTCAAG
507658 TT
1 TT
507660 TAAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.14, C:0.16, G:0.35, T:0.35
Consensus pattern (18 bp):
TTCGGGTTCGAGTTCAAG
Found at i:508298 original size:56 final size:56
Alignment explanation
Indices: 508212--508329 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 56
508202 AAGTAGAAGT
*
508212 AGGCAACAACAACAAAACCAAACCTAGATTGAAGCTTAGACCGAATTAACAGCAAC
1 AGGCAACAACAACAAAACCAAACCTAGATTGAAGCTTAGACCAAATTAACAGCAAC
* * * *
508268 AGGCAACAACAA-TAAACCTAAACGC-AGATTGAAGTTTAGACTAAATTAATAGCAAC
1 AGGCAACAACAACAAAACC-AAAC-CTAGATTGAAGCTTAGACCAAATTAACAGCAAC
508324 -GGCAAC
1 AGGCAAC
508330 GGCAACAGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
55 11 0.20
56 43 0.78
57 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.15, T:0.15
Consensus pattern (56 bp):
AGGCAACAACAACAAAACCAAACCTAGATTGAAGCTTAGACCAAATTAACAGCAAC
Found at i:508823 original size:16 final size:15
Alignment explanation
Indices: 508796--508825 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
508786 ATGTTAACTT
508796 TATATTCTATTCTAC
1 TATATTCTATTCTAC
508811 TATATTGCTATTCTA
1 TATATT-CTATTCTA
508826 AGTGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:512584 original size:45 final size:45
Alignment explanation
Indices: 512499--512585 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
512489 GTGGTTTTAG
* *
512499 TTAAAATTTTTATTATTTTTTAAATATATAAAAATTAAATTTATA
1 TTAAAATTTTTATTATTTTTTAAATAAATAAAAATAAAATTTATA
* * **
512544 TTAATATTTTTA-TATTTTTATAATTAAATTTAAATAAAATTT
1 TTAAAATTTTTATTATTTTT-TAAATAAATAAAAATAAAATTT
512586 TTTATTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 7 0.20
45 28 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (45 bp):
TTAAAATTTTTATTATTTTTTAAATAAATAAAAATAAAATTTATA
Found at i:512875 original size:21 final size:21
Alignment explanation
Indices: 512850--512890 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
512840 TCCGATTTAT
*
512850 AAGTAAATTTAATTTTAATTA
1 AAGTAAATTTAATTTAAATTA
* *
512871 AAGTAATTTTTATTTAAATT
1 AAGTAAATTTAATTTAAATT
512891 TTATTAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
AAGTAAATTTAATTTAAATTA
Found at i:513389 original size:35 final size:36
Alignment explanation
Indices: 513339--513425 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 36
513329 TTATATTTGT
*
513339 GTATAT-TTTTATATATTAATAATTTATTT-TATTATA
1 GTATATATTTT-TATATTAAT-ATATATTTGTATTATA
* *
513375 -TATATATTTTTATATTTATGTATATTTGTATTATA
1 GTATATATTTTTATATTAATATATATTTGTATTATA
513410 TGTATATCATTTTTAT
1 -GTATAT-ATTTTTAT
513426 GTTATGTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
34 6 0.14
35 20 0.47
36 4 0.09
37 5 0.12
38 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (36 bp):
GTATATATTTTTATATTAATATATATTTGTATTATA
Found at i:513416 original size:37 final size:37
Alignment explanation
Indices: 513299--513425 Score: 99
Period size: 37 Copynumber: 3.5 Consensus size: 37
513289 TATGTGTTGA
* * *
513299 TATT-TATAT-TATTTTTTTATATT--TAAAATATTA
1 TATTATATATATATTTTTATATATTAATAATATATTT
* * *
513332 TATT-TGTGTATATTTTTATATATTAATAATTTATTT
1 TATTATATATATATTTTTATATATTAATAATATATTT
*
513368 TATTATATATATATTTTTATAT-TT-AT-GTATATTT
1 TATTATATATATATTTTTATATATTAATAATATATTT
513402 GTATTATATGTATATCATTTTTAT
1 -TATTATA--TATAT-ATTTTTAT
513426 GTTATGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
33 7 0.09
34 19 0.25
35 9 0.12
36 13 0.17
37 20 0.26
38 8 0.11
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (37 bp):
TATTATATATATATTTTTATATATTAATAATATATTT
Found at i:513577 original size:12 final size:12
Alignment explanation
Indices: 513560--513599 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
513550 TCGTATCATG
513560 TTTATATTATTT
1 TTTATATTATTT
*
513572 TTTATATTATGT
1 TTTATATTATTT
513584 TTTA-ATT-TTT
1 TTTATATTATTT
513594 TTTATA
1 TTTATA
513600 CCTATCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.24
11 4 0.16
12 15 0.60
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:513705 original size:4 final size:4
Alignment explanation
Indices: 513690--513751 Score: 61
Period size: 4 Copynumber: 14.8 Consensus size: 4
513680 TCAAGAGGGA
* * * *
513690 AAAG AGAG AAAG AAAG AAAG AAAG AAAA AATGAG AAAA AAAG AAAAA AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA--AG AAAG AAAG -AAAG AAAG
513741 AAAG AAAG AAA
1 AAAG AAAG AAA
513752 AAGAGAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
4 41 0.87
5 3 0.06
6 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:513727 original size:10 final size:8
Alignment explanation
Indices: 513696--513761 Score: 69
Period size: 8 Copynumber: 7.9 Consensus size: 8
513686 GGGAAAAGAG
*
513696 AGAAAGAA
1 AGAAAAAA
*
513704 AGAAAGAA
1 AGAAAAAA
513712 AGAAAAAA
1 AGAAAAAA
513720 TGAGAAAAAA
1 --AGAAAAAA
513730 AGAAAAAAA
1 AG-AAAAAA
*
513739 AGAAAGAA
1 AGAAAAAA
*
513747 AGAAAAAG
1 AGAAAAAA
513755 AGAAAAA
1 AGAAAAA
513762 GTTTACGTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
8 35 0.69
9 8 0.16
10 8 0.16
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AGAAAAAA
Found at i:513835 original size:38 final size:37
Alignment explanation
Indices: 513785--513865 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
513775 TCTTTGTGTT
513785 ATTTTTTTATATTTAA-AATATTATAAT-TTTTATATAA
1 ATTTTTTTATA-TTAATAAT-TTATAATATTTTATATAA
** *
513822 ATTTTTTATATATTAATAATTTATTTTATTTTATATAT
1 ATTTTTT-TATATTAATAATTTATAATATTTTATATAA
513860 ATTTTT
1 ATTTTT
513866 ATACATACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 16 0.42
38 22 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (37 bp):
ATTTTTTTATATTAATAATTTATAATATTTTATATAA
Found at i:514093 original size:9 final size:9
Alignment explanation
Indices: 514079--514104 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
514069 AGAAAAATGG
514079 AAAGAAAAA
1 AAAGAAAAA
514088 AAAGAAAAA
1 AAAGAAAAA
514097 AAAGAAAA
1 AAAGAAAA
514105 GGAGAGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:514269 original size:11 final size:12
Alignment explanation
Indices: 514238--514287 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
514228 CGTGTCATAT
514238 TTATTTTTTATA
1 TTATTTTTTATA
*
514250 TTATGTTTTA-A
1 TTATTTTTTATA
*
514261 TTATTTTTTATG
1 TTATTTTTTATA
*
514273 TCATATTTTTATA
1 TTAT-TTTTTATA
514286 TT
1 TT
514288 TCGTATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 8 0.27
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:514281 original size:23 final size:23
Alignment explanation
Indices: 514238--514281 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
514228 CGTGTCATAT
* *
514238 TTATTTTTTATATTATGTTTTAA
1 TTATTTTTTATATCATATTTTAA
*
514261 TTATTTTTTATGTCATATTTT
1 TTATTTTTTATATCATATTTT
514282 TATATTTCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (23 bp):
TTATTTTTTATATCATATTTTAA
Found at i:514684 original size:15 final size:14
Alignment explanation
Indices: 514662--514698 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
514652 TTTATTTGAT
514662 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
514676 AAAAGAAAGAAAAAG
1 AAAA-AAAGAAAAAG
514691 AGAAAAAA
1 A-AAAAAA
514699 ATTTATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 14 0.67
16 3 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:515967 original size:4 final size:4
Alignment explanation
Indices: 515953--515984 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
515943 TTTAGCCACA
515953 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
515985 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:516231 original size:25 final size:26
Alignment explanation
Indices: 516202--516265 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
516192 ATGTTTTCTT
516202 TTATATATTTA-AAATATTAAAT-AAA
1 TTATATATTTATAAA-ATTAAATAAAA
* *
516227 TTATATTTTTATAAAATTATATAAAA
1 TTATATATTTATAAAATTAAATAAAA
*
516253 TTTTATATGTTAT
1 TTATATAT-TTAT
516266 TAATTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 16 0.50
26 12 0.38
27 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TTATATATTTATAAAATTAAATAAAA
Found at i:516294 original size:18 final size:19
Alignment explanation
Indices: 516252--516300 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
516242 ATTATATAAA
*
516252 ATTTTATATGTTATTAATTT
1 ATTTTATAT-TTATTAATAT
*
516272 ATTTTATATTT-TTTATAT
1 ATTTTATATTTATTAATAT
516290 ATTTTCATATT
1 ATTTT-ATATT
516301 CTTATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 10 0.38
19 7 0.27
20 9 0.35
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTATATTTATTAATAT
Found at i:517418 original size:26 final size:25
Alignment explanation
Indices: 517359--517418 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
517349 CAACCCAAAA
517359 AAATAATTTTAAATTAATATAATACAT
1 AAAT-ATTTTAAATTAATATAATA-AT
**
517386 ATTTATTTTAAATTTAATTATAAT-AT
1 AAATATTTTAAA-TTAA-TATAATAAT
517412 AAATATT
1 AAATATT
517419 AATTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
26 15 0.56
27 6 0.22
28 6 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATATTTTAAATTAATATAATAAT
Found at i:517441 original size:21 final size:20
Alignment explanation
Indices: 517415--517455 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
517405 ATAATATAAA
*
517415 TATTAATTAAAAAATATATTT
1 TATTAAATAAAAAATA-ATTT
*
517436 TATTAAATAAATAATAATTT
1 TATTAAATAAAAAATAATTT
517456 AAATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAAATAAAAAATAATTT
Found at i:517887 original size:23 final size:23
Alignment explanation
Indices: 517834--517892 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
517824 TTTTTTAATT
* *
517834 ATTTATATTATATATTTAAATGTG
1 ATTTATA-TATATATATAAATGTA
* *
517858 ATGTATATATATATATATATGTA
1 ATTTATATATATATATAAATGTA
*
517881 ATTTATAAATAT
1 ATTTATATATAT
517893 GTAAAATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
ATTTATATATATATATAAATGTA
Found at i:518056 original size:13 final size:14
Alignment explanation
Indices: 518027--518063 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
518017 TTATATAATA
*
518027 AAATATTAAATTTT
1 AAATATTAAATTGT
518041 AAATATT-AATTGT
1 AAATATTAAATTGT
518054 AAATA-TAAAT
1 AAATATTAAAT
518064 GATGAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 1 0.05
13 13 0.62
14 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
AAATATTAAATTGT
Found at i:518533 original size:20 final size:20
Alignment explanation
Indices: 518510--518558 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
518500 TTTTATAGAT
518510 TTTTATATATTAATTATTGA
1 TTTTATATATTAATTATTGA
*
518530 TTTTACATATTAATTATTGA
1 TTTTATATATTAATTATTGA
518550 TTTTATATA
1 TTTTATATA
518559 AGTTTTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTATATATTAATTATTGA
Found at i:519368 original size:20 final size:21
Alignment explanation
Indices: 519343--519382 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
519333 ATAATATAAA
*
519343 TATTAATTAAA-AATAATTTT
1 TATTAAATAAATAATAATTTT
519363 TATTAAATAAATAATAATTT
1 TATTAAATAAATAATAATTT
519383 AAATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTAAATAAATAATAATTTT
Found at i:519420 original size:19 final size:19
Alignment explanation
Indices: 519370--519410 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
519360 TTTTATTAAA
*
519370 TAAATA-ATAATTTAAATT
1 TAAATATATAAATTAAATT
519388 TAAATATATAAATTAAATT
1 TAAATATATAAATTAAATT
519407 TAAA
1 TAAA
519411 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATATAAATTAAATT
Found at i:519790 original size:14 final size:14
Alignment explanation
Indices: 519760--519811 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
519750 TCCATTTTAA
*
519760 TTATT-TTTTAATTT
1 TTATTATTTT-ATAT
519774 TTATTATTTTATAT
1 TTATTATTTTATAT
519788 TTATTA-TTTATAT
1 TTATTATTTTATAT
519801 TATATATATTT
1 T-TAT-TATTT
519812 AAATATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.24
14 17 0.52
15 6 0.18
16 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTTTATAT
Found at i:521532 original size:27 final size:26
Alignment explanation
Indices: 521496--521547 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
521486 TTATTTTATT
*
521496 TTAATTATTATTTATATAATAAAAATA
1 TTAATTATTAATTATA-AATAAAAATA
*
521523 TTAATTATTAATTATAAATATAAAT
1 TTAATTATTAATTATAAATAAAAAT
521548 GATGAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATTATTAATTATAAATAAAAATA
Found at i:526854 original size:18 final size:19
Alignment explanation
Indices: 526825--526862 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
526815 ATTTATATTT
526825 TTAAACTTAATAAAAATTA
1 TTAAACTTAATAAAAATTA
526844 TTAAA-TTAATAAAAATTA
1 TTAAACTTAATAAAAATTA
526862 T
1 T
526863 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAACTTAATAAAAATTA
Found at i:529322 original size:28 final size:27
Alignment explanation
Indices: 529260--529322 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
529250 TTAACGTATC
* * *
529260 AAAATTAATATAAATATAAAATAACTT
1 AAAATGAATATAAATACAAAATAACTG
529287 AAACATGAATATAACATACAAAATACAC-G
1 AAA-ATGAATATAA-ATACAAAATA-ACTG
529316 AAAATGA
1 AAAATGA
529323 CACTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 13 0.43
29 12 0.40
30 2 0.07
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (27 bp):
AAAATGAATATAAATACAAAATAACTG
Found at i:534232 original size:4 final size:4
Alignment explanation
Indices: 534223--534254 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
534213 AGAATAAAAT
534223 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
534255 AACTTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:534618 original size:14 final size:15
Alignment explanation
Indices: 534601--534629 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
534591 CACATTTACT
534601 TTTTCT-TTGATTAA
1 TTTTCTATTGATTAA
534615 TTTTCTATTGATTAA
1 TTTTCTATTGATTAA
534630 GGCTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTCTATTGATTAA
Found at i:536929 original size:17 final size:17
Alignment explanation
Indices: 536889--536958 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
536879 ATACTAGAGA
536889 TTATTTATTAATTAAATAT
1 TTATTT-TT-ATTAAATAT
* *
536908 ATATTTTTATTAATTAT
1 TTATTTTTATTAAATAT
536925 TTATTTTATATTAAA-A-
1 TTATTTT-TATTAAATAT
*
536941 ATATTTTTA-T-AATAT
1 TTATTTTTATTAAATAT
536956 TTA
1 TTA
536959 AAATTATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 4 0.10
16 6 0.14
17 15 0.36
18 8 0.19
19 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTTTATTAAATAT
Found at i:539138 original size:23 final size:18
Alignment explanation
Indices: 539087--539124 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
539077 CCACAGCCAA
539087 GACTTATTACAATTGACC
1 GACTTATTACAATTGACC
539105 GACTTATTACAATTGACC
1 GACTTATTACAATTGACC
539123 GA
1 GA
539125 TAACATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (18 bp):
GACTTATTACAATTGACC
Found at i:540390 original size:35 final size:36
Alignment explanation
Indices: 540345--540422 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 36
540335 TAATATTTAC
* *
540345 ATTTTAAATATTTAT-ATATATAATAAAAAAATTAT
1 ATTTTAAATATTTATAATATAAAATAAAAAAATTAG
* *
540380 ATTTTTAATATTTATACATATAAAATAAAATAATTAG
1 ATTTTAAATATTTATA-ATATAAAATAAAAAAATTAG
540417 ATTTTA
1 ATTTTA
540423 TTAGTGAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 14 0.39
37 22 0.61
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTTTAAATATTTATAATATAAAATAAAAAAATTAG
Found at i:540415 original size:37 final size:35
Alignment explanation
Indices: 540336--540422 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 35
540326 TATCTTAAAT
* *
540336 AATATTTACATTTTAAATATTTATATATATAATAA
1 AATAATTACATTTTAAATATTTATATATAAAATAA
* * *
540371 AAAAATTATATTTTTAATATTTATACATATAAAATAA
1 AATAATTACATTTTAAATATTTAT--ATATAAAATAA
*
540408 AATAATTAGATTTTA
1 AATAATTACATTTTA
540423 TTAGTGAGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 20 0.48
37 22 0.52
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (35 bp):
AATAATTACATTTTAAATATTTATATATAAAATAA
Found at i:540681 original size:12 final size:13
Alignment explanation
Indices: 540640--540686 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
540630 AAAGTTCGTT
540640 TATTTTATTAAAAA
1 TATTTT-TTAAAAA
540654 TATTTTTTGAAAAA
1 TATTTTTT-AAAAA
*
540668 TATTTTTT-ATAA
1 TATTTTTTAAAAA
540680 TATTTTT
1 TATTTTT
540687 GTTTGTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 10 0.32
13 2 0.06
14 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATTTTTTAAAAA
Found at i:540720 original size:19 final size:21
Alignment explanation
Indices: 540696--540745 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
540686 TGTTTGTTTT
540696 ATAAAAAAT-AATTTAGATA-
1 ATAAAAAATGAATTTAGATAG
*
540715 ATAAAAAATGACTTTAGATAG
1 ATAAAAAATGAATTTAGATAG
540736 ATGAAAAAAT
1 AT-AAAAAAT
540746 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.33
20 9 0.33
21 2 0.07
22 7 0.26
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (21 bp):
ATAAAAAATGAATTTAGATAG
Found at i:540849 original size:4 final size:4
Alignment explanation
Indices: 540840--540900 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 4
540830 GATGGCTAAT
* * * * * * *
540840 TATA TATA TATA TATG TATG TATG TATG TAGA TATG TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
540888 TATA TGTA TATA T
1 TATA TATA TATA T
540901 TTATGCAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:546754 original size:2 final size:2
Alignment explanation
Indices: 546747--546778 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
546737 GGCCCCTTTC
546747 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
546779 TCATATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548525 original size:3 final size:3
Alignment explanation
Indices: 548517--548555 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
548507 TTTGATTTGA
548517 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
548556 ATTTTGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:549185 original size:10 final size:10
Alignment explanation
Indices: 549157--549189 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
549147 TTAAAATATT
549157 ATTATATAAA
1 ATTATATAAA
*
549167 AAT-TATAAA
1 ATTATATAAA
549176 ATTATATAAA
1 ATTATATAAA
549186 ATTA
1 ATTA
549190 AATTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTATATAAA
Found at i:549517 original size:21 final size:22
Alignment explanation
Indices: 549493--549566 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 22
549483 GATTTAAAAA
549493 AATAAAAAAATATTTTAT-ATT
1 AATAAAAAAATATTTTATAATT
** *
549514 AATATTAATATATTTTTATAATT
1 AATAAAAAAATA-TTTTATAATT
549537 AAATAATATAAAAT-TTATTATAATT
1 -AATAA-A-AAAATATT-TTATAATT
549562 AATAA
1 AATAA
549567 TGATGGAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 3 0.07
24 11 0.27
25 8 0.20
26 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAAAAAAATATTTTATAATT
Found at i:553192 original size:13 final size:13
Alignment explanation
Indices: 553176--553200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553166 AAAGTAAATA
553176 TTAAAATTTTAAT
1 TTAAAATTTTAAT
553189 TTAAAATTTTAA
1 TTAAAATTTTAA
553201 ATATTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAAATTTTAAT
Found at i:553889 original size:3 final size:3
Alignment explanation
Indices: 553881--553912 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
553871 CTCCAGTTTT
553881 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
553913 GGCTAACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:555265 original size:17 final size:18
Alignment explanation
Indices: 555245--555313 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
555235 AATATAAAAA
555245 ATTTATTAATA-TTATAT
1 ATTTATTAATATTTATAT
* *
555262 ATTTGTTTGATTTATTTATAT
1 ATTT-ATT-A-ATATTTATAT
555283 ATTTATATAATATTTATAT
1 ATTTAT-TAATATTTATAT
*
555302 TTTTATT-ATATT
1 ATTTATTAATATT
555314 ATTTTTAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 9 0.21
18 3 0.07
19 15 0.36
20 4 0.10
21 11 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTATTAATATTTATAT
Found at i:555296 original size:19 final size:20
Alignment explanation
Indices: 555274--555317 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
555264 TTGTTTGATT
555274 TATTTATATATTTA-TATAA
1 TATTTATATATTTATTATAA
* *
555293 TATTTATATTTTTATTATAT
1 TATTTATATATTTATTATAA
555313 TATTT
1 TATTT
555318 TTAAGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTATATATTTATTATAA
Found at i:555320 original size:22 final size:24
Alignment explanation
Indices: 555285--555329 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
555275 ATTTATATAT
555285 TTATATAATATTT-A-TATTTTTA
1 TTATATAATATTTAAGTATTTTTA
* *
555307 TTATATTATTTTTAAGTATTTTT
1 TTATATAATATTTAAGTATTTTT
555330 GATATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATATAATATTTAAGTATTTTTA
Found at i:555542 original size:16 final size:16
Alignment explanation
Indices: 555517--555547 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
555507 AATAATAACA
555517 AATGTAAAAATAAATT
1 AATGTAAAAATAAATT
*
555533 AATGTGAAAATAAAT
1 AATGTAAAAATAAAT
555548 AAATTTAATA
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:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (16 bp):
AATGTAAAAATAAATT
Found at i:555714 original size:16 final size:15
Alignment explanation
Indices: 555677--555717 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
555667 CAATCACAAC
555677 ATAAAATAAATTTTAT
1 ATAAAAT-AATTTTAT
555693 AT-AAATAATTTTAT
1 ATAAAATAATTTTAT
555707 ATTAAAATAAT
1 A-TAAAATAAT
555718 AAAATGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.39
15 5 0.22
16 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAATAATTTTAT
Found at i:556083 original size:23 final size:23
Alignment explanation
Indices: 556057--556103 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
556047 TTATTTAAAG
*
556057 TTTATGTTAATATATTTTTATTT
1 TTTATGTTAATATATTTTAATTT
* *
556080 TTTATTTTAATTTATTTTAATTT
1 TTTATGTTAATATATTTTAATTT
556103 T
1 T
556104 AATTTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTATGTTAATATATTTTAATTT
Found at i:556095 original size:10 final size:10
Alignment explanation
Indices: 556080--556137 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
556070 ATTTTTATTT
556080 TTTATTTTAA
1 TTTATTTTAA
556090 TTTATTTTAA
1 TTTATTTTAA
*
556100 TTTTAATTTGAA
1 -TTT-ATTTTAA
*
556112 --TATATTAA
1 TTTATTTTAA
*
556120 -TTATTTAAA
1 TTTATTTTAA
556129 TTTATTTTA
1 TTTATTTTA
556138 TTTGAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
8 5 0.13
9 7 0.18
10 17 0.45
11 3 0.08
12 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:556102 original size:16 final size:17
Alignment explanation
Indices: 556073--556108 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
556063 TTAATATATT
*
556073 TTTATTTTTTATTTTAA
1 TTTATTTTTAATTTTAA
556090 TTTA-TTTTAATTTTAA
1 TTTATTTTTAATTTTAA
556106 TTT
1 TTT
556109 GAATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTAATTTTAA
Found at i:556334 original size:13 final size:15
Alignment explanation
Indices: 556304--556335 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
556294 ATTTAAATTT
556304 AAATATTTAAAATAA
1 AAATATTTAAAATAA
556319 AAATA-TTAAAATAA
1 AAATATTTAAAATAA
556333 AAA
1 AAA
556336 ATATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATATTTAAAATAA
Found at i:557312 original size:18 final size:16
Alignment explanation
Indices: 557282--557329 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
557272 TTAAATTATT
557282 ATTTTTTATTTATAAA
1 ATTTTTTATTTATAAA
* *
557298 ATTTTTATAATTTATGAG
1 ATTTTT-T-ATTTATAAA
557316 ATTTTTTATTTATA
1 ATTTTTTATTTATA
557330 TATTTACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
ATTTTTTATTTATAAA
Found at i:557404 original size:13 final size:13
Alignment explanation
Indices: 557386--557412 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
557376 ATATTTATTT
557386 TTAATTTAATTAA
1 TTAATTTAATTAA
557399 TTAATTTAATTAA
1 TTAATTTAATTAA
557412 T
1 T
557413 CGAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:557573 original size:10 final size:11
Alignment explanation
Indices: 557558--557590 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
557548 TTAGATATAA
557558 AATTAAAA-AT
1 AATTAAAATAT
557568 AATTAAAATAT
1 AATTAAAATAT
557579 AATATAAAATAT
1 AAT-TAAAATAT
557591 TATATGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 5 0.24
12 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTAAAATAT
Found at i:557629 original size:28 final size:27
Alignment explanation
Indices: 557565--557643 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 27
557555 TAAAATTAAA
* *
557565 AATAATTAAAATATAATATAAA-ATAT
1 AATATTTAAAAAATAATATAAATATAT
* **
557591 TATATGAAAAAAATAATATAAATATAT
1 AATATTTAAAAAATAATATAAATATAT
* *
557618 GAATATTTAAAAATTTATAT-AATATA
1 -AATATTTAAAAAATAATATAAATATA
557644 AATTATTAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
26 17 0.41
27 10 0.24
28 14 0.34
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
AATATTTAAAAAATAATATAAATATAT
Found at i:557640 original size:33 final size:33
Alignment explanation
Indices: 557603--557676 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
557593 TATGAAAAAA
**
557603 ATAATATAAATATATGAAT-ATTTAAAAATTTAT
1 ATAATATAAAT-TATGAATAATAAAAAAATTTAT
*
557636 ATAATATAAATTATTAATACATAAAAAAATTTAT
1 ATAATATAAATTATGAATA-ATAAAAAAATTTAT
557670 ATAATAT
1 ATAATAT
557677 GAGATAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 6 0.17
33 11 0.31
34 19 0.53
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
ATAATATAAATTATGAATAATAAAAAAATTTAT
Found at i:559713 original size:30 final size:27
Alignment explanation
Indices: 559679--559740 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
559669 GTATTTTTAT
559679 ATATTTTATTATATTATA-AATATATTTAAA
1 ATATTTTA-TAT-TTATATAA-AT-TTTAAA
*
559709 ATATTTTATATTTATATAAATTTTAAT
1 ATATTTTATATTTATATAAATTTTAAA
559736 ATATT
1 ATATT
559741 AATAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.33
28 7 0.23
29 5 0.17
30 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATTTTATATTTATATAAATTTTAAA
Found at i:559737 original size:18 final size:17
Alignment explanation
Indices: 559699--559765 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
559689 ATATTATAAA
559699 TATATTTA-A-AATATTT
1 TATATTTATATAA-ATTT
559715 TATATTTATATAAATTT
1 TATATTTATATAAATTT
559732 TAATATATTA-AT-AA-TT
1 T-ATAT-TTATATAAATTT
*
559748 TATA-TTATATAAAATT
1 TATATTTATATAAATTT
559764 TA
1 TA
559766 AGATACTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 5 0.11
16 15 0.34
17 8 0.18
18 8 0.18
19 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTTATATAAATTT
Found at i:559759 original size:32 final size:33
Alignment explanation
Indices: 559708--559775 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
559698 ATATATTTAA
* * * *
559708 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTATATAAAATTTAAGATACT
559741 AATAATTTATA-TTATATAAAATTTAAGATACT
1 AATAATTTATATTTATATAAAATTTAAGATACT
559773 AAT
1 AAT
559776 TTTTTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (33 bp):
AATAATTTATATTTATATAAAATTTAAGATACT
Found at i:559783 original size:33 final size:32
Alignment explanation
Indices: 559708--559790 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
559698 ATATATTTAA
* * *
559708 AATATTTTATATTTATATAAATTTTAATATATT
1 AATATTTTATA-TTATATAAAATTTAAGATACT
*
559741 AATAATTTATATTATATAAAATTTAAGATACT
1 AATATTTTATATTATATAAAATTTAAGATACT
* *
559773 AATTTTTTTATATAATAT
1 AA-TATTTTATATTATAT
559791 TTATATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 20 0.48
33 22 0.52
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
AATATTTTATATTATATAAAATTTAAGATACT
Found at i:565500 original size:21 final size:23
Alignment explanation
Indices: 565476--565522 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
565466 ACTCTAGCTT
565476 AAATTA-TT-ATTTAATAATAAA
1 AAATTATTTAATTTAATAATAAA
*
565497 AAATTATTTAAATTTAATTATAAA
1 AAATTATTT-AATTTAATAATAAA
565521 AA
1 AA
565523 TATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
24 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTATTTAATTTAATAATAAA
Found at i:565519 original size:24 final size:23
Alignment explanation
Indices: 565484--565570 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 23
565474 TTAAATTATT
565484 ATTTAATAATAAAAAATTATTTAA
1 ATTTAATAATAAAAAA-TATTTAA
* *
565508 ATTTAATTAT-AAAAATATATAA
1 ATTTAATAATAAAAAATATTTAA
565530 ATATTAAT-ATAAAATAATATTTTAA
1 AT-TTAATAATAAAA-AATA-TTTAA
565555 TATTTTAATAATAAAA
1 -A-TTTAATAATAAAA
565571 TGGGTCAGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
22 10 0.19
23 13 0.25
24 13 0.25
25 4 0.08
26 6 0.11
27 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAATAATAAAAAATATTTAA
Found at i:565549 original size:22 final size:21
Alignment explanation
Indices: 565490--565549 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
565480 TATTATTTAA
* * *
565490 TAATAAAAAATTATTTAAATT
1 TAATATAAAATAATATAAATT
565511 TAATTATAAAA-ATATATAAATAT
1 TAA-TATAAAATA-ATATAAAT-T
565534 TAATATAAAATAATAT
1 TAATATAAAATAATAT
565550 TTTAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 3 0.09
22 24 0.75
23 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATATAAAATAATATAAATT
Found at i:568338 original size:107 final size:107
Alignment explanation
Indices: 568152--568369 Score: 346
Period size: 107 Copynumber: 2.0 Consensus size: 107
568142 CATGATAAAA
* * * *
568152 TTCTACAAAATTCACCTACAACCTATTTAAATAAGTAGCGTTACACAAGGTATCATCCTTTTCTA
1 TTCTACAAAATTCACCTACAACCTACTTAAATAAGCAGCGTTAAAAAAGGTATCATCCTTTTCTA
568217 AACTATCCAAAGAAATTAAGATCAAAACTGAAAAAGTAATCT
66 AACTATCCAAAGAAATTAAGATCAAAACTGAAAAAGTAATCT
** * *
568259 TTCTACAAAATTTGCCTACAACCTACTTAAATATGCAGTGTTAAAAAAGGTATCATCCTTTTCTA
1 TTCTACAAAATTCACCTACAACCTACTTAAATAAGCAGCGTTAAAAAAGGTATCATCCTTTTCTA
* *
568324 AACTATCCAAAGAAATTAAGATTAAAACTGAAAAAGTAATTT
66 AACTATCCAAAGAAATTAAGATCAAAACTGAAAAAGTAATCT
568366 TTCT
1 TTCT
568370 CTTCCATTAT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (107 bp):
TTCTACAAAATTCACCTACAACCTACTTAAATAAGCAGCGTTAAAAAAGGTATCATCCTTTTCTA
AACTATCCAAAGAAATTAAGATCAAAACTGAAAAAGTAATCT
Found at i:570121 original size:10 final size:11
Alignment explanation
Indices: 570096--570232 Score: 57
Period size: 11 Copynumber: 13.4 Consensus size: 11
570086 CTTCGATCCG
570096 ATTTAAATTAA
1 ATTTAAATTAA
*
570107 ATTTAAGTT-A
1 ATTTAAATTAA
570117 ATTT--A-TAA
1 ATTTAAATTAA
** *
570125 ATTTATTTTATT
1 ATTTAAATTA-A
*
570137 ATTAAAATTAA
1 ATTTAAATTAA
570148 ATTTAAA-TAA
1 ATTTAAATTAA
* **
570158 TTTTTTATT-A
1 ATTTAAATTAA
570168 A-TTAAATAATAA
1 ATTTAAAT--TAA
570180 A-TTAAATTAA
1 ATTTAAATTAA
570190 A-TTAAATT-A
1 ATTTAAATTAA
* *
570199 ATTTATATAAA
1 ATTTAAATTAA
570210 ATTT---TTAA
1 ATTTAAATTAA
*
570218 ATTTAAATTTA
1 ATTTAAATTAA
570229 ATTT
1 ATTT
570233 GATTAAAACT
Statistics
Matches: 93, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
7 1 0.01
8 12 0.13
9 6 0.06
10 29 0.31
11 30 0.32
12 15 0.16
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:570223 original size:29 final size:29
Alignment explanation
Indices: 570186--570248 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
570176 ATAAATTAAA
*
570186 TTAAATTAAA-TTAATTT-ATATAAAATTT
1 TTAAATTAAATTTAATTTGAT-TAAAACTT
570214 TTAAATTTAAATTTAATTTGATTAAAACTT
1 TTAAA-TTAAATTTAATTTGATTAAAACTT
570244 TTAAA
1 TTAAA
570249 CAGTTATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 5 0.16
29 5 0.16
30 19 0.61
31 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAATTAAATTTAATTTGATTAAAACTT
Found at i:570665 original size:2 final size:2
Alignment explanation
Indices: 570653--570682 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
570643 ATCTCCTTTG
*
570653 AT AT GT 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
570683 TTTGTTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:575408 original size:22 final size:21
Alignment explanation
Indices: 575362--575405 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
575352 AAAAATATAT
*
575362 ATTTTTTATTAATTATTAATTA
1 ATTTTTTATTAATAATT-ATTA
575384 ATTTTTTATATAATAATT-TTA
1 ATTTTTTAT-TAATAATTATTA
575405 A
1 A
575406 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTTATTAATAATTATTA
Found at i:576424 original size:20 final size:18
Alignment explanation
Indices: 576401--576450 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
576391 TAAAATAATT
576401 ATAATATTTTTAAATAATAA
1 ATAATATTTTTAAAT--TAA
*
576421 ATAA-GTTTTTAAATTAA
1 ATAATATTTTTAAATTAA
576438 A-AATATTTGTTAA
1 ATAATATTT-TTAA
576451 TTTTGATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 7 0.27
18 4 0.15
19 9 0.35
20 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAATATTTTTAAATTAA
Found at i:576496 original size:28 final size:29
Alignment explanation
Indices: 576465--576536 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 29
576455 GATTAGTTTA
*
576465 ATTTATATTA-TT-ATTTAATATTAAAAAT
1 ATTTATATTATTTAATTTAAT-TAAAAAAT
* *
576493 ATTTTTTTTATTTAAATTTAATTAAAAAAT
1 ATTTATATTATTT-AATTTAATTAAAAAAT
* *
576523 ATTTAAATTTTTTA
1 ATTTATATTATTTA
576537 TTAATATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
28 8 0.24
29 3 0.09
30 16 0.47
31 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTATATTATTTAATTTAATTAAAAAAT
Found at i:577182 original size:2 final size:2
Alignment explanation
Indices: 577175--577204 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
577165 CCCTCAGGTC
577175 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
577205 CATTTGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577517 original size:16 final size:17
Alignment explanation
Indices: 577496--577572 Score: 65
Period size: 16 Copynumber: 4.7 Consensus size: 17
577486 CATTGCTATC
577496 TATTTTAAAT-TATTTA
1 TATTTTAAATATATTTA
**
577512 TATTTTTTATATATTTA
1 TATTTTAAATATATTTA
* *
577529 -AATATAAATATATTTA
1 TATTTTAAATATATTTA
577545 TATTTTATTAA-A-ATTTA
1 TATTTTA--AATATATTTA
577562 TA-TTTAAATAT
1 TATTTTAAATAT
577573 TAAATAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 24 0.51
17 17 0.36
18 1 0.02
19 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTAAATATATTTA
Found at i:577581 original size:23 final size:22
Alignment explanation
Indices: 577521--577608 Score: 87
Period size: 23 Copynumber: 4.1 Consensus size: 22
577511 ATATTTTTTA
*
577521 TATATTTAAATATAAATATATT
1 TATATTTAAATATAAATAAATT
*
577543 TATATTT---TAT-TA-AAATT
1 TATATTTAAATATAAATAAATT
577560 TATATTTAAATATTAAATAAATT
1 TATATTTAAATA-TAAATAAATT
* *
577583 TATATATTTAATATAAATATATT
1 TATAT-TTAAATATAAATAAATT
577606 TAT
1 TAT
577609 TTTTTTATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
17 11 0.20
18 1 0.02
19 3 0.06
20 2 0.04
21 1 0.02
22 8 0.15
23 22 0.41
24 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATTTAAATATAAATAAATT
Found at i:577583 original size:17 final size:19
Alignment explanation
Indices: 577563--577600 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
577553 TAAAATTTAT
577563 ATTTAAATA-TTAA-ATAA
1 ATTTAAATATTTAATATAA
*
577580 ATTTATATATTTAATATAA
1 ATTTAAATATTTAATATAA
577599 AT
1 AT
577601 ATATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 4 0.22
19 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATATTTAATATAA
Found at i:577795 original size:22 final size:21
Alignment explanation
Indices: 577767--577824 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
577757 GCGTGATCCG
577767 TTTTATTGATTTTTTTAAAA-A
1 TTTTATT-ATTTTTTTAAAATA
*
577788 TTATTATTTTATTTTTTAAAATA
1 TT-TTATTAT-TTTTTTAAAATA
577811 TTTTATATATTTTT
1 TTTTAT-TATTTTT
577825 ATATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 3 0.10
22 23 0.74
23 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATTATTTTTTTAAAATA
Found at i:577808 original size:21 final size:19
Alignment explanation
Indices: 577777--577825 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
577767 TTTTATTGAT
*
577777 TTTTTTAAAAATTATTATTTTA
1 TTTTTT-AAAA-TATT-TTATA
577799 TTTTTTAAAATATTTTATA
1 TTTTTTAAAATATTTTATA
577818 TATTTTTA
1 T-TTTTTA
577826 TATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 10 0.40
21 4 0.16
22 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTTAAAATATTTTATA
Found at i:577824 original size:10 final size:10
Alignment explanation
Indices: 577811--577839 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
577801 TTTTAAAATA
577811 TTTTATATAT
1 TTTTATATAT
577821 TTTTATATAT
1 TTTTATATAT
577831 TTTTA-ATAT
1 TTTTATATAT
577840 AAATAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:577930 original size:26 final size:27
Alignment explanation
Indices: 577856--577930 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
577846 ACTAATATAT
* *
577856 TAAAT-AATTATATATAAATTATATTTA
1 TAAATAAATAATA-ATAAATTATTTTTA
*
577883 TAAATAAATAATAATACA-TATTTTTA
1 TAAATAAATAATAATAAATTATTTTTA
*
577909 TAACATAAA-ACTAA-AAATTATT
1 TAA-ATAAATAATAATAAATTATT
577931 AGTAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 2 0.05
26 18 0.45
27 14 0.35
28 6 0.15
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATAAATAATAATAAATTATTTTTA
Found at i:578132 original size:3 final size:3
Alignment explanation
Indices: 578124--578154 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
578114 TATTTAACCA
578124 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
578155 GTGATGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:578825 original size:17 final size:20
Alignment explanation
Indices: 578789--578825 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
578779 TTCTTTGATT
578789 TAAACAAATATTTATATTAA
1 TAAACAAATATTTATATTAA
578809 TAAA-AAAT-TTTAT-TTAA
1 TAAACAAATATTTATATTAA
578826 ATTTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 4 0.24
20 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAACAAATATTTATATTAA
Found at i:579131 original size:2 final size:2
Alignment explanation
Indices: 579126--579157 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
579116 TGAAAATTTC
579126 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
579158 TGGAATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:579282 original size:14 final size:14
Alignment explanation
Indices: 579239--579285 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
579229 GAATGAAATT
579239 TTTTAATTCTTATA
1 TTTTAATTCTTATA
* *
579253 TTATTAAAAT-TAATA
1 TT-TT-AATTCTTATA
579268 TTTTAATTCTTATA
1 TTTTAATTCTTATA
579282 TTTT
1 TTTT
579286 TAAAAGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.12
14 12 0.46
15 8 0.31
16 3 0.12
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAATTCTTATA
Found at i:579286 original size:15 final size:15
Alignment explanation
Indices: 579238--579288 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
579228 TGAATGAAAT
579238 TTTTTAATTCTTATA
1 TTTTTAATTCTTATA
* **
579253 TTATTAA-AATTA-A
1 TTTTTAATTCTTATA
579266 TATTTTAATTCTTATA
1 T-TTTTAATTCTTATA
579282 TTTTTAA
1 TTTTTAA
579289 AAGTTATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAATTCTTATA
Found at i:580270 original size:19 final size:19
Alignment explanation
Indices: 580246--580286 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
580236 AAAATTGATT
*
580246 AAATCGAATA-AACTTATAA
1 AAATCGAA-AGAACTAATAA
580265 AAATCGAAAGAACTAATAA
1 AAATCGAAAGAACTAATAA
580284 AAA
1 AAA
580287 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATCGAAAGAACTAATAA
Found at i:588103 original size:99 final size:100
Alignment explanation
Indices: 587916--588103 Score: 226
Period size: 99 Copynumber: 1.9 Consensus size: 100
587906 TTCATTTAGT
587916 GGTAAATGTTTCGTGAGTTAAATTAATTATTTAAATTTAAAAATTTATTATATTAAAAAATAATA
1 GGTAAATGTTTCGTGAGTTAAATTAATTATTTAAATTTAAAAATTTATTATATTAAAAAATAATA
** * **
587981 TTTTTTAACATACATTATTTTTTATCTTAATAATA
66 TTTAATAACAAACATTAAATTTTATCTTAATAATA
*
588016 GGTAAATGTTTACG-G-GTTAAATTAGTTATTTAAATTTAAAAATTTATCTAATAATT-AAAAA-
1 GGTAAATGTTT-CGTGAGTTAAATTAATTATTTAAATTTAAAAATTTAT-T-AT-ATTAAAAAAT
*
588077 AAT-TTTAAATAA-AAATATTAAATTTTA
62 AATATTT-AATAACAAACATTAAATTTTA
588104 AAAAATAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
99 45 0.59
100 19 0.25
101 9 0.12
102 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (100 bp):
GGTAAATGTTTCGTGAGTTAAATTAATTATTTAAATTTAAAAATTTATTATATTAAAAAATAATA
TTTAATAACAAACATTAAATTTTATCTTAATAATA
Found at i:588409 original size:10 final size:10
Alignment explanation
Indices: 588394--588440 Score: 60
Period size: 10 Copynumber: 4.5 Consensus size: 10
588384 ATACAAACAA
588394 ATTTAAATAT
1 ATTTAAATAT
588404 ATTTAAATTATTT
1 ATTTAAA-TA--T
588417 ATTTAAATAT
1 ATTTAAATAT
588427 ATTTAAAT-T
1 ATTTAAATAT
588436 ATTTA
1 ATTTA
588441 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.18
10 16 0.47
11 2 0.06
12 2 0.06
13 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTTAAATAT
Found at i:588420 original size:23 final size:23
Alignment explanation
Indices: 588394--588452 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
588384 ATACAAACAA
588394 ATTTAAATATATTTAAATTATTT
1 ATTTAAATATATTTAAATTATTT
588417 ATTTAAATATATTTAAATTATTT
1 ATTTAAATATATTTAAATTATTT
*
588440 ATTTAAAAATATT
1 ATTTAAATATATT
588453 AATAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTAAATATATTTAAATTATTT
Found at i:588431 original size:14 final size:13
Alignment explanation
Indices: 588403--588446 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
588393 AATTTAAATA
588403 TATTTAAATTATT
1 TATTTAAATTATT
588416 TATTTAAA-TA--
1 TATTTAAATTATT
588426 TATTTAAATTATT
1 TATTTAAATTATT
588439 TATTTAAA
1 TATTTAAA
588447 AATATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 2 0.07
13 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTAAATTATT
Found at i:589014 original size:15 final size:16
Alignment explanation
Indices: 588984--589033 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 16
588974 ATTTTATTTT
588984 TATATAAATATTATAAA
1 TATATAAAT-TTATAAA
*
589001 TTTAT-AATTTAT-AA
1 TATATAAATTTATAAA
589015 TATATAAATTT-TAAA
1 TATATAAATTTATAAA
589030 -ATAT
1 TATAT
589034 TTATATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 11 0.38
15 11 0.38
16 3 0.10
17 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATAAATTTATAAA
Found at i:589690 original size:24 final size:24
Alignment explanation
Indices: 589661--589712 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
589651 TTGATATTAA
* *
589661 ATTATATTTTTA-TTATTTTATATT
1 ATTATATTTGTATTTATATT-TATT
589685 ATTATATTTGTATTTATATTTATT
1 ATTATATTTGTATTTATATTTATT
589709 ATTA
1 ATTA
589713 AATCTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTATATTTGTATTTATATTTATT
Found at i:590065 original size:13 final size:13
Alignment explanation
Indices: 590043--590085 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
590033 TACATATATA
*
590043 AATATAAATATTT
1 AATATTAATATTT
590056 AATATTAATATTT
1 AATATTAATATTT
*
590069 AAATATATAAAATTT
1 -AATAT-TAATATTT
590084 AA
1 AA
590086 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 12 0.46
14 7 0.27
15 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATTAATATTT
Done.