Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 13 of 19
Found at i:5285256 original size:15 final size:15
Alignment explanation
Indices: 5285238--5285282 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
5285228 CATTGCCATT
*
5285238 ATTATCATTATCTTC
1 ATTATCATCATCTTC
5285253 ATTATCATCATTCTT-
1 ATTATCATCA-TCTTC
*
5285268 ATTAGCATCATCTTC
1 ATTATCATCATCTTC
5285283 GTTACTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTATCATCATCTTC
Found at i:5290182 original size:140 final size:140
Alignment explanation
Indices: 5289930--5290209 Score: 542
Period size: 140 Copynumber: 2.0 Consensus size: 140
5289920 TCAGCTGGTT
*
5289930 CTATGTTTACTTCAGTGTTTTGTTTCTTTGAAGAGACTAGCAAACATAATATAATCGCCATATTT
1 CTATGTTTACATCAGTGTTTTGTTTCTTTGAAGAGACTAGCAAACATAATATAATCGCCATATTT
*
5289995 TTGGTCAAAACTCTTCCATCTTTGATTAGTAAATGATTTTGGTGATTTCTTATGTAGGCTTTGGA
66 TTGGTCAAAACTCTTCCATCTTTGATTAGAAAATGATTTTGGTGATTTCTTATGTAGGCTTTGGA
5290060 AAGTGTTGAA
131 AAGTGTTGAA
5290070 CTATGTTTACATCAGTGTTTTGTTTCTTTGAAGAGACTAGCAAACATAATATAATCGCCATATTT
1 CTATGTTTACATCAGTGTTTTGTTTCTTTGAAGAGACTAGCAAACATAATATAATCGCCATATTT
5290135 TTGGTCAAAACTCTTCCATCTTTGATTAGAAAATGATTTTGGTGATTTCTTATGTAGGCTTTGGA
66 TTGGTCAAAACTCTTCCATCTTTGATTAGAAAATGATTTTGGTGATTTCTTATGTAGGCTTTGGA
5290200 AAGTGTTGAA
131 AAGTGTTGAA
5290210 TTCAACAGGG
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (140 bp):
CTATGTTTACATCAGTGTTTTGTTTCTTTGAAGAGACTAGCAAACATAATATAATCGCCATATTT
TTGGTCAAAACTCTTCCATCTTTGATTAGAAAATGATTTTGGTGATTTCTTATGTAGGCTTTGGA
AAGTGTTGAA
Found at i:5291374 original size:2 final size:2
Alignment explanation
Indices: 5291367--5291400 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5291357 AAAGCAATAC
**
5291367 AT AT AT AT AT AT AT AT AT AT AT AT CC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5291401 GACAGTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5295530 original size:28 final size:29
Alignment explanation
Indices: 5295498--5295552 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
5295488 ATTGAAAAAA
5295498 ATTTAAATAA-TTTTGTAT-TTTTTATTAT
1 ATTTAAATAAGTTTT-TATATTTTTATTAT
*
5295526 ATTTAATTAAGTTTTTATATTTTTATT
1 ATTTAAATAAGTTTTTATATTTTTATT
5295553 TTAAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (29 bp):
ATTTAAATAAGTTTTTATATTTTTATTAT
Found at i:5295838 original size:30 final size:30
Alignment explanation
Indices: 5295804--5295864 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5295794 TTATAAGGAC
*
5295804 TTATTTAATTCAAAATAAAAATAT-AAAGTT
1 TTATTTAACT-AAAATAAAAATATAAAAGTT
* *
5295834 TTATTTGACTAAAATAAAAATCTAAAAGTT
1 TTATTTAACTAAAATAAAAATATAAAAGTT
5295864 T
1 T
5295865 GATTAAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (30 bp):
TTATTTAACTAAAATAAAAATATAAAAGTT
Found at i:5295918 original size:20 final size:21
Alignment explanation
Indices: 5295895--5295933 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5295885 CCAAAATTTA
5295895 TTAA-AAAATTTTTAAATAGT
1 TTAAGAAAATTTTTAAATAGT
*
5295915 TTAAGAAATTTTTTAAATA
1 TTAAGAAAATTTTTAAATA
5295934 TTATGTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TTAAGAAAATTTTTAAATAGT
Found at i:5316107 original size:110 final size:110
Alignment explanation
Indices: 5315911--5316131 Score: 293
Period size: 110 Copynumber: 2.0 Consensus size: 110
5315901 AGAAATCAAT
** *
5315911 TACATCAAACATTTAGGAACAACTGCCTCAGTAAATCAATTAAACCAAACCGTTTAATCCAAATC
1 TACATCAAACATTTAGGAACAACTAACTCAATAAATCAATTAAACCAAACCGTTTAATCCAAATC
* *
5315976 GTAATTAATTTGTGTAAATAATCACTT-TGAT-ATGATTTTACTCAC
66 ATAATTAATTTGAGTAAATAATCA-TTCTGATCA-GATTTTACTCAC
* * * * * *
5316021 TACATCAAACATTTAGGAACAATTAACTTAATAAATTAATTAAACCGAACCGTTTAATCTAAATT
1 TACATCAAACATTTAGGAACAACTAACTCAATAAATCAATTAAACCAAACCGTTTAATCCAAATC
* *
5316086 ATAATTAATTTGAGTAGATAATTATTCTGATCAGATTTTACTCAC
66 ATAATTAATTTGAGTAAATAATCATTCTGATCAGATTTTACTCAC
5316131 T
1 T
5316132 CCGCAGGTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
109 2 0.02
110 93 0.97
111 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (110 bp):
TACATCAAACATTTAGGAACAACTAACTCAATAAATCAATTAAACCAAACCGTTTAATCCAAATC
ATAATTAATTTGAGTAAATAATCATTCTGATCAGATTTTACTCAC
Found at i:5319553 original size:27 final size:27
Alignment explanation
Indices: 5319486--5319559 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
5319476 GATCACGAAA
5319486 AATTATTAATTAATAAAAATAATATTT
1 AATTATTAATTAATAAAAATAATATTT
* * * *
5319513 AATTAATAAATAAT-AAATTATTAATTT
1 AATTATTAATTAATAAAAATAAT-ATTT
5319540 -ATATATTAATTAATAAAAAT
1 AAT-TATTAATTAATAAAAAT
5319560 TTAATTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 8 0.22
27 25 0.68
28 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTATTAATTAATAAAAATAATATTT
Found at i:5319563 original size:27 final size:27
Alignment explanation
Indices: 5319489--5319568 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 27
5319479 CACGAAAAAT
5319489 TATTAATTAATAAAAA--TAATATT-TA
1 TATTAATTAATAAAAATTTAAT-TTATA
*
5319514 -ATTAATAAATAATAAATTATTAATTTATA
1 TATTAATTAATAA-AAA-T-TTAATTTATA
5319543 TATTAATTAATAAAAATTTAATTTAT
1 TATTAATTAATAAAAATTTAATTTAT
5319569 TAACTTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
24 11 0.24
25 3 0.07
27 9 0.20
28 3 0.07
29 9 0.20
30 11 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TATTAATTAATAAAAATTTAATTTATA
Found at i:5319569 original size:35 final size:33
Alignment explanation
Indices: 5319507--5319576 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
5319497 AATAAAAATA
*
5319507 ATATTTAATTAATAAATAATAAATTATTAATTT
1 ATATTTAATTAATAAATAATAAATTATTAACTT
*
5319540 ATATATTAATTAATAAA-AATTTAATTTATTAACTT
1 ATAT-TTAATTAATAAATAA--TAAATTATTAACTT
5319575 AT
1 AT
5319577 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 6 0.19
34 12 0.38
35 14 0.44
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
ATATTTAATTAATAAATAATAAATTATTAACTT
Found at i:5319925 original size:26 final size:27
Alignment explanation
Indices: 5319882--5319936 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
5319872 AGTCATTTTG
5319882 TACAAAGCCTTCTAATTAAGTTAT-TA
1 TACAAAGCCTTCTAATTAAGTTATGTA
* * *
5319908 TACAAAGCTTTTTCATTAAGTTATGTA
1 TACAAAGCCTTCTAATTAAGTTATGTA
5319935 TA
1 TA
5319937 TATATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (27 bp):
TACAAAGCCTTCTAATTAAGTTATGTA
Found at i:5320107 original size:17 final size:18
Alignment explanation
Indices: 5320069--5320107 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5320059 TCTATCAAAA
*
5320069 ATATTATTTTATTAACAT
1 ATATTAATTTATTAACAT
5320087 -TATTAATTTATTAA-AT
1 ATATTAATTTATTAACAT
5320103 ATATT
1 ATATT
5320108 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTAATTTATTAACAT
Found at i:5321103 original size:2 final size:2
Alignment explanation
Indices: 5321066--5321091 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5321056 TAACTCTCCA
5321066 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
5321092 GCGTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5338336 original size:2 final size:2
Alignment explanation
Indices: 5338329--5338364 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5338319 TGTTTGTCTG
5338329 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
5338365 GGCCTTGAAT
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:5349409 original size:32 final size:32
Alignment explanation
Indices: 5349368--5349430 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
5349358 TTATATATAG
* *
5349368 TGATGGACTGCCCTTATCCTGTTAATTAGAAA
1 TGATGGACTGCCCTCATCCTGCTAATTAGAAA
*
5349400 TGATGGACTGCCCTCATTCTGCTAATTAGAA
1 TGATGGACTGCCCTCATCCTGCTAATTAGAA
5349431 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (32 bp):
TGATGGACTGCCCTCATCCTGCTAATTAGAAA
Found at i:5351049 original size:2 final size:2
Alignment explanation
Indices: 5351044--5351079 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5351034 CAGGGAGAGA
* *
5351044 AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5351080 GATTGCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5360815 original size:2 final size:2
Alignment explanation
Indices: 5360810--5360849 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5360800 TCTCTCTCTC
*
5360810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5360850 TGGGTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5366952 original size:1 final size:1
Alignment explanation
Indices: 5366946--5366982 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
5366936 AGAGAATTTC
* *
5366946 TTTTTTTTTTTTTTTTTTTTTTTTATTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5366983 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:5366983 original size:13 final size:12
Alignment explanation
Indices: 5366947--5366986 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
5366937 GAGAATTTCT
*
5366947 TTTTTTTTTTTT
1 TTTTTTTTTTTA
5366959 TTTTTTTTTTTA
1 TTTTTTTTTTTA
5366971 TTTTATTTTTTTA
1 TTTT-TTTTTTTA
5366984 TTT
1 TTT
5366987 AAAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:5384904 original size:13 final size:13
Alignment explanation
Indices: 5384886--5384919 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5384876 AAAAAATTGA
5384886 AATTGAATCAATC
1 AATTGAATCAATC
*
5384899 AATTGAATCGATC
1 AATTGAATCAATC
5384912 AGATTGAA
1 A-ATTGAA
5384920 AACACCATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (13 bp):
AATTGAATCAATC
Found at i:5385550 original size:22 final size:22
Alignment explanation
Indices: 5385514--5385575 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
5385504 TAATTTTGGT
* * *
5385514 AGTTTTTAAGCATTACGTAACC
1 AGTTTTTAGGTATTACATAACC
* *
5385536 AGTTTTTAGGTATTATATAACT
1 AGTTTTTAGGTATTACATAACC
5385558 AGTTTTTAGGTATTACAT
1 AGTTTTTAGGTATTACAT
5385576 GATTAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (22 bp):
AGTTTTTAGGTATTACATAACC
Found at i:5385585 original size:22 final size:22
Alignment explanation
Indices: 5385538--5385623 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
5385528 ACGTAACCAG
* * *
5385538 TTTTTAGGTATTATATAACTAG
1 TTTTTAGGTATTACATGACTAA
*
5385560 TTTTTAGGTATTACATGATTAA
1 TTTTTAGGTATTACATGACTAA
*
5385582 TTTTTAGATATTACATGACTAA
1 TTTTTAGGTATTACATGACTAA
** *
5385604 TTTTTAAATATTACGTGACT
1 TTTTTAGGTATTACATGACT
5385624 GATTAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (22 bp):
TTTTTAGGTATTACATGACTAA
Found at i:5387199 original size:2 final size:2
Alignment explanation
Indices: 5387192--5387230 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5387182 TGCAGATGTG
5387192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5387231 TTCTTGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5388741 original size:22 final size:23
Alignment explanation
Indices: 5388700--5388742 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5388690 TGTCTTAAAC
* *
5388700 ATTTTATTCAAGATATAATTGAG
1 ATTTTATTCAAGAAAAAATTGAG
5388723 ATTTTATT-AAGAAAAAATTG
1 ATTTTATTCAAGAAAAAATTG
5388743 GCACAAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (23 bp):
ATTTTATTCAAGAAAAAATTGAG
Found at i:5403076 original size:21 final size:22
Alignment explanation
Indices: 5403050--5403090 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5403040 TAATATCCCA
*
5403050 AAAAAATTAAA-AATTATTTTT
1 AAAAAATTAAATAAATATTTTT
5403071 AAAAAATTAAATAAATATTT
1 AAAAAATTAAATAAATATTT
5403091 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAAATTAAATAAATATTTTT
Found at i:5403282 original size:20 final size:21
Alignment explanation
Indices: 5403259--5403304 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
5403249 AAAAAATAAA
* *
5403259 AATTCATTTAAAAA-TTTTTT
1 AATTAATTTAAAAACTTTTTC
5403279 AATTAATTTAAAAACTTTTTC
1 AATTAATTTAAAAACTTTTTC
5403300 AATTA
1 AATTA
5403305 TTGCATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAATTTAAAAACTTTTTC
Found at i:5406284 original size:30 final size:29
Alignment explanation
Indices: 5406208--5406284 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
5406198 TATTTTAAAA
5406208 AATT-AAATAAATTTTTATTTTTTATTAT
1 AATTCAAATAAATTTTTATTTTTTATTAT
* * *
5406236 -ATTCAATTAAAATCTTTATGTTTTTATTTT
1 AATTCAAAT-AAATTTTTAT-TTTTTATTAT
5406266 AATTCAAATAAATTTTTAT
1 AATTCAAATAAATTTTTAT
5406285 AATTAATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.08
28 3 0.08
29 9 0.22
30 18 0.45
31 7 0.17
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
AATTCAAATAAATTTTTATTTTTTATTAT
Found at i:5406560 original size:30 final size:30
Alignment explanation
Indices: 5406524--5406582 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5406514 AATTATCAAG
5406524 AACTTATTTGATTCAAAATAAAAATATAAT
1 AACTTATTTGATTCAAAATAAAAATATAAT
5406554 AACTTATTTGATTCAAAATAAAAATATAA
1 AACTTATTTGATTCAAAATAAAAATATAA
5406583 AATTTGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (30 bp):
AACTTATTTGATTCAAAATAAAAATATAAT
Found at i:5407602 original size:11 final size:12
Alignment explanation
Indices: 5407585--5407613 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5407575 AATTTTTCTG
5407585 GGAAAAAAAAAA
1 GGAAAAAAAAAA
5407597 -GAAAAAAAAAA
1 GGAAAAAAAAAA
5407608 GGAAAA
1 GGAAAA
5407614 TCTTGTGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
GGAAAAAAAAAA
Found at i:5413908 original size:17 final size:19
Alignment explanation
Indices: 5413888--5413925 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5413878 GATTCACTAA
5413888 ATTA-ATTTT-TTATTTTT
1 ATTATATTTTCTTATTTTT
5413905 ATTATATTTTCCTTATTTTT
1 ATTATATTTT-CTTATTTTT
5413925 A
1 A
5413926 ATGATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
20 9 0.50
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTATATTTTCTTATTTTT
Found at i:5423497 original size:3 final size:3
Alignment explanation
Indices: 5423489--5423516 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5423479 GGAACCAAAA
5423489 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
5423517 GATAGACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5426107 original size:44 final size:47
Alignment explanation
Indices: 5425991--5426132 Score: 146
Period size: 50 Copynumber: 3.0 Consensus size: 47
5425981 ACTACTCGAG
* * *
5425991 AGAAAATGAGACAATTGTAGAGTTATTGAATGATAAGCAAATTATTAAGA
1 AGAAAAT-AGACAATTGTAGAGTTATTGAGTGACAAGCAAATTGTT--GA
* * *
5426041 AGAAAATGAGACTATTATAGAGTTATTGAGTGACAAGTAAATTGTTGA
1 AGAAAAT-AGACAATTGTAGAGTTATTGAGTGACAAGCAAATTGTTGA
* * *
5426089 A-AAAAT-G-CAATTGTAGAGTTGTTGGGTGACAAGCAAAATGTTGA
1 AGAAAATAGACAATTGTAGAGTTATTGAGTGACAAGCAAATTGTTGA
5426133 GAACGTAATG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
44 31 0.39
45 1 0.01
47 5 0.06
48 3 0.04
50 40 0.50
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (47 bp):
AGAAAATAGACAATTGTAGAGTTATTGAGTGACAAGCAAATTGTTGA
Found at i:5426531 original size:17 final size:17
Alignment explanation
Indices: 5426493--5426535 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
5426483 CGGAATTGAT
5426493 TAAAAA-TATTATTTAA
1 TAAAAATTATTATTTAA
*
5426509 TTAAAATTATTAATTT-A
1 TAAAAATTATT-ATTTAA
5426526 TAAAAATTAT
1 TAAAAATTAT
5426536 CTTGTACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATTATTATTTAA
Found at i:5456221 original size:15 final size:15
Alignment explanation
Indices: 5456200--5456609 Score: 117
Period size: 15 Copynumber: 26.9 Consensus size: 15
5456190 TTTTAATGTC
5456200 ATATATTTTATTTTT
1 ATATATTTTATTTTT
* * *
5456215 ATTTATTATATATTT
1 ATATATTTTATTTTT
5456230 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
5456245 AATATATTATATTTATT
1 -ATATATTTTATTT-TT
*
5456262 AT-TA-TTAATTTTT
1 ATATATTTTATTTTT
* * *
5456275 ATATAATATCATCTCTTAA
1 ATAT-ATTTTAT-T-TT-T
* *
5456294 ATATATTTT-TGATGTC
1 ATATATTTTAT--TTTT
5456310 ATATATTTTATTTTT
1 ATATATTTTATTTTT
* *
5456325 ATTTATTATTATAATCTT
1 ATATATT-TTAT--TTTT
5456343 ATATATTTTATTTTT
1 ATATATTTTATTTTT
5456358 AATATATTTATATTTTT
1 -ATATATTT-TATTTTT
*
5456375 -TAT-TGTTAATTTTT
1 ATATAT-TTTATTTTT
* * *
5456389 ATATAATATCATCTCTT
1 ATAT-ATTTTAT-TTTT
*
5456406 A-A-A-TATATTTTT
1 ATATATTTTATTTTT
* **
5456418 A-ATGTCATATATTTT
1 ATATATTTTAT-TTTT
* *
5456433 ATTTCA-TTTATTATT
1 ATAT-ATTTTATTTTT
*
5456448 ATA-ATCTTATATATTT
1 ATATAT-TT-TATTTTT
5456464 -TAT-TTTTATTTTT
1 ATATATTTTATTTTT
5456477 AATATATTTT-TTATATT
1 -ATATATTTTATT-T-TT
*
5456494 ATATATTTTATTTTA
1 ATATATTTTATTTTT
* *
5456509 ATTTGTTTTACCTATATTAT
1 ATATATTTTA--T-T-TT-T
* *
5456529 ATAAATTTTAATTTT
1 ATATATTTTATTTTT
5456544 A-ATATTTTA--TTT
1 ATATATTTTATTTTT
*
5456556 -TAT-TTTAATTTTT
1 ATATATTTTATTTTT
* *
5456569 A-AT-TCTTA-TATT
1 ATATATTTTATTTTT
*
5456581 ATATATTTTATTTTA
1 ATATATTTTATTTTT
*
5456596 ATATTTTTTATTTT
1 ATATATTTTATTTT
5456610 AATTATAACA
Statistics
Matches: 289, Mismatches: 59, Indels: 94
0.65 0.13 0.21
Matches are distributed among these distances:
11 4 0.01
12 14 0.05
13 23 0.08
14 31 0.11
15 92 0.32
16 68 0.24
17 28 0.10
18 16 0.06
19 6 0.02
20 7 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:5456224 original size:20 final size:20
Alignment explanation
Indices: 5456201--5456266 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 20
5456191 TTTAATGTCA
5456201 TATATTTTATTTTTATTTATT
1 TATATTTTATTTTTATTTA-T
5456222 ATATATTTATATATTTTATTT-T
1 -TATATTT-TAT-TTTTATTTAT
* *
5456244 TAATATATTATATTTA-TTAT
1 T-ATATTTTATTTTTATTTAT
5456264 TAT
1 TAT
5456267 TAATTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
19 4 0.11
20 6 0.16
21 4 0.11
22 13 0.34
23 3 0.08
24 8 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATATTTTATTTTTATTTAT
Found at i:5456375 original size:24 final size:24
Alignment explanation
Indices: 5456310--5456392 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
5456300 TTTTGATGTC
5456310 ATATATTT-TA-TTTTTATTTATTA
1 ATATATTTATATTTTTTATTT-TTA
* *
5456333 TTATAATCTTATATATTTTATTTTTA
1 ATAT-AT-TTATATTTTTTATTTTTA
*
5456359 ATATATTTATATTTTTTATTGTTA
1 ATATATTTATATTTTTTATTTTTA
5456383 AT-T-TTTATAT
1 ATATATTTATAT
5456393 AATATCATCT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.14
23 4 0.08
24 20 0.39
25 4 0.08
26 8 0.16
27 8 0.16
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (24 bp):
ATATATTTATATTTTTTATTTTTA
Found at i:5456393 original size:24 final size:24
Alignment explanation
Indices: 5456200--5456279 Score: 66
Period size: 23 Copynumber: 3.5 Consensus size: 24
5456190 TTTTAATGTC
*
5456200 ATATATTT-TAT-TTTTATT-TATT
1 ATATATTTATATATTTTATTGT-TA
*
5456222 ATATATTTATATATTTTATTTTTA
1 ATATATTTATATATTTTATTGTTA
*
5456246 ATATA-TTATAT-TTATTATTATTA
1 ATATATTTATATATT-TTATTGTTA
5456269 AT-T-TTTATATA
1 ATATATTTATATA
5456280 ATATCATCTC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
22 17 0.34
23 19 0.38
24 13 0.26
25 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
ATATATTTATATATTTTATTGTTA
Found at i:5456449 original size:113 final size:114
Alignment explanation
Indices: 5456132--5456504 Score: 602
Period size: 113 Copynumber: 3.3 Consensus size: 114
5456122 AAAATACAAG
5456132 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTT-AATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
5456196 TGTCATATATTTTATTTTTATTTATTA-TAT-AT-TTATATATTTTATT
66 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
* *
5456242 TTTAATATA-TTATATTTATTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTGA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
5456306 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
*
5456355 TTTAATATATTTATATTTTTTATTGTTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
5456420 TGTCATATATTTTA-TTTCATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
*
5456468 TTT-AT-TTTTAATATATTTTTTA-TATTATATATTTTAT
1 TTTAATATATT--TATATTTTTTATTATTA-AT-TTTTAT
5456505 TTTAATTTGT
Statistics
Matches: 246, Mismatches: 8, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
109 40 0.16
110 48 0.20
111 6 0.02
112 8 0.03
113 72 0.29
114 72 0.29
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
Found at i:5456579 original size:54 final size:49
Alignment explanation
Indices: 5456478--5456613 Score: 145
Period size: 54 Copynumber: 2.7 Consensus size: 49
5456468 TTTATTTTTA
* *
5456478 ATATATTTT-TTATATTATATATTTTATTTTAATTTGTTTTACCTATATT
1 ATATATTTTATTTTAATAT-TATTTTATTTTAATTTGTTTTACCTATATT
*
5456527 ATATAAATTTTAATTTTAATATTTTATTTTATTTTAATTT-TTAATT-CTTATATT
1 ATAT--ATTTT-ATTTTAATA--TTATTTTATTTTAATTTGTT--TTACCTATATT
5456581 ATATATTTTATTTTAATATT-TTTTATTTTAATT
1 ATATATTTTATTTTAATATTATTTTATTTTAATT
5456614 ATAACAGTAT
Statistics
Matches: 76, Mismatches: 3, Indels: 17
0.79 0.03 0.18
Matches are distributed among these distances:
48 13 0.17
49 6 0.08
51 14 0.18
52 5 0.07
53 8 0.11
54 27 0.36
55 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (49 bp):
ATATATTTTATTTTAATATTATTTTATTTTAATTTGTTTTACCTATATT
Found at i:5456615 original size:33 final size:32
Alignment explanation
Indices: 5456457--5456616 Score: 98
Period size: 33 Copynumber: 4.8 Consensus size: 32
5456447 TATAATCTTA
* *
5456457 TATATTTTA-TTTTTATTTTTAA-TATATTTTT
1 TATATTATATTTTTTA-TTTTAATTATATATTT
* *
5456488 TATATTATATATTTTATTTTAATT-TGT-TTT
1 TATATTATATTTTTTATTTTAATTATATATTT
* *
5456518 ACCTATATTATATAAATTTTAATTTTAA-TATTTTATTT
1 ---TATATTATAT---TTTTTATTTTAATTA-TATATTT
* *
5456556 TATTTTA-ATTTTTAATTCTTATATTATATATTT
1 TATATTATATTTTTTATT-TTA-ATTATATATTT
*
5456589 TATTTTAATATTTTTTATTTTAATTATA
1 TATATT-ATATTTTTTATTTTAATTATA
5456617 ACAGTATAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
30 3 0.03
31 24 0.23
32 9 0.09
33 29 0.28
34 8 0.08
35 16 0.15
36 10 0.10
37 2 0.02
38 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (32 bp):
TATATTATATTTTTTATTTTAATTATATATTT
Found at i:5457119 original size:3 final size:3
Alignment explanation
Indices: 5457111--5457135 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5457101 TTTTTATAAA
5457111 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5457136 TATTTTGTTT
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:5462670 original size:17 final size:19
Alignment explanation
Indices: 5462648--5462682 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5462638 ACTTTAAAAA
5462648 AATTAAA-A-AGTTTTAAG
1 AATTAAACATAGTTTTAAG
5462665 AATTAAACATAGTTTTAA
1 AATTAAACATAGTTTTAA
5462683 ATTTTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (19 bp):
AATTAAACATAGTTTTAAG
Found at i:5464910 original size:14 final size:14
Alignment explanation
Indices: 5464891--5464987 Score: 51
Period size: 14 Copynumber: 7.0 Consensus size: 14
5464881 TTATTTTTAT
*
5464891 TTAAATTTAAAATA
1 TTAAATATAAAATA
5464905 TTAAATATAAAAT-
1 TTAAATATAAAATA
*
5464918 TGTAATGTATAAAATA
1 T-TAA-ATATAAAATA
*
5464934 -TAAATAATTAAATA
1 TTAAAT-ATAAAATA
** *
5464948 CGACATATAAAAT-
1 TTAAATATAAAATA
* *
5464961 TT-TATATAATA-A
1 TTAAATATAAAATA
5464973 TTAAATATATAAATA
1 TTAAATATA-AAATA
5464988 GTCAAATAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 17
0.67 0.14 0.19
Matches are distributed among these distances:
12 9 0.15
13 7 0.11
14 33 0.54
15 12 0.20
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (14 bp):
TTAAATATAAAATA
Found at i:5466904 original size:15 final size:16
Alignment explanation
Indices: 5466878--5466908 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5466868 TTCTTTTTAC
5466878 AACTTATTTTTCTCTT
1 AACTTATTTTTCTCTT
5466894 AACTT-TTTTTCTCTT
1 AACTTATTTTTCTCTT
5466909 GTTTGTGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (16 bp):
AACTTATTTTTCTCTT
Found at i:5473330 original size:2 final size:2
Alignment explanation
Indices: 5473323--5473352 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5473313 GACTTGATTA
5473323 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5473353 ATACAATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5481031 original size:35 final size:35
Alignment explanation
Indices: 5480964--5481048 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
5480954 TATAAAAAAT
* *
5480964 AATAAATATAAAATATTATTTTAAGTAAAATAATTAA
1 AATAAAT-T-AAATACTACTTTAAGTAAAATAATTAA
* *
5481001 AATAAATTAAATACTACTTTATGTAGAATAATTAA
1 AATAAATTAAATACTACTTTAAGTAAAATAATTAA
*
5481036 AATAAATAAAATA
1 AATAAATTAAATA
5481049 TTATTTCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 35 0.81
36 1 0.02
37 7 0.16
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (35 bp):
AATAAATTAAATACTACTTTAAGTAAAATAATTAA
Found at i:5502429 original size:7 final size:7
Alignment explanation
Indices: 5502417--5502459 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
5502407 TGGAAAAAAT
5502417 AAATAAA
1 AAATAAA
5502424 AAATAAA
1 AAATAAA
**
5502431 AGGTAAA
1 AAATAAA
*
5502438 AACTTAAA
1 AA-ATAAA
5502446 AAATAAA
1 AAATAAA
5502453 AAATAAA
1 AAATAAA
5502460 CAGCGGAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:5512516 original size:17 final size:17
Alignment explanation
Indices: 5512491--5512525 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5512481 AATATTTAAG
5512491 ATAAATTTATTATATTA
1 ATAAATTTATTATATTA
* *
5512508 ATAATTTTATTATTTTA
1 ATAAATTTATTATATTA
5512525 A
1 A
5512526 AATATAGTTT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAAATTTATTATATTA
Found at i:5517135 original size:2 final size:2
Alignment explanation
Indices: 5517130--5517159 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5517120 ATATAGCCAC
5517130 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
5517160 GATTTATAAG
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:5532770 original size:30 final size:31
Alignment explanation
Indices: 5532708--5532770 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
5532698 TCTAAAATCT
* *
5532708 TATTTTTATATTATATTTAATCAAACTTTTA
1 TATTTTTATATTAAATTAAATCAAACTTTTA
* *
5532739 TATTTTTATTTTAAATTAAAT-AAATTTTTA
1 TATTTTTATATTAAATTAAATCAAACTTTTA
5532769 TA
1 TA
5532771 ATTAACAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTTTTATATTAAATTAAATCAAACTTTTA
Found at i:5535091 original size:15 final size:14
Alignment explanation
Indices: 5535071--5535122 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 14
5535061 TTTTTATAAT
5535071 ATAATATAATTATA
1 ATAATATAATTATA
*
5535085 GATAATATGATTATA
1 -ATAATATAATTATA
5535100 AGTAATATAATTATA
1 A-TAATATAATTATA
5535115 AGTAATAT
1 A-TAATAT
5535123 TATTGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 1 0.03
15 33 0.97
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (14 bp):
ATAATATAATTATA
Found at i:5535407 original size:33 final size:33
Alignment explanation
Indices: 5535276--5535408 Score: 105
Period size: 33 Copynumber: 4.1 Consensus size: 33
5535266 AAAATATAAG
*
5535276 TTTAATAT-A-TTTATAT-TT-TTTATTATTATT
1 TTTAATATAATTTTATATATTATATATT-TTATT
* * * *
5535306 TTTTATATAATATCATATCATAAATATATTTTATT
1 TTTAATATAATTTTATAT-AT-TATATATTTTATT
* * *
5535341 TTTATTGTAATTTTATATATT-TTTATTTTTATT
1 TTTAATATAATTTTATATATTATATA-TTTTATT
* *
5535374 TTTAATATAATTTTTTATATTATATATTATATT
1 TTTAATATAATTTTATATATTATATATTTTATT
5535407 TT
1 TT
5535409 AATTTTTTTC
Statistics
Matches: 78, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
30 7 0.09
31 1 0.01
32 8 0.10
33 33 0.42
34 6 0.08
35 18 0.23
36 5 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (33 bp):
TTTAATATAATTTTATATATTATATATTTTATT
Found at i:5535662 original size:16 final size:17
Alignment explanation
Indices: 5535641--5535673 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5535631 AAGATCTCAA
5535641 GAAAAAATT-ATAAAAT
1 GAAAAAATTCATAAAAT
*
5535657 GAAAAATTTCATAAAAT
1 GAAAAAATTCATAAAAT
5535674 CCTAGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
GAAAAAATTCATAAAAT
Found at i:5536023 original size:28 final size:25
Alignment explanation
Indices: 5535967--5536028 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
5535957 AATTTTGGAC
*
5535967 GAAGAAGAAGCATGGACCTTAGCTA
1 GAAGAAGAAGCAAGGACCTTAGCTA
* *
5535992 GAAGAAGAAGCAAGGACTTTAGTTA
1 GAAGAAGAAGCAAGGACCTTAGCTA
5536017 -AATGAAGAAGCA
1 GAA-GAAGAAGCA
5536029 GCAAGGAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.45, C:0.11, G:0.27, T:0.16
Consensus pattern (25 bp):
GAAGAAGAAGCAAGGACCTTAGCTA
Found at i:5542181 original size:15 final size:16
Alignment explanation
Indices: 5542152--5542187 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
5542142 AATATAAAAG
5542152 AAAGTATTTAAAGAGAA
1 AAAGTATTT-AAGAGAA
5542169 AAAGTATTT-AGAGAA
1 AAAGTATTTAAGAGAA
5542184 AAAG
1 AAAG
5542188 AAAAAATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
17 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (16 bp):
AAAGTATTTAAGAGAA
Found at i:5583285 original size:20 final size:20
Alignment explanation
Indices: 5583256--5583303 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5583246 TTACATGGTC
5583256 TGTA-TTGCATG-AAATTAAG
1 TGTATTTGCATGAAAATT-AG
5583275 TGTATTTGCATGAAAATTAG
1 TGTATTTGCATGAAAATTAG
5583295 TGTATTTGC
1 TGTATTTGC
5583304 CTTGAGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (20 bp):
TGTATTTGCATGAAAATTAG
Found at i:5591339 original size:21 final size:22
Alignment explanation
Indices: 5591281--5591339 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5591271 TTACTTTTTC
*
5591281 ATATAAAAAACATTAAATAGTT
1 ATATAAAAAATATTAAATAGTT
* *
5591303 ATATAAAAAATTTTAAAT-TTT
1 ATATAAAAAATATTAAATAGTT
* *
5591324 ATATAATATATATTAA
1 ATATAAAAAATATTAA
5591340 GATTAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATAAAAAATATTAAATAGTT
Found at i:5591961 original size:105 final size:106
Alignment explanation
Indices: 5591773--5591963 Score: 235
Period size: 105 Copynumber: 1.8 Consensus size: 106
5591763 CTTTGTTTAA
* * *
5591773 CAATTTTTATTATTTAATAAATATTCTACTAAATCTTTTCCAAAAAAAATCTAAAAGGAAGATTC
1 CAATTTTTATTATCTAATAAATATTCTACTAAATCTTTTCCAAAAAAAATCTAAAAGAAAGATCC
* * *
5591838 TTAAAAATTCAGAGAAAATTACAAGTGAAATAAGTTATAAC
66 ATAAAAATCCAAAGAAAATTACAAGTGAAATAAGTTATAAC
* * * * *
5591879 CAATTTTTATTATCTAATAAATATAT-TA-TTAATGTTTTTGC-AAGAAAATTTAAAAGAAAGAT
1 CAATTTTTATTATCTAATAAATAT-TCTACTAAAT-CTTTTCCAAAAAAAATCTAAAAGAAAGAT
*
5591941 CCATATAAATCCAAAGAAAATTA
64 CCATAAAAATCCAAAGAAAATTA
5591964 AAGGCCAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
105 40 0.56
106 30 0.42
107 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (106 bp):
CAATTTTTATTATCTAATAAATATTCTACTAAATCTTTTCCAAAAAAAATCTAAAAGAAAGATCC
ATAAAAATCCAAAGAAAATTACAAGTGAAATAAGTTATAAC
Found at i:5592133 original size:91 final size:92
Alignment explanation
Indices: 5591957--5592142 Score: 252
Period size: 91 Copynumber: 2.0 Consensus size: 92
5591947 AAATCCAAAG
* * *
5591957 AAAATTAAAGGCCAAACAAATTATAATCAATTTTTAGTTGAAAAATTCAAAAAAAAATTATCACT
1 AAAATTAAAGGCCAAACAAACTATAACCAATTTTGAGTTGAAAAATTCAAAAAAAAATTATCACT
* *
5592022 TTCAATTTATTTTACGGG-AAATAGAT
66 CTCAATTTATTTTACGGGAAAATAAAT
* * *
5592048 AAAATTAAAGGCCAAACAAACTATAACCAATTTTGAGTTGAAATA-TCAGATGAAAAATTTATCA
1 AAAATTAAAGGCCAAACAAACTATAACCAATTTTGAGTTGAAAAATTCA-A-AAAAAAATTATCA
*
5592112 CTCTCAATTTATTTTA-TGGAAAATAAAT
64 CTCTCAATTTATTTTACGGGAAAATAAAT
5592140 AAA
1 AAA
5592143 CTAAACTGTG
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
90 3 0.04
91 44 0.53
92 36 0.43
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (92 bp):
AAAATTAAAGGCCAAACAAACTATAACCAATTTTGAGTTGAAAAATTCAAAAAAAAATTATCACT
CTCAATTTATTTTACGGGAAAATAAAT
Found at i:5593065 original size:39 final size:40
Alignment explanation
Indices: 5593013--5593099 Score: 160
Period size: 39 Copynumber: 2.2 Consensus size: 40
5593003 AACCATATGT
5593013 AAAAGA-ATGGGTAATGTTTTCTATATTTTCTTATTTATA
1 AAAAGATATGGGTAATGTTTTCTATATTTTCTTATTTATA
5593052 AAAAGATA-GGGTAATGTTTTCTATATTTTCTTATTTATA
1 AAAAGATATGGGTAATGTTTTCTATATTTTCTTATTTATA
5593091 AAAAGATAT
1 AAAAGATAT
5593100 TCTTTTCCCC
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (40 bp):
AAAAGATATGGGTAATGTTTTCTATATTTTCTTATTTATA
Found at i:5596837 original size:17 final size:17
Alignment explanation
Indices: 5596811--5596843 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5596801 GCGTTTTCTC
5596811 TTTTTCCCTTCTTTTTT
1 TTTTTCCCTTCTTTTTT
*
5596828 TTTTTTCCTTCTTTTT
1 TTTTTCCCTTCTTTTT
5596844 GGAGGGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCCCTTCTTTTTT
Found at i:5599352 original size:30 final size:31
Alignment explanation
Indices: 5599311--5599395 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
5599301 AACTATGAAT
* *
5599311 TAAGTTATTATATTTTTATTTTGAGA-CAAA
1 TAAGTTTTTATAATTTTATTTTGAGATCAAA
*
5599341 TAAGTTTTTATAATTTTATTTTTA-ATCAAA
1 TAAGTTTTTATAATTTTATTTTGAGATCAAA
* *
5599371 TAAATTTTTATACTTTTATTTTGAG
1 TAAGTTTTTATAATTTTATTTTGAG
5599396 TTAAAGAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.02
30 46 0.98
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (31 bp):
TAAGTTTTTATAATTTTATTTTGAGATCAAA
Found at i:5599410 original size:30 final size:30
Alignment explanation
Indices: 5599318--5599411 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
5599308 AATTAAGTTA
* * *
5599318 TTATATTTTTATTTTGAGACAAATAAGTTT
1 TTATAATTTTATTTTGAGTCAAATAAATTT
* *
5599348 TTATAATTTTATTTTTAATCAAATAAATTT
1 TTATAATTTTATTTTGAGTCAAATAAATTT
* * * *
5599378 TTATACTTTTATTTTGAGTTAAAGAAACTT
1 TTATAATTTTATTTTGAGTCAAATAAATTT
5599408 TTAT
1 TTAT
5599412 GATTAATGAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (30 bp):
TTATAATTTTATTTTGAGTCAAATAAATTT
Found at i:5599724 original size:89 final size:88
Alignment explanation
Indices: 5599625--5599800 Score: 343
Period size: 89 Copynumber: 2.0 Consensus size: 88
5599615 TAAGTGATAT
5599625 TTTAATTAATAATAATTAATTATAAAAATTTATTTAATTCGAAATAAAAATAAAAAAACTTGATT
1 TTTAATTAATAATAATTAATTATAAAAATTTATTTAATTCGAAATAAAAATAAAAAAACTTGATT
5599690 GAATAGAAAAAAAATAAAAAAAAA
66 GAATAG-AAAAAAATAAAAAAAAA
5599714 TTTAATTAATAATAATTAATTATAAAAATTTATTTAATTCGAAATAAAAATAAAAAAACTTGATT
1 TTTAATTAATAATAATTAATTATAAAAATTTATTTAATTCGAAATAAAAATAAAAAAACTTGATT
5599779 GAATAGAAAAAAATAAAAAAAA
66 GAATAGAAAAAAATAAAAAAAA
5599801 TTAAATTTTT
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 16 0.18
89 71 0.82
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (88 bp):
TTTAATTAATAATAATTAATTATAAAAATTTATTTAATTCGAAATAAAAATAAAAAAACTTGATT
GAATAGAAAAAAATAAAAAAAAA
Found at i:5599766 original size:28 final size:28
Alignment explanation
Indices: 5599646--5599769 Score: 92
Period size: 32 Copynumber: 4.2 Consensus size: 28
5599636 ATAATTAATT
5599646 ATAAAAATTTATTTAATTCGAAATAAAA
1 ATAAAAATTTATTTAATTCGAAATAAAA
* * *
5599674 ATAAAAAAACTTGATTGAA-TAGAAA-AAAA
1 AT--AAAAA-TTTATTTAATTCGAAATAAAA
*** *
5599703 ATAAAAAAAAATTTAATT-AATAATAATTAA
1 ATAAAAATTTATTTAATTCGA-AATAA--AA
5599733 TTATAAAAATTTATTTAATTCGAAATAAAA
1 --ATAAAAATTTATTTAATTCGAAATAAAA
5599763 ATAAAAA
1 ATAAAAA
5599770 AACTTGATTG
Statistics
Matches: 73, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
26 6 0.08
27 8 0.11
28 11 0.15
29 6 0.08
30 14 0.19
31 7 0.10
32 20 0.27
33 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (28 bp):
ATAAAAATTTATTTAATTCGAAATAAAA
Found at i:5599790 original size:28 final size:29
Alignment explanation
Indices: 5599665--5599799 Score: 107
Period size: 30 Copynumber: 4.6 Consensus size: 29
5599655 TATTTAATTC
5599665 GAAATAAAAATAAAAAAACTTGATTGAATA
1 GAAA-AAAAATAAAAAAACTTGATTGAATA
* *
5599695 GAAAAAAAATAAAAAAAAATTTAATT-AATA
1 GAAAAAAAAT--AAAAAAACTTGATTGAATA
** * * * * *
5599725 -ATAATTAATTATAAAAA-TTTATTTAATTC
1 GA-AAAAAAATAAAAAAACTTGATTGAA-TA
5599754 GAAATAAAAATAAAAAAACTTGATTGAATA
1 GAAA-AAAAATAAAAAAACTTGATTGAATA
5599784 G-AAAAAAATAAAAAAA
1 GAAAAAAAATAAAAAAA
5599800 ATTAAATTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
27 5 0.06
28 21 0.26
29 12 0.15
30 25 0.30
31 19 0.23
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (29 bp):
GAAAAAAAATAAAAAAACTTGATTGAATA
Found at i:5608097 original size:20 final size:20
Alignment explanation
Indices: 5608072--5608113 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5608062 AGACCATCTG
5608072 AGGCCACTAAAATCTAAGTT
1 AGGCCACTAAAATCTAAGTT
5608092 AGGCCACTAAAATCTAAGTT
1 AGGCCACTAAAATCTAAGTT
5608112 AG
1 AG
5608114 ACATAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (20 bp):
AGGCCACTAAAATCTAAGTT
Found at i:5617066 original size:17 final size:18
Alignment explanation
Indices: 5617044--5617085 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5617034 AGTTGGGGCC
5617044 AATCAAAAATATT-ATTT
1 AATCAAAAATATTAATTT
**
5617061 AATCAAAGTTATTAATTT
1 AATCAAAAATATTAATTT
5617079 -ATCAAAA
1 AATCAAAA
5617086 TTTTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (18 bp):
AATCAAAAATATTAATTT
Found at i:5617111 original size:21 final size:20
Alignment explanation
Indices: 5617087--5617126 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5617077 TTATCAAAAT
5617087 TTTATAATAATTATTTTTATC
1 TTTATAATAATT-TTTTTATC
* *
5617108 TTTATTATTATTTTTTTAT
1 TTTATAATAATTTTTTTAT
5617127 AAATTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATAATAATTTTTTTATC
Found at i:5617926 original size:15 final size:15
Alignment explanation
Indices: 5617900--5617940 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5617890 TTTAATTTAT
5617900 AAATAAATAATAATAA
1 AAATAAA-AATAATAA
*
5617916 AAATAAAAATAATTA
1 AAATAAAAATAATAA
*
5617931 AAGTAAAAAT
1 AAATAAAAAT
5617941 TAGCAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAAAAATAATAA
Found at i:5618163 original size:252 final size:251
Alignment explanation
Indices: 5617523--5618203 Score: 840
Period size: 253 Copynumber: 2.7 Consensus size: 251
5617513 TATTGATGTC
* *
5617523 AATGTGT-TAAATTGAACATAATAAATCAATTAAGTAAAAATAAATATAATTTTTTTGAAAATTA
1 AATGTGTGT-AATTTAACATAATAAGTCAATTAAGTAAAAATAAATATAA-TTTTTTGAAAATTA
* * * *
5617587 AACATTTACATTTATATTATCAAGTTAAAAATATTTAATGATTTAATAATTTTAATTTATAAATG
64 AACATTTAAATTTATATTATCGAGCT-AAAATATTTTATGATTT-ATAATTTTAATTTATAAATG
* * * * *
5617652 -AATAATAATAAAGATAAAAATAATTATAGTGAAAATTAGTAATTGAAAAACCTTGACATAAACT
127 AAATAATAATAAAAATAAAAATAATTAAAGTAAAAATTAGCAATTAAAAAACCTTGACATAAACT
* * ** * ** * * *
5617716 TGTAAGAATTAATGTAAAAAATTATAAAAGTGGAACAAATATTGTTAAAATATTAACATA
192 TGTAAAAATCAACATAAAAAATTACAAAAGTAAAACAAACATTGTCAAAATATTAAAATA
* * *
5617776 AATTTGTGTAATTTAACATAATAAGACAATTAAGTCAAAATAAATATAATTTTTATGAAAATTAA
1 AATGTGTGTAATTTAACATAATAAGTCAATTAAGTAAAAATAAATATAATTTTT-TGAAAATTAA
* *
5617841 ACATTTAAATTTATATTATCGAGCTTAAAATATTTTAT-AGGTTACAAATTTTAATTTATAAAT-
65 ACATTTAAATTTATATTATCGAGC-TAAAATATTTTATGA-TTTA-TAATTTTAATTTATAAATG
* *
5617904 AAATAATAATAAAAATAAAAATAATTAAAGTAAAAATTAGCAGA-TAAAAAACTTTGACATAAAT
127 AAATAATAATAAAAATAAAAATAATTAAAGTAAAAATTAGCA-ATTAAAAAACCTTGACATAAAC
* *
5617968 TTGTAAAAATCAACAT-AAAAATTACGAAGGTAAAACAAACATTGTCAAAATATTAAAATA
191 TTGTAAAAATCAACATAAAAAATTACAAAAGTAAAACAAACATTGTCAAAATATTAAAATA
* * *
5618028 AATGTGTGTGATTTAACATAATAAGTCAATTAAGTTAAAATAAATATAATTTTTTAAAAATTAAA
1 AATGTGTGTAATTTAACATAATAAGTCAATTAAGTAAAAATAAATATAATTTTTTGAAAATTAAA
* *
5618093 TATTTAAATTTATATTATTGAGCTAAAAGTATTTTATGATTTATAA-TTTAATTTATAAATG-AA
66 CATTTAAATTTATATTATCGAGCTAAAA-TATTTTATGATTTATAATTTTAATTTATAAATGAAA
** * * * *
5618156 TAATAATAAGGAT-AAAATAATTATAGTGAAAATTAACAATTGAAAAAC
130 TAATAATAAAAATAAAAATAATTAAAGTAAAAATTAGCAATTAAAAAAC
5618204 ATTTGCATAA
Statistics
Matches: 372, Mismatches: 45, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
247 1 0.00
248 29 0.08
249 27 0.07
250 7 0.02
251 42 0.11
252 94 0.25
253 169 0.45
254 3 0.01
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (251 bp):
AATGTGTGTAATTTAACATAATAAGTCAATTAAGTAAAAATAAATATAATTTTTTGAAAATTAAA
CATTTAAATTTATATTATCGAGCTAAAATATTTTATGATTTATAATTTTAATTTATAAATGAAAT
AATAATAAAAATAAAAATAATTAAAGTAAAAATTAGCAATTAAAAAACCTTGACATAAACTTGTA
AAAATCAACATAAAAAATTACAAAAGTAAAACAAACATTGTCAAAATATTAAAATA
Found at i:5618267 original size:28 final size:28
Alignment explanation
Indices: 5618230--5618347 Score: 87
Period size: 31 Copynumber: 4.0 Consensus size: 28
5618220 TTTATTCTTC
*
5618230 TTATTATTTATTAAACTAATTTTTATTT
1 TTATTTTTTATTAAACTAATTTTTATTT
*
5618258 TTATTTTTTA-TAATAATAATTTATTTATTTAT
1 TTATTTTTTATTAA-ACTAA-TT-TTTA-TT-T
* * *
5618290 TTAATTTTTATTATAA-TTATTTCTATTT
1 TTATTTTTTATTA-AACTAATTTTTATTT
*
5618318 TTACTATTATTTATTAACCTAATTTTTATT
1 TTA-T-TT-TTTATTAAACTAATTTTTATT
5618348 ATAATATTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
27 3 0.04
28 17 0.24
29 4 0.06
30 10 0.14
31 20 0.29
32 12 0.17
33 3 0.04
34 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (28 bp):
TTATTTTTTATTAAACTAATTTTTATTT
Found at i:5618285 original size:45 final size:46
Alignment explanation
Indices: 5618231--5618358 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 46
5618221 TTATTCTTCT
* * *
5618231 TATTATTTATTAAACTAATTTTTATTTTTATTTTTTATAATAATAA
1 TATTATTTATTAAACTAATTTTTATTATAATTATTTATAATAATAA
* ** * * ** *
5618277 T-TTATTTATTTATTTAATTTTTATTATAATTATTTCTATTTTTAC
1 TATTATTTATTAAACTAATTTTTATTATAATTATTTATAATAATAA
*
5618322 TATTATTTATTAACCTAATTTTTATTATAA-TATTTAT
1 TATTATTTATTAAACTAATTTTTATTATAATTATTTAT
5618359 TTTAAAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
45 40 0.61
46 26 0.39
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (46 bp):
TATTATTTATTAAACTAATTTTTATTATAATTATTTATAATAATAA
Found at i:5652424 original size:21 final size:21
Alignment explanation
Indices: 5652359--5652422 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
5652349 CAAAATAAAT
* * *
5652359 AACTCTAAAATTGGTTCAATA
1 AACTCTAAAATCGATTCAACA
*
5652380 AA-TGCTAAAATCAATTCAACA
1 AACT-CTAAAATCGATTCAACA
5652401 AACTCTAAAATCGATTC-ACA
1 AACTCTAAAATCGATTCAACA
5652421 AA
1 AA
5652423 ACCATTATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.17
21 29 0.81
22 1 0.03
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (21 bp):
AACTCTAAAATCGATTCAACA
Found at i:5652466 original size:21 final size:21
Alignment explanation
Indices: 5652387--5652503 Score: 62
Period size: 21 Copynumber: 5.6 Consensus size: 21
5652377 ATAAATGCTA
* *
5652387 AAATCAATTCAACAAACTCTA
1 AAATCAATTCAACAAACCCTT
* *
5652408 AAATCGATTC-ACAAAACCATT
1 AAATCAATTCAAC-AAACCCTT
* * *
5652429 ATA-CTAATTTAATAAACCCTT
1 AAATC-AATTCAACAAACCCTT
*
5652450 AAATCGATTCAACAAA-CCTT
1 AAATCAATTCAACAAACCCTT
* * *
5652470 AAAACCAATTCGACAAA-ACTT
1 -AAATCAATTCAACAAACCCTT
*
5652491 AAAATCGATTCAA
1 -AAATCAATTCAA
5652504 AAAGCTCTCA
Statistics
Matches: 71, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
20 7 0.10
21 62 0.87
22 2 0.03
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.26
Consensus pattern (21 bp):
AAATCAATTCAACAAACCCTT
Found at i:5653922 original size:21 final size:21
Alignment explanation
Indices: 5653880--5653924 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5653870 GCATGAAGTG
* *
5653880 AGATGAACGTTGCAGCAAATT
1 AGATGAACGTTGAACCAAATT
*
5653901 AGATGAACGTTGAACCAGATT
1 AGATGAACGTTGAACCAAATT
5653922 AGA
1 AGA
5653925 GAGTTAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (21 bp):
AGATGAACGTTGAACCAAATT
Found at i:5654214 original size:222 final size:222
Alignment explanation
Indices: 5653808--5654248 Score: 722
Period size: 222 Copynumber: 2.0 Consensus size: 222
5653798 AAGCAAAGAA
* *
5653808 AGCTCAGAAGATGAAAGACTTTGATGTGTGTTGAGAGTGAAAGTGTGAGACTGTATTTATAGGCA
1 AGCTCAAAAGATGAAAGACTTTGATGTGTGTCGAGAGTGAAAGTGTGAGACTGTATTTATAGGCA
* * *
5653873 TGAAGTGAGATGAACGTTGCAGCAAATTAGATGAACGTTGAACCAGATTAGAGAGTTAAGAAAAA
66 TGAAGTGAGATGAACATTGCAGCAAATAAGATGAACGTTAAACCAGATTAGAGAGTTAAGAAAAA
* * * *
5653938 GACTCAAGGAGTTAAAGAAAAACCTGGTCAGCTTGTATACTGAGTCAGGTATCCGTTGTAAAACT
131 AACTCAAGCAGTTAAAGAAAAACCTGGTCAGCTTGTATACTAAGTCAAGTATCCGTTGTAAAACT
5654003 TAGACAGATAAACATTGGAGCTAAACC
196 TAGACAGATAAACATTGGAGCTAAACC
* * * *
5654030 AGCTCAAAAGATGAAAGACTTTGGTGTGTGTCGAGAGTG-AAGATGTGAGGCTGTATTTATGGGT
1 AGCTCAAAAGATGAAAGACTTTGATGTGTGTCGAGAGTGAAAG-TGTGAGACTGTATTTATAGGC
* *
5654094 ATGAAGTGAGGTGAACATTGCAGCAAATAAGATGAACGTTAAACCAGATTAGAGAGTTGAGAAAA
65 ATGAAGTGAGATGAACATTGCAGCAAATAAGATGAACGTTAAACCAGATTAGAGAGTTAAGAAAA
5654159 AAACTCAAGCAGTTAAAGAAAAACCTGGTCAGCTTGTATACTAAGTCAAGTATCCGTTGTAAAAC
130 AAACTCAAGCAGTTAAAGAAAAACCTGGTCAGCTTGTATACTAAGTCAAGTATCCGTTGTAAAAC
*
5654224 TTAGTCAGATAAACATTGGAGCTAA
195 TTAGACAGATAAACATTGGAGCTAA
5654249 GCCAAGTAAG
Statistics
Matches: 202, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
221 3 0.01
222 199 0.99
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (222 bp):
AGCTCAAAAGATGAAAGACTTTGATGTGTGTCGAGAGTGAAAGTGTGAGACTGTATTTATAGGCA
TGAAGTGAGATGAACATTGCAGCAAATAAGATGAACGTTAAACCAGATTAGAGAGTTAAGAAAAA
AACTCAAGCAGTTAAAGAAAAACCTGGTCAGCTTGTATACTAAGTCAAGTATCCGTTGTAAAACT
TAGACAGATAAACATTGGAGCTAAACC
Found at i:5664800 original size:25 final size:26
Alignment explanation
Indices: 5664749--5664803 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
5664739 AAATTAAATA
*
5664749 AAATTTTATTTTTATTATATTTAATT
1 AAATTTTATATTTATTATATTTAATT
*
5664775 AAATTTATATATTT-TTAT-TTTTATT
1 AAATTT-TATATTTATTATATTTAATT
5664800 AAAT
1 AAAT
5664804 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 10 0.38
27 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
AAATTTTATATTTATTATATTTAATT
Found at i:5664801 original size:29 final size:29
Alignment explanation
Indices: 5664742--5664814 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
5664732 TCAAAAAAAA
*
5664742 TTAAATAAAATT-T-TATTTTTATTATAT
1 TTAAATAAATTTATATATTTTTATTATAT
* *
5664769 TTAATTAAATTTATATATTTTTATT-TTT
1 TTAAATAAATTTATATATTTTTATTATAT
*
5664797 ATTAAATAAATTTTTATA
1 -TTAAATAAATTTATATA
5664815 ATTAATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 10 0.26
28 3 0.08
29 25 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTAAATAAATTTATATATTTTTATTATAT
Found at i:5667046 original size:90 final size:91
Alignment explanation
Indices: 5666892--5667061 Score: 288
Period size: 90 Copynumber: 1.9 Consensus size: 91
5666882 TCTCTCAAGG
* * *
5666892 ATGCTGTTCGGTGTTAATAACAAACTCTTGCACTGCAATTCATGCTGGTTAAGAACGCTAGACTG
1 ATGCTGTTCGGTGTAAATAACAAACTCTTGCACTGCAATTCATGCTGATTAAGAACACTAGACTG
5666957 TTGCATGTTGGTAGTTGTGCTGCATT
66 TTGCATGTTGGTAGTTGTGCTGCATT
* *
5666983 ATGCTGTTCGGTGTAAAT-ACTAACTCTTGCACTGCAATTCATGCTGATTAAGAACACTGGACTG
1 ATGCTGTTCGGTGTAAATAACAAACTCTTGCACTGCAATTCATGCTGATTAAGAACACTAGACTG
5667047 TTGCATGTTGGTAGT
66 TTGCATGTTGGTAGT
5667062 CGGACTGCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 57 0.77
91 17 0.23
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (91 bp):
ATGCTGTTCGGTGTAAATAACAAACTCTTGCACTGCAATTCATGCTGATTAAGAACACTAGACTG
TTGCATGTTGGTAGTTGTGCTGCATT
Found at i:5672931 original size:21 final size:21
Alignment explanation
Indices: 5672907--5672950 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5672897 AAATGGTGGT
*
5672907 GGTGGTGGTAGGTACTCTGGA
1 GGTGGTAGTAGGTACTCTGGA
*
5672928 GGTGGTAGTAGGTTCTCTGGA
1 GGTGGTAGTAGGTACTCTGGA
5672949 GG
1 GG
5672951 CAAAGGTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.09, G:0.48, T:0.30
Consensus pattern (21 bp):
GGTGGTAGTAGGTACTCTGGA
Found at i:5681421 original size:16 final size:16
Alignment explanation
Indices: 5681397--5681429 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5681387 GATAAACTTT
5681397 ATAAATGCGGACATGA
1 ATAAATGCGGACATGA
*
5681413 ATAAGTGCGGACATGA
1 ATAAATGCGGACATGA
5681429 A
1 A
5681430 ATTATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (16 bp):
ATAAATGCGGACATGA
Found at i:5690534 original size:12 final size:12
Alignment explanation
Indices: 5690517--5690551 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5690507 CCCCTTTTAG
*
5690517 TCTATATCTATA
1 TCTATATATATA
5690529 TCTATATATATA
1 TCTATATATATA
*
5690541 TATATATATAT
1 TCTATATATAT
5690552 TATCATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTATATATATA
Found at i:5693050 original size:28 final size:27
Alignment explanation
Indices: 5692982--5693053 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
5692972 TTTTATCACA
5692982 ATGTATAATAATTAAATTTTTTAATAT
1 ATGTATAATAATTAAATTTTTTAATAT
* *
5693009 ATCGTGTAATAATTATATTTTTTAATAT
1 AT-GTATAATAATTAAATTTTTTAATAT
5693037 GATGTAT-ATCAATTAAA
1 -ATGTATAAT-AATTAAA
5693054 ATTTAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 4 0.11
28 32 0.84
29 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (27 bp):
ATGTATAATAATTAAATTTTTTAATAT
Found at i:5704390 original size:27 final size:27
Alignment explanation
Indices: 5704360--5704455 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
5704350 CTAAAGCACC
*
5704360 AAGGATGTTCTAAGCACGAAAGTGCCT
1 AAGGATGTTCTAAGCACAAAAGTGCCT
* * * * *
5704387 AAGGGTGTTTTAAGTATAGAAGTGCCT
1 AAGGATGTTCTAAGCACAAAAGTGCCT
*
5704414 AA-GAGTGTTTTAAGTC-CAAAAGTG-CT
1 AAGGA-TGTTCTAAG-CACAAAAGTGCCT
5704440 GAAGGATGTTCTAAGC
1 -AAGGATGTTCTAAGC
5704456 GTGGAAGCAC
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
26 4 0.07
27 48 0.89
28 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (27 bp):
AAGGATGTTCTAAGCACAAAAGTGCCT
Found at i:5704534 original size:27 final size:26
Alignment explanation
Indices: 5704471--5704534 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
5704461 AGCACCCAAG
* *
5704471 GGTGTTTCAAGTATGGAAGCGCTTAT
1 GGTGTTTCAAGTATGGAAGCGCTAAA
* * **
5704497 GGTGTTCCAAGTGTGGAAGTTCTCAAA
1 GGTGTTTCAAGTATGGAAGCGCT-AAA
5704524 GGTGTTTCAAG
1 GGTGTTTCAAG
5704535 CATAAAAGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.33
Consensus pattern (26 bp):
GGTGTTTCAAGTATGGAAGCGCTAAA
Found at i:5707777 original size:22 final size:19
Alignment explanation
Indices: 5707730--5707778 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 19
5707720 TATAAATTTT
5707730 AATTTAA-ATATATTTAAA
1 AATTTAATATATATTTAAA
5707748 AATATTAATATATATTAATAATA
1 AAT-TTAATATATATT--TAA-A
5707771 AATTTAAT
1 AATTTAAT
5707779 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 4 0.15
20 7 0.27
22 8 0.31
23 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTAATATATATTTAAA
Found at i:5716155 original size:16 final size:16
Alignment explanation
Indices: 5716134--5716167 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5716124 CTAATATATT
5716134 TTAAGTATATCATTAA
1 TTAAGTATATCATTAA
* *
5716150 TTAAGTTTATTATTAA
1 TTAAGTATATCATTAA
5716166 TT
1 TT
5716168 TTTTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATATCATTAA
Found at i:5716190 original size:14 final size:14
Alignment explanation
Indices: 5716173--5716205 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5716163 TAATTTTTTA
5716173 ATATATA-TAATATT
1 ATATATATTAATA-T
5716187 ATATATATTAATAT
1 ATATATATTAATAT
5716201 ATATA
1 ATATA
5716206 AAACAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATATTAATAT
Found at i:5716191 original size:12 final size:12
Alignment explanation
Indices: 5716171--5716206 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5716161 ATTAATTTTT
5716171 TAATATATATAA
1 TAATATATATAA
* *
5716183 TATTATATATAT
1 TAATATATATAA
5716195 TAATATATATAA
1 TAATATATATAA
5716207 AACAATTAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATATATATAA
Found at i:5718336 original size:19 final size:19
Alignment explanation
Indices: 5718312--5718358 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
5718302 TTACATGGTC
5718312 TGTATTTGCATGAAATTAG
1 TGTATTTGCATGAAATTAG
5718331 TGTATTTGCATGAAATTAG
1 TGTATTTGCATGAAATTAG
5718350 TGTATTTGC
1 TGTATTTGC
5718359 CTTGGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (19 bp):
TGTATTTGCATGAAATTAG
Found at i:5724720 original size:201 final size:200
Alignment explanation
Indices: 5724109--5724873 Score: 747
Period size: 201 Copynumber: 3.8 Consensus size: 200
5724099 CTATATGGTG
* * * * *
5724109 TAATGGTGCATATTAGATATTTAAAGTACTTGACGTGGCATTCCTATTGTGTAAAAACGGCACAG
1 TAATGATGCAAATTAGATATTTAAAGTACTTGACATGGCATTCCTATTGTGTAAAAATGGCACAA
* * ** * * * *
5724174 TGGTGCTTATAGAAAGAAAAAACTTTAAATGTGTGGGCAT-TG-GGCATTCTTATTATACATTCA
66 TGGTGCTTATAGAAATAAAACACCCTAAA-GTGTAGGCATGTGTAGCATTCCTATTATACATTAA
* * *
5724237 GGTATAATGGTGCCAATGTGTGAA-ATTGAAATCTTAGTATGTGGTGCATTTCTATTATATGATT
130 GGTATAATGGTGCCAATCTGTGAATA-TGAAATCTTAGTATATGGTGCATTCCTATTATATGATT
*
5724301 GAAGTTA
194 GAAGGTA
* * * * * * * ** **
5724308 TAAT-AGTACATATTATACATTTAAACTACTTGATATGGCATACAAATTGTGTAATTATGGCACA
1 TAATGA-TGCAAATTAGATATTTAAAGTACTTGACATGGCATTCCTATTGTGTAAAAATGGCACA
* * * * * * *
5724372 ATGGTGCTTATAGACATAAAGA-A-CTTTAAGGGTTGG-GTATGTAGCATTCCTATTATACATTA
65 ATGGTGCTTATAGAAATAAA-ACACCCTAAAGTGTAGGCATGTGTAGCATTCCTATTATACATTA
* * ** * * * * * ** * * *
5724434 CGGAATAATAATGCCAATATATGAATTTCAAATCTGAACATATAGTGCATTCCTATTATGTAATT
129 AGGTATAATGGTGCCAATCTGTGAATATGAAATCTTAGTATATGGTGCATTCCTATTATATGATT
5724499 GAAGGTA
194 GAAGGTA
** * * * * *
5724506 TAATGGCGCAAATTAGATATTTAAAATGCATGACATGGCATCCCCATTGTGTAAAAATGGCACAA
1 TAATGATGCAAATTAGATATTTAAAGTACTTGACATGGCATTCCTATTGTGTAAAAATGGCACAA
* * *
5724571 TGGTGCTTTTAGGAATAATAACACCCTAAAGTGTAAGCATGTGTAGCATTCCTATTATACATTAA
66 TGGTGCTTATAGAAATAA-AACACCCTAAAGTGTAGGCATGTGTAGCATTCCTATTATACATTAA
* *
5724636 GGTATAATGGTGCCTATCTGTGAATATGAAATCTTAGTATATGGTGCATTCCTATTA-ATTGATC
130 GGTATAATGGTGCCAATCTGTGAATATGAAATCTTAGTATATGGTGCATTCCTATTATA-TGATT
*
5724700 GAAGGTG
194 GAAGGTA
** * * * *
5724707 TCGTGATGCAAATTATATATTTAAAGTACTTGACGTGGCATTCCTATTGTATAATAATGGCACAA
1 TAATGATGCAAATTAGATATTTAAAGTACTTGACATGGCATTCCTATTGTGTAAAAATGGCACAA
* * *
5724772 TGGTGTTTTTAGAAATAATAACACCCTAAAGTTTAGGCATGTGTAGCATTCCTATTATACATTAA
66 TGGTGCTTATAGAAATAA-AACACCCTAAAGTGTAGGCATGTGTAGCATTCCTATTATACATTAA
*
5724837 GGTATAATGGTGCCTATAC-GTGAATATGAAATCTTAG
130 GGTATAATGGTGCCAAT-CTGTGAATATGAAATCTTAG
5724874 CATTCCTATT
Statistics
Matches: 454, Mismatches: 100, Indels: 22
0.79 0.17 0.04
Matches are distributed among these distances:
196 1 0.00
197 7 0.02
198 140 0.31
199 70 0.15
200 9 0.02
201 226 0.50
202 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (200 bp):
TAATGATGCAAATTAGATATTTAAAGTACTTGACATGGCATTCCTATTGTGTAAAAATGGCACAA
TGGTGCTTATAGAAATAAAACACCCTAAAGTGTAGGCATGTGTAGCATTCCTATTATACATTAAG
GTATAATGGTGCCAATCTGTGAATATGAAATCTTAGTATATGGTGCATTCCTATTATATGATTGA
AGGTA
Found at i:5724882 original size:56 final size:56
Alignment explanation
Indices: 5724815--5724929 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
5724805 TAGGCATGTG
5724815 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATACGTGAATATGAAATCT
1 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATACGTGAATATGAAATCT
5724871 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATACGTGAATATGAAATCT
1 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATACGTGAATATGAAATCT
5724927 TAG
1 TAG
5724930 AATATGGTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (56 bp):
TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATACGTGAATATGAAATCT
Found at i:5725070 original size:257 final size:256
Alignment explanation
Indices: 5724614--5725132 Score: 815
Period size: 257 Copynumber: 2.0 Consensus size: 256
5724604 TAAGCATGTG
*
5724614 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATCTGTGAATATGAAATCTTAGTATATG
1 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATCTGTGAATATGAAATCTTAGAATATG
* * *
5724679 GTGCATTCCTATTAATTGATCGAAGGTGTCGTGATGCAAATTATATATTTAAAGTACTTGACGTG
66 GTGCATTCCTATTAATTGATCGAAGGCGTAGTGATGCAAATTAGATATTTAAAGTACTTGACGTG
5724744 GCATTCCTATTGTATAATAATGGCACAATGGTGTTTTTAGAAATAATAACACCCTAAAGTTTAGG
131 GCATTCCTATTGTATAATAATGGCACAATGGTGTTTTTAGAAATAATAACACCCTAAAGTTTAGG
*
5724809 CATGTGTAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATACGTGAATATGAAATCT
196 CATGTGTAGCATTCCTATTATACATTAAGGTACAATGGTGCCTATACGTGAAT-TGAAATCT
5724871 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATAC-GTGAATATGAAATCTTAGAATAT
1 TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTAT-CTGTGAATATGAAATCTTAGAATAT
5724935 GGTGCATTCCTATTAATTGATCGAAGGCGTAGTGATGCAAATTAGATATTTAAAGTACTTGACGT
65 GGTGCATTCCTATTAATTGATCGAAGGCGTAGTGATGCAAATTAGATATTTAAAGTACTTGACGT
* ****************
5725000 GGCATTCCTATTGTGTAATAATGGCACANNNNNNNNNNNNNNNNTAATAACACCCTAAAGTTTAG
130 GGCATTCCTATTGTATAATAATGGCACAATGGTGTTTTTAGAAATAATAACACCCTAAAGTTTAG
5725065 GCATGTGTAGCATTCCTATTATACATTAAGGTACAATGGTGCCTATACGTGAATTGAAATCT
195 GCATGTGTAGCATTCCTATTATACATTAAGGTACAATGGTGCCTATACGTGAATTGAAATCT
5725127 TAGCAT
1 TAGCAT
5725133 ATGGTGCATT
Statistics
Matches: 239, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
256 14 0.06
257 224 0.94
258 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.34
Consensus pattern (256 bp):
TAGCATTCCTATTATACATTAAGGTATAATGGTGCCTATCTGTGAATATGAAATCTTAGAATATG
GTGCATTCCTATTAATTGATCGAAGGCGTAGTGATGCAAATTAGATATTTAAAGTACTTGACGTG
GCATTCCTATTGTATAATAATGGCACAATGGTGTTTTTAGAAATAATAACACCCTAAAGTTTAGG
CATGTGTAGCATTCCTATTATACATTAAGGTACAATGGTGCCTATACGTGAATTGAAATCT
Found at i:5729937 original size:148 final size:145
Alignment explanation
Indices: 5729715--5730008 Score: 396
Period size: 148 Copynumber: 2.0 Consensus size: 145
5729705 AAAATTAAAT
* *
5729715 ATTATATATTACAAAAAAATATTTTAAATTTAAAAATAGATAAAATTATCAATATTTTAATCATC
1 ATTATATATTACAAAAAAATATTTCAAATTTAAAAATAGATAAAATTATCAATATTTTAATCATA
* * *
5729780 ATAACATTTAAATTATAAATACACTATTAATGTTT-AATTATCAATTATTAATATTATTATAAAA
66 ATAACATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTATTATAAAA
** *
5729844 AAGTTTAAATTTTTA
131 AAACTTAAATTATTA
* *
5729859 ATTATATATTTGA-AAAAATAATATTTCACATTTTAAAAATTA-ATTAAAATTATTAATATTTTA
1 ATTATATA-TT-ACAAAAA-AATATTTCA-AATTTAAAAA-TAGA-TAAAATTATCAATATTTTA
* * *
5729922 ATCATAATAATATTTAAATTATAAATAAAATATTCATATTTAAATTATTAATTATTAATATTATT
60 ATCATAATAACATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTATT
5729987 ATAAAAAAACTTAAATTATTA
125 ATAAAAAAACTTAAATTATTA
5730008 A
1 A
5730009 GTAAAAAATA
Statistics
Matches: 130, Mismatches: 13, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
144 8 0.06
145 7 0.05
146 9 0.07
147 10 0.08
148 55 0.42
149 41 0.32
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (145 bp):
ATTATATATTACAAAAAAATATTTCAAATTTAAAAATAGATAAAATTATCAATATTTTAATCATA
ATAACATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTATTATAAAA
AAACTTAAATTATTA
Found at i:5729945 original size:17 final size:17
Alignment explanation
Indices: 5729912--5729945 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5729902 TTAAAATTAT
*
5729912 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
5729929 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
5729946 ATAAAATATT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:5730019 original size:29 final size:27
Alignment explanation
Indices: 5729987--5730045 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
5729977 TAATATTATT
*
5729987 ATAAAAAAACTTAAATTATTAAGTAAAAA
1 ATAAAAAAACTCAAATTA-TAA-TAAAAA
* * *
5730016 ATAAATAATCTCATATTATAATAAAAA
1 ATAAAAAAACTCAAATTATAATAAAAA
5730043 ATA
1 ATA
5730046 TTTTCATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 9 0.35
28 3 0.12
29 14 0.54
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (27 bp):
ATAAAAAAACTCAAATTATAATAAAAA
Found at i:5748481 original size:12 final size:13
Alignment explanation
Indices: 5748464--5748512 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
5748454 AACATCCAAC
5748464 ATATTA-AATACA
1 ATATTACAATACA
**
5748476 ATATTACAATATTG
1 ATATTACAATA-CA
5748490 ATATTA-AATACA
1 ATATTACAATACA
5748502 ATATTACAATA
1 ATATTACAATA
5748513 TTGATAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 12 0.40
13 12 0.40
14 6 0.20
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (13 bp):
ATATTACAATACA
Found at i:5748500 original size:26 final size:26
Alignment explanation
Indices: 5748464--5748518 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5748454 AACATCCAAC
5748464 ATATTAAATACAATATTACAATATTG
1 ATATTAAATACAATATTACAATATTG
5748490 ATATTAAATACAATATTACAATATTG
1 ATATTAAATACAATATTACAATATTG
5748516 ATA
1 ATA
5748519 ATCTAATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (26 bp):
ATATTAAATACAATATTACAATATTG
Found at i:5752223 original size:25 final size:24
Alignment explanation
Indices: 5752166--5752223 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
5752156 TAAAATTTTT
*
5752166 TTATAT-TTAATAATTAATTATTA
1 TTATATATTAAAAATTAATTATTA
*
5752189 TTAT-TAATTAAAATATTACTTATTA
1 TTATAT-ATTAAAA-ATTAATTATTA
5752214 TTATATATTA
1 TTATATATTA
5752224 TGTCATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 4 0.14
24 5 0.17
25 18 0.62
26 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATATATTAAAAATTAATTATTA
Found at i:5752396 original size:24 final size:25
Alignment explanation
Indices: 5752365--5752429 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
5752355 AATTAAATTT
*
5752365 ATTTAATTTAAAATAAAAATA-AAA
1 ATTTAATTTAAAATAAAAAAATAAA
5752389 ATTTAATTTAATATAATAAAAAAATAAA
1 ATTTAATTT-A-A-AATAAAAAAATAAA
5752417 ATTT-ATTTAAAAT
1 ATTTAATTTAAAAT
5752430 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 12 0.33
25 2 0.06
26 2 0.06
27 13 0.36
28 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTAATTTAAAATAAAAAAATAAA
Found at i:5752400 original size:29 final size:27
Alignment explanation
Indices: 5752359--5752426 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 27
5752349 AATTGTAATT
*
5752359 AAATTTATTTAATTTAA-AATAAAAATAA
1 AAATTTATTTAATATAATAA-AAAAAT-A
5752387 AAATTTAATTTAATATAATAAAAAAATA
1 AAATTT-ATTTAATATAATAAAAAAATA
5752415 AAATTTATTTAA
1 AAATTTATTTAA
5752427 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 6 0.16
28 13 0.35
29 16 0.43
30 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATTTATTTAATATAATAAAAAAATA
Found at i:5755086 original size:25 final size:26
Alignment explanation
Indices: 5755045--5755109 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 26
5755035 CAATTTTTCC
5755045 CCTCCC-TCCTCCTTCCTCTCTCCTT
1 CCTCCCTTCCTCCTTCCTCTCTCCTT
*
5755070 CCTCCCTTTCTCC-TCCTCTCTCCTT
1 CCTCCCTTCCTCCTTCCTCTCTCCTT
5755095 CCTCCCTATCC-CCTT
1 CCTCCCT-TCCTCCTT
5755110 ATAAATTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 27 0.77
26 8 0.23
ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40
Consensus pattern (26 bp):
CCTCCCTTCCTCCTTCCTCTCTCCTT
Found at i:5755093 original size:10 final size:11
Alignment explanation
Indices: 5755049--5755098 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
5755039 TTTTCCCCTC
5755049 CCTC-CTCCTT
1 CCTCTCTCCTT
5755059 CCTCTCTCCTT
1 CCTCTCTCCTT
5755070 CCTCCCTTTCTCC-T
1 CCT--C--TCTCCTT
5755084 CCTCTCTCCTT
1 CCTCTCTCCTT
5755095 CCTC
1 CCTC
5755099 CCTATCCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
10 9 0.26
11 14 0.41
12 1 0.03
13 1 0.03
14 4 0.12
15 5 0.15
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (11 bp):
CCTCTCTCCTT
Found at i:5765183 original size:15 final size:16
Alignment explanation
Indices: 5765160--5765193 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5765150 CTTCGCCTCC
5765160 TCCCACTTCCTCGCCT
1 TCCCACTTCCTCGCCT
*
5765176 TCCC-CTTCCTCTCCT
1 TCCCACTTCCTCGCCT
5765191 TCC
1 TCC
5765194 TCTCTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.03, C:0.59, G:0.03, T:0.35
Consensus pattern (16 bp):
TCCCACTTCCTCGCCT
Found at i:5779398 original size:2 final size:2
Alignment explanation
Indices: 5779391--5779425 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5779381 TGTAACCGCT
5779391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5779426 CAACACTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5781026 original size:45 final size:42
Alignment explanation
Indices: 5780927--5781030 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
5780917 ATACTCCCTA
* * * *
5780927 GTTACAATTTTTTGTTATTTCTTGTTAGATTTTTTATTACGT
1 GTTACAATTATTTGTTATTCCTTATTAAATTTTTTATTACGT
* ** *
5780969 GTAACACCTATTTGTTATTCCTTATTACAATTTTTTTTGTCACGT
1 GTTACAATTATTTGTTATTCCTTATTA-AATTTTTTAT-T-ACGT
5781014 GTTACAATTATTTGTTA
1 GTTACAATTATTTGTTA
5781031 ATCTTTGTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 21 0.44
43 8 0.17
44 1 0.02
45 18 0.38
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.56
Consensus pattern (42 bp):
GTTACAATTATTTGTTATTCCTTATTAAATTTTTTATTACGT
Found at i:5781292 original size:16 final size:16
Alignment explanation
Indices: 5781273--5781322 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
5781263 AAAAATCCAA
*
5781273 AAAACAAAAAAAAAAG
1 AAAACAAATAAAAAAG
* *
5781289 AAAAC-TATAAAAAAT
1 AAAACAAATAAAAAAG
*
5781304 AAAAGAAATAAAAAAG
1 AAAACAAATAAAAAAG
5781320 AAA
1 AAA
5781323 GATAGGAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.82, C:0.04, G:0.06, T:0.08
Consensus pattern (16 bp):
AAAACAAATAAAAAAG
Found at i:5788121 original size:28 final size:28
Alignment explanation
Indices: 5788090--5788145 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5788080 AAAACATATT
5788090 ATAAACAAATAAATTACATCAAAAATAA
1 ATAAACAAATAAATTACATCAAAAATAA
* * *
5788118 ATAAGCAAATACATTACATCAAATATAA
1 ATAAACAAATAAATTACATCAAAAATAA
5788146 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (28 bp):
ATAAACAAATAAATTACATCAAAAATAA
Found at i:5794336 original size:39 final size:39
Alignment explanation
Indices: 5794273--5794367 Score: 137
Period size: 39 Copynumber: 2.6 Consensus size: 39
5794263 TTTAAGTTAA
*
5794273 AATATTTTAA-TTAAATATT---ATTTTTT-AATTTTTT
1 AATATTTTAAGTTAAATATTAACATTTTTTGTATTTTTT
*
5794307 AATATTTTAAGTTAGATATTAACATTTTTTGTATTTTTT
1 AATATTTTAAGTTAAATATTAACATTTTTTGTATTTTTT
5794346 AATATTTTAAGTTAAATATTAA
1 AATATTTTAAGTTAAATATTAA
5794368 TACTCATCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
34 10 0.19
35 8 0.15
38 7 0.13
39 28 0.53
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (39 bp):
AATATTTTAAGTTAAATATTAACATTTTTTGTATTTTTT
Found at i:5794382 original size:39 final size:39
Alignment explanation
Indices: 5794299--5794383 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 39
5794289 ATTATTTTTT
* * ** **
5794299 AATTTTTTAATATTTTAAGTTAGATATTAACATTTTTTG
1 AATTTTTTAATATTTTAAGTTAAATATTAACACTCATCA
* *
5794338 TATTTTTTAATATTTTAAGTTAAATATTAATACTCATCA
1 AATTTTTTAATATTTTAAGTTAAATATTAACACTCATCA
5794377 AATTTTT
1 AATTTTT
5794384 ACTACTGTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (39 bp):
AATTTTTTAATATTTTAAGTTAAATATTAACACTCATCA
Found at i:5796057 original size:6 final size:6
Alignment explanation
Indices: 5796048--5796072 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5796038 TTATGATGGG
5796048 AGCCCC AGCCCC AGCCCC AGCCCC A
1 AGCCCC AGCCCC AGCCCC AGCCCC A
5796073 ACCAGTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.64, G:0.16, T:0.00
Consensus pattern (6 bp):
AGCCCC
Found at i:5802274 original size:2 final size:2
Alignment explanation
Indices: 5802267--5802299 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5802257 AATTATGTAC
5802267 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
5802300 CACACACACA
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:5808814 original size:17 final size:18
Alignment explanation
Indices: 5808792--5808827 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5808782 AAAATAAATA
5808792 AAAAATATCAT-AATTTT
1 AAAAATATCATAAATTTT
*
5808809 AAAAATATTATAAATTTT
1 AAAAATATCATAAATTTT
5808827 A
1 A
5808828 CGTCAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATATCATAAATTTT
Found at i:5813323 original size:29 final size:30
Alignment explanation
Indices: 5813289--5813346 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
5813279 AAATAAATTT
**
5813289 AATTTTTATCTTTTTATTAT-AATTAAATA
1 AATTTTTAAATTTTTATTATAAATTAAATA
*
5813318 AATTTTTAAATTTTTATTTTAAATTAAAT
1 AATTTTTAAATTTTTATTATAAATTAAAT
5813347 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
AATTTTTAAATTTTTATTATAAATTAAATA
Found at i:5819333 original size:40 final size:40
Alignment explanation
Indices: 5819287--5819366 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
5819277 GAAGCACCAT
*
5819287 CTTGAAATATCAAAGTGTAACAAGAAGGTTTTATAAGCAC
1 CTTGAAATATCAAAGTGTAACAAGAAGGTTCTATAAGCAC
**
5819327 CTTGAAATATCAAAGTGTAGGAAGAAGGTTCTATAAGCAC
1 CTTGAAATATCAAAGTGTAACAAGAAGGTTCTATAAGCAC
5819367 AACAACATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (40 bp):
CTTGAAATATCAAAGTGTAACAAGAAGGTTCTATAAGCAC
Found at i:5821412 original size:6 final size:6
Alignment explanation
Indices: 5821364--5821422 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
5821354 TATTCATAAG
* * * *
5821364 TCTCTT TTTCCTT TC-CTT TTTCTT T-TACTT TCTCTT CCCCTT TCTCTT
1 TCTCTT TCT-CTT TCTCTT TCTCTT TCT-CTT TCTCTT TCTCTT TCTCTT
5821412 TCTCTT TCTCT
1 TCTCTT TCTCT
5821423 CGGTTGCTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (6 bp):
TCTCTT
Found at i:5834326 original size:2 final size:2
Alignment explanation
Indices: 5834319--5834352 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5834309 CCTGTGCTGA
5834319 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
5834353 TGGTATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5839624 original size:2 final size:2
Alignment explanation
Indices: 5839617--5839649 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5839607 AATTTATGCA
*
5839617 AT AT AT AT AT AC 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
5839650 AATTTTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5845718 original size:26 final size:24
Alignment explanation
Indices: 5845679--5845727 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
5845669 TCCATAGATT
*
5845679 TTATATATCATTAATTAATCAAATG
1 TTATATATCATTAATAAAT-AAATG
*
5845704 TTATGATATCGTTAATAAATAAAT
1 TTAT-ATATCATTAATAAATAAAT
5845728 TTAAAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (24 bp):
TTATATATCATTAATAAATAAATG
Done.