Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015861.1 Corchorus capsularis cultivar CVL-1 contig15882, 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: 92614
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:2535 original size:22 final size:22
Alignment explanation
Indices: 2510--2570 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2500 ATAGCAAAGT
* * * *
2510 TTATTAAAATTTCATATGGTGG
1 TTATCAAAATTTCATAAGATAG
2532 TTATCAAAA-TTCAATAAGATAG
1 TTATCAAAATTTC-ATAAGATAG
2554 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
2571 AAATATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 27 0.82
23 3 0.09
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGATAG
Found at i:3815 original size:178 final size:179
Alignment explanation
Indices: 3546--3884 Score: 463
Period size: 178 Copynumber: 1.9 Consensus size: 179
3536 TCGATTAAGG
*
3546 TGATTTAAGTGTATATTAAAAGATTGTTCCATGATCTGAAACTTTCATACAGGACTCGAAAACTA
1 TGATTCAAGTGTATATTAAAAGATTGTTCCATGATCTGAAACTTTCATACAGGACTCGAAAACTA
* * * *
3611 AATGTAATGTTTCAAGTACCAAAAATGCTTCC-GAAAAATTTGATGTTTCGGTTAACGGGAATAG
66 AATGTAATGTTTCAAGTACAAAAAATGCTTCCAAAAAAATTAGATGTTTCGGTTAACGGAAATAG
*
3675 ACGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATGGAGA
131 ACGGTCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATGGAGA
* * * * *
3724 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCT-ACAACTTTCATGA-AGGACTCGAAACC
1 TGATTCAAGTGTATATTAAAAGATTGTTCCATGATCTGA-AACTTTCAT-ACAGGACTCGAAAAC
* * * *
3787 TGAATTTAATG-TTCAAGATATAAAAAATGCTTCCAAAAAAATTAGTTGTTTCGGTTAACGGAAA
64 TAAATGTAATGTTTCAAG-TACAAAAAATGCTTCCAAAAAAATTAGATGTTTCGGTTAACGGAAA
*
3851 TAGACGGTCTACTTAATATTACATAATTTGTGCT
128 TAGACGGTCCACTTAATATTACATAATTTGTGCT
3885 TATGGTGGAA
Statistics
Matches: 140, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
177 7 0.05
178 79 0.56
179 54 0.39
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (179 bp):
TGATTCAAGTGTATATTAAAAGATTGTTCCATGATCTGAAACTTTCATACAGGACTCGAAAACTA
AATGTAATGTTTCAAGTACAAAAAATGCTTCCAAAAAAATTAGATGTTTCGGTTAACGGAAATAG
ACGGTCCACTTAATATTACATAATTTGTGCTCCAGATGTCTGATGGAGA
Found at i:4427 original size:27 final size:27
Alignment explanation
Indices: 4374--4427 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4364 TAAAGTGAAA
* ** *
4374 CAATTTCTTTTTCTTTTTTTTTTAAAT
1 CAATTTCTTTATCTTTTAATTTCAAAT
4401 CAATTTCTTTATCTTTTAATTTCAAAT
1 CAATTTCTTTATCTTTTAATTTCAAAT
4428 ATAAAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (27 bp):
CAATTTCTTTATCTTTTAATTTCAAAT
Found at i:4732 original size:21 final size:21
Alignment explanation
Indices: 4668--4736 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4658 CTACTAAAGG
*
4668 CTACTCAAAAAGCTTATAAGA
1 CTACTAAAAAAGCTTATAAGA
*
4689 CTACTAAAAAAGC---TAAGT
1 CTACTAAAAAAGCTTATAAGA
* **
4707 TTACTACCAAAGCTTATAAGA
1 CTACTAAAAAAGCTTATAAGA
4728 CTACTAAAA
1 CTACTAAAA
4737 GCTGGCAAGG
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
18 14 0.39
21 22 0.61
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.25
Consensus pattern (21 bp):
CTACTAAAAAAGCTTATAAGA
Found at i:12105 original size:30 final size:30
Alignment explanation
Indices: 12071--12132 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12061 AATGGGTCGA
* *
12071 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
1 ATGGCCGGTTGTGGCCAGATGGCCCATGCG
*
12101 ATGGCCGGTTGTGGCCAGATGGCTCATGCG
1 ATGGCCGGTTGTGGCCAGATGGCCCATGCG
12131 AT
1 AT
12133 ATCCCGTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.11, C:0.24, G:0.42, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCAGATGGCCCATGCG
Found at i:17713 original size:36 final size:36
Alignment explanation
Indices: 17663--17766 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 36
17653 AGTAAGAACA
* *
17663 AAAGAAGACAGACTGGCTTAGTTTCAAGGAAACTAGGT
1 AAAGAA-A-AGACTGGCTTAATTTCAAGGAAACTAAGT
* *
17701 AAAGAAAAGACTGGTTTAATTTCAAGGAAATTAAGT
1 AAAGAAAAGACTGGCTTAATTTCAAGGAAACTAAGT
* * *
17737 AAA-TATAGACTGACTTTAATTTCAAGGAAA
1 AAAGAAAAGACTGGC-TTAATTTCAAGGAAA
17767 GAAGACTGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
35 7 0.12
36 43 0.75
37 1 0.02
38 6 0.11
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (36 bp):
AAAGAAAAGACTGGCTTAATTTCAAGGAAACTAAGT
Found at i:17781 original size:12 final size:12
Alignment explanation
Indices: 17764--17789 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17754 AATTTCAAGG
17764 AAAGAAGACTGA
1 AAAGAAGACTGA
17776 AAAGAAGACTGA
1 AAAGAAGACTGA
17788 AA
1 AA
17790 TTAGACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (12 bp):
AAAGAAGACTGA
Found at i:17795 original size:11 final size:11
Alignment explanation
Indices: 17781--18407 Score: 439
Period size: 11 Copynumber: 56.6 Consensus size: 11
17771 ACTGAAAAGA
17781 AGACTGAAATT
1 AGACTGAAATT
17792 AGACT-AAATT
1 AGACTGAAATT
*
17802 AGACTGAAATG
1 AGACTGAAATT
**
17813 AGACTGAAAAA
1 AGACTGAAATT
* *
17824 ATACTGATATT
1 AGACTGAAATT
17835 AGACTGAAATT
1 AGACTGAAATT
* *
17846 AGACTGATATA
1 AGACTGAAATT
*
17857 AGACTGATATT
1 AGACTGAAATT
* * **
17868 AAACTAAAACC
1 AGACTGAAATT
**
17879 AGACTGAAAGA
1 AGACTGAAATT
*
17890 ATACTGAAATT
1 AGACTGAAATT
*
17901 AGACTGAAAAT
1 AGACTGAAATT
**
17912 AGACTGAAAAA
1 AGACTGAAATT
*
17923 AGACTGATATT
1 AGACTGAAATT
* *
17934 AAACTGAAATG
1 AGACTGAAATT
**
17945 AGACTGAAAAA
1 AGACTGAAATT
*
17956 AGACTGATATT
1 AGACTGAAATT
17967 AGACTGAAATT
1 AGACTGAAATT
* *
17978 AAACTGATA-T
1 AGACTGAAATT
*
17988 ACGACTGATATT
1 A-GACTGAAATT
* *
18000 AAACTGAAATC
1 AGACTGAAATT
**
18011 AGACTGAAAGA
1 AGACTGAAATT
*
18022 ATACTGAAATT
1 AGACTGAAATT
** **
18033 AGACTGGTAGA
1 AGACTGAAATT
18044 AGACTGAAATT
1 AGACTGAAATT
**
18055 AGACTGAAAAA
1 AGACTGAAATT
*
18066 AGACTGATATT
1 AGACTGAAATT
18077 AGACTGAAATT
1 AGACTGAAATT
* *
18088 AGACTGATATA
1 AGACTGAAATT
*
18099 AGACTGATATT
1 AGACTGAAATT
* *
18110 AAACTGAAATC
1 AGACTGAAATT
*
18121 AGACTGAAATA
1 AGACTGAAATT
* *
18132 ATAGTGAAATT
1 AGACTGAAATT
*
18143 AGACTGAAAAT
1 AGACTGAAATT
*
18154 AGACTGATATT
1 AGACTGAAATT
*
18165 AAACTGAAATT
1 AGACTGAAATT
* **
18176 AGACTAAAAAA
1 AGACTGAAATT
*
18187 AGACTGATATT
1 AGACTGAAATT
* *
18198 AAACTGAAATC
1 AGACTGAAATT
**
18209 AGACTGAAAGA
1 AGACTGAAATT
*
18220 ATACTGAAATT
1 AGACTGAAATT
**
18231 AGACTGAAAAA
1 AGACTGAAATT
**
18242 AGACTGAAAAA
1 AGACTGAAATT
*
18253 AGACTGATATT
1 AGACTGAAATT
*
18264 AAACTGAAATT
1 AGACTGAAATT
* **
18275 AGACTAAAAAA
1 AGACTGAAATT
*
18286 AGACTGATATT
1 AGACTGAAATT
**
18297 AGACAAAAATT
1 AGACTGAAATT
* *
18308 AGACTGATATA
1 AGACTGAAATT
*
18319 AGACTGATATTAAATC
1 AGACTG-----AAATT
**
18335 AGACTGAAAGA
1 AGACTGAAATT
* **
18346 AAACTGAAAAA
1 AGACTGAAATT
*
18357 AGACTGATATT
1 AGACTGAAATT
*
18368 AAACTGAAATT
1 AGACTGAAATT
**
18379 AGACTGAAAGA
1 AGACTGAAATT
18390 AGACTGAAATT
1 AGACTGAAATT
18401 AGACTGA
1 AGACTGA
18408 TAAAAGACTG
Statistics
Matches: 466, Mismatches: 142, Indels: 16
0.75 0.23 0.03
Matches are distributed among these distances:
10 12 0.03
11 443 0.95
12 2 0.00
16 9 0.02
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.24
Consensus pattern (11 bp):
AGACTGAAATT
Found at i:17836 original size:33 final size:33
Alignment explanation
Indices: 17808--18407 Score: 561
Period size: 33 Copynumber: 18.0 Consensus size: 33
17798 AATTAGACTG
* *
17808 AAATGAGACTGAAAAAATACTGATATTAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* * * *
17841 AAATTAGACTGATATAAGACTGATATTAAACTA
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
** * * *
17874 AAACCAGACTGAAAGAATACTGAAATTAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* *
17907 AAAATAGACTGAAAAAAGACTGATATTAAACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
*
17940 AAATGAGACTGAAAAAAGACTGATATTAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* * * * *
17973 AAATTAAACTGATATACGACTGATATTAAACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* * * *
18006 AAATCAGACTGAAAGAATACTGAAATTAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
** ** ** * **
18039 GTAGAAGACTGAAATTAGACTGAAAAAAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* ** *
18072 ATATTAGACTGAAATTAGACTGATATAAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* * ** * * * *
18105 ATATTAAACTGAAATCAGACTGAAATAATAGTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* *
18138 AAATTAGACTGAAAATAGACTGATATTAAACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* *
18171 AAATTAGACTAAAAAAAGACTGATATTAAACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* * * *
18204 AAATCAGACTGAAAGAATACTGAAATTAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
** *
18237 AAAAAAGACTGAAAAAAGACTGATATTAAACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* **
18270 AAATTAGACTAAAAAAAGACTGATATTAGACAA
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* *
18303 AAATTAGACTGATATAAGACTGATATTAAATCAGACTG
1 AAATTAGACTGAAAAAAGACTGATA-T---T-AGACTG
** * *
18341 AAAGAAAACTGAAAAAAGACTGATATTAAACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
* *
18374 AAATTAGACTGAAAGAAGACTGAAATTAGACTG
1 AAATTAGACTGAAAAAAGACTGATATTAGACTG
18407 A
1 A
18408 TAAAAGACTG
Statistics
Matches: 461, Mismatches: 101, Indels: 10
0.81 0.18 0.02
Matches are distributed among these distances:
33 433 0.94
34 2 0.00
37 2 0.00
38 24 0.05
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (33 bp):
AAATTAGACTGAAAAAAGACTGATATTAGACTG
Found at i:18537 original size:36 final size:36
Alignment explanation
Indices: 18409--18928 Score: 626
Period size: 36 Copynumber: 14.6 Consensus size: 36
18399 TTAGACTGAT
*
18409 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGT---AAAG
* * * *
18448 AAAAGAATGTCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
18484 --AAGACTGGTTTAATTTCAAGGAAATTAAGTAAA-
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
18517 AAAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAA-GACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * * *
18554 AAAAGATTGGCTTAGTTTCAAAGAAACTAGGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
18590 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
18626 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * * * *
18662 -ATAGACTAG---AGTTTCAAAGAAACTAGGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * * *
18694 AAAAGACTGGCTTAGTTTCAAAGAAACTAGGTGAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
18730 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
18766 AAAAGACTAGCTTAATTTCAAGGAAATTAGGCAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
18802 -ATAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * *
18837 AAAAGACTGGCTTAGTTTCGAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
18873 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * *
18908 AAGACACAGGCTTAATTTCAA
1 AAAAGACTGGCTTAATTTCAA
18929 ACAAGGAAAT
Statistics
Matches: 417, Mismatches: 55, Indels: 22
0.84 0.11 0.04
Matches are distributed among these distances:
32 20 0.05
33 7 0.02
34 27 0.06
35 58 0.14
36 274 0.66
37 4 0.01
39 27 0.06
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (36 bp):
AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
Found at i:18705 original size:140 final size:141
Alignment explanation
Indices: 18409--18928 Score: 697
Period size: 140 Copynumber: 3.7 Consensus size: 141
18399 TTAGACTGAT
* * * * * * *
18409 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGAAAAGAATGTCTTAGTTTCAAGGAAA
1 AAAAGACTGGCTTAGTTTCAAAGAAACTAGGT---AAAGAAAAGACTGGCTTAATTTCAAGGAAA
* * * * * *
18474 CTAGGTAAAG--AAGACTGGTTTAATTTCAAGGAAATTAAGTAAAAAAAGGACTGGCTTAGTTTC
63 TTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATA-GACTGG--TAGTTTC
18537 AAGGAAACTAGGTAAAG
125 AAGGAAACTAGGTAAAG
*
18554 AAAAGATTGGCTTAGTTTCAAAGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAAGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
* *
18619 AGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTAG-AGTTTCAAAGAA
66 AGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGTAGTTTCAAGGAA
18683 ACTAGGTAAAG
131 ACTAGGTAAAG
*
18694 AAAAGACTGGCTTAGTTTCAAAGAAACTAGGTGAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAAGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
* * *
18759 AGTAAAGAAAAGACTAGCTTAATTTCAAGGAAATTAGGCAAAGATAGACTGGCTTAATTTCAAGG
66 AGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGG--TAGTTTCAAGG
* *
18824 AAATTAAGTAAAG
129 AAACTAGGTAAAG
* *
18837 AAAAGACTGGCTTAGTTTCGAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAAGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
* * *
18902 AGTAAA-AAGACACAGGCTTAATTTCAA
66 AGTAAAGAAAAGACTGGCTTAATTTCAA
18929 ACAAGGAAAT
Statistics
Matches: 338, Mismatches: 32, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
140 134 0.40
142 52 0.15
143 92 0.27
144 33 0.10
145 27 0.08
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (141 bp):
AAAAGACTGGCTTAGTTTCAAAGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
AGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGTAGTTTCAAGGAA
ACTAGGTAAAG
Found at i:18995 original size:36 final size:34
Alignment explanation
Indices: 18946--19064 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 34
18936 AATTAAGTAA
*
18946 AATAAAGAACTTAATTCAGTGTAATTAAGTGAGGTC
1 AATAAAGAGCTTAATTCAG-GTAATTAAGTGA-GTC
18982 AATAAA-AGGCTTAATTCAGGGTAATTAAGT-AG--
1 AATAAAGA-GCTTAATTCA-GGTAATTAAGTGAGTC
*
19014 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAGCTTAATTC-AGGTAATTAAGTG-AGTC
19050 AATAAAGAGCTTAAT
1 AATAAAGAGCTTAAT
19065 CTAGAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
32 25 0.35
33 2 0.03
34 3 0.04
35 2 0.03
36 39 0.54
37 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (34 bp):
AATAAAGAGCTTAATTCAGGTAATTAAGTGAGTC
Found at i:19018 original size:68 final size:68
Alignment explanation
Indices: 18936--19064 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 68
18926 CAAACAAGGA
*
18936 AATTAAGTAAAATAAAGAACTTAATTC-AGTGTAATTAAGTGAGGTCAATAAA-AGGCTTAATTC
1 AATTAAGTAAAATAAAGAACTTAATTCAAG-GTAATTAAGTGAAGTCAATAAAGA-GCTTAATTC
18999 AGGGT
64 AGGGT
*
19004 AATTAAGTAGAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
19065 CTAGAAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
68 54 0.95
69 3 0.05
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAATTCAG
GGT
Found at i:19027 original size:32 final size:32
Alignment explanation
Indices: 18936--19043 Score: 128
Period size: 32 Copynumber: 3.2 Consensus size: 32
18926 CAAACAAGGA
* *
18936 AATTAAGTAAAATAAAGAACTTAATTCAGTGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
*
18968 AATTAAGTGAGGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-A-G--AATAAAGA-ACTTAATTCAGGGT
*
19004 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
19036 AATTAAGT
1 AATTAAGT
19044 GAAGTCAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
32 34 0.52
33 2 0.03
34 1 0.02
35 2 0.03
36 26 0.40
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (32 bp):
AATTAAGTAGAATAAAGAACTTAATTCAGGGT
Found at i:22122 original size:25 final size:25
Alignment explanation
Indices: 22094--22153 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
22084 AAATCTGAAA
22094 TTCAAAGTTGAATCGGCTATGAATT
1 TTCAAAGTTGAATCGGCTATGAATT
22119 TTCAAAGTTGAATCGGCTATGAATT
1 TTCAAAGTTGAATCGGCTATGAATT
22144 TTCAAAGTTG
1 TTCAAAGTTG
22154 CTTATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (25 bp):
TTCAAAGTTGAATCGGCTATGAATT
Found at i:23109 original size:30 final size:30
Alignment explanation
Indices: 23075--23136 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
23065 AATGGGTCGA
*
23075 ATGGCCGGTTGTGACCGGATGGCCCGTGCG
1 ATGGCCGGTTGTGACCGGATGGCCCATGCG
* *
23105 ATGGCCGGTTGTGGCCGGATGGCTCATGCG
1 ATGGCCGGTTGTGACCGGATGGCCCATGCG
23135 AT
1 AT
23137 ATCCCGTGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.11, C:0.24, G:0.42, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTGACCGGATGGCCCATGCG
Found at i:26180 original size:5 final size:5
Alignment explanation
Indices: 26158--26195 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
26148 GTGTGTGTGT
26158 ATATA TATATA TATATA ATATA ATATA ATATA ATATA A
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA A
26196 GAGGTAGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 21 0.66
6 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:27857 original size:158 final size:158
Alignment explanation
Indices: 27569--27886 Score: 636
Period size: 158 Copynumber: 2.0 Consensus size: 158
27559 CCATACTTTG
27569 TAGGGAAATAGAAGATGAAACTAATCAATGTCAAGGCGCGAGTGGAAGAAATTTATTACCTTTTA
1 TAGGGAAATAGAAGATGAAACTAATCAATGTCAAGGCGCGAGTGGAAGAAATTTATTACCTTTTA
27634 AGTTGATGTAAGATTTTAGATTTGAGTTTTGTAAATTAAGAAAACAGTAAAAGAGTTTTCTCTTG
66 AGTTGATGTAAGATTTTAGATTTGAGTTTTGTAAATTAAGAAAACAGTAAAAGAGTTTTCTCTTG
27699 ACAATTGACTTCATACTATATAATTTTC
131 ACAATTGACTTCATACTATATAATTTTC
27727 TAGGGAAATAGAAGATGAAACTAATCAATGTCAAGGCGCGAGTGGAAGAAATTTATTACCTTTTA
1 TAGGGAAATAGAAGATGAAACTAATCAATGTCAAGGCGCGAGTGGAAGAAATTTATTACCTTTTA
27792 AGTTGATGTAAGATTTTAGATTTGAGTTTTGTAAATTAAGAAAACAGTAAAAGAGTTTTCTCTTG
66 AGTTGATGTAAGATTTTAGATTTGAGTTTTGTAAATTAAGAAAACAGTAAAAGAGTTTTCTCTTG
27857 ACAATTGACTTCATACTATATAATTTTC
131 ACAATTGACTTCATACTATATAATTTTC
27885 TA
1 TA
27887 CCCTGGCAAA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 160 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (158 bp):
TAGGGAAATAGAAGATGAAACTAATCAATGTCAAGGCGCGAGTGGAAGAAATTTATTACCTTTTA
AGTTGATGTAAGATTTTAGATTTGAGTTTTGTAAATTAAGAAAACAGTAAAAGAGTTTTCTCTTG
ACAATTGACTTCATACTATATAATTTTC
Found at i:30128 original size:12 final size:12
Alignment explanation
Indices: 30111--30136 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30101 CCATTGCTAA
30111 AGATTTTTGTAG
1 AGATTTTTGTAG
30123 AGATTTTTGTAG
1 AGATTTTTGTAG
30135 AG
1 AG
30137 GAAGGAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (12 bp):
AGATTTTTGTAG
Found at i:33408 original size:22 final size:21
Alignment explanation
Indices: 33269--33633 Score: 170
Period size: 22 Copynumber: 16.8 Consensus size: 21
33259 TTTCGAACAG
*
33269 GGTTATCAAAATTTCATAGTA
1 GGTTATCAAAATTTCATAGGA
* *
33290 TGTAAATCAAAATTTCATAGGGA
1 GGT-TATCAAAATTTCATA-GGA
* * *
33313 GATTAACAAAATTTCATAATGA
1 GGTTATCAAAATTTCAT-AGGA
** **
33335 AATTATCAAAAAATCATAGGAA
1 GGTTATCAAAATTTCATAGG-A
*
33357 GGTTATCAAAA-TT--T-GTA
1 GGTTATCAAAATTTCATAGGA
* *
33374 -GTTATTAAGATTTCATAAGGA
1 GGTTATCAAAATTTCAT-AGGA
*
33395 GGTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGG-A
*
33417 GGTTTATCAAAATTTCATAGCAA
1 GG-TTATCAAAATTTCATAG-GA
* *
33440 GGTTATCACAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
33462 GATTATCAAAATTTCAAAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
33484 GATTACTGACAA-TTCATATGGA
1 GGTTA-TCAAAATTTCATA-GGA
* * * * *
33506 GGTTCTTAAATTTTCATAACGT
1 GGTTATCAAAATTTCAT-AGGA
* *
33528 GGTTATCAATATATCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* * *
33550 GGTTATCAACATCTT-ATGGTGTT
1 GGTTATCAAAAT-TTCATAG-G-A
33573 GGTTATCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATAG-GA
* *
33595 GGTCT-TCAAAATTCCTTATGGA
1 GGT-TATCAAAATTTCATA-GGA
*
33617 GGTTAACAAAATTTCAT
1 GGTTATCAAAATTTCAT
33634 TAGAAGGCTA
Statistics
Matches: 257, Mismatches: 62, Indels: 49
0.70 0.17 0.13
Matches are distributed among these distances:
16 8 0.03
17 3 0.01
18 1 0.00
19 2 0.01
21 16 0.06
22 179 0.70
23 48 0.19
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:33759 original size:62 final size:62
Alignment explanation
Indices: 33693--33844 Score: 225
Period size: 62 Copynumber: 2.5 Consensus size: 62
33683 TCATTATTGA
*
33693 AATTTCATAGGAACGTTATCCAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCTT
1 AATTTCATAGGAACGTTATCCAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* * * *
33755 AATTTCATAGGAATGTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAACGTTATCCAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
33817 AATTTAATAGGAAGGTTAT-CATAATTTC
1 AATTTCATAGGAACGTTATCCA-AATTTC
33845 GTATGAATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
61 1 0.01
62 80 0.99
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (62 bp):
AATTTCATAGGAACGTTATCCAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
Found at i:33802 original size:23 final size:22
Alignment explanation
Indices: 33755--33800 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
33745 TAATTATCTT
*
33755 AATTTCATAGGAATGTTATCAA
1 AATTTCATAGGAATGTCATCAA
33777 AATTTCATAAGG-ATGTCATCAA
1 AATTTCAT-AGGAATGTCATCAA
33799 AA
1 AA
33801 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
AATTTCATAGGAATGTCATCAA
Found at i:52953 original size:137 final size:137
Alignment explanation
Indices: 52707--52983 Score: 554
Period size: 137 Copynumber: 2.0 Consensus size: 137
52697 GGTGCATATA
52707 CTTCTAATATTAGTAATCACAAACCTATGAAGATTTTCAAATTCTTGATGCCTTTAGATACATAA
1 CTTCTAATATTAGTAATCACAAACCTATGAAGATTTTCAAATTCTTGATGCCTTTAGATACATAA
52772 ATTAGGTTAAAATATTGTAGTCAATCTAAATATAAGATGTTACTATTGGTTTTTTGTGAAACTAT
66 ATTAGGTTAAAATATTGTAGTCAATCTAAATATAAGATGTTACTATTGGTTTTTTGTGAAACTAT
52837 TGACATC
131 TGACATC
52844 CTTCTAATATTAGTAATCACAAACCTATGAAGATTTTCAAATTCTTGATGCCTTTAGATACATAA
1 CTTCTAATATTAGTAATCACAAACCTATGAAGATTTTCAAATTCTTGATGCCTTTAGATACATAA
52909 ATTAGGTTAAAATATTGTAGTCAATCTAAATATAAGATGTTACTATTGGTTTTTTGTGAAACTAT
66 ATTAGGTTAAAATATTGTAGTCAATCTAAATATAAGATGTTACTATTGGTTTTTTGTGAAACTAT
52974 TGACATC
131 TGACATC
52981 CTT
1 CTT
52984 AAAGCATAGA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 140 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (137 bp):
CTTCTAATATTAGTAATCACAAACCTATGAAGATTTTCAAATTCTTGATGCCTTTAGATACATAA
ATTAGGTTAAAATATTGTAGTCAATCTAAATATAAGATGTTACTATTGGTTTTTTGTGAAACTAT
TGACATC
Found at i:54750 original size:30 final size:30
Alignment explanation
Indices: 54716--54777 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
54706 GCGATGACTT
54716 AAGGATAAATCGGTTAAAAGTGACAATTAA
1 AAGGATAAATCGGTTAAAAGTGACAATTAA
54746 AAGGATAAATCGGTTAAAAGTGACAATTAA
1 AAGGATAAATCGGTTAAAAGTGACAATTAA
54776 AA
1 AA
54778 ATGAACGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (30 bp):
AAGGATAAATCGGTTAAAAGTGACAATTAA
Found at i:54810 original size:37 final size:37
Alignment explanation
Indices: 54758--54829 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
54748 GGATAAATCG
*
54758 GTTAAAAGTGACAATTAAAAATGAACGGAGGTAGTCA
1 GTTAAAAGGGACAATTAAAAATGAACGGAGGTAGTCA
* *
54795 GTTAAAAGGGGCAATTAAAAATGAATGGAGGTAGT
1 GTTAAAAGGGACAATTAAAAATGAACGGAGGTAGT
54830 ATATCCTACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (37 bp):
GTTAAAAGGGACAATTAAAAATGAACGGAGGTAGTCA
Found at i:56720 original size:70 final size:70
Alignment explanation
Indices: 56636--56789 Score: 229
Period size: 70 Copynumber: 2.2 Consensus size: 70
56626 GAGTAAAATT
* * * * *
56636 GTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTA
1 GTAAAATAGTAAAATAAAATAACTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
56701 GTTGA
66 GTTGA
* *
56706 GTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
1 GTAAAATAGTAAAATAAAATAACTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
56771 GTTGA
66 GTTGA
56776 GTAAAACTA-TAAAA
1 GTAAAA-TAGTAAAA
56790 ACCTAAATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
70 74 0.97
71 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (70 bp):
GTAAAATAGTAAAATAAAATAACTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
GTTGA
Found at i:57806 original size:5 final size:5
Alignment explanation
Indices: 57798--57825 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
57788 AAAAAAAATG
57798 CAATA CAATA CAATA CAATA CAATA CAA
1 CAATA CAATA CAATA CAATA CAATA CAA
57826 GTGCTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (5 bp):
CAATA
Found at i:61534 original size:11 final size:11
Alignment explanation
Indices: 61518--61543 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61508 ATTGCTAGAT
61518 GTGATTAGTAG
1 GTGATTAGTAG
61529 GTGATTAGTAG
1 GTGATTAGTAG
61540 GTGA
1 GTGA
61544 CACGTGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (11 bp):
GTGATTAGTAG
Found at i:61588 original size:15 final size:15
Alignment explanation
Indices: 61560--61592 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
61550 GAATAAAAAA
61560 TTAAATATTATTATT
1 TTAAATATTATTATT
61575 TTAATATATT-TTATT
1 TTAA-ATATTATTATT
61590 TTA
1 TTA
61593 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAATATTATTATT
Found at i:63621 original size:14 final size:15
Alignment explanation
Indices: 63596--63624 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
63586 ATTTCAATTG
63596 AATTAGATTTTCCTT
1 AATTAGATTTTCCTT
63611 AATTA-ATTTTCCTT
1 AATTAGATTTTCCTT
63625 TTATATCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTAGATTTTCCTT
Found at i:65046 original size:19 final size:19
Alignment explanation
Indices: 65018--65055 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
65008 CATATAAAAT
*
65018 AATAAAAACTAATTTTTAA
1 AATAAAAACTAATTATTAA
*
65037 AATAATAACTAATTATTAA
1 AATAAAAACTAATTATTAA
65056 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAAAACTAATTATTAA
Found at i:69061 original size:33 final size:35
Alignment explanation
Indices: 69019--69143 Score: 133
Period size: 33 Copynumber: 3.8 Consensus size: 35
69009 TTGGTCGCGA
*
69019 CGCGGGTCGCG-CGCAGATCGCGA-CCAGCCATGG
1 CGCGGGTCGCGACGCAGATTGCGACCCAGCCATGG
*
69052 CGCGGGTCGCGATCCGC-G--TGCGATCCAGCCATGG
1 CGCGGGTCGCGA--CGCAGATTGCGACCCAGCCATGG
*
69086 -GCGGGTCGCGGC-CAGATTGCGACCCA-CCATGG
1 CGCGGGTCGCGACGCAGATTGCGACCCAGCCATGG
*
69118 TGCGGGTCGCGAC-CAGATTGCGACCC
1 CGCGGGTCGCGACGCAGATTGCGACCC
69144 GCACCATGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
30 1 0.01
31 2 0.03
32 6 0.08
33 57 0.71
34 10 0.12
35 1 0.01
36 3 0.04
ACGTcount: A:0.14, C:0.35, G:0.38, T:0.13
Consensus pattern (35 bp):
CGCGGGTCGCGACGCAGATTGCGACCCAGCCATGG
Found at i:69085 original size:34 final size:33
Alignment explanation
Indices: 69020--69199 Score: 117
Period size: 33 Copynumber: 5.5 Consensus size: 33
69010 TGGTCGCGAC
*
69020 GCGGGTCGCGCG-CAGA-TCGCGACCAGCCATGG
1 GCGGGTCGCGAGCCAGAGT-GCGACCAGCCATGG
* *
69052 CGCGGGTCGCGATCC-GCGTGCGATCCAGCCATGG
1 -GCGGGTCGCGAGCCAGAGTGCGA-CCAGCCATGG
*
69086 GCGGGTCGCG-GCCAGATTGCGACCCA-CCATGG
1 GCGGGTCGCGAGCCAGAGTGCGA-CCAGCCATGG
* *
69118 TGCGGGTCGCGA-CCAGATTGCGACCCGCACCAT-G
1 -GCGGGTCGCGAGCCAGAGTGCGACCAG--CCATGG
** * * **
69152 GATGGTCGCGATCCA-CGTGCGACCCAGTTATGG
1 GCGGGTCGCGAGCCAGAGTGCGA-CCAGCCATGG
69185 GCGGGTCGCGA-CCAG
1 GCGGGTCGCGAGCCAG
69200 TCCTTTTCTG
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
32 15 0.13
33 79 0.68
34 19 0.16
35 4 0.03
ACGTcount: A:0.16, C:0.33, G:0.37, T:0.14
Consensus pattern (33 bp):
GCGGGTCGCGAGCCAGAGTGCGACCAGCCATGG
Found at i:69898 original size:22 final size:22
Alignment explanation
Indices: 69774--69932 Score: 74
Period size: 22 Copynumber: 7.2 Consensus size: 22
69764 TTAATCTTCT
* * *
69774 TATGAAATTTTGTTAACCTCCC
1 TATGAAATATTGATAACCTCCA
* * * *
69796 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATATTGATA-ACCTCCA
* * *
69818 TATGGAATTTTGATAACTTCCCA
1 TATGAAATATTGATAACCT-CCA
* **
69841 -ATGAAATTTTGATAACCAACA
1 TATGAAATATTGATAACCTCCA
* *
69862 CTATGAGATACTGATAACCTCCA
1 -TATGAAATATTGATAACCTCCA
* *
69885 TATGATATATTGATAACC-ACA
1 TATGAAATATTGATAACCTCCA
* *
69906 TTATGAAA-ATTTAAAAACCTCCA
1 -TATGAAATA-TTGATAACCTCCA
69929 TATG
1 TATG
69933 GATTGTTAGT
Statistics
Matches: 105, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
21 6 0.06
22 78 0.74
23 21 0.20
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (22 bp):
TATGAAATATTGATAACCTCCA
Found at i:69970 original size:22 final size:22
Alignment explanation
Indices: 69942--69988 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
69932 GGATTGTTAG
* * *
69942 TAATCACACTCTGAAATTTTGA
1 TAATCACAATATGAAATTGTGA
69964 TAATCACAATATGAAATTGTGA
1 TAATCACAATATGAAATTGTGA
69986 TAA
1 TAA
69989 CCTCGTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
TAATCACAATATGAAATTGTGA
Found at i:69998 original size:22 final size:21
Alignment explanation
Indices: 69953--70244 Score: 152
Period size: 22 Copynumber: 13.6 Consensus size: 21
69943 AATCACACTC
* * *
69953 TGAAATTTTGATAATCACAATA
1 TGAAATTTTGATAACCTC-TTA
*
69975 TGAAATTGTGATAACCTCGTTA
1 TGAAATTTTGATAACCTC-TTA
* *
69997 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AA-CCTCTTA
*
70020 TAAAATTTTGATAAACCTCTTTA
1 TGAAATTTTGAT-AACCTC-TTA
* *
70043 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAAC-CTCTTA
*
70065 TGAAATCTTGATAA---C-TA
1 TGAAATTTTGATAACCTCTTA
* * *
70082 -CAAATTGTGATAACCTCCCTA
1 TGAAATTTTGATAACCT-CTTA
**
70103 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTC-TTA
* * *
70125 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCT-CTTA
* *
70147 TGAAATTTTGATCTACATAC-TA
1 TGAAATTTTGAT-AACCT-CTTA
70169 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCTTA
* *
70191 TGAAAATTTGA-AAACTAAAC-TA
1 TGAAATTTTGATAACCT---CTTA
* **
70213 TGAAATTTTGATATCCTC-CC
1 TGAAATTTTGATAACCTCTTA
70233 TGAAATTTTGAT
1 TGAAATTTTGAT
70245 TACTCCATAA
Statistics
Matches: 210, Mismatches: 41, Indels: 40
0.72 0.14 0.14
Matches are distributed among these distances:
16 10 0.05
17 2 0.01
18 1 0.00
20 16 0.08
21 7 0.03
22 129 0.61
23 42 0.20
24 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCTTA
Found at i:70027 original size:23 final size:22
Alignment explanation
Indices: 69999--70078 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 22
69989 CCTCGTTATG
69999 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTT-CTATA
70022 AAATTTTGATAAACCTCTT-TATA
1 AAATTTTGATAAA--TCTTCTATA
* *
70045 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTC-TATA
*
70067 AAATCTTGATAA
1 AAATTTTGATAA
70079 CTACAAATTG
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 14 0.28
23 29 0.58
25 4 0.08
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (22 bp):
AAATTTTGATAAATCTTCTATA
Found at i:70077 original size:45 final size:45
Alignment explanation
Indices: 69973--70078 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 45
69963 ATAATCACAA
*
69973 TATGAAATTGTGAT-AACCTCGTTATGAAATTTTGATAAATCTTCC
1 TATGAAATT-TGATAAACCTCGTTATAAAATTTTGATAAATCTTCC
* * * *
70018 TATAAAATTTTGATAAACCTCTTTATAAAATTTTGATAACT-TTCT
1 TATGAAA-TTTGATAAACCTCGTTATAAAATTTTGATAAATCTTCC
70063 TATGAAATCTTGATAA
1 TATGAAAT-TTGATAA
70079 CTACAAATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 26 0.50
46 25 0.48
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.42
Consensus pattern (45 bp):
TATGAAATTTGATAAACCTCGTTATAAAATTTTGATAAATCTTCC
Found at i:70630 original size:22 final size:21
Alignment explanation
Indices: 70350--70826 Score: 125
Period size: 22 Copynumber: 21.8 Consensus size: 21
70340 AATCACATTT
* *
70350 TGAAAATTTGATAACCTCTTCA
1 TGAAATTTTGATAACCTCCT-A
* * * *
70372 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
70394 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTC-CTA
* * *
70416 TGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAACC-TCCTA
**
70438 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTC-CTA
*
70460 TGAAATTTTGATAACCTTCTA
1 TGAAATTTTGATAACCTCCTA
* *
70481 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCC-TA
* * *
70501 TGAAATTGAGACTTTTATAACATTCATA
1 TGAAA-T-----TTTGATAAC-CTCCTA
* *
70529 TGAAATTTTGATAATCTCCCCA
1 TGAAATTTTGATAACCT-CCTA
*
70551 TGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGA-TAACCTCCT-A
* *
70573 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
70595 TAAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-CTA
* * *
70617 TGACATTTTGATAATCT-CTT
1 TGAAATTTTGATAACCTCCTA
* ** *
70637 TGGTAACCTTTCT-ATAAAAT--TG
1 T-G-AA-ATTT-TGATAACCTCCTA
* *
70659 TGAAA--AT--TAACCACCCTA
1 TGAAATTTTGATAACC-TCCTA
** *
70677 TGAAATTTCAATAACCAACCTA
1 TGAAATTTTGATAACC-TCCTA
* *
70699 AGAAATTTTAATAACCTGATCCTA
1 TGAAATTTTGATAACC---TCCTA
* *
70723 TGAAATTTTGATTACTTCCATA
1 TGAAATTTTGATAACCTCC-TA
* *
70745 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
70767 TGGAAA-TTTGATAACCTCCTCA
1 T-GAAATTTTGATAACCTCCT-A
* * * *
70789 TGAAATTATAATAACTATCTTA
1 TGAAATTTTGATAAC-CTCCTA
70811 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
70827 ACATAGAGAC
Statistics
Matches: 326, Mismatches: 90, Indels: 79
0.66 0.18 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
18 6 0.02
19 3 0.01
20 12 0.04
21 31 0.10
22 216 0.66
23 21 0.06
24 18 0.06
26 4 0.01
27 2 0.01
28 7 0.02
29 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:71628 original size:42 final size:42
Alignment explanation
Indices: 71581--71666 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
71571 TGTACTCTTC
*
71581 AAATGAGCTCATTTCCACAAAAGAAGTTACAAAATCAGGAAT
1 AAATGAGCTCATTTCCACAAAAAAAGTTACAAAATCAGGAAT
71623 AAATGAGCTCATTTCCACAAAAAAAGTTACAAAATCAGGAAT
1 AAATGAGCTCATTTCCACAAAAAAAGTTACAAAATCAGGAAT
71665 AA
1 AA
71667 GTAAAAGACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (42 bp):
AAATGAGCTCATTTCCACAAAAAAAGTTACAAAATCAGGAAT
Found at i:72348 original size:2 final size:2
Alignment explanation
Indices: 72341--72365 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72331 GATGAGAAAA
72341 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 A
72366 AGTAGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72525 original size:39 final size:39
Alignment explanation
Indices: 72468--72544 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
72458 TAATCAAATT
* * *
72468 GAATTCTTTTAGTCCAATTCCAACTATGTATTACGGGTA
1 GAATTCTTTTAGTACAATTCAAACTATATATTACGGGTA
* *
72507 GAATT-TTATTAGTACAATTCAAATTATATTTTACGGGT
1 GAATTCTT-TTAGTACAATTCAAACTATATATTACGGGT
72545 TCTCTTAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 2 0.06
39 30 0.94
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (39 bp):
GAATTCTTTTAGTACAATTCAAACTATATATTACGGGTA
Found at i:72559 original size:34 final size:34
Alignment explanation
Indices: 72515--72579 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
72505 TAGAATTTTA
*
72515 TTAGTACAATT-CAAATTATATTTTACGGGTTCTC
1 TTAGTACAATTGC-AATTATATATTACGGGTTCTC
*
72549 TTAGTCCAATTGCAATTATATATTACGGGTT
1 TTAGTACAATTGCAATTATATATTACGGGTT
72580 AAGTGTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (34 bp):
TTAGTACAATTGCAATTATATATTACGGGTTCTC
Found at i:72694 original size:28 final size:26
Alignment explanation
Indices: 72635--72696 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
72625 AAGTAATCTT
* *
72635 GAAGAGATTGGTTGAGATTAAAATTG
1 GAAGAGTTTGGTTGAGATTAAAAATG
72661 G--GAGTTTGGTTGAGATTAAAAATG
1 GAAGAGTTTGGTTGAGATTAAAAATG
72685 GTTAAGAGTTTG
1 G--AAGAGTTTG
72697 TCTAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 22 0.73
26 1 0.03
28 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (26 bp):
GAAGAGTTTGGTTGAGATTAAAAATG
Found at i:73827 original size:30 final size:31
Alignment explanation
Indices: 73791--73849 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
73781 GGCAATTTAG
*
73791 AAATATATTTTTTAAAA-AA-GGTACAATTAA
1 AAATATA-TTTTAAAAATAAGGGTACAATTAA
73821 AAATATATTTTAAAAATAAGGGTACAATT
1 AAATATATTTTAAAAATAAGGGTACAATT
73850 GGAAAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 9 0.35
31 9 0.35
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (31 bp):
AAATATATTTTAAAAATAAGGGTACAATTAA
Found at i:73946 original size:155 final size:157
Alignment explanation
Indices: 73712--74025 Score: 481
Period size: 155 Copynumber: 2.0 Consensus size: 157
73702 ATTATATAAT
*
73712 CTAATAATTAATAATGGAATAATTTATGATTAAAAAGATAATGGAATAATTAAAATATTATTTAT
1 CTAATAATTAATAATGGAATAATTTATGATTAAAAAGATAATGGAATAATTAAAATATTATTTAG
* *
73777 TAATGGCAATTTAGAAATATATTTTTTAAAAAA-GGTACAATTAAAAATATATTTTAAAAATAAG
66 TAATGGCAATTTAGAAATAT-GTTTTAAAAAAATGGTACAATTAAAAATATATTTTAAAAATAAG
* *
73841 GGTACAATTGGAAAACATAAAG-TTTCC
130 GGTACAATCGAAAAACATAAAGTTTTCC
*
73868 CTAATAATTAATAATGGAATAATTTATGATTAAAAA-ATACTGGAATAATTAAAATATTATTTAG
1 CTAATAATTAATAATGGAATAATTTATGATTAAAAAGATAATGGAATAATTAAAATATTATTTAG
* * ** * *
73932 TAATGGTAATTTAGAAATGTGTTTTAAAAAAATGGTACAATTGGAAATATGTTTTAAAAATAATG
66 TAATGGCAATTTAGAAATATGTTTTAAAAAAATGGTACAATTAAAAATATATTTTAAAAATAAGG
*
73997 GTACAATCGAAAAATATAAAGTTTTCC
131 GTACAATCGAAAAACATAAAGTTTTCC
74024 CT
1 CT
74026 TATTCGTACT
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
154 10 0.07
155 90 0.63
156 43 0.30
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (157 bp):
CTAATAATTAATAATGGAATAATTTATGATTAAAAAGATAATGGAATAATTAAAATATTATTTAG
TAATGGCAATTTAGAAATATGTTTTAAAAAAATGGTACAATTAAAAATATATTTTAAAAATAAGG
GTACAATCGAAAAACATAAAGTTTTCC
Found at i:74000 original size:31 final size:31
Alignment explanation
Indices: 73932--74003 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
73922 TATTATTTAG
* *
73932 TAATGGTA-ATTTAGAAATGTGTTTTAAAAA
1 TAATGGTACAATTAGAAATATGTTTTAAAAA
*
73962 -AATGGTACAATTGGAAATATGTTTTAAAAA
1 TAATGGTACAATTAGAAATATGTTTTAAAAA
73992 TAATGGTACAAT
1 TAATGGTACAAT
74004 CGAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.19
30 19 0.51
31 11 0.30
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (31 bp):
TAATGGTACAATTAGAAATATGTTTTAAAAA
Found at i:74999 original size:2 final size:2
Alignment explanation
Indices: 74950--74980 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74940 TTAACAGGAA
74950 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 A
74981 CATGTGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75004 original size:12 final size:12
Alignment explanation
Indices: 74987--75011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
74977 TATACATGTG
74987 TGTGTGTATATA
1 TGTGTGTATATA
74999 TGTGTGTATATA
1 TGTGTGTATATA
75011 T
1 T
75012 CTATACTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TGTGTGTATATA
Found at i:75465 original size:19 final size:21
Alignment explanation
Indices: 75433--75475 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
75423 TTCTTTAATA
75433 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
75454 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
75473 TTA
1 TTA
75476 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:75665 original size:22 final size:22
Alignment explanation
Indices: 75640--75743 Score: 95
Period size: 22 Copynumber: 4.6 Consensus size: 22
75630 TTGTCTCTAT
75640 ATGGTTATCAAAATTTCATAAG
1 ATGGTTATCAAAATTTCATAAG
* * *
75662 ATGGTTATTATAATTTCATGAGG
1 ATGGTTATCAAAATTTCAT-AAG
75685 A-GGTTATCAAAATTTCAT-AG
1 ATGGTTATCAAAATTTCATAAG
* * *
75705 TGTGGTTACCAAAATTTCATAGG
1 -ATGGTTATCAAAATTTCATAAG
*
75728 ATCAGGTTATTAAAAT
1 AT--GGTTATCAAAAT
75744 CTCTTAGGTT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
22 49 0.77
23 4 0.06
24 10 0.16
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAAG
Found at i:75721 original size:44 final size:43
Alignment explanation
Indices: 75642--75728 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
75632 GTCTCTATAT
** *
75642 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCAT-AGGA
*
75686 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAAG-ATGGTTACCAAAATTTCATAGGA
75729 TCAGGTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCATAGGA
Found at i:75777 original size:26 final size:26
Alignment explanation
Indices: 75715--75782 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
75705 TGTGGTTACC
* *
75715 AAAATTTCATAGGAT--CAGGTTATT
1 AAAATCTCATAGGATGGTAGGTTATT
* *
75739 AAAATCTCTTAGGTTGGTAGGTTATT
1 AAAATCTCATAGGATGGTAGGTTATT
* *
75765 GAAATTTCATAGGATGGT
1 AAAATCTCATAGGATGGT
75783 TAATTATCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 12 0.35
26 22 0.65
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.38
Consensus pattern (26 bp):
AAAATCTCATAGGATGGTAGGTTATT
Found at i:75845 original size:22 final size:22
Alignment explanation
Indices: 75820--75878 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
75810 ATCAAAGAGA
*
75820 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
75842 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
75864 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
75879 TAAATATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:75943 original size:22 final size:21
Alignment explanation
Indices: 75884--76201 Score: 126
Period size: 22 Copynumber: 14.3 Consensus size: 21
75874 TTCATTAAAT
*
75884 ATTTCATGGAGAGGTTATCAAA
1 ATTTCATAGA-AGGTTATCAAA
* **
75906 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
*
75928 ATTTCATATGAAGGTTATAAAAGTCTCA
1 ATTTCATA-GAAGGTTAT-CAA-----A
* * *
75956 ATTTCATA-AGGGGTACCAAA
1 ATTTCATAGAAGGTTATCAAA
* ** *
75976 ATTTGATAGAAATTTATC-GA
1 ATTTCATAGAAGGTTATCAAA
* *
75996 ATCTCATAG-AGTGATTATCGAA
1 ATTTCATAGAAG-G-TTATCAAA
76018 ATTTCATAGAGATCGGATTATCAAA
1 ATTTCATAGA-A--GG-TTATCAAA
*
76043 ATTT-ATAGAAAGATTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
* *
76064 ATTCCATAG-TGTTGTTATCAAA
1 ATTTCATAGAAG--GTTATCAAA
* *
76086 ATTTCAAAGCGAGGTTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
* * *
76108 ATTACATA-ATGTGATTATCAGA
1 ATTTCATAGAAG-G-TTATCAAA
* *
76130 ATTTCATAGAGGGATTAACAAA
1 ATTTCATAGAAGG-TTATCAAA
* *
76152 ATTTTATAAAGAGGTTATCAAA
1 ATTTCATAGA-AGGTTATCAAA
*
76174 ATTTCATAAAGAGGTTATCAAA
1 ATTTCATAGA-AGGTTATCAAA
*
76196 TTTTCA
1 ATTTCA
76202 AAATGTGATT
Statistics
Matches: 222, Mismatches: 48, Indels: 52
0.69 0.15 0.16
Matches are distributed among these distances:
19 1 0.00
20 18 0.08
21 21 0.09
22 137 0.62
23 7 0.03
24 7 0.03
25 16 0.07
26 6 0.03
28 9 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTTCATAGAAGGTTATCAAA
Found at i:76126 original size:44 final size:44
Alignment explanation
Indices: 76033--76223 Score: 167
Period size: 44 Copynumber: 4.4 Consensus size: 44
76023 ATAGAGATCG
* * * * *
76033 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTCCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
76077 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * *
76120 GATTATCAGAATTTCATAGAG-GGATTAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGG-TTATCAAAATTTCATAATGT
* * *
76164 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
76208 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
76224 TAGTGGTATT
Statistics
Matches: 117, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
43 17 0.15
44 97 0.83
45 3 0.03
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:76439 original size:22 final size:22
Alignment explanation
Indices: 76321--76884 Score: 210
Period size: 22 Copynumber: 25.9 Consensus size: 22
76311 AAATCTCAAT
*
76321 GAGGATATCAAAA-TT--TAGG
1 GAGGTTATCAAAATTTCATAGG
* *
76340 GAGGATATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAG-G
* * * *
76363 TA-GTTTTCAAAATTTCACA-A
1 GAGGTTATCAAAATTTCATAGG
*
76383 GAGGGTTATCAAAATTTCAT-CG
1 GA-GGTTATCAAAATTTCATAGG
* * *
76405 TATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAATTTCATAGG
* * **
76428 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAGG
**
76450 GAGGTTATCAAAAAATCATAGG
1 GAGGTTATCAAAATTTCATAGG
76472 GAGGTTATCAAAA-TT--T--G
1 GAGGTTATCAAAATTTCATAGG
* * *
76489 TA-GTTATCAAGATTTCATAAG
1 GAGGTTATCAAAATTTCATAGG
* ** *
76510 AAAATTATCAAAATTTTATAGG
1 GAGGTTATCAAAATTTCATAGG
*
76532 GAGGTTTATCAAAATTTTATAGG
1 GAGG-TTATCAAAATTTCATAGG
* * **
76555 AAGATTGATCAAAATTTCATAAC
1 GAGGTT-ATCAAAATTTCATAGG
* **
76578 GAGGTTATCACAATTTCATAAT
1 GAGGTTATCAAAATTTCATAGG
* * * *
76600 GTGATTATCAAAATTTCAGAGT
1 GAGGTTATCAAAATTTCATAGG
* * *
76622 GTGATTA-CTAACAA-TTCATATG
1 GAGGTTATC-AA-AATTTCATAGG
* * * * **
76644 GAGCTTTTTAAATTTTCATAAC
1 GAGGTTATCAAAATTTCATAGG
* * * *
76666 GTGGTTATCAATATATCATATG
1 GAGGTTATCAAAATTTCATAGG
* *
76688 GAGGTTATCAACATCTCAT-GG
1 GAGGTTATCAAAATTTCATAGG
* *
76709 TGTTGGTTATCAAAATTTCATTGG
1 -G-AGGTTATCAAAATTTCATAGG
* **
76733 GAAGTTATCAAAATTTCATATT
1 GAGGTTATCAAAATTTCATAGG
* *
76755 GAGGTCT-TCAAAATTCCTTAGG
1 GAGGT-TATCAAAATTTCATAGG
* * * *
76777 GAGGTAAACCAAATTTCATAAG
1 GAGGTTATCAAAATTTCATAGG
* ** **
76799 AAGGTTGAAAAAAATTT-ATAAA
1 GAGGTT-ATCAAAATTTCATAGG
* * * *
76821 AAGGTTCTCGAAATTCCATA-G
1 GAGGTTATCAAAATTTCATAGG
* * *
76842 TATCGTTATTAAAATTTCATAGG
1 GA-GGTTATCAAAATTTCATAGG
* *
76865 AAGATTATCAAAATTTCATA
1 GAGGTTATCAAAATTTCATA
76885 ATGGGATCAT
Statistics
Matches: 400, Mismatches: 115, Indels: 57
0.70 0.20 0.10
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 15 0.04
20 3 0.01
21 14 0.04
22 283 0.71
23 70 0.17
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGG
Found at i:76460 original size:44 final size:44
Alignment explanation
Indices: 76318--76887 Score: 237
Period size: 44 Copynumber: 13.1 Consensus size: 44
76308 TGAAAATCTC
*
76318 AATGAGGATATCAAAA-TT--TAGGGAGGA-TATCAAAATTTCAT
1 AATGAGGTTATCAAAATTTCATAGGGA-GATTATCAAAATTTCAT
* * * *
76359 AGTTTA-GTTTTCAAAATTTCACAAGAGG-G-TTATCAAAATTTCAT
1 A-ATGAGGTTATCAAAATTTCA-TAG-GGAGATTATCAAAATTTCAT
** * * *
76403 CGT-ATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCAT
1 AATGAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
** *
76447 AATGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T
1 AATGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
* * * * * *
76488 -GT-A-GTTATCAAGATTTCATAAGAAAATTATCAAAATTTTAT
1 AATGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
** * *
76529 AGGGAGGTTTATCAAAATTTTATAGGAAGATTGATCAAAATTTCAT
1 AATGAGG-TTATCAAAATTTCATAGGGAGATT-ATCAAAATTTCAT
* * ** * *
76575 AACGAGGTTATCACAATTTCATAATGTGATTATCAAAATTTCAG
1 AATGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
* * * * * * * *
76619 AGTGTGATTA-CTAACAA-TTCATATGGAGCTTTTTAAATTTTCAT
1 AATGAGGTTATC-AA-AATTTCATAGGGAGATTATCAAAATTTCAT
* * * * * * * *
76663 AACGTGGTTATCAATATATCATATGGAGGTTATCAACATCTCAT
1 AATGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
** * *
76707 GGTGTTGGTTATCAAAATTTCATTGGGA-AGTTATCAAAATTTCAT
1 AATG-AGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCAT
* * * * * * *
76752 ATTGAGGTCT-TCAAAATTCCTTAGGGAGGTAAACCAAATTTCAT
1 AATGAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
** *** * * * *
76796 AA-GAAGGTTGAAAAAAATTT-ATAAAAAGGTTCTCGAAATTCCAT
1 AATG-AGGTT-ATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
* * * *
76840 AGT-ATCGTTATTAAAATTTCATAGGAAGATTATCAAAATTTCAT
1 AATGA-GGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
76884 AATG
1 AATG
76888 GGATCATAAA
Statistics
Matches: 384, Mismatches: 110, Indels: 66
0.69 0.20 0.12
Matches are distributed among these distances:
38 25 0.07
39 3 0.01
40 1 0.00
41 11 0.03
42 8 0.02
43 22 0.06
44 208 0.54
45 87 0.23
46 19 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
AATGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCAT
Found at i:76542 original size:23 final size:23
Alignment explanation
Indices: 76514--76593 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
76504 CATAAGAAAA
76514 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
76537 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* * **
76560 TGATCAAAATTTCATAACGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
76582 TTATCACAATTT
1 TTATCAAAATTT
76594 CATAATGTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 10 0.21
23 37 0.79
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:78335 original size:31 final size:31
Alignment explanation
Indices: 78300--78365 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
78290 AATTTTACGC
* **
78300 TTTCCGATTGTA-CCTTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTT-TTTAAAAAACATA
78331 TTTCCAATTGTACCCTTTTTTAAAAAACATA
1 TTTCCAATTGTACCCTTTTTTAAAAAACATA
78362 TTTC
1 TTTC
78366 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTAAAAAACATA
Found at i:78372 original size:32 final size:31
Alignment explanation
Indices: 78306--78372 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
78296 ACGCTTTCCG
** *
78306 ATTGTACCTTTATTTTTAAAACATATTTCCA
1 ATTGTACCTTTATTTAAAAAACATATTTCAA
78337 ATTGTACCCTTT-TTTAAAAAACATATTTCTAA
1 ATTGTA-CCTTTATTTAAAAAACATATTTC-AA
78369 ATTG
1 ATTG
78373 CCATTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTGTACCTTTATTTAAAAAACATATTTCAA
Found at i:78469 original size:163 final size:162
Alignment explanation
Indices: 78253--78581 Score: 588
Period size: 163 Copynumber: 2.0 Consensus size: 162
78243 AGAAAATCTA
* *
78253 ATCTATACTATATATAAAAGTACTACGAATAAGGGGAAATTTTACGCTTTCCGATTGTACCTTTA
1 ATCTATACTATATATAAAAG-A-TACGAATAAGGGGAAACTTTACGCTTTCCGATTGTACCCTTA
78318 TTTTTAAAACATATTTCCAATTGTACCCTTTTTTAAAAAACATATTTCTAAATTGCCATTACTAA
64 TTTTTAAAACATATTTCCAATTGTACCCTTTTTTAAAAAACATATTTCTAAATTGCCATTACTAA
78383 ATAATATATTTTAATTATTCCATTATTTTTTTAATC
129 AT-A-ATATTTTAATTATTCCATTATTTTTTTAATC
*
78419 ATCTATACTATATATAAAAG-TACGAATAAGGGGAAACTTTACGTTTTCCGATTGTACCCTTATT
1 ATCTATACTATATATAAAAGATACGAATAAGGGGAAACTTTACGCTTTCCGATTGTACCCTTATT
78483 TTTAAAACATATTTCCAATTGTACCCTTTTTTAAAAAACATATTTCTAAATTGCCATTACTAAAT
66 TTTAAAACATATTTCCAATTGTACCCTTTTTTAAAAAACATATTTCTAAATTGCCATTACTAAAT
78548 AATATTTTAATTATTCCATTATTTTTTTAATC
131 AATATTTTAATTATTCCATTATTTTTTTAATC
78580 AT
1 AT
78582 AAATTATTCC
Statistics
Matches: 160, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
161 33 0.21
162 1 0.01
163 106 0.66
166 20 0.12
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (162 bp):
ATCTATACTATATATAAAAGATACGAATAAGGGGAAACTTTACGCTTTCCGATTGTACCCTTATT
TTTAAAACATATTTCCAATTGTACCCTTTTTTAAAAAACATATTTCTAAATTGCCATTACTAAAT
AATATTTTAATTATTCCATTATTTTTTTAATC
Found at i:78498 original size:31 final size:31
Alignment explanation
Indices: 78463--78528 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
78453 AACTTTACGT
* *
78463 TTTCCGATTGTACCCTTATTTT-TAAAACATA
1 TTTCCAATTGTACCCTT-TTTTAAAAAACATA
78494 TTTCCAATTGTACCCTTTTTTAAAAAACATA
1 TTTCCAATTGTACCCTTTTTTAAAAAACATA
78525 TTTC
1 TTTC
78529 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTAAAAAACATA
Found at i:78931 original size:23 final size:22
Alignment explanation
Indices: 78852--78985 Score: 127
Period size: 23 Copynumber: 6.3 Consensus size: 22
78842 ATAAAAAAAA
78852 TCATAGGGAGGTTATCAAAATT
1 TCATAGGGAGGTTATCAAAATT
* *
78874 T-GTA---A--TTATCAAGATT
1 TCATAGGGAGGTTATCAAAATT
*
78890 TCATAAGGAGGTTATCAAAATT
1 TCATAGGGAGGTTATCAAAATT
*
78912 TTATAGGGAGGTTTATCAAAATT
1 TCATAGGGAGG-TTATCAAAATT
** *
78935 TCATAGCAAGGTTTATCACAATT
1 TCATAGGGAGG-TTATCAAAATT
* *
78958 TCATAGTGTGGTTATCAAAATT
1 TCATAGGGAGGTTATCAAAATT
78980 TCATAG
1 TCATAG
78986 TGTGATTACT
Statistics
Matches: 91, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
16 11 0.12
17 2 0.02
18 1 0.01
20 1 0.01
21 2 0.02
22 36 0.40
23 38 0.42
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TCATAGGGAGGTTATCAAAATT
Found at i:78947 original size:45 final size:44
Alignment explanation
Indices: 78879--78985 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
78869 AAATTTGTAA
* * *
78879 TTATCAAGATTTCATAAGGAGG-TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCAT-AGAAGGTTTATCAAAATTTCATAGGGAGG
* * *
78923 TTTATCAAAATTTCATAGCAAGGTTTATCACAATTTCATAGTGTGG
1 -TTATCAAAATTTCATAG-AAGGTTTATCAAAATTTCATAGGGAGG
78969 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
78986 TGTGATTACT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
44 2 0.04
45 34 0.63
46 18 0.33
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATAGAAGGTTTATCAAAATTTCATAGGGAGG
Found at i:79004 original size:22 final size:22
Alignment explanation
Indices: 78947--79006 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
78937 ATAGCAAGGT
*
78947 TTATCACAATTTCATAGTGTGG
1 TTATCACAATTTCATAGTGTGA
*
78969 TTATCAAAATTTCATAGTGTGA
1 TTATCACAATTTCATAGTGTGA
*
78991 TTACTGACAA-TTCATA
1 TTA-TCACAATTTCATA
79007 TGGAGGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCACAATTTCATAGTGTGA
Found at i:79218 original size:22 final size:22
Alignment explanation
Indices: 79168--79231 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
79158 AATTTATAAA
* *
79168 AAGGTTCTCGAAATTTCATAGT
1 AAGGTTATCGAAATTTCATAGG
** *
79190 ATTGTTATTGAAATTTCATAGG
1 AAGGTTATCGAAATTTCATAGG
*
79212 AAGGTTATCAAAATTTCATA
1 AAGGTTATCGAAATTTCATA
79232 AGGTCGTCAT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
AAGGTTATCGAAATTTCATAGG
Found at i:79272 original size:62 final size:62
Alignment explanation
Indices: 79201--79355 Score: 265
Period size: 62 Copynumber: 2.5 Consensus size: 62
79191 TTGTTATTGA
*
79201 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGTCGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
79263 AATTTCATAGGAATGTTATCAAAATTTCATAAGGACGTTATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
79325 AATTTAATAGGAAGGTTATCATAATTTCATA
1 AATTTCATAGGAAGGTTATCAAAATTTCATA
79356 TGAATATTTC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 87 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
Found at i:79281 original size:22 final size:22
Alignment explanation
Indices: 79256--79360 Score: 71
Period size: 22 Copynumber: 5.0 Consensus size: 22
79246 AATAGTGTAA
79256 TTATCATAATTTCATAGGAATG
1 TTATCATAATTTCATAGGAATG
* *
79278 TTATCAAAATTTCATAAGG-ACG
1 TTATCATAATTTCAT-AGGAATG
**
79300 TTAT-A-AA--AAATAGTGTAA--
1 TTATCATAATTTCATAG-G-AATG
* *
79318 TTATCATAATTTAATAGGAAGG
1 TTATCATAATTTCATAGGAATG
*
79340 TTATCATAATTTCATATGAAT
1 TTATCATAATTTCATAGGAAT
79361 ATTTCATTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
17 2 0.03
18 7 0.11
19 1 0.02
20 7 0.11
21 2 0.03
22 43 0.66
23 3 0.05
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (22 bp):
TTATCATAATTTCATAGGAATG
Found at i:79420 original size:2 final size:2
Alignment explanation
Indices: 79413--79452 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
79403 GCCAAAACTA
79413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79453 CAAGTTGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86067 original size:20 final size:19
Alignment explanation
Indices: 86038--86089 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
86028 TGAACATAAT
86038 ATGAATAAAGGTTTTGTAAA
1 ATGAA-AAAGGTTTTGTAAA
86058 ATGAAGAAAGGTTTTGTAAA
1 ATGAA-AAAGGTTTTGTAAA
*
86078 AAGAAAAAGGTT
1 ATGAAAAAGGTT
86090 ATGAACTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (19 bp):
ATGAAAAAGGTTTTGTAAA
Found at i:86278 original size:37 final size:37
Alignment explanation
Indices: 86220--86295 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
86210 CACGAAGAAG
**
86220 TTTAATGGGTAACCAACTTAATAGGGAGTGATTTTTT
1 TTTAATGGGTAACCAACTTAATAGGGAGCAATTTTTT
* *
86257 TTTAATGGGTAACTAATTTAATAGGGAGCAATTTTTT
1 TTTAATGGGTAACCAACTTAATAGGGAGCAATTTTTT
86294 TT
1 TT
86296 ATTTAAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (37 bp):
TTTAATGGGTAACCAACTTAATAGGGAGCAATTTTTT
Found at i:87803 original size:20 final size:18
Alignment explanation
Indices: 87778--87822 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
87768 ACATATGTTT
87778 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
87798 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
87816 TACTAAT
1 TACTAAT
87823 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:91394 original size:16 final size:17
Alignment explanation
Indices: 91373--91410 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
91363 AGCAAAAATT
*
91373 GGAAGAGGAG-AGAAAA
1 GGAAGAGGAGTAAAAAA
*
91389 GGAAGATGAGTAAAAAA
1 GGAAGAGGAGTAAAAAA
91406 GGAAG
1 GGAAG
91411 GGAAAGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.05
Consensus pattern (17 bp):
GGAAGAGGAGTAAAAAA
Found at i:92102 original size:291 final size:291
Alignment explanation
Indices: 91578--92153 Score: 1080
Period size: 291 Copynumber: 2.0 Consensus size: 291
91568 AGAAGAGAGG
91578 GTGGGAAGGGAGAGAAAATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATT
1 GTGGGAAGGGAGAGAAAATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATT
91643 TTCAGGCAATGAAAACAGTGGAAAACAAGGAGTATTTTTTTAAAGGGCTCTGTTAACCCCGATTT
66 TTCAGGCAATGAAAACAGTGGAAAACAAGGAGTATTTTTTTAAAGGGCTCTGTTAACCCCGATTT
* *
91708 TTTTAGGGATTTCCACTAAGCTATCAAGTGGTGGTTTTAATATAGTTTTGCCATTGTGTTCTGTC
131 TTTTAGGGATTTCCACTAACCTATCAAGGGGTGGTTTTAATATAGTTTTGCCATTGTGTTCTGTC
*
91773 GGGGCTATCTGGTTTTGGGCTTATGCCCACCTCTCGTGGCCCAGAAAGTTTTCTTTTTCTTTAAT
196 GGGGCTATCTGGTTTTGGGCTTATGCCCACCTCTCGTGGCCCAGAAAGTTTTCTTTTTCTTTAAC
91838 ATGAATAAAAAAATTTACTATTATTCATGAT
261 ATGAATAAAAAAATTTACTATTATTCATGAT
91869 GTGGGAAGGGAGAGAAAATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATT
1 GTGGGAAGGGAGAGAAAATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATT
* *
91934 TTCAGGCAATGAAAACAGTGGAAAACAGGGAGTATTTTTTTAAAGGGCTCTGTTAACCCCGGTTT
66 TTCAGGCAATGAAAACAGTGGAAAACAAGGAGTATTTTTTTAAAGGGCTCTGTTAACCCCGATTT
* *
91999 TTTTGGGGATTTCCACTAACCTATCAAGGGGTGGTTTTAATATAGTTTTGTCATTGTGTTCTGTC
131 TTTTAGGGATTTCCACTAACCTATCAAGGGGTGGTTTTAATATAGTTTTGCCATTGTGTTCTGTC
*
92064 GGGGCTATCTGGTTTTGGGCTTATGCCCATCTCTCGTGGCCCAGAAAGTTTTCTTTTTCTTTAAC
196 GGGGCTATCTGGTTTTGGGCTTATGCCCACCTCTCGTGGCCCAGAAAGTTTTCTTTTTCTTTAAC
92129 ATGAATAAAAAAATTTACTATTATT
261 ATGAATAAAAAAATTTACTATTATT
92154 TATCACACCA
Statistics
Matches: 277, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
291 277 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (291 bp):
GTGGGAAGGGAGAGAAAATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATT
TTCAGGCAATGAAAACAGTGGAAAACAAGGAGTATTTTTTTAAAGGGCTCTGTTAACCCCGATTT
TTTTAGGGATTTCCACTAACCTATCAAGGGGTGGTTTTAATATAGTTTTGCCATTGTGTTCTGTC
GGGGCTATCTGGTTTTGGGCTTATGCCCACCTCTCGTGGCCCAGAAAGTTTTCTTTTTCTTTAAC
ATGAATAAAAAAATTTACTATTATTCATGAT
Done.