Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 27 of 171
Found at i:12394709 original size:30 final size:31
Alignment explanation
Indices: 12394611--12394709 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 31
12394601 CATAATTTTG
* *
12394611 AAATTTAACTATTTTATTTTTT--ATTTCAAA
1 AAATTTAA-TCTTTTATTTTTTAAAATTCAAA
12394641 AAATTTAATCTTTTTATTTTTTAAAATTTTTCAAA
1 AAATTTAATC-TTTTATTTTTTAAAA---TTCAAA
12394676 AAATTTAATCTTTTATTTTTTAAAATT-AAA
1 AAATTTAATCTTTTATTTTTTAAAATTCAAA
12394706 AAAT
1 AAAT
12394710 ACAAATTTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
29 1 0.02
30 26 0.43
31 2 0.03
32 1 0.02
34 15 0.25
35 16 0.26
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (31 bp):
AAATTTAATCTTTTATTTTTTAAAATTCAAA
Found at i:12396831 original size:18 final size:18
Alignment explanation
Indices: 12396808--12396865 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
12396798 CATCATTATA
12396808 TTATTATTTAAATAACAT
1 TTATTATTTAAATAACAT
* *
12396826 TTATTA-TTATATTA-A-
1 TTATTATTTAAATAACAT
12396841 --ATTATTTAAATAACAT
1 TTATTATTTAAATAACAT
*
12396857 TTATAATTT
1 TTATTATTT
12396866 CATGTATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
13 4 0.13
14 6 0.20
15 1 0.03
16 1 0.03
17 6 0.20
18 12 0.40
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATTATTTAAATAACAT
Found at i:12396832 original size:21 final size:23
Alignment explanation
Indices: 12396801--12396842 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
12396791 TATCATCCAT
12396801 CATTATATTATTAT-TTAAATAA
1 CATTATATTATTATATTAAATAA
12396823 CATT-TATTATTATATTAAAT
1 CATTATATTATTATATTAAAT
12396843 TATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
CATTATATTATTATATTAAATAA
Found at i:12396845 original size:31 final size:29
Alignment explanation
Indices: 12396802--12396860 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 29
12396792 ATCATCCATC
12396802 ATTATATTATTATTTAAATAACATTTATT
1 ATTATATTATTATTTAAATAACATTTATT
12396831 ATTATATTAAATTATTTAAATAACATTTAT
1 ATTATATT--ATTATTTAAATAACATTTAT
12396861 AATTTCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.29
31 20 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTATATTATTATTTAAATAACATTTATT
Found at i:12402331 original size:16 final size:15
Alignment explanation
Indices: 12402306--12402335 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12402296 TTATTTCTCA
12402306 AAAATATTTTTAAAT
1 AAAATATTTTTAAAT
12402321 AAAATATTTTTAAAT
1 AAAATATTTTTAAAT
12402336 TTTTTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTTTTAAAT
Found at i:12404919 original size:16 final size:16
Alignment explanation
Indices: 12404895--12404925 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12404885 TTTATTTTTT
12404895 ATATCTATCTATATTC
1 ATATCTATCTATATTC
*
12404911 ATATTTATCTATATT
1 ATATCTATCTATATT
12404926 ATTAATCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATCTATCTATATTC
Found at i:12406213 original size:27 final size:24
Alignment explanation
Indices: 12406171--12406219 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
12406161 CTCGGTGGAG
*
12406171 TGGATACCTGACTCGGACGATGGGT
1 TGGATACCTGAATCGGA-GATGGGT
12406196 TGGATGACGCTGAATCGGAGATGG
1 TGGAT-AC-CTGAATCGGAGATGG
12406220 TGCCACCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 7 0.33
27 9 0.43
ACGTcount: A:0.22, C:0.16, G:0.39, T:0.22
Consensus pattern (24 bp):
TGGATACCTGAATCGGAGATGGGT
Found at i:12414865 original size:2 final size:2
Alignment explanation
Indices: 12414860--12414896 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12414850 ATGAAAAAAG
*
12414860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12414897 GCTGCCTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12439346 original size:13 final size:12
Alignment explanation
Indices: 12439328--12439389 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
12439318 TTTGATGGTT
12439328 TTTAATTTAATAA
1 TTTAA-TTAATAA
12439341 TTTAA-TAATAA
1 TTTAATTAATAA
*
12439352 --TATTTAATAA
1 TTTAATTAATAA
12439362 TGTTAATTAATTAA
1 T-TTAATTAA-TAA
*
12439376 TTT-ATTATTAA
1 TTTAATTAATAA
12439387 TTT
1 TTT
12439390 TTTGTAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 12 0.29
12 4 0.10
13 13 0.32
14 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTTAATTAATAA
Found at i:12444619 original size:3 final size:3
Alignment explanation
Indices: 12444613--12444637 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12444603 TCAAAACGCA
12444613 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
12444638 GGGATTATCT
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:12445366 original size:21 final size:21
Alignment explanation
Indices: 12445328--12445368 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12445318 ATTCAAACCA
*
12445328 TAAATCTTAAACTCTAAACTT
1 TAAACCTTAAACTCTAAACTT
12445349 TAAACCTTAAAC-CTTAAACT
1 TAAACCTTAAACTC-TAAACT
12445369 CTGACCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAACCTTAAACTCTAAACTT
Found at i:12456514 original size:49 final size:49
Alignment explanation
Indices: 12456435--12456583 Score: 145
Period size: 53 Copynumber: 2.9 Consensus size: 49
12456425 TTTTTTTGGA
* *
12456435 TGTCGCTCATGCCGTGGCCGACACCCCCTTTATCGGATAAAAAAATTTG
1 TGTCGCCCATGCCATGGCCGACACCCCCTTTATCGGATAAAAAAATTTG
* * * * *
12456484 TGTCGCCCTTGCCATGGCTGACACCTCCTTTATCTGATAAAAAAATATTTTTT
1 TGTCGCCCATGCCATGGCCGACACCCCCTTTATCGGAT-AAAAAA-A--TTTG
* * * * *
12456537 TGTCTCCTATGCCATGGTCGACACCCGCTTTATCTGATTAAAAAAAT
1 TGTCGCCCATGCCATGGCCGACACCCCCTTTATCGGA-TAAAAAAAT
12456584 CACTCATGCC
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
49 32 0.40
50 7 0.09
51 1 0.01
52 1 0.01
53 39 0.48
54 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (49 bp):
TGTCGCCCATGCCATGGCCGACACCCCCTTTATCGGATAAAAAAATTTG
Found at i:12456568 original size:53 final size:48
Alignment explanation
Indices: 12456435--12456583 Score: 140
Period size: 49 Copynumber: 2.9 Consensus size: 48
12456425 TTTTTTTGGA
* * *
12456435 TGTCGCTC-ATGCCGTGGCCGACACCCCCTTTATCGGATAAAAAAATTTG
1 TGTCGCCCTATGCCATGG-CGACA-CCCCTTTATCTGATAAAAAAATTTG
*
12456484 TGTCGCCCT-TGCCATGGCTGACACCTCCTTTATCTGATAAAAAAATATTT
1 TGTCGCCCTATGCCATGGC-GACACC-CCTTTATCTGATAAAAAAAT-TTG
* *
12456534 TTTTGTCTCCTATGCCATGGTCGACACCCGCTTTATCTGATTAAAAAAAT
1 TGTCG-C-CCTATGCCATGG-CGACACCC-CTTTATCTGA-TAAAAAAAT
12456584 CACTCATGCC
Statistics
Matches: 84, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
48 3 0.04
49 37 0.44
50 5 0.06
51 1 0.01
52 4 0.05
53 24 0.29
54 10 0.12
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (48 bp):
TGTCGCCCTATGCCATGGCGACACCCCTTTATCTGATAAAAAAATTTG
Found at i:12456680 original size:97 final size:95
Alignment explanation
Indices: 12456493--12456679 Score: 209
Period size: 97 Copynumber: 1.9 Consensus size: 95
12456483 GTGTCGCCCT
**
12456493 TGCCATGGCTGACACCTCCTTTATCTGATAAAAAAATATTTTTTTGTCTCCTATGCCATGGTCGA
1 TGCCATGGCTGACACCTCCTTTATCTGATAAAAAAATATTTTTTTGTCTCCTATGCCATGACCGA
12456558 CACCCGCTTTATCTGATTAAAAAAATCACTCA
66 CACCCGCTTTATCTGATT--AAAAATCACTCA
* * *
12456590 TGCCATGG-TCGACA-CTACCTTTATCTGAT-AAAAAATATTTTTTTTGGTGTTGTCTATGTCAT
1 TGCCATGGCT-GACACCT-CCTTTATCTGATAAAAAAATA-TTTTTTT-GT-CT-CCTATGCCAT
***
12456652 GACCGACACCTTTTTTATCTGATTAAAA
60 GACCGACACCCGCTTTATCTGATTAAAA
12456680 TTTTTTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
96 11 0.14
97 31 0.41
98 6 0.08
99 1 0.01
100 27 0.36
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (95 bp):
TGCCATGGCTGACACCTCCTTTATCTGATAAAAAAATATTTTTTTGTCTCCTATGCCATGACCGA
CACCCGCTTTATCTGATTAAAAATCACTCA
Found at i:12469898 original size:30 final size:30
Alignment explanation
Indices: 12469864--12469933 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
12469854 ATTTCGTTTT
*
12469864 TATTTTAAATTTAATTTCGAATTTCTTGTA
1 TATTTTAAATTTAATTTCGAATTTCATGTA
* ** *
12469894 TATTTTAATTTTTCTTTCTAATTTCATGTA
1 TATTTTAAATTTAATTTCGAATTTCATGTA
*
12469924 TATTCTAAAT
1 TATTTTAAAT
12469934 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.59
Consensus pattern (30 bp):
TATTTTAAATTTAATTTCGAATTTCATGTA
Found at i:12470901 original size:62 final size:61
Alignment explanation
Indices: 12470753--12470943 Score: 271
Period size: 61 Copynumber: 3.1 Consensus size: 61
12470743 GGAAAATGAT
* *
12470753 CAACACCAAGAAAATTTGAAA-TTTTTTCTCGAGAAAAAAGGGGTGTCGGCCATTTG-ATGGC
1 CAACACCAAAAAAATTTGAAATTTTTTTCTCGAG-AAAAGGGGGTGTCGGCCA-TTGCATGGC
* * *
12470814 CCACACCAAAAAAA-TTAAAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTGCATAGC
1 CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCATTGCATGGC
*
12470875 CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAATAGGGGGTGTCGGCAATTGCATGGC
1 CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAA-AGGGGGTGTCGGCCATTGCATGGC
12470937 CAACACC
1 CAACACC
12470944 CCAAATTTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
60 12 0.10
61 54 0.47
62 49 0.42
63 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (61 bp):
CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTGCATGGC
Found at i:12471381 original size:11 final size:11
Alignment explanation
Indices: 12471362--12471418 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
12471352 AGTTTAAATT
12471362 TTTTATTATTA
1 TTTTATTATTA
* *
12471373 TTTTCTTATCA
1 TTTTATTATTA
**
12471384 TTTTGCTATTA
1 TTTTATTATTA
**
12471395 CATTATTATTA
1 TTTTATTATTA
*
12471406 TTTTATTGTTA
1 TTTTATTATTA
12471417 TT
1 TT
12471419 ATTTAGATAT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.67
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:12482515 original size:18 final size:18
Alignment explanation
Indices: 12482494--12482535 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12482484 TGGAGGCTTA
* *
12482494 GGTGGTGGGGGAGGTGGT
1 GGTGGCGGGGGAGGTGGG
*
12482512 GGTGGCGGTGGAGGTGGG
1 GGTGGCGGGGGAGGTGGG
12482530 GGTGGC
1 GGTGGC
12482536 AATGGTGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.05, G:0.71, T:0.19
Consensus pattern (18 bp):
GGTGGCGGGGGAGGTGGG
Found at i:12482638 original size:15 final size:15
Alignment explanation
Indices: 12482604--12482652 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
12482594 ATGGAGGGCT
* *
12482604 TGGTGGCGGAGGAGG
1 TGGTGGAGGAGGTGG
* *
12482619 AGGTGGAGGCGGTGG
1 TGGTGGAGGAGGTGG
*
12482634 TGGTGGGGGAGGTGG
1 TGGTGGAGGAGGTGG
12482649 TGGT
1 TGGT
12482653 TCCCATGGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.10, C:0.04, G:0.67, T:0.18
Consensus pattern (15 bp):
TGGTGGAGGAGGTGG
Found at i:12483933 original size:16 final size:18
Alignment explanation
Indices: 12483897--12483935 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12483887 ATAAGTTTAA
12483897 TTATTAATATTTACGTTTT
1 TTATTAATATTTAC-TTTT
*
12483916 TTATTAA-ATTTATTTTT
1 TTATTAATATTTACTTTT
12483933 TTA
1 TTA
12483936 ATATTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTAATATTTACTTTT
Found at i:12493874 original size:63 final size:63
Alignment explanation
Indices: 12493806--12493931 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
12493796 TTGATGCCGA
12493806 GGCTCGCCAAAATGCACATTTGACACGGGTCACAGTTGCTGCAAATATTGCTATACACAGTCC
1 GGCTCGCCAAAATGCACATTTGACACGGGTCACAGTTGCTGCAAATATTGCTATACACAGTCC
12493869 GGCTCGCCAAAATGCACATTTGACACGGGTCACAGTTGCTGCAAATATTGCTATACACAGTCC
1 GGCTCGCCAAAATGCACATTTGACACGGGTCACAGTTGCTGCAAATATTGCTATACACAGTCC
12493932 TGCTACTGGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (63 bp):
GGCTCGCCAAAATGCACATTTGACACGGGTCACAGTTGCTGCAAATATTGCTATACACAGTCC
Found at i:12495432 original size:23 final size:21
Alignment explanation
Indices: 12495384--12495454 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 21
12495374 CAACTTATTT
12495384 TTATTTAAATAAATAATA-TAATA
1 TTATTTAAAT-AATAA-ACTAA-A
12495407 TTATTTAAATTAAGTAAACTAAA
1 TTATTTAAA-TAA-TAAACTAAA
*
12495430 TTACTTGTTAATAATAAACTAAA
1 TTA-TT-TAAATAATAAACTAAA
12495453 TT
1 TT
12495455 TGTTAATACT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
23 27 0.64
24 12 0.29
25 3 0.07
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATTTAAATAATAAACTAAA
Found at i:12495475 original size:20 final size:20
Alignment explanation
Indices: 12495429--12495476 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
12495419 AGTAAACTAA
*
12495429 ATTACTTGTTAATAATAAAC
1 ATTATTTGTTAATAATAAAC
* *
12495449 -TAAATTTGTTAATACTAAAC
1 AT-TATTTGTTAATAATAAAC
12495469 ATTATTTG
1 ATTATTTG
12495477 AAAACGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (20 bp):
ATTATTTGTTAATAATAAAC
Found at i:12499164 original size:15 final size:16
Alignment explanation
Indices: 12499144--12499186 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
12499134 AAAGTTAGTT
12499144 TGTAATTATT-TTTTA
1 TGTAATTATTATTTTA
12499159 TGTAATT-TTATTTTA
1 TGTAATTATTATTTTA
* *
12499174 TGTTATTACTATT
1 TGTAATTATTATT
12499187 ATGTGACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 18 0.75
16 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (16 bp):
TGTAATTATTATTTTA
Found at i:12500027 original size:25 final size:25
Alignment explanation
Indices: 12499993--12500048 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12499983 CATTTACCAT
* * *
12499993 TTTTCAAAAATTAAAGAATAAAATTA
1 TTTT-AAAAATAAAAGAAAAAAAGTA
*
12500019 TTTTAAAAATAAAATAAAAAAAGTA
1 TTTTAAAAATAAAAGAAAAAAAGTA
12500044 TTTTA
1 TTTTA
12500049 TTAAATCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
TTTTAAAAATAAAAGAAAAAAAGTA
Found at i:12535990 original size:37 final size:36
Alignment explanation
Indices: 12535927--12536033 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 36
12535917 ATTCCAAAAA
12535927 TAATATTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTTTAATATT-AATTTAATAT
**
12535963 TAATACTTATTTTAATA-TTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTT-TAATATTAATTTAATAT
* *
12536000 TAAAGTGATTATCTTAATA-TTAAAT-TTAATTTAA
1 T-AA-T-ATTATTTTAATAGTTTAATATTAATTTAA
12536034 AGTTTAACTT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
36 15 0.25
37 27 0.46
38 3 0.05
39 13 0.22
40 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATTTTAATAGTTTAATATTAATTTAATAT
Found at i:12536002 original size:11 final size:11
Alignment explanation
Indices: 12535927--12536002 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
12535917 ATTCCAAAAA
*
12535927 TAATATTATTT
1 TAATATTAATT
12535938 TAATAGTTTAATAT
1 TAATA--TTAAT-T
12535952 TAA-ATTTAATT
1 TAATA-TTAATT
*
12535963 TAATACTTATTT
1 TAATA-TTAATT
12535975 TAATATT-ATT
1 TAATATTAATT
12535985 T--TATTAATT
1 TAATATTAATT
12535994 TAATATTAA
1 TAATATTAA
12536003 AGTGATTATC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 3 0.06
11 17 0.31
12 17 0.31
13 5 0.09
14 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TAATATTAATT
Found at i:12536239 original size:22 final size:20
Alignment explanation
Indices: 12536188--12536239 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
12536178 ATAAAGTAAA
*
12536188 ATTAAATTAATTAAAATTAAT
1 ATTAAATT-TTTAAAATTAAT
* *
12536209 ATGATATTTTTAGAAATTTAAT
1 ATTAAATTTTTA-AAA-TTAAT
12536231 ATTAAATTT
1 ATTAAATTT
12536240 AATTTAATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
22 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
ATTAAATTTTTAAAATTAAT
Found at i:12539062 original size:17 final size:17
Alignment explanation
Indices: 12539042--12539075 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12539032 TTATAAATGA
12539042 TTTGAGTGCTTAAACAG
1 TTTGAGTGCTTAAACAG
12539059 TTTGAGTGCTTAAACAG
1 TTTGAGTGCTTAAACAG
12539076 AAAAGATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
TTTGAGTGCTTAAACAG
Found at i:12539903 original size:7 final size:7
Alignment explanation
Indices: 12539891--12539925 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
12539881 AGTACAAGTA
12539891 CCAAATT
1 CCAAATT
12539898 CCAAATT
1 CCAAATT
12539905 CCAAATT
1 CCAAATT
12539912 CCAAATT
1 CCAAATT
12539919 CCAAATT
1 CCAAATT
12539926 TTGAACGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (7 bp):
CCAAATT
Found at i:12552185 original size:21 final size:24
Alignment explanation
Indices: 12552152--12552194 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
12552142 GTAAAAATTT
12552152 AATAAGAATATTTCGA-AATTTTA
1 AATAAGAATATTTCGATAATTTTA
*
12552175 AATAA-AA-ATTTGGATAATTT
1 AATAAGAATATTTCGATAATTT
12552195 ATTTATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (24 bp):
AATAAGAATATTTCGATAATTTTA
Found at i:12554504 original size:51 final size:51
Alignment explanation
Indices: 12554424--12554520 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
12554414 CAAATTTAAC
* *
12554424 CCTCAATATTTACAAAACTTGTCACTTTAGTTCTAATTCAAAAAAAAATGA
1 CCTCAATATTTACAAAACTTGTCAATTTAGTTCTAACTCAAAAAAAAATGA
* *
12554475 CCTCAATATTTACAAATA-TTGTTAATTTAGTTCTAACTCTAAAAAA
1 CCTCAATATTTACAAA-ACTTGTCAATTTAGTTCTAACTCAAAAAAA
12554521 TAAAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.36
Consensus pattern (51 bp):
CCTCAATATTTACAAAACTTGTCAATTTAGTTCTAACTCAAAAAAAAATGA
Found at i:12555278 original size:2 final size:2
Alignment explanation
Indices: 12555271--12555325 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
12555261 ATCCTTTATG
12555271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12555313 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
12555326 TTATTAGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12558941 original size:20 final size:20
Alignment explanation
Indices: 12558916--12558955 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12558906 CTCTATATAT
*
12558916 TTTTATATGTTTAGAATTTA
1 TTTTATATGTTTAAAATTTA
* *
12558936 TTTTATTTTTTTAAAATTTA
1 TTTTATATGTTTAAAATTTA
12558956 AAATTTCAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATATGTTTAAAATTTA
Found at i:12579026 original size:22 final size:22
Alignment explanation
Indices: 12578977--12579036 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
12578967 GGAGGTGGAA
**
12578977 ATTAAATTATAATTTTTATGAT
1 ATTAAATTATAATTTTTAAAAT
*
12578999 AGTAAATATATAA-TTTTAAAAT
1 ATTAAAT-TATAATTTTTAAAAT
* *
12579021 ATTAAATCAAAATTTT
1 ATTAAATTATAATTTT
12579037 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.10
22 22 0.73
23 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTAAATTATAATTTTTAAAAT
Found at i:12586615 original size:6 final size:6
Alignment explanation
Indices: 12586604--12586628 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12586594 CTTCCATCCG
12586604 TAACCA TAACCA TAACCA TAACCA T
1 TAACCA TAACCA TAACCA TAACCA T
12586629 GCCTTTTGTC
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:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TAACCA
Found at i:12588281 original size:6 final size:6
Alignment explanation
Indices: 12588258--12588297 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
12588248 CTCTGATTTT
12588258 TCTTT- TCTTTC T-TCTTC TCTTTC TCTTTC TCTTTC TCTTT
1 TCTTTC TCTTTC TCT-TTC TCTTTC TCTTTC TCTTTC TCTTT
12588298 ATCCTTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 6 0.19
6 25 0.78
7 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TCTTTC
Found at i:12590680 original size:7 final size:7
Alignment explanation
Indices: 12590668--12590717 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
12590658 GTAATTCTCT
12590668 CCGTCAC
1 CCGTCAC
12590675 CCGTCAC
1 CCGTCAC
12590682 CCGTCAC
1 CCGTCAC
12590689 CCGTCAC
1 CCGTCAC
12590696 CCGTCAC
1 CCGTCAC
12590703 CCGTCAC
1 CCGTCAC
12590710 CCGTCAC
1 CCGTCAC
12590717 C
1 C
12590718 ACCAACCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.14, C:0.58, G:0.14, T:0.14
Consensus pattern (7 bp):
CCGTCAC
Found at i:12593796 original size:18 final size:16
Alignment explanation
Indices: 12593756--12593799 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
12593746 TTAACCCCCC
12593756 AAAAAGAAG-G-GAAA
1 AAAAAGAAGAGTGAAA
12593770 AAAAAGAAGAGTGAAA
1 AAAAAGAAGAGTGAAA
12593786 ACAAAACGAAGAGT
1 A-AAAA-GAAGAGT
12593800 CATTTTCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.35
15 1 0.04
16 5 0.19
17 4 0.15
18 7 0.27
ACGTcount: A:0.66, C:0.05, G:0.25, T:0.05
Consensus pattern (16 bp):
AAAAAGAAGAGTGAAA
Found at i:12608150 original size:22 final size:21
Alignment explanation
Indices: 12608120--12608160 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
12608110 ACTATAATAT
12608120 TTTTCATTTTTACCCCCAAACCC
1 TTTTCATTTTT--CCCCAAACCC
12608143 TTTT-ATTTTTCCCCAAAC
1 TTTTCATTTTTCCCCAAAC
12608161 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTCATTTTTCCCCAAACCC
Found at i:12613607 original size:23 final size:21
Alignment explanation
Indices: 12613581--12613623 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
12613571 CATTTCCAGA
*
12613581 AAGTAAGGATTTGAGACACTTTT
1 AAGTAAGAATTT-AGA-ACTTTT
*
12613604 AAGTTAGAATTTAGAACTTT
1 AAGTAAGAATTTAGAACTTT
12613624 CCAATTTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (21 bp):
AAGTAAGAATTTAGAACTTTT
Found at i:12616753 original size:80 final size:80
Alignment explanation
Indices: 12616614--12616778 Score: 208
Period size: 80 Copynumber: 2.1 Consensus size: 80
12616604 TCTTTATTTT
* * * * * *
12616614 CAACCAAATCCGTCAATTCATTGCACCCGGTGCCTAGTGGATAAACCGCGATAAGTGAGCGCAGC
1 CAACGAAATCCGTCAATTCATTGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAAC
*
12616679 TCTAGTTGGATTAAC
66 TCTAATTGGATTAAC
* * *
12616694 CAACGAAATCCGTCAATTC-TTGGTATCCAGTGCCTAGCGGATAAACCGTAATGAA-TGAGCCCA
1 CAACGAAATCCGTCAATTCATT-GCACCCAGTGCCTAGCGGATAAACCGCAAT-AAGTGAGCCCA
12616757 ACTCTAATTGGATTAAC
64 ACTCTAATTGGATTAAC
12616774 CAACG
1 CAACG
12616779 GTTTGCGCCC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 2 0.03
80 69 0.95
81 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (80 bp):
CAACGAAATCCGTCAATTCATTGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAAC
TCTAATTGGATTAAC
Found at i:12617005 original size:79 final size:80
Alignment explanation
Indices: 12616822--12617024 Score: 304
Period size: 79 Copynumber: 2.5 Consensus size: 80
12616812 ATTTTGGCAT
* *
12616822 CTAGTGCCTAGCGGATAAACCGTAAAGGTGAGCCCAGCTCTAGTTGGATTAACCAACAAATATCC
1 CTAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAATATCC
12616887 GTCAAATCCTGACAC
66 GTCAAATCCTGACAC
*
12616902 CTAGTGCCTAGC-GAGTAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAA-TAATATC
1 CTAGTGCCTAGCGGA-TAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAATATC
12616965 CGTCAAATCCTGACA-
65 CGTCAAATCCTGACAC
* * * *
12616980 CTCAGTGCCTAGCGGATAAATCGCAAATGTGTGCCCAGCACTAGT
1 CT-AGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGT
12617025 AAATTAAACT
Statistics
Matches: 113, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
78 2 0.02
79 58 0.51
80 53 0.47
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
CTAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCAACAAATATCC
GTCAAATCCTGACAC
Found at i:12626093 original size:23 final size:23
Alignment explanation
Indices: 12626067--12626112 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
12626057 CTCACCTTTG
*
12626067 GATTATGATCCAAGGAACATAAT
1 GATTATGATCCAAGCAACATAAT
*
12626090 GATTATGATCTAAGCAACATAAT
1 GATTATGATCCAAGCAACATAAT
12626113 AAGCATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (23 bp):
GATTATGATCCAAGCAACATAAT
Found at i:12628285 original size:1 final size:1
Alignment explanation
Indices: 12628279--12628305 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
12628269 CACGGTGTGT
12628279 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
12628306 CAAAACAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:12628886 original size:23 final size:24
Alignment explanation
Indices: 12628860--12628929 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 24
12628850 TTAATGTTCA
**
12628860 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCATCGAACATTAAT
12628883 CGAACATGTTCA-CGAACATTAAT
1 CGAACATGTTCATCGAACATTAAT
12628906 CGAACATGTTCAT-GAACATATAAT
1 CGAACATGTTCATCGAACAT-TAAT
12628930 TGAAAACCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
22 3 0.07
23 35 0.83
24 4 0.10
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (24 bp):
CGAACATGTTCATCGAACATTAAT
Found at i:12632890 original size:26 final size:28
Alignment explanation
Indices: 12632831--12632893 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
12632821 ATTTTTAATT
* * *
12632831 TTTTTAAAAATATTATTTTTTATTTTAA
1 TTTTTAATAATATTAATTTTTATTTAAA
*
12632859 TATTTAATAAT-TTAATTTTTA-TTAAA
1 TTTTTAATAATATTAATTTTTATTTAAA
12632885 TTTTTAATA
1 TTTTTAATA
12632894 TAAACATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 12 0.40
27 9 0.30
28 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTAATAATATTAATTTTTATTTAAA
Found at i:12632996 original size:17 final size:16
Alignment explanation
Indices: 12632971--12633013 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12632961 AATATGTTCT
*
12632971 AAATTATATAACATATA
1 AAATAATATAA-ATATA
12632988 AAATAATAT-AATATA
1 AAATAATATAAATATA
*
12633003 AAATATTATAA
1 AAATAATATAA
12633014 TTTAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATATAAATATA
Found at i:12633003 original size:15 final size:15
Alignment explanation
Indices: 12632983--12633021 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
12632973 ATTATATAAC
12632983 ATATAAAATAATATA
1 ATATAAAATAATATA
*
12632998 ATATAAAATATTATA
1 ATATAAAATAATATA
*
12633013 ATTTAAAAT
1 ATATAAAAT
12633022 TGACTGAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAAAATAATATA
Found at i:12634718 original size:28 final size:29
Alignment explanation
Indices: 12634665--12634735 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
12634655 ATTGAAAGGA
* *
12634665 GCCCAAAATTATTTTTTTAATTTTTAAGAG
1 GCCC-AAATTATTTTTTCAATCTTTAAGAG
*
12634695 GCCCAAATT-TTTTTTCAATCTTTAAGGG
1 GCCCAAATTATTTTTTCAATCTTTAAGAG
*
12634723 GCCCAAATAATTT
1 GCCCAAATTATTT
12634736 ATCAACTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 24 0.67
29 8 0.22
30 4 0.11
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.42
Consensus pattern (29 bp):
GCCCAAATTATTTTTTCAATCTTTAAGAG
Found at i:12634740 original size:28 final size:28
Alignment explanation
Indices: 12634686--12634751 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
12634676 TTTTTTTAAT
* ** *
12634686 TTTTAAGAGGCCCAAATTTTTTTTCAA-
1 TTTTAAGGGGCCCAAATAATTTATCAAC
12634713 TCTTTAAGGGGCCCAAATAATTTATCAAC
1 T-TTTAAGGGGCCCAAATAATTTATCAAC
12634742 TTTTAAGGGG
1 TTTTAAGGGG
12634752 TCTAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 31 0.94
29 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (28 bp):
TTTTAAGGGGCCCAAATAATTTATCAAC
Found at i:12635845 original size:1 final size:1
Alignment explanation
Indices: 12635839--12635868 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
12635829 TCTTTCACTC
*
12635839 TTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12635869 GGGTTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:12637764 original size:6 final size:6
Alignment explanation
Indices: 12637753--12637778 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12637743 ATATTTTTTG
12637753 TAATTA TAATTA TAATTA TAATTA TA
1 TAATTA TAATTA TAATTA TAATTA TA
12637779 CGTGCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:12642898 original size:15 final size:17
Alignment explanation
Indices: 12642877--12642917 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
12642867 TAATTATTTA
12642877 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
12642893 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
12642909 AAAATTATA
1 AAAATTATA
12642918 TTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:12642902 original size:25 final size:24
Alignment explanation
Indices: 12642868--12642944 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 24
12642858 AAATTAATTT
12642868 AATTATTTAAAAATTATAAAAATATA
1 AATTA-TT-AAAATTATAAAAATATA
* *
12642894 AATTATTAAAATAATAAAATTATA
1 AATTATTAAAATTATAAAAATATA
* ** *
12642918 TTATTATTATTATTGTAAAAATATA
1 -AATTATTAAAATTATAAAAATATA
12642943 AA
1 AA
12642945 ATTTAATTCA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 16 0.39
25 20 0.49
26 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (24 bp):
AATTATTAAAATTATAAAAATATA
Found at i:12644873 original size:44 final size:44
Alignment explanation
Indices: 12644810--12644893 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
12644800 CTGGTGCATC
*
12644810 TAAGTTTTGTTTAATCATGACTATGCCAGTTGAGGAAACTCATT
1 TAAGTTTTGTTTAATCATGACTATGCCAGTAGAGGAAACTCATT
12644854 TAAGTTTTGTTTAATCATGACTATGCCAGTAGAGGAAACT
1 TAAGTTTTGTTTAATCATGACTATGCCAGTAGAGGAAACT
12644894 GCTATGCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (44 bp):
TAAGTTTTGTTTAATCATGACTATGCCAGTAGAGGAAACTCATT
Found at i:12655026 original size:18 final size:16
Alignment explanation
Indices: 12654993--12655026 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
12654983 GTAATTCACC
12654993 AAAAAAATAATAAATT
1 AAAAAAATAATAAATT
12655009 AAAATAAATAACTAAATT
1 AAAA-AAATAA-TAAATT
12655027 TCAAATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAATAATAAATT
Found at i:12656517 original size:2 final size:2
Alignment explanation
Indices: 12656510--12656546 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12656500 AGTTGATTTA
12656510 AT AT 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 AT AT A
12656547 ATTTATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12660632 original size:19 final size:19
Alignment explanation
Indices: 12660610--12660646 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12660600 ATAGTATTTT
12660610 ATTAATTTAATATTAAATG
1 ATTAATTTAATATTAAATG
*
12660629 ATTATTTTAATATTAAAT
1 ATTAATTTAATATTAAAT
12660647 TAAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTAATTTAATATTAAATG
Found at i:12660745 original size:16 final size:16
Alignment explanation
Indices: 12660695--12660745 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
12660685 TTTTAATAAG
*
12660695 ATTTAATATTAAATTA
1 ATTTAATATTAAAATA
* **
12660711 ATATAATATTTATCA-A
1 ATTTAATA-TTAAAATA
12660727 ATTTAATATTAAAATA
1 ATTTAATATTAAAATA
12660743 ATT
1 ATT
12660746 AAGTTTAATC
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
15 4 0.15
16 19 0.73
17 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAATATTAAAATA
Found at i:12663068 original size:29 final size:29
Alignment explanation
Indices: 12663025--12663109 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 29
12663015 GTCACGTCAC
*
12663025 AATTGTATACATAAATTTTAATTTGGTAT
1 AATTATATACATAAATTTTAATTTGGTAT
* *
12663054 AATTATATACGTAAAATTTTAATTGTGGTTT
1 AATTATATACAT-AAATTTTAATT-TGGTAT
* *
12663085 AAATATATACTTTAAATTTTAATTT
1 AATTATATAC-ATAAATTTTAATTT
12663110 TAATTTAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.21
30 12 0.25
31 25 0.52
32 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (29 bp):
AATTATATACATAAATTTTAATTTGGTAT
Found at i:12663102 original size:31 final size:30
Alignment explanation
Indices: 12663036--12663109 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
12663026 ATTGTATACA
*
12663036 TAAATTTTAATTTGGTATAATTATATACGT
1 TAAATTTTAATTTGGTATAAATATATACGT
* * *
12663066 AAAATTTTAATTGTGGTTTAAATATATACTT
1 TAAATTTTAATT-TGGTATAAATATATACGT
12663097 TAAATTTTAATTT
1 TAAATTTTAATTT
12663110 TAATTTAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (30 bp):
TAAATTTTAATTTGGTATAAATATATACGT
Found at i:12663117 original size:31 final size:31
Alignment explanation
Indices: 12663057--12663117 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
12663047 TTGGTATAAT
**
12663057 TATATACGTAAAATTTTAATTGTGGTTTAAA
1 TATATACGTAAAATTTTAATTGTAATTTAAA
* * *
12663088 TATATACTTTAAATTTTAATTTTAATTTAA
1 TATATACGTAAAATTTTAATTGTAATTTAA
12663118 TCATACACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (31 bp):
TATATACGTAAAATTTTAATTGTAATTTAAA
Found at i:12677070 original size:1 final size:1
Alignment explanation
Indices: 12677064--12677088 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12677054 TTGCAACTTG
12677064 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
12677089 TTTAGGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:12678223 original size:38 final size:40
Alignment explanation
Indices: 12678181--12678261 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
12678171 ATGGATATCT
*
12678181 TTTG-AAAAGTCACAATCC-TTTCATATT-AGATGGACACC
1 TTTGAAAAAGTCACAACCCTTTTCATATTGA-ATGGACACC
12678219 TTTGAAAAAGTCACAACCCTTTTCATATTGAATGGACACC
1 TTTGAAAAAGTCACAACCCTTTTCATATTGAATGGACACC
12678259 TTT
1 TTT
12678262 TGGAAGAGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 4 0.10
39 13 0.33
40 21 0.54
41 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (40 bp):
TTTGAAAAAGTCACAACCCTTTTCATATTGAATGGACACC
Found at i:12681017 original size:7 final size:7
Alignment explanation
Indices: 12680991--12681040 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
12680981 TTAGAATTAA
12680991 TATTCTTT
1 TATT-TTT
12680999 TGATTGTTT
1 T-ATT-TTT
12681008 TATTTTT
1 TATTTTT
12681015 TATTTTT
1 TATTTTT
12681022 TATTTTT
1 TATTTTT
12681029 TATTTTT
1 TATTTTT
12681036 T-TTTT
1 TATTTT
12681041 GTGAACAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 4 0.10
7 25 0.62
8 4 0.10
9 7 0.17
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (7 bp):
TATTTTT
Found at i:12684288 original size:13 final size:13
Alignment explanation
Indices: 12684270--12684296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12684260 CATGAGAATC
12684270 TCTCTTTATGTCA
1 TCTCTTTATGTCA
12684283 TCTCTTTATGTCA
1 TCTCTTTATGTCA
12684296 T
1 T
12684297 TAAGGATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (13 bp):
TCTCTTTATGTCA
Found at i:12688557 original size:428 final size:427
Alignment explanation
Indices: 12687751--12689037 Score: 2119
Period size: 428 Copynumber: 3.0 Consensus size: 427
12687741 CTTAATCACA
*
12687751 TAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTCATAAAATACTATTA
1 TAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTAATAAAATACTATTA
* **
12687816 ATATGATTATTAAATTAAATTTTTATAAATGTTTATTTTTTAAATATGCTTATTATATTATATGG
66 ATATGATTATTAAATTTAATTTTTATAAATGTTTATTTTTTAAATATGCTTATTATATTATGCGG
* ** *
12687881 GACGGGTGGAGATGGGATAGGTACAAGATCATACCCATACTTGTTCCACCACCCACGACGGGTCT
131 GACGGGTGGAGATGGGACAGGTACAAGATCATACCCACGCTTGTCCCACCACCCACGACGGGTCT
* * *
12687946 AATTTTTTTCTCATCTCCATCCTACCACCCGCGAAACCAATACCTATCTCCGCTTAATCGGGTGT
196 AATTTTTTTCTCATCTCCATCCTACCACCCGCGAAACCAATACCCATCTCCGTTTAATTGGGTGT
12688011 GAAATGGGGCGAGGGCCCGCAAAACTCGCCCCACTAATTCAACTAGAGATTAAAAAAAATTATAT
261 GAAATGGGGCGAGGGCCCGCAAAACTCGCCCCACTAATTCAACTAGAGATTAAAAAAAATTATAT
* * * * *
12688076 ATATAAGACCTCCACCAATATTTTAATGAATAATTTCTTTTATATAATTTTTTCTCACTTCAATC
326 ATATAAGACCTCCACCTATATTTCAAGGAATAACTTCTTTTATATATTTTTTTCTCACTTCAATC
12688141 GAAAAGTGTGAAATAATAATAATAATATTATTATTAT
391 GAAAAGTGTGAAATAATAATAATAATATTATTATTAT
*
12688178 TAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTAATAAAAAAACTATT
1 TAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTAAT-AAAATACTATT
*
12688243 AATATGATTATTAAATTTAATTTTTATAAATGTTTATTTTTTAAATATACTTATTATATTATGCG
65 AATATGATTATTAAATTTAATTTTTATAAATGTTTATTTTTTAAATATGCTTATTATATTATGCG
*
12688308 GGACGGGTGGAGATGGGACAGGTACAATATCATACCCACGCTTGTCCCACCACCCACGACGGGTC
130 GGACGGGTGGAGATGGGACAGGTACAAGATCATACCCACGCTTGTCCCACCACCCACGACGGGTC
* *
12688373 TAATTTTTTTCTCATATCCATCCTACCACCCGC-AGAACCAATACCCATCTCCGTTTAATTAGGT
195 TAATTTTTTTCTCATCTCCATCCTACCACCCGCGA-AACCAATACCCATCTCCGTTTAATTGGGT
* *
12688437 GTGAAATAGGGCGAGGGCCCGCAAAACTCGCCCCACTAATTCAACTAGAGATTAAAGAAAATTAT
259 GTGAAATGGGGCGAGGGCCCGCAAAACTCGCCCCACTAATTCAACTAGAGATTAAAAAAAATTAT
12688502 ATATATAAGACCTCCACCTATATTTCAAGGAATAACTTCTTTTATATATTTTTTTCTCACTTCAA
324 ATATATAAGACCTCCACCTATATTTCAAGGAATAACTTCTTTTATATATTTTTTTCTCACTTCAA
* *
12688567 TCGAAAAGTGTGAAATAATAATAATAATAATAATAATAATAT
389 TCGAAAAGTGTGAAATAATAATAATAAT-AT--TATTATTAT
*
12688609 TAAATATTAGATTAAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATACTATTA
1 TAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTAATAAAATACTATTA
* *
12688674 ATATGATTATTAAA-TTAAATTTTATAAATATTTATTTTTTAAATATGCTTATTATATTATGCGG
66 ATATGATTATTAAATTTAATTTTTATAAATGTTTATTTTTTAAATATGCTTATTATATTATGCGG
* * * *
12688738 GATGGGTGAAGATGGGACAGGTACAAGATCATACCCACGCTTGTCCCACCATCCACGACAGGTCT
131 GACGGGTGGAGATGGGACAGGTACAAGATCATACCCACGCTTGTCCCACCACCCACGACGGGTCT
* *
12688803 AATTTTTTTCTCATCTCCATCCTACCACTCGCGAAACCAATATCCATCTCCGTTTAATTGGGTGT
196 AATTTTTTTCTCATCTCCATCCTACCACCCGCGAAACCAATACCCATCTCCGTTTAATTGGGTGT
* * *
12688868 GAAATGGGGCGAGGACCCGCAAAACTCGCCCCACTAATTAAACTAGAGATTAAATAAAATTATAT
261 GAAATGGGGCGAGGGCCCGCAAAACTCGCCCCACTAATTCAACTAGAGATTAAAAAAAATTATAT
* *
12688933 ATATAAGACCTCCATCTATATTTCAAGGAATAACTTCTTTTGTATAATTTTTTTCTCACTTCAAT
326 ATATAAGACCTCCACCTATATTTCAAGGAATAACTTCTTTTATAT-ATTTTTTTCTCACTTCAAT
* * * *
12688998 CGAAAAGTGTGAAATATTATTATTATTATTATTATTAT
390 CGAAAAGTGTGAAATAATAATAATAATATTATTATTAT
12689036 TA
1 TA
12689038 TACAAGTAAT
Statistics
Matches: 802, Mismatches: 51, Indels: 14
0.93 0.06 0.02
Matches are distributed among these distances:
427 62 0.08
428 339 0.42
429 274 0.34
430 68 0.08
431 59 0.07
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (427 bp):
TAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTAATAAAATACTATTA
ATATGATTATTAAATTTAATTTTTATAAATGTTTATTTTTTAAATATGCTTATTATATTATGCGG
GACGGGTGGAGATGGGACAGGTACAAGATCATACCCACGCTTGTCCCACCACCCACGACGGGTCT
AATTTTTTTCTCATCTCCATCCTACCACCCGCGAAACCAATACCCATCTCCGTTTAATTGGGTGT
GAAATGGGGCGAGGGCCCGCAAAACTCGCCCCACTAATTCAACTAGAGATTAAAAAAAATTATAT
ATATAAGACCTCCACCTATATTTCAAGGAATAACTTCTTTTATATATTTTTTTCTCACTTCAATC
GAAAAGTGTGAAATAATAATAATAATATTATTATTAT
Found at i:12688588 original size:3 final size:3
Alignment explanation
Indices: 12688580--12688607 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12688570 AAAAGTGTGA
12688580 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12688608 TTAAATATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12688659 original size:25 final size:26
Alignment explanation
Indices: 12688626--12688686 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
12688616 TAGATTAAAT
12688626 TTAATATTAA-AATAATCACT-TTAATA
1 TTAATATTAATAA-AAT-ACTATTAATA
12688652 TTAA-ATTAATAAAATACTATTAATA
1 TTAATATTAATAAAATACTATTAATA
* *
12688677 TGATTATTAA
1 TTAATATTAA
12688687 ATTAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
25 16 0.53
26 11 0.37
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (26 bp):
TTAATATTAATAAAATACTATTAATA
Found at i:12689020 original size:3 final size:3
Alignment explanation
Indices: 12689012--12689038 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12689002 AAGTGTGAAA
12689012 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
12689039 ACAAGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12710957 original size:3 final size:3
Alignment explanation
Indices: 12710949--12710984 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
12710939 GGCAATCCAA
12710949 AAG AAG AAG AAG AAG AAAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AA
12710985 ACAGAGGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12710967 original size:16 final size:16
Alignment explanation
Indices: 12710948--12710981 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12710938 TGGCAATCCA
12710948 AAAGAAGAAGAAGAAG
1 AAAGAAGAAGAAGAAG
12710964 AAAGAAGAAGAAGAAG
1 AAAGAAGAAGAAGAAG
12710980 AA
1 AA
12710982 GAAACAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAGAAGAAG
Found at i:12710973 original size:19 final size:19
Alignment explanation
Indices: 12710949--12710985 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12710939 GGCAATCCAA
12710949 AAGAAGAAGAAGAAGAAAG
1 AAGAAGAAGAAGAAGAAAG
12710968 AAGAAGAAGAAGAAGAAA
1 AAGAAGAAGAAGAAGAAA
12710986 CAGAGGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGAAGAAGAAGAAGAAAG
Found at i:12717158 original size:3 final size:3
Alignment explanation
Indices: 12717150--12717175 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12717140 TACTATATCT
12717150 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12717176 CAATACCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12717508 original size:21 final size:21
Alignment explanation
Indices: 12717456--12717509 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
12717446 AAATAAAATG
12717456 ATCAACATAAAAAAAAATTCA
1 ATCAACATAAAAAAAAATTCA
* * * *
12717477 GTTAACGTAAAAAAAATTTCA
1 ATCAACATAAAAAAAAATTCA
12717498 ATCAACATAAAA
1 ATCAACATAAAA
12717510 TTATTCTCTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (21 bp):
ATCAACATAAAAAAAAATTCA
Found at i:12722766 original size:13 final size:13
Alignment explanation
Indices: 12722748--12722773 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12722738 GATATTTAAT
12722748 TATTCAAAATATA
1 TATTCAAAATATA
12722761 TATTCAAAATATA
1 TATTCAAAATATA
12722774 AAATTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTCAAAATATA
Found at i:12723716 original size:5 final size:5
Alignment explanation
Indices: 12723706--12723733 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12723696 CCAGTAGAAT
12723706 ATGCA ATGCA ATGCA ATGCA ATGCA ATG
1 ATGCA ATGCA ATGCA ATGCA ATGCA ATG
12723734 AGAAGGGAAC
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:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (5 bp):
ATGCA
Found at i:12733596 original size:24 final size:25
Alignment explanation
Indices: 12733550--12733596 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
12733540 TAATTAATTT
* **
12733550 AACTTAATTTTTAATTGTGTTAAAA
1 AACTAAATTTTTAATTGAATTAAAA
12733575 AACTAAATTTTTAATT-AATTAA
1 AACTAAATTTTTAATTGAATTAA
12733597 TATTTTTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
AACTAAATTTTTAATTGAATTAAAA
Found at i:12744146 original size:15 final size:15
Alignment explanation
Indices: 12744126--12744163 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12744116 AACAATAAAA
12744126 TATAATTTA-ATTATT
1 TATAATTTATA-TATT
*
12744141 TATAATTTATATCTT
1 TATAATTTATATATT
12744156 TATAATTT
1 TATAATTT
12744164 TTAAATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATAATTTATATATT
Found at i:12744215 original size:30 final size:30
Alignment explanation
Indices: 12744149--12744205 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12744139 TTTATAATTT
* * *
12744149 ATATCTTTATAATTTTTAAATGATTAAATC
1 ATATTTTTATAATTTTTAAAAGATAAAATC
12744179 ATATTTTTATAATTTTTAAAAG-TAAAA
1 ATATTTTTATAATTTTTAAAAGATAAAA
12744206 GTATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (30 bp):
ATATTTTTATAATTTTTAAAAGATAAAATC
Found at i:12744216 original size:29 final size:30
Alignment explanation
Indices: 12744154--12744226 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
12744144 AATTTATATC
* * *
12744154 TTTATAATTTTTAAATGATTAAATCATATT
1 TTTATAATTTTTAAAAGATAAAATCATAAT
12744184 TTTATAATTTTTAAAAG-TAAAAGT-ATAAT
1 TTTATAATTTTTAAAAGATAAAA-TCATAAT
* *
12744213 TTTATTATTATTAA
1 TTTATAATTTTTAA
12744227 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTTAAAAGATAAAATCATAAT
Found at i:12745175 original size:19 final size:20
Alignment explanation
Indices: 12745132--12745181 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12745122 TTACAAAAAG
* *
12745132 AATTCAAAATAATTTTTTAA
1 AATTCAAAATAATTTATAAA
*
12745152 TATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTTATAAA
12745171 AATTCCAAAAT
1 AATT-CAAAAT
12745182 TTGTATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTCAAAATAATTTATAAA
Found at i:12750361 original size:19 final size:20
Alignment explanation
Indices: 12750318--12750366 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12750308 TTACAAAAAG
* *
12750318 AATTCAAAATAATTTTTTAA
1 AATTCAAAATAATTTATAAA
*
12750338 TATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTTATAAA
12750357 AATTCCAAAA
1 AATT-CAAAA
12750367 CTTGTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTCAAAATAATTTATAAA
Found at i:12750605 original size:21 final size:20
Alignment explanation
Indices: 12750576--12750615 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12750566 ATTTCATTCT
*
12750576 ATTTGACTCGACTCGAATTTC
1 ATTTCACTCGACTC-AATTTC
*
12750597 ATTTCACTCTACTCAATTT
1 ATTTCACTCGACTCAATTT
12750616 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (20 bp):
ATTTCACTCGACTCAATTTC
Found at i:12753123 original size:47 final size:47
Alignment explanation
Indices: 12753054--12753150 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
12753044 ACTGGTGGTT
12753054 ACTGGTAGTTAAGATGGTTAGTAGTTAGTGTCAGTTATAGTTACCTA
1 ACTGGTAGTTAAGATGGTTAGTAGTTAGTGTCAGTTATAGTTACCTA
*
12753101 ACTGGTAGTTAAGATGGTTAGTAGTTAGTGTCAGTTATAGTTAGCTA
1 ACTGGTAGTTAAGATGGTTAGTAGTTAGTGTCAGTTATAGTTACCTA
12753148 ACT
1 ACT
12753151 ACTATACCAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (47 bp):
ACTGGTAGTTAAGATGGTTAGTAGTTAGTGTCAGTTATAGTTACCTA
Found at i:12754978 original size:17 final size:16
Alignment explanation
Indices: 12754936--12754967 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12754926 TTTAATATTT
12754936 TAAAAATT-ATAAAAA
1 TAAAAATTAATAAAAA
12754951 TAAAAATTAATAAAAA
1 TAAAAATTAATAAAAA
12754967 T
1 T
12754968 TACAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATTAATAAAAA
Found at i:12755460 original size:30 final size:30
Alignment explanation
Indices: 12755426--12755490 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
12755416 ACTTATTTTA
*
12755426 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
12755456 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
12755486 TTGTT
1 TTGTT
12755491 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGACAT
Found at i:12757979 original size:24 final size:24
Alignment explanation
Indices: 12757947--12758005 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
12757937 GCCGGTGTTT
*
12757947 CTGGTGGTTGCCGCTGTAAAATAG
1 CTGGTGGTTGCCGCGGTAAAATAG
*
12757971 CTGGTGGTTGCCGCGGTAAAGTAG
1 CTGGTGGTTGCCGCGGTAAAATAG
12757995 CTGGTGGTTGC
1 CTGGTGGTTGC
12758006 TGCGTAGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.39, T:0.29
Consensus pattern (24 bp):
CTGGTGGTTGCCGCGGTAAAATAG
Found at i:12758885 original size:13 final size:13
Alignment explanation
Indices: 12758867--12758892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12758857 ACAATATATT
12758867 TATTAATTAAAAA
1 TATTAATTAAAAA
12758880 TATTAATTAAAAA
1 TATTAATTAAAAA
12758893 ATTTGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:12770593 original size:16 final size:16
Alignment explanation
Indices: 12770572--12770610 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12770562 ATTTGGTTCA
12770572 TTGTAATGGAATAAGG
1 TTGTAATGGAATAAGG
*
12770588 TTGTAATGGAATAGGG
1 TTGTAATGGAATAAGG
*
12770604 CTGTAAT
1 TTGTAAT
12770611 CGATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (16 bp):
TTGTAATGGAATAAGG
Found at i:12770909 original size:19 final size:18
Alignment explanation
Indices: 12770887--12770935 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
12770877 AAATAAATAG
*
12770887 AATTTAAAATAAATATTTT
1 AATTTAAAA-AAATATGTT
*
12770906 AA-TTAAAAAATTATGTT
1 AATTTAAAAAAATATGTT
12770923 AATTTTAAAAAAA
1 AA-TTTAAAAAAA
12770936 AGTTATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
19 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTTAAAAAAATATGTT
Found at i:12774855 original size:12 final size:12
Alignment explanation
Indices: 12774840--12774868 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12774830 GCCTCCTCCT
12774840 CCGCCTCTGGAG
1 CCGCCTCTGGAG
12774852 CCGCCTCTGGAG
1 CCGCCTCTGGAG
12774864 CCGCC
1 CCGCC
12774869 GCCTCTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.48, G:0.31, T:0.14
Consensus pattern (12 bp):
CCGCCTCTGGAG
Found at i:12774871 original size:15 final size:15
Alignment explanation
Indices: 12774840--12774886 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12774830 GCCTCCTCCT
12774840 CCGCCTCTGGA---G
1 CCGCCTCTGGAGCCG
12774852 CCGCCTCTGGAGCCG
1 CCGCCTCTGGAGCCG
**
12774867 CCGCCTCTGCTGCCG
1 CCGCCTCTGGAGCCG
12774882 CCGCC
1 CCGCC
12774887 AATGCTAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 11 0.37
15 19 0.63
ACGTcount: A:0.04, C:0.51, G:0.30, T:0.15
Consensus pattern (15 bp):
CCGCCTCTGGAGCCG
Found at i:12799309 original size:11 final size:11
Alignment explanation
Indices: 12799290--12799321 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12799280 ATGGCATAAA
12799290 TGATATCATAG
1 TGATATCATAG
*
12799301 TGGTATCATAG
1 TGATATCATAG
12799312 TGATATCATA
1 TGATATCATA
12799322 ATTTAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (11 bp):
TGATATCATAG
Found at i:12811322 original size:84 final size:86
Alignment explanation
Indices: 12811151--12811354 Score: 245
Period size: 84 Copynumber: 2.4 Consensus size: 86
12811141 ATTTTGGATT
* * * * * **
12811151 CCTCGATTTACCCGAA-GATGCACTGTGTATGCCAGTATAGATGCCTCTATTTACCCGATGATGC
1 CCTCGGTTTACCC-AATGATGCACTATGTGTGCCAGTATAGATGCCTCGATTTACCCAATGATAA
*
12811215 ATTATGTGTGACAGTACAGATC
65 ATTATGTGTGACAGTACAAATC
* * *
12811237 CCTTGGTTTACCCAATGATGCA-T-TGTGTGCCAGTATAGATGCCTCGGTTTACTCAATGATAAA
1 CCTCGGTTTACCCAATGATGCACTATGTGTGCCAGTATAGATGCCTCGATTTACCCAATGATAAA
*
12811300 TTATGTGT-ACCAGTATAAATC
66 TTATGTGTGA-CAGTACAAATC
*
12811321 CCTCGGTTTACCCGATGATGCACTATGTGTGCCA
1 CCTCGGTTTACCCAATGATGCACTATGTGTGCCA
12811355 ATATCGATAA
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
83 1 0.01
84 70 0.69
85 4 0.04
86 26 0.26
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (86 bp):
CCTCGGTTTACCCAATGATGCACTATGTGTGCCAGTATAGATGCCTCGATTTACCCAATGATAAA
TTATGTGTGACAGTACAAATC
Found at i:12811443 original size:43 final size:43
Alignment explanation
Indices: 12807018--12811448 Score: 2834
Period size: 43 Copynumber: 104.6 Consensus size: 43
12807008 ATATCTGACA
* * * * ** * * *
12807018 ATGCACTATGTGTGTCGGTATAGAAGATTCGATTTATCCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12807061 ATGCACTGTGTGTGTCAGTATAGAAGCTTTGATTTATCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12807104 ATGCACTGTGTGT--CAGTATAGATGCTTCGGTTTA-TCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * ** * *
12807144 ATACACTGTGTGTGCCAGTATATG-TACTTCGATTTATTCAATT
1 ATGCACTGTGTGTGCCAGTATA-GATGCCTCGGTTTACCCGATG
* * * * * * *
12807187 ATTCATTCTGTGTGCCAGTATAGATGTCTCTGTTTACTCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12807230 ATGCATTATTTCTGCCAGTATAGATGCCTTGATTTA-CCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12807272 ATGCTCTGTGTGCGCCAGTATAGATGCCTTGATTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12807315 ATGCTCTGTGTGCGTCAGTATAGATGCCTTGATTTACCCGATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12807358 ATGCAC--TGTGTGCCAGTATAGATGCCTCGATTTACACAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* *
12807399 ATGCACTGTGTGT--TAGTATAGATGCCTCGGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * *
12807440 CTACACTATGTGTACCAGTATAGATGCTTCGATTTA-CCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12807482 ATGCACTGTGTGTGCTAGTATAGATGCCTCGGTTTACTCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12807525 ATGTACTGTGTGTGCCAGTACAGATGCCTCGATTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* *
12807568 ATGCA-T-TGTGTGCCAGTATAAATGCCTCGATTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12807609 ATGCAC--TGTGTGCAAGTATAAATGCCTCGATTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** * ** * *
12807650 ATGCACTGTGTGCGGTAGTATAGATGTCTCAATTTACTCAAT-
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12807692 AT--ACTGTGTGTGCTAGTATAGATGCCTTGGTTTATCCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12807733 ATTCACTGTGTATGCCAGTATAGATGTCTCGGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * **
12807776 ACGCACTGTGTGTGCCAATATAGATACCTCAATTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12807819 ATGCACCGTGTGTGCTAATATAGATGCCTCAGTTTACCTGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* **
12807862 ATGCACTGTGTGTGCCAGTATAGATCCCTCGGTTTAGTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12807905 ATGCATTGTGTATGCCAATATAGATGCATCGGCTTACCCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * **
12807948 ATGCACTGTATGTACCAATATAGATGCCTCGGCTTACCAAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** *
12807991 ATGCAC--TGTGTGCCAGTATATATGCCTTAGTTTACTCGAT-
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12808031 ATTGCACTATGTGTACCAGTATAGATGCCTCGATTTATCAGATG
1 A-TGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** ** *
12808075 ATATAC--TGTGTGCCAGTATAGATGCCTCAATTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12808116 TATGCAC--TGTGTGCCATTATAGATACATCGATTTACTCGATG
1 -ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * ** *
12808158 ATGCACAGTATGTGCCAGTATAGATGCCTCGATTTATTCGGT-
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * ** * *
12808200 AT-TACATTTGTGTATCAGTATAGATGCCTCAGTTTACTCGATG
1 ATGCAC-TGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12808243 AGGCAC--TATGTGCCAGTATAGATGCCTCGGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * *
12808284 ATGCAC--TGTGTACTAGAATAGATGCCACGATTTACTCGATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12808325 ATGCAC--TGTGTACCAATATAGATACGTCGATTTAGCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12808366 ATGCAC--TGTGTGCTAGCATAGATGCCTTGATTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * ** * *
12808407 ACGAACTGTGTGTGCCAAAATAGATGCCTCCGCTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12808450 ATGCATTATGTGTGCCAGTATAGATACCACGTTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * * *
12808493 ATCCATTATGTATGCCAATATAGATACCTCAGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* *
12808536 ATGCACTGTGTGTGCCAATATAGATGCCTCGGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * * **
12808579 ATACACTGTTTGTGCTAATATAGATGCATTGATTTACCAAAT-
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12808621 ATCGCAC--TGTGTACCAGTATAGATACCTCGATTTATCAGATG
1 AT-GCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** *
12808663 ATACACTGTGTGTGTTAGTATAGATGCCTCGGCTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * *
12808706 ATGCAC--TGTGT-CCAGTATAGATGCCTCAATTTACCCAATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12808746 ATTCACTGTGTGT--TAATGTAGATGCCTCGATTTA-CCTACTG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGA-TG
* * * * *** ***
12808787 TTGTACTCTATGTGCCAGTATAGATGCCTTTATTTATTAGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * ***
12808830 ATATATTGTGTGTGCCAGTATAGATGCCTCGATTTATTTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * *
12808873 ATATACTATGTGTGCCAGTATAAATGCCTTGGTTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12808916 ATGCACTATGTATGCTAGTATAGATGCCTCGGTTTACCCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * ** **
12808959 ATGAATTGTGTGTGCCAATATAGATATCTCGGTTTACTTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12809002 ATGCATTGTGTGTGTCAGTTTAAATGCCTCGGTTTACCCGAAG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * ** *
12809045 ATACACTGTGTGTACCAGTATAGATGCCTCGACTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
*
12809088 ATGCAC--TGTGTGCCAGTATAGATGCCTCAGTTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * * *
12809129 ATGCATTGTATGTACCAGTATAGATACTTCGATTT-CTCGATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12809171 ATGCATTATGTGTGCCAATATAGATGCCTCGATTTACCTGAT-
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * ***
12809213 ATTGCACTCTATGTGTCAGTATAGATGCCTCGATTTATTAGATG
1 A-TGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * * ***
12809257 ATATATTGTGTATGCCAGTATAGATGCCTCGATTTATTTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * * * * * * *
12809300 ATATATTATGTGTGCTAATAT-GAATACCTTGGTTTACCCGGTA
1 ATGCACTGTGTGTGCCAGTATAG-ATGCCTCGGTTTACCCGATG
** * *** *
12809343 ATGCACTACGTGTGCTAGTATAGATGCCTCAACTTACCCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12809386 ATGAATTGTGTGTGGCAGTATAAATACCTCGGTTTA--C-TTG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * *
12809426 ATGCACTATGTGTGCCATTTTAGATGCATCGATTTACTCGAAG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* *
12809469 ATACAC--TGTGTGCCAGTATAGATGCCTCAGTTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * ** * * ** * *
12809510 ATGCACTGTGTACGACAGTCGATATCCCTTTGTTTGCCCGATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** ** *
12809553 ATGCAC--TGTGTGCCAGCATAGATGAATCAATTTACCTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * ** * ***
12809594 ATACACTGTATGTGCCAGTATAGACGTTTCGTTTTATTAGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * *
12809637 ATATA-T-TGTGTACCAGTATAGATGCCTCGATTTATCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** * * ** *
12809678 ATGAACTACGTGTGCTAGTAT---TACCTCGACTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12809718 GTGCAC--TGTGTGCCAGTATAGATACCTCGATTTACTCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** * *
12809759 ATGCACTGTGTGTGTCAGTATAGATAACTTGGTTTACCCAAT-
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * ** * * * *
12809801 ATCGTATTGTGTGTACTTGTATAGATGCCTCGATTTATCAGATT
1 AT-GCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12809845 ATACAGTATGTGTGCCAATATAAATGCCTCGGTATACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * ** **
12809888 ATGAATTGTGTATGCCAATATAAATGTTTCGGTTTACCTAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * ** *
12809931 ATGCACTTTGTGTGCCAGTATAAATACCTCGATTTACCTTATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12809974 ATGCACTGTGTGTGCCAGTAAAGATGCATCGGTTTACCCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12810017 ATGCAC--TGTGTACTAGTACAGAT-CCTTCGGTTTACCAGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCC-TCGGTTTACCCGATG
* * ** * *
12810058 ATGTATTGTGTGTTTCAGTAAAGATGCCTCGGTTTACCCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * ** *
12810101 AAGCACTGTGTGTGCCAGTATAGATGCCTTGGTTTTTCCTATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* ** * * *
12810144 ATGCACTGTGTATGTTAGTACAGATACCTCGATTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * ** * *
12810187 ATTCACTATGTACGCTAGTATAAATGCCTCGGTTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * *
12810230 ATGCACTGTGTGTGCCAGTATAGATATCTCAGCTTACCTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12810273 ATGCACTCTGTGTGCCTGTTTAGATGCCTCGGGTTACCTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12810316 ATGCACTGTG-GTTACCAGTATAGA-GTCCTCGATTTACTCGATG
1 ATGCACTGTGTG-TGCCAGTATAGATG-CCTCGGTTTACCCGATG
** * *** *
12810359 ATGCACTGTGTGTGCCAACATAGATGCCTCAGTTTATTTGACG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * ***
12810402 TTGCATTATGTGTGCCAGTATAGATGTCTCGATTTATTAGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** *
12810445 ATAAACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12810488 ATGCACTATGTGTGCTAGTATAAATG-CTTGAGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCG-GTTTACCCGATG
* * * * *
12810531 ATGAACTGTGTATGCTAGAATAGATGCCTCGGTTTACCCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12810574 ATGCAC--TGTGTACTAATATAGATGCCTCAGTTTACTCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * **
12810615 ATGCACTGTGTGTGCTAGTATAGATACCTCGGTTTACTTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * *
12810658 ATGTACCGTTTGTGCCAGTATAGATGCCAT-GATTTACCCTAT-
1 ATGCACTGTGTGTGCCAGTATAGATGCC-TCGGTTTACCCGATG
* * * * **
12810700 ATCGTACTGTGTGTACCAGTATAGATGCCTCGATTTATCAAATG
1 AT-GCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12810744 ATGCACTGCGTGTGCTAGTATAGATACCTCAGCTTACCTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * **
12810787 ATGCA--ATGTGTGCC-GCTATAGATGCGTTAGTTTACCCGATG
1 ATGCACTGTGTGTGCCAG-TATAGATGCCTCGGTTTACCCGATG
** * * *
12810828 ATGCACTGTGTGTGCCAGTATAGATATCTCGATTTACTCGATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * **
12810871 ATTCATTTTGTGTGCCAATATAGATGCCTCGGTTTACATGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * * *** *
12810914 TTGCACTCTATATGCCAGTATAGATGCTTTGATTTATTAGATT
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * ****
12810957 ATGTACTGTGTGTGCCAGTATAGATGTCTCGATTTATTATATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * *
12811000 ATATAC--TATGTGCCAGTATAGATGCCTCGGTTTACCTGATA
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * *
12811041 ATGTACTATGTGTGCTAGTATAGATGCGTCGATTTACCCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * *
12811084 ATAAACTGTGT-T-CCAGTATAGATACCTCGGTTTACCTGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * * *
12811125 ATGCACTGTTTATGCCATTTTGGATTCCTCGATTTACCCGAAG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* **
12811168 ATGCACTGTGTATGCCAGTATAGATGCCTCTATTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * * * * *
12811211 ATGCATTATGTGTGACAGTACAGATCCCTTGGTTTACCCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* *
12811254 ATGCA-T-TGTGTGCCAGTATAGATGCCTCGGTTTACTCAATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
** * * * * *
12811295 ATAAATTATGTGTACCAGTATAAATCCCTCGGTTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * ** ** * *
12811338 ATGCACTATGTGTGCCAATATCGATAACTTAGCTTACACGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * * *
12811381 ATACACTGTGTGTGCCAATATAGATGCTTCAGTTTACCCGATG
1 ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
* * *
12811424 ATGCACTGTGTATGTCAATATAGAT
1 ATGCACTGTGTGTGCCAGTATAGAT
12811449 TGTAACATCC
Statistics
Matches: 3418, Mismatches: 882, Indels: 176
0.76 0.20 0.04
Matches are distributed among these distances:
38 11 0.00
40 125 0.04
41 760 0.22
42 214 0.06
43 2289 0.67
44 19 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (43 bp):
ATGCACTGTGTGTGCCAGTATAGATGCCTCGGTTTACCCGATG
Found at i:12811793 original size:18 final size:18
Alignment explanation
Indices: 12811772--12811821 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
12811762 TTATTAAAGA
*
12811772 TATATTAATTAATAATAT
1 TATATTAAATAATAATAT
*
12811790 TATAATAAATAATAATAT
1 TATATTAAATAATAATAT
* *
12811808 TTTATTATATAATA
1 TATATTAAATAATA
12811822 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTAAATAATAATAT
Found at i:12813922 original size:41 final size:40
Alignment explanation
Indices: 12813857--12813976 Score: 150
Period size: 43 Copynumber: 2.9 Consensus size: 40
12813847 AAGGTCTCAC
*
12813857 ATAGATACCTCGGTATACCCGATGATAAACTGTGTGCCAGT
1 ATAGATACCTCGGTTTA-CCGATGATAAACTGTGTGCCAGT
* * *
12813898 ATAGATGCCTCGATTTACCTGATGATAAACTTTGTGTGGCAGT
1 ATAGATACCTCGGTTTACC-GATGATAAAC--TGTGTGCCAGT
*
12813941 ATAGATACCTCGGTTTAACCGATGATACACTGTGTG
1 ATAGATACCTCGGTTT-ACCGATGATAAACTGTGTG
12813977 AGCCAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.03
41 30 0.44
43 33 0.49
44 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (40 bp):
ATAGATACCTCGGTTTACCGATGATAAACTGTGTGCCAGT
Found at i:12814778 original size:213 final size:214
Alignment explanation
Indices: 12813887--12818886 Score: 2281
Period size: 213 Copynumber: 23.5 Consensus size: 214
12813877 GATGATAAAC
* * * ** * * * *
12813887 TGTGTGCCAGTATAGATGCCTCGATTTAC-CTGATGATAAACTTTGTGTGGCAGTATAGATACCT
1 TGTGTGCCAGTATAGATGCTTTGGTTTACTC-GATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * * * * * * *
12813951 CGGTTTAACCGATGATACACTGTGTGAGCCAATAT-GAATGCTTC-AGTTTA-CTCGATGTTGCA
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAG-ATGCTTCGA-TTTATCT-GAAGATGCA
* * * * * * * * *
12814013 -TTGTATGTGCCAGTA-AGGATTCCTCAGTTTA-CCAAATAATGCATTGTGTGTGCCAGAATAGA
127 CTTAT-TGTGCCAGTATA-GATGCTTCTGTTTATCC-GATGATGCACTATGTGTGCCAGTATAGA
** * * * *
12814075 TGCCTCGGTTTATACGATGAGGCATT
189 TGTTTCGATTTATCCGATGATGCACT
* * ** * *
12814101 GTGTGTGCTAGTATAGATGCTTTTGTTTGTTAGATGATGCACTGTGTGTGCTAGTATAGATGCTT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* *
12814166 CGGTTTAT-TAGATGAAGCACTATGTGTGCTAGTATAGATGCTTCGATTTAT-T--AGATGCACT
65 CGGTTTATCT-GATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAAGATGCACT
* * * ** * ** *
12814227 GT-GTGTGCCAGTATAAATCCTTCAATTTTTTAGATAATGCACTATGTGTGCTC-GTATAGATGC
129 -TATTGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGC-CAGTATAGATG-
* * ** *
12814290 ATT-AATTTATGAGATGTTGCACCT
191 TTTCGATTTATCCGATGATGCA-CT
* * * * * *
12814314 TGTGTGACAGTATAGATGCTTCGATTTA-TCCGATAATGCACTGTGTTTGCCTGTATAGATGCTT
1 TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * * * * * * *
12814378 CGGTTCACCCGACGATGCAC--TGTGTGCTAGTATAGATGCTTCGATTTACCCGATA-ATACAC-
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGA-AGATGCACT
* * * * * * *
12814439 TATGTGTGCCAGTACAAATGCTT-TGATTTACCCGATAATACATTATGTGT--CAGTATAGATGC
129 TAT-TGTGCCAGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTGTGCCAGTATAGATGT
*
12814501 TTCGATTTA-CCTGATAAT-CACT
192 TTCGATTTATCC-GATGATGCACT
* ** * * * *
12814523 GTGTGTGCCAGTATAGATGCTTTGATTTACTCGACAATGCACTGTGTTTGCTACTATAGATGTTT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * ** * *
12814588 CGGTTTATCTGATGATACACTTTGTGTGTTAGTATAGATGCTTTGATTTATCTGAAGAAGCACTT
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAAGATGCACTT
* * *
12814653 ATTGTGCCACTATAGATGCTTCTGTTTATCCGATGATGCACAATGTGTGCCAGTATAAATGTTTC
130 ATTGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGATGTTTC
* * *
12814718 CATTTACCCGATAATGCA-T
195 GATTTATCCGATGATGCACT
* * *
12814737 TATGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTATGTGTGCCAGTATAGATGTTTC
1 TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTTC
* * * * * * * * *
12814802 AGTTTAT-TCGATGATGTACTGTGTGTGCCAATATAAATACTTCGATTTAT-TCGATGAGGC-GT
66 GGTTTATCT-GATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGATGCACT
* * * * * ** * ** * * **
12814864 T-GTGTGTCAGTATAGATTCTT-TCGTTGATTCGATGACACACTGTGTGTATCATTGTAGATAAT
129 TATTGTGCCAGTATAGATGCTTCT-GTTTATCCGATGATGCACTATGTGTGCCAGTATAGATGTT
* *
12814927 TCGGTTTA-CTCGATGATGCATT
193 TCGATTTATC-CGATGATGCACT
* * ***
12814949 ATGTTTTCCAGTATAGATGCTTCAATTTAC-CGGATGATGCACTGTGTGTGCCAGTATAGATGCT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACTC-GATGATGCACTGTGTGTGCCAGTATAGATGCT
** * * *
12815013 TCTATTTA-CTCGATAATACACTATGTGTGCCAGTATAGATGCTTC-AGTTTA-CTCGACGATGC
64 TCGGTTTATCT-GATGATGCACTATGTGTGCCAGTATAGATGCTTCGA-TTTATCT-GAAGATGC
* * ** * * *
12815075 ACTGTGTT-TGCCAGTATAGATACTTCAATTTATCCGAAT-ATGCACTTTTTGTGCCACTATAGA
126 ACT-TATTGTGCCAGTATAGATGCTTCTGTTTATCCG-ATGATGCACTATGTGTGCCAGTATAGA
* ** * *
12815138 TGCTTCTTTTTATCCGATGAAGCACAA
189 TGTTTCGATTTATCCGATGATGCAC-T
* * *
12815165 TGTGTGCCAGTATAGATG-TTTCAGTTTATTCGATAATGCA-T-TGTGTGCCAGTATAGATGCTT
1 TGTGTGCCAGTATAGATGCTTT-GGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * ** * * * *
12815227 TGGTTTACCCAATGATGCACTATGTGTGCCAGTATCGATGCTTTGATTTAT-TCGATGGTGCAC-
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGATGCACT
* * * ** *
12815290 -AGTGTGTGCCAATATAGATGCTTC-GATTTATTCGATGAGGTGCTATGTGTGCTAGTATAGATG
129 TA-T-TGTGCCAGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTGTGCCAGTATAGATG
* ** *
12815353 TTT-TAGTTTATTGGATGACGCACT
191 TTTCGA-TTTATCCGATGATGCACT
* * * * * * *
12815377 GTGTGTGCCAATGTAGATGCTTCGATTTACTCGAGGATGCACTCTGTGTACCAGTATAGATGCTT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * * * *
12815442 CGATTTATTCT-ATTATGCACTGTGTGTACCAGTATAGATACTTCGATTTATCT-AATGATGCA-
65 CGGTTTA-TCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAA-GATGCAC
* * * * * * * * *
12815504 TTATGTGTGCTAGTATAGATGTTTCGGTGTATCGGATGATGTACCATGTGTGCCAGTATAAATGC
128 TTAT-TGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGATGT
12815569 TTCGATTTATCCGATGATGCACT
192 TTCGATTTATCCGATGATGCACT
* * *
12815592 GTGTGGGTGCGAGTATAGATGCTTCGGTTTATTCGATGATGCACTGTGTGGCTGCCAGTATAGAT
1 -TGT--GTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGT-G-TGCCAGTATAGAT
* * * * * *** * *
12815657 GCTTCGGTTTATCCGATGA-GAAACTGTGTAGGTGCTAGTATAAATGCTTCGGGATATCCGATGA
61 GCTTCGGTTTATCTGATGATG-CACTATGT--GTGCCAGTATAGATGCTTCGATTTATCTGAAGA
* * * * * * * ** * *
12815721 TGCACTGTA-TGTGTCAGTATAG-TCTCTTCGGTATATTCGTTGATGCATTATCCGTGTCAATAT
123 TGCACT-TATTGTGCCAGTATAGAT-GCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTAT
* * *
12815784 AAATGTTTTGATTTA-CTCGATGATGCAGTT
186 AGATGTTTCGATTTATC-CGATGATGCA-CT
* * * * * **
12815814 TTTGTGCCAGTATAGATGCTTT-GTTTACGCGAAGATGCACTGTATATGTTAGTATAGATGCTTC
1 TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTTC
* * * * * *
12815878 TGTTTA-CTCGATGATGCACTATGTGTGTCAATATAGATGCTTAG-TTTATCCGATGATGCAC-T
66 GGTTTATCT-GATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAAGATGCACTT
* * * * * *
12815940 -GTGTGTCCGAGTATAGATGTTTC-GATTTATCCGATGATGTACTACGTGTGCCATTATAGTTGT
130 ATTGTG-CC-AGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTGTGCCAGTATAGATGT
*
12816003 TTCGATTTATCCGATGTTGCACT
192 TTCGATTTATCCGATGATGCACT
* * ** * * * * * ** *
12816026 GTGTGTGCCAGTATATATGCTTTGGTTTATTTTATTATGCATTTTATATATCAGTATAAATGCTT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * * * * * * * *
12816091 CTGTTTATCCGATAATG-AATCGTGTGTGCCAGTATAGATGTTTCGATGTAT-TCGATGATGTAC
65 CGGTTTATCTGATGATGCACT-ATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGATGCAC
* * *
12816154 -TA-TGCTTGTCAGTATAGATGCTTCAGTTTATCC---GATGCAC--TGTGTGCTAGTATAGATG
128 TTATTG--TGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGATG
* * *
12816212 CTTC-ATTTTATCCGGTGATACACTT
191 TTTCGA-TTTATCCGATGATGCAC-T
* * ***
12816237 TGTGTGTCAGTATAAATGCTTCAATTTA-TCCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
1 TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCTT
* * * * * * **
12816301 TGATTTACCCGATGATGCAC--TGTGTGCCAGTATAGATGCTTCGCTTTAT-TCGATGATTAAC-
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGATGCACT
* * * * * * *
12816362 T-GTGTGCCAGTATAAATGCTT-TAGTTTATCCAATGATGTACTGTGTGTGTCAGTATAAATGTT
129 TATTGTGCCAGTATAGATGCTTCT-GTTTATCCGATGATGCACTATGTGTGCCAGTATAGATGTT
* * *
12816425 TCTG-TGTATTCGATGATGCACGA
193 TC-GATTTATCCGATGATGCAC-T
* * * * *** * * * **
12816448 TATATGCTAGTATATATGCTTCAATTTA-TCCGATAATACACTATGTGTGCCAGTATAGATTTTT
1 TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCTT
** * * * * ** * * * * * *
12816512 TAGTCTATCCGATAATG--CTTTGTGTGTGAGCATAGATGCTTCGGTCTATC-CAATGATGTAAT
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAA-GATGCACT
* * * * * * *
12816574 GT-GTGTGCCAGTGTAGATGCTTC-GATTTATTCAATGATGCATTGTGTGTGCAAGTAT---T-T
129 -TATTGTGCCAGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTGTGCCAGTATAGATGT
* *
12816633 TT-G-TGTATCCGATGATGAACT
192 TTCGATTTATCCGATGATGCACT
* * * ** ** * * *
12816654 GTGTGTGCCAATGTATATTTTTTTTTTGTA-TCCGATAATGCACTATGTGTGTCAGTATAGAAT-
1 -TGTGTGCCAGTATAGATGCTTTGGTT-TACT-CGATGATGCACTGTGTGTGCCAGTATAG-ATG
*** ** * * * * * *
12816717 CTTTAATTTGCCCGATGATGCACTCTGTGTGCCTA-TATAGATGCTTTGGTTTATCCGATGAT-C
62 CTTCGGTTTATCTGATGATGCACTATGTGTGCC-AGTATAGATGCTTCGATTTATCTGAAGATGC
* * ** * * * *
12816780 TACTGT-GTGTGCCAATATAGATGCTTGGGTTTACCCGATGATGTAC--TGTATGCCAATATAGA
126 -ACT-TATTGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGA
*
12816842 TGCTTCGATTTA-CCTGATGATGCACT
189 TGTTTCGATTTATCC-GATGATGCACT
** ** * ** * **
12816868 TGACT-TGTTAGTATAGATGCTTCAGTTTATTTTATGATGCACTGTGTGTACTTGTATAGATGCT
1 TG--TGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCT
* ** * * * *
12816932 TCGATTTAT-TCGATGGGGCACTGTGTGTGCAAGTATAAATGCTTCGATTTAT-TCGATGATGCA
64 TCGGTTTATCT-GATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGATGCA
* * * * * * *
12816995 -TTTTGTGTGCTAGTATAGATCCTTC-GATTTATTCGATGATGCACTGTGCGCT-CCAATATAGA
127 CTTAT-TGTGCCAGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTG-TGCCAGTATAGA
* *
12817057 TGCTTTTG-TCTA-CTCGATGATGCAC-
189 TG-TTTCGATTTATC-CGATGATGCACT
** * * * * * *
12817082 TGCTGGTGCCAGTATAGATG-TTTCAATTTACCCAATGATGGACTATGTGTGTCAGTATAGATGT
1 TG-T-GTGCCAGTATAGATGCTTT-GGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGC
* * * * * * * * *
12817146 TTCAGTGTATCCGATGATGCACTGTGTGTGCCAGTATACATGTTTCGGTGTATCCGATA-ATGCA
63 TTCGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGA-AGATGCA
** * * *
12817210 C-TATGTGTTTCAATATAGATGCTTCAGTTTATCCGATGATGCGCTATGTGTGCCAGTATAGATG
127 CTTAT-TGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGATG
* * *
12817274 TTTCAATTTATCCAATGATGTACT
191 TTTCGATTTATCCGATGATGCACT
* * * ** * * *
12817298 CTATGTGTCAGTATAGATGATTCAGTTTA-TCCAATGATGCACTGTATGTGCTAGTATAGATGCT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCT
* * * * * * * * *
12817362 TCGGTTTATTTAATGATGCACTGTATGTACCAATATAGATGCTT-TAGTTTATCCGATGATGCAC
64 TCGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGA-TTTATCTGAAGATGCAC
** * * * * * *
12817426 TGTA-TGTTTCAGTTTAGATGCTT-TAGTTTATCCAATGATGCATTGTATGTTCCAGTATAGATG
128 T-TATTGTGCCAGTATAGATGCTTCT-GTTTATCCGATGATGCACTATGTGTGCCAGTATAGATG
* * *
12817489 -TTCGGTGTATCCAATGATGCAC-
191 TTTCGATTTATCCGATGATGCACT
* * * * ** * * *
12817511 TGTGTGCCGGTATAGATGATTCGATTTA-TCCGATGATATACTGTGTGT--CAATAGAGATTCTT
1 TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCTT
** * * * * * * * *
12817573 TAGTTTATCCGATGTTGCA--GTGTGTGCCATTATAGATGCTTCGGTTTATC-CAATGTTGTA-T
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAA-GATGCACT
* ** * * *** * *
12817634 T-TTGTGTCAGGGTAGAT-TTTTTGATTTATTTAATGATACACTGTGTGTGCCAG--T--AT-TT
129 TATTGTGCCAGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTGTGCCAGTATAGATGTT
* * *
12817692 TCGATGTA-CCTAATGATACACT
193 TCGATTTATCC-GATGATGCACT
* * * * * * *
12817714 ATGTGTGCCAGTGTAGATG-TTTCGGTGTA-TCTGATGATGCAGTATGTGTGTCAGTATTGATTC
1 -TGTGTGCCAGTATAGATGCTTT-GGTTTACTC-GATGATGCACTGTGTGTGCCAGTATAGATGC
* * ** *
12817777 TTCTGTTTATCTGATGATGCACTGTGTGTGATAGTATAGATGCTTC-AGTTTATCTGATGATGCA
63 TTCGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGA-TTTATCTGAAGATGCA
* * * * *
12817841 C-TATGTGTGCTAGTATAGATG-TTTTAGTTTATTCGATGATGCACTATGTGTGCCAATGTAGAT
127 CTTAT-TGTGCCAGTATAGATGCTTCT-GTTTATCCGATGATGCACTATGTGTGCCAGTATAGAT
* *
12817904 GTTTCGGTTTATTCGATGATGCACT
190 GTTTCGATTTATCCGATGATGCACT
* *
12817929 GTGTGTGCCAGTATAGATGCTTTGGTTTA-TACGATGATGCACAGTGTGTGCCAGTATAAATGCT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCT
* * * * ** * * *
12817993 TTGGTTTACCCGAT-AGTGCACTTTGCT-TTTCAGTAAAGATTCTTC-AGTTTATCCT-ATGATG
64 TCGGTTTATCTGATGA-TGCACTATG-TGTGCCAGTATAGATGCTTCGA-TTTAT-CTGAAGATG
* * * * * * * * *
12818054 CA-TT-GTGTGCTAGTATAGATGTTTCGGTTTTTTCAATGATGCATTGTGTGTGCCAGTATAGAT
125 CACTTATTGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGAT
* * *
12818117 -TCTTCGGTTTATTCGTTGATGCACT
190 GT-TTCGATTTATCCGATGATGCACT
* * * * * * * *
12818142 GTGTGTGCTAGTATTGATGCTTCGATTTA-TCCAATGATGCA--ATGTGTACCAGTATAAATGCT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACT-CGATGATGCACTGTGTGTGCCAGTATAGATGCT
* ** * * * * * * * * *
12818204 TCGGTTTACCCAATGATGCACTGTTTATGCCAATATAGATGCTTTGGTATATCCGATGATGCACT
64 TCGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAAGATGCACT
* * * * * * * *
12818269 GTA-TGTGCTAGTATGGTTACTTCGGTATATTCGATGATGC-CT-TGTCCGTGTCAGTATAGATG
129 -TATTGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGT--GTGCCAGTATAGATG
* * *
12818331 CTTCGGTTTATCCCATGATGCACT
191 TTTCGATTTATCCGATGATGCACT
* * * * *
12818355 ATGTGGGTGCTAGTATAGATGCTTTGGTTTA-TCTGATGAGGCACTATGTGAGTGCTAGTATTGA
1 -TGT--GTGCCAGTATAGATGCTTTGGTTTACTC-GATGATGCAC--TGTGTGTGCCAGTATAGA
*** * * * * * * * * * ** *
12818419 TGCTTTTATATATCTGATAATGCACTGTATGTCCCAGTATAGTTACTTCGGTATAT-TCGGTGAC
60 TGCTTCGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGAT
* ** * * * *
12818483 GCA-TTATCCGTGTTAGTATAGATTCTTCGGTTTACCCGATGATGCAC--TGTGTTCCAGTATAG
124 GCACTTAT-TGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAG
* *
12818545 ATGCTTAGATTTATCCGATGATGCACTT
188 ATGTTTCGATTTATCCGATGATGCAC-T
* ** * **
12818573 TGTATGTTAATATAGATGCTTCAGTTTA-TCTGATGATGCACTGTGTGTGCCAGTATAGATGCTT
1 TGTGTGCCAGTATAGATGCTTTGGTTTACTC-GATGATGCACTGTGTGTGCCAGTATAGATGCTT
** * * * *
12818637 CTATTTATCCGATGATGCACTGTGTGTGCCAGTATAAATGCTTCGATTTAT-TCGATGATGCACT
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCT-GAAGATGCACT
* * * * * * *
12818701 GT-GTGTACCAGTTTAGACGCTTC-GATTTATCCGATAATGCATTGTGTGTGCCAGTATAGATGT
129 -TATTGTGCCAGTATAGATGCTTCTG-TTTATCCGATGATGCACTATGTGTGCCAGTATAGATGT
* * *
12818764 TTCGGTGTA-CCTAATGATGCACT
192 TTCGATTTATCC-GATGATGCACT
* * ** * * *
12818787 ATGTGTGTC-GTATTGATGCTTTAATTTATTCGATGATGCACTGTGTGTGCCAATATAGATGTTT
1 -TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTT
** * * * *
12818851 CAATTTATCCGGTGATGCATTATGTGTGTCAGTATA
65 CGGTTTATCTGATGATGCACTATGTGTGCCAGTATA
12818887 AAAAATACTA
Statistics
Matches: 3681, Mismatches: 859, Indels: 491
0.73 0.17 0.10
Matches are distributed among these distances:
201 2 0.00
202 19 0.01
203 3 0.00
204 35 0.01
205 3 0.00
206 86 0.02
207 34 0.01
208 153 0.04
209 18 0.00
210 323 0.09
211 284 0.08
212 266 0.07
213 914 0.25
214 256 0.07
215 880 0.24
216 64 0.02
217 80 0.02
218 25 0.01
219 140 0.04
220 3 0.00
221 88 0.02
222 3 0.00
223 2 0.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (214 bp):
TGTGTGCCAGTATAGATGCTTTGGTTTACTCGATGATGCACTGTGTGTGCCAGTATAGATGCTTC
GGTTTATCTGATGATGCACTATGTGTGCCAGTATAGATGCTTCGATTTATCTGAAGATGCACTTA
TTGTGCCAGTATAGATGCTTCTGTTTATCCGATGATGCACTATGTGTGCCAGTATAGATGTTTCG
ATTTATCCGATGATGCACT
Found at i:12818877 original size:43 final size:43
Alignment explanation
Indices: 12813887--12818886 Score: 2730
Period size: 43 Copynumber: 117.3 Consensus size: 43
12813877 GATGATAAAC
* * ** *
12813887 TGTGTGCCAGTATAGATGCCTCGATTTA-CCTGATGATAAACTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCC-GATGATGCACTG
* * * ** * *
12813930 TGTGTGGCAGTATAGATACCTCGGTTTAACCGATGATACACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12813973 TGTGAGCCAATAT-GAATGCTTCAGTTTA-CTCGATGTTGCATTG
1 TGTGTGCCAGTATAG-ATGCTTCAATTTATC-CGATGATGCACTG
* * * * * * *
12814016 TATGTGCCAGTA-AGGATTCCTCAGTTTA-CCAAATAATGCATTG
1 TGTGTGCCAGTATA-GATGCTTCAATTTATCC-GATGATGCACTG
* * ** * * *
12814059 TGTGTGCCAGAATAGATGCCTCGGTTTATACGATGAGGCATTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *** * **
12814102 TGTGTGCTAGTATAGATGCTTTTGTTTGTTAGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** ** * *
12814145 TGTGTGCTAGTATAGATGCTTCGGTTTATTAGATGAAGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * *
12814188 TGTGTGCTAGTATAGATGCTTCGATTTAT--TA-GATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** * *
12814228 TGTGTGCCAGTATAAATCCTTCAATTTTTTAGATAATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** *
12814271 TGTGTGCTC-GTATAGATGCATT-AATTTATGAGATGTTGCACCT-
1 TGTGTGC-CAGTATAGATGC-TTCAATTTATCCGATGATGCA-CTG
* * *
12814314 TGTGTGACAGTATAGATGCTTCGATTTATCCGATAATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * * *
12814357 TGTTTGCCTGTATAGATGCTTCGGTTCACCCGACGATGCAC--
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * *
12814398 TGTGTGCTAGTATAGATGCTTCGATTTACCCGATAATACACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * * *
12814441 TGTGTGCCAGTACAAATGCTTTGATTTACCCGATAATACA-T-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *
12814482 TATGTGTCAGTATAGATGCTTCGATTTA-CCTGATAAT-CACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCC-GATGATGCACTG
** **
12814524 TGTGTGCCAGTATAGATGCTTTGATTTA-CTCGACAATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * * * ** * * *
12814567 TGTTTGCTACTATAGATGTTTCGGTTTATCTGATGATACACTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** ** * * *
12814610 TGTGTGTTAGTATAGATGCTTTGATTTATCTGAAGAAGCACT-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** **
12814652 TATTGTGCCACTATAGATGCTTCTGTTTATCCGATGATGCACAA
1 T-GTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12814696 TGTGTGCCAGTATAAATGTTTCCATTTACCCGATAATGCA-T-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *** *
12814737 TATGTGCCAGTATAGATGCTTTGGTTTA-CTCGATGATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * * *
12814780 TGTGTGCCAGTATAGATGTTTCAGTTTATTCGATGATGTACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * * *
12814823 TGTGTGCCAATATAAATACTTCGATTTATTCGATGAGGC-GT-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * **
12814864 TGTGTGTCAGTATAGATTCTTTC-GTTGATTCGATGACACACTG
1 TGTGTGCCAGTATAGATGC-TTCAATTTATCCGATGATGCACTG
** * * ** ** * *
12814907 TGTGTATCATTGTAGATAATTCGGTTTA-CTCGATGATGCATTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* *
12814950 TGTTTTCCAGTATAGATGCTTCAATTTA-CCGGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCC-GATGATGCACTG
* * * *
12814993 TGTGTGCCAGTATAGATGCTTCTATTTA-CTCGATAATACACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* *
12815036 TGTGTGCCAGTATAGATGCTTCAGTTTA-CTCGACGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * *
12815079 TGTTTGCCAGTATAGATACTTCAATTTATCCGAAT-ATGCACTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCG-ATGATGCACTG
* * ** * **
12815122 TTTGTGCCACTATAGATGCTTCTTTTTATCCGATGAAGCACAA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *
12815165 TGTGTGCCAGTATAGATGTTTCAGTTTATTCGATAATGCA-T-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
*** * * *
12815206 TGTGTGCCAGTATAGATGCTTTGGTTTACCCAATGATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * * *
12815249 TGTGTGCCAGTATCGATGCTTTGATTTATTCGATGGTGCACAG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * ** *
12815292 TGTGTGCCAATATAGATGCTTCGATTTATTCGATGAGGTGCTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * ** *
12815335 TGTGTGCTAGTATAGATGTTTTAGTTTATTGGATGACGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12815378 TGTGTGCCAATGTAGATGCTTCGATTTA-CTCGAGGATGCACTC
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * * * *
12815421 TGTGTACCAGTATAGATGCTTCGATTTATTCTATTATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** * *
12815464 TGTGTACCAGTATAGATACTTCGATTTATCTAATGATGCATTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * * * **
12815507 TGTGTGCTAGTATAGATGTTTCGGTGTATCGGATGATGTACCA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *
12815550 TGTGTGCCAGTATAAATGCTTCGATTTATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** *
12815593 TGTGGGTGCGAGTATAGATGCTTCGGTTTATTCGATGATGCACTG
1 TGT--GTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** *
12815638 TGTGGCTGCCAGTATAGATGCTTCGGTTTATCCGATGA-GAAACTG
1 TGT-G-TGCCAGTATAGATGCTTCAATTTATCCGATGATG-CACTG
* * ****
12815683 TGTAGGTGCTAGTATAAATGCTTCGGGATATCCGATGATGCACTG
1 TGT--GTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** * * * * *
12815728 TATGTGTCAGTATAG-TCTCTTCGGTATATTCGTTGATGCATTA
1 TGTGTGCCAGTATAGAT-GCTTCAATTTATCCGATGATGCACTG
** * * * * ** * *
12815771 TCCGTGTCAATATAAATGTTTTGATTTA-CTCGATGATGCAGTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* ** *
12815814 TTTGTGCCAGTATAGATGCTT-TGTTTA-CGCGAAGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * ** ** *
12815856 TATATGTTAGTATAGATGCTTCTGTTTA-CTCGATGATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * *
12815899 TGTGTGTCAATATAGATGCTT-AGTTTATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *
12815941 TGTGT-CCGAGTATAGATGTTTCGATTTATCCGATGATGTACTA
1 TGTGTGCC-AGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * *
12815984 CGTGTGCCATTATAGTTGTTTCGATTTATCCGATGTTGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *** *** * * *
12816027 TGTGTGCCAGTATATATGCTTTGGTTTATTTTATTATGCATTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * ** * *
12816070 TATATATCAGTATAAATGCTTCTGTTTATCCGATAATG-AATCG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACT-G
* * * * * *
12816113 TGTGTGCCAGTATAGATGTTTCGATGTATTCGATGATGTACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *
12816156 TGCT-TGTCAGTATAGATGCTTCAGTTTATCC---GATGCAC--
1 TG-TGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12816194 TGTGTGCTAGTATAGATGCTTCATTTTATCCGGTGATACACTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *
12816237 TGTGTGTCAGTATAAATGCTTCAATTTATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** *
12816280 TGTGTGCCAGTATAGATGCTTTGATTTACCCGATGATGCAC--
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** * **
12816321 TGTGTGCCAGTATAGATGCTTCGCTTTATTCGATGATTAAC--
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12816362 TGTGTGCCAGTATAAATGCTTTAGTTTATCCAATGATGTACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** * *
12816405 TGTGTGTCAGTATAAATGTTTCTGTGTATTCGATGATGCAC-G
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * * *
12816447 ATATATGCTAGTATATATGCTTCAATTTATCCGATAATACACTA
1 -TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** * * * * **
12816491 TGTGTGCCAGTATAGATTTTTTAGTCTATCCGATAATGCTTTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * * * *
12816534 TGTGTG--AGCATAGATGCTTCGGTCTATCCAATGATGTAATG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12816575 TGTGTGCCAGTGTAGATGCTTCGATTTATTCAATGATGCATTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * *
12816618 TGTGTGCAAGTAT---T--TT-TGTGTATCCGATGATGAACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** *** * *
12816655 TGTGTGCCAATGTATATTTTTTTTTTGTATCCGATAATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATT-TATCCGATGATGCACTG
* * ** *
12816699 TGTGTGTCAGTATAGAAT-CTTTAATTTGCCCGATGATGCACTC
1 TGTGTGCCAGTATAG-ATGCTTCAATTTATCCGATGATGCACTG
***
12816742 TGTGTGCCTA-TATAGATGCTTTGGTTTATCCGATGAT-CTACTG
1 TGTGTGCC-AGTATAGATGCTTCAATTTATCCGATGATGC-ACTG
* *** * *
12816785 TGTGTGCCAATATAGATGCTTGGGTTTACCCGATGATGTAC--
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * *
12816826 TGTATGCCAATATAGATGCTTCGATTTA-CCTGATGATGCACT-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCC-GATGATGCACTG
** * ***
12816868 TGACT-TGTTAGTATAGATGCTTCAGTTTATTTTATGATGCACTG
1 TG--TGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * * **
12816912 TGTGTACTTGTATAGATGCTTCGATTTATTCGATGGGGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * *
12816955 TGTGTGCAAGTATAAATGCTTCGATTTATTCGATGATGCATTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *
12816998 TGTGTGCTAGTATAGATCCTTCGATTTATTCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * *** *
12817041 TGCGCT-CCAATATAGATGCTTTTGTCTA-CTCGATGATGCACTG
1 TGTG-TGCCAGTATAGATGCTTCAATTTATC-CGATGATGCACTG
* * * * *
12817084 CTG-GTGCCAGTATAGATGTTTCAATTTACCCAATGATGGACTA
1 -TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *
12817127 TGTGTGTCAGTATAGATGTTTCAGTGTATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * * *
12817170 TGTGTGCCAGTATACATGTTTCGGTGTATCCGATAATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** * * * *
12817213 TGTGTTTCAATATAGATGCTTCAGTTTATCCGATGATGCGCTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *
12817256 TGTGTGCCAGTATAGATGTTTCAATTTATCCAATGATGTACTC
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12817299 TATGTGTCAGTATAGATGATTCAGTTTATCCAATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** ***
12817342 TATGTGCTAGTATAGATGCTTCGGTTTATTTAATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12817385 TATGTACCAATATAGATGCTTTAGTTTATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * * * * *
12817428 TATGTTTCAGTTTAGATGCTTTAGTTTATCCAATGATGCATTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * *
12817471 TATGTTCCAGTATAGATG-TTCGGTGTATCCAATGATGCAC--
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * **
12817511 TGTGTGCCGGTATAGATGATTCGATTTATCCGATGATATACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * *
12817554 TGTGT--CAATAGAGATTCTTTAGTTTATCCGATGTTGCA--G
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * * *
12817593 TGTGTGCCATTATAGATGCTTCGGTTTATCCAATGTTGTA-T-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** ** ** *** *
12817634 TTTGTGTCAGGGTAGATTTTTTGATTTATTTAATGATACACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12817677 TGTGTGCCAGTAT---T--TTCGATGTA-CCTAATGATACACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCC-GATGATGCACTG
* * ** * * * *
12817715 TGTGTGCCAGTGTAGATGTTTCGGTGTATCTGATGATGCAGTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** *
12817758 TGTGTGTCAGTATTGATTCTTCTGTTTATCTGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** * * *
12817801 TGTGTGATAGTATAGATGCTTCAGTTTATCTGATGATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * *
12817844 TGTGTGCTAGTATAGATGTTTTAGTTTATTCGATGATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * ** *
12817887 TGTGTGCCAATGTAGATGTTTCGGTTTATTCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
*** * *
12817930 TGTGTGCCAGTATAGATGCTTTGGTTTATACGATGATGCACAG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* *** * *
12817973 TGTGTGCCAGTATAAATGCTTTGGTTTACCCGAT-AGTGCACTT
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGA-TGCACTG
** * * * *
12818016 TGCT-TTTCAGTAAAGATTCTTCAGTTTATCCTATGATGCA-T-
1 TG-TGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * * * *
12818057 TGTGTGCTAGTATAGATGTTTCGGTTTTTTCAATGATGCATTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * *
12818100 TGTGTGCCAGTATAGATTCTTCGGTTTATTCGTTGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12818143 TGTGTGCTAGTATTGATGCTTCGATTTATCCAATGATGCA--A
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * ** * *
12818184 TGTGTACCAGTATAAATGCTTCGGTTTACCCAATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * *** *
12818227 TTTATGCCAATATAGATGCTTTGGTATATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * ** * *
12818270 TATGTGCTAGTATGGTTACTTCGGTATATTCGATGATGC-CT-
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** *
12818311 TGTCCGTGTCAGTATAGATGCTTCGGTTTATCCCATGATGCACTATG
1 TGT--GTGCCAGTATAGATGCTTCAATTTATCCGATGATGCAC--TG
* * *** * *
12818358 TGGGTGCTAGTATAGATGCTTTGGTTTATCTGATGAGGCACTATG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCAC--TG
* * * ** * * *
12818403 TGAGTGCTAGTATTGATGCTTTTATATATCTGATAATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * ** * * * * * *
12818446 TATGTCCCAGTATAGTTACTTCGGTATATTCGGTGACGCATTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
** ** * ** *
12818489 TCCGTGTTAGTATAGATTCTTCGGTTTACCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
*
12818532 TGT-T-CCAGTATAGATGCTT-AGATTTATCCGATGATGCACTT
1 TGTGTGCCAGTATAGATGCTTCA-ATTTATCCGATGATGCACTG
* ** * * *
12818573 TGTATGTTAATATAGATGCTTCAGTTTATCTGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
*
12818616 TGTGTGCCAGTATAGATGCTTCTATTTATCCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * *
12818659 TGTGTGCCAGTATAAATGCTTCGATTTATTCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * * *
12818702 TGTGTACCAGTTTAGACGCTTCGATTTATCCGATAATGCATTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* ** * * *
12818745 TGTGTGCCAGTATAGATGTTTCGGTGTA-CCTAATGATGCACTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCC-GATGATGCACTG
* * * *
12818788 TGTGTGTC-GTATTGATGCTTTAATTTATTCGATGATGCACTG
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
* * * * *
12818830 TGTGTGCCAATATAGATGTTTCAATTTATCCGGTGATGCATTA
1 TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
*
12818873 TGTGTGTCAGTATA
1 TGTGTGCCAGTATA
12818887 AAAAATACTA
Statistics
Matches: 3892, Mismatches: 929, Indels: 272
0.76 0.18 0.05
Matches are distributed among these distances:
37 25 0.01
38 58 0.01
39 6 0.00
40 63 0.02
41 483 0.12
42 194 0.05
43 2808 0.72
44 67 0.02
45 182 0.05
46 4 0.00
47 2 0.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (43 bp):
TGTGTGCCAGTATAGATGCTTCAATTTATCCGATGATGCACTG
Found at i:12819376 original size:10 final size:10
Alignment explanation
Indices: 12819361--12819400 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 10
12819351 TTAATTTTGT
12819361 TTTTTAAATA
1 TTTTTAAATA
12819371 TTTTT--ATA
1 TTTTTAAATA
12819379 TTTTTAAATTA
1 TTTTTAAA-TA
12819390 TTTTTAAATA
1 TTTTTAAATA
12819400 T
1 T
12819401 GATATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.30
10 9 0.33
11 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:12819394 original size:30 final size:29
Alignment explanation
Indices: 12819341--12819400 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
12819331 CATTTTATTT
* *
12819341 TTTTTATTTTTTAATTTTGTTTTTTAAATA
1 TTTTTATTTTTTAATATT-ATTTTTAAATA
12819371 TTTTTATATTTTTAA-ATTATTTTTAAATA
1 TTTTTAT-TTTTTAATATTATTTTTAAATA
12819400 T
1 T
12819401 GATATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 9 0.33
31 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTTATTTTTTAATATTATTTTTAAATA
Found at i:12819816 original size:22 final size:22
Alignment explanation
Indices: 12819766--12819818 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
12819756 AATTAATAAT
* *
12819766 CAAATTTAATTCAAAAAAATTA
1 CAAATTAAATTCAAAAAAAATA
12819788 -AAGATTAAATT-AATAAAAAATA
1 CAA-ATTAAATTCAA-AAAAAATA
12819810 CAAATTAAA
1 CAAATTAAA
12819819 AGTTAGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (22 bp):
CAAATTAAATTCAAAAAAAATA
Found at i:12826323 original size:9 final size:9
Alignment explanation
Indices: 12826308--12826340 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
12826298 TTGAATCTCT
12826308 CTTCTTCTG
1 CTTCTTCTG
*
12826317 TTTCTTCTG
1 CTTCTTCTG
12826326 CTTCTTCTG
1 CTTCTTCTG
12826335 CTTCTT
1 CTTCTT
12826341 TTTTTTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.09, T:0.61
Consensus pattern (9 bp):
CTTCTTCTG
Found at i:12836170 original size:21 final size:22
Alignment explanation
Indices: 12836144--12836337 Score: 151
Period size: 23 Copynumber: 8.4 Consensus size: 22
12836134 ACGGAACAAG
* *
12836144 CAGAGAGTAC-CAAAGTACTAA
1 CAGAGAGCACACAAAGTGCTAA
*
12836165 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT----AA
*
12836190 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCT-AA
* *
12836213 CAGAGAGTACACAAAGTACTAA
1 CAGAGAGCACACAAAGTGCTAA
12836235 TCAGAGAGCACACAAAGTGCTAA
1 -CAGAGAGCACACAAAGTGCTAA
* *
12836258 TCAGAAAGCACACACAGTGCTAATAA
1 -CAGAGAGCACACAAAGTGC---TAA
* *
12836284 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCT-AA
*
12836307 CAGAGAGCACACACAGTGCTAA
1 CAGAGAGCACACAAAGTGCTAA
12836329 TCAGAGAGC
1 -CAGAGAGC
12836338 GCGCTAGTGT
Statistics
Matches: 139, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
21 15 0.11
22 6 0.04
23 82 0.59
25 26 0.19
26 10 0.07
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGAGAGCACACAAAGTGCTAA
Found at i:12836214 original size:23 final size:23
Alignment explanation
Indices: 12836188--12836337 Score: 185
Period size: 23 Copynumber: 6.4 Consensus size: 23
12836178 AGTGCTGGGC
12836188 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
12836211 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
12836234 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
12836257 ATCAGAAAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
12836281 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
12836305 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
12836328 ATCAGAGAGC
1 AACAGAGAGC
12836338 GCGCTAGTGT
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
22 3 0.03
23 87 0.79
24 2 0.02
25 15 0.14
26 3 0.03
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:12836288 original size:71 final size:68
Alignment explanation
Indices: 12836144--12836333 Score: 210
Period size: 71 Copynumber: 2.7 Consensus size: 68
12836134 ACGGAACAAG
* *
12836144 CAGAGAGTAC-CAAAGTACTAACAGAGAGCACA-TAAGTGCTGGGCAA-CAGAGAGCACACACAG
1 CAGAGAGTACACAAAGTACTAACAGAGAGCACACAAAGTGCT----AATCAGAAAGCACACACAG
12836206 TGCTAAA
62 TGCTAAA
12836213 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAAAGCACACACAGTGC
1 CAGAGAGTACACAAAGTACTAA-CAGAGAGCACACAAAGTGCTAATCAGAAAGCACACACAGTGC
12836278 TAATAA
65 T-A-AA
* * *
12836284 CAGAGAG--CACGAGACGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
1 CAGAGAGTACAC-A-AAGTACT-AACAGAGAGCACACAAAGTGCTAATCAGA
12836334 GAGCGCGCTA
Statistics
Matches: 107, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
68 2 0.02
69 32 0.30
70 13 0.12
71 51 0.48
72 9 0.08
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (68 bp):
CAGAGAGTACACAAAGTACTAACAGAGAGCACACAAAGTGCTAATCAGAAAGCACACACAGTGCT
AAA
Found at i:12838651 original size:10 final size:11
Alignment explanation
Indices: 12838604--12838654 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
12838594 ATTTAAGATA
*
12838604 TTATTTTTTAT
1 TTATTTTGTAT
12838615 TTAATTTTGTAT
1 TT-ATTTTGTAT
12838627 TTATTTATGTTTAT
1 TTATTT-TG--TAT
12838641 TT-TTTTGTAT
1 TTATTTTGTAT
12838651 TTAT
1 TTAT
12838655 CTTTTAGAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 14 0.41
13 3 0.09
14 5 0.15
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (11 bp):
TTATTTTGTAT
Found at i:12839459 original size:16 final size:16
Alignment explanation
Indices: 12839438--12839472 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12839428 CTATTTTCTA
12839438 TTTCTTTTAATTTTGT
1 TTTCTTTTAATTTTGT
*
12839454 TTTCTTTTATTTTTGT
1 TTTCTTTTAATTTTGT
12839470 TTT
1 TTT
12839473 TCCCCAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTCTTTTAATTTTGT
Found at i:12870820 original size:25 final size:26
Alignment explanation
Indices: 12870789--12870844 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
12870779 ACAAAAAAAC
*
12870789 AACATAATAAC-TACACTAAATTAAA
1 AACATAATAACAAACACTAAATTAAA
* *
12870814 AACATAATAACAAACAGTACATTAAA
1 AACATAATAACAAACACTAAATTAAA
12870840 AACAT
1 AACAT
12870845 CAATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.21
Consensus pattern (26 bp):
AACATAATAACAAACACTAAATTAAA
Found at i:12872037 original size:23 final size:23
Alignment explanation
Indices: 12871981--12872041 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
12871971 AACTATTCTC
*
12871981 ATATTTATTAAATTTTAAAATCTT
1 ATATTAATTAAATTTT-AAATCTT
12872005 ATATTAATTAAATTTT-AATCGTT
1 ATATTAATTAAATTTTAAATC-TT
*
12872028 ATATTCATTAAATT
1 ATATTAATTAAATT
12872042 AAATTATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 4 0.12
23 15 0.44
24 15 0.44
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTAATTAAATTTTAAATCTT
Found at i:12872809 original size:2 final size:2
Alignment explanation
Indices: 12872802--12872835 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12872792 ATTAATATTA
12872802 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
12872836 TAAATTCACA
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:12877731 original size:19 final size:19
Alignment explanation
Indices: 12877707--12877747 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12877697 AAATATTTTG
*
12877707 AAATTTAAA-GATCAATTTA
1 AAATTTAAATCAT-AATTTA
12877726 AAATTTAAATCATAATTTA
1 AAATTTAAATCATAATTTA
12877745 AAA
1 AAA
12877748 ATATATAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTTAAATCATAATTTA
Found at i:12886748 original size:2 final size:2
Alignment explanation
Indices: 12886743--12886774 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12886733 GTGTGTGTGT
*
12886743 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12886775 TTGAAGGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12903729 original size:30 final size:30
Alignment explanation
Indices: 12903693--12903757 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
12903683 ACTTATTTTA
*
12903693 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTACTATTTTAGAGGTAT
*
12903723 TTGTTAATTTTGTTACTATTTTATAGGTAT
1 TTGTTAATTTTGTTACTATTTTAGAGGTAT
12903753 TTGTT
1 TTGTT
12903758 TATTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.02, G:0.15, T:0.62
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGGTAT
Found at i:12914520 original size:3 final size:3
Alignment explanation
Indices: 12914512--12914552 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12914502 TTAGTCAAGT
12914512 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12914553 GCATTTTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12935647 original size:38 final size:37
Alignment explanation
Indices: 12935605--12935680 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
12935595 CTTATACCCC
12935605 TTATTTAACCAAA-ATATTA-AATATTTGTAACAATTTGT
1 TTATTT-A-CAAATATATTACAATA-TTGTAACAATTTGT
*
12935643 TTATTTACAAATATATTACTAATATTGTAATAATTTGT
1 TTATTTACAAATATATTAC-AATATTGTAACAATTTGT
12935681 GTAATTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
36 4 0.12
37 7 0.21
38 19 0.56
39 4 0.12
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (37 bp):
TTATTTACAAATATATTACAATATTGTAACAATTTGT
Found at i:12955220 original size:6 final size:6
Alignment explanation
Indices: 12955209--12955234 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12955199 TAAAAGAATT
12955209 TGCAAG TGCAAG TGCAAG TGCAAG TG
1 TGCAAG TGCAAG TGCAAG TGCAAG TG
12955235 GGGCGTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (6 bp):
TGCAAG
Found at i:12957211 original size:18 final size:18
Alignment explanation
Indices: 12957188--12957224 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12957178 TATGCACATA
12957188 TTGACTTGCAACATCGAG
1 TTGACTTGCAACATCGAG
12957206 TTGACTTGCAACATCGAG
1 TTGACTTGCAACATCGAG
12957224 T
1 T
12957225 ATCTTAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (18 bp):
TTGACTTGCAACATCGAG
Done.