Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014005.1 Kokia drynarioides strain JFW-HI SEQ_129036, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 328869
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 158 characters in sequence are not A, C, G, or T
Found at i:19640 original size:71 final size:71
Alignment explanation
Indices: 19524--19665 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
19514 CACAAAAAAT
19524 GGTAACTAAGTTGCAGCTTTAAGACATAAGTTTCTTTGGGTTAATGGGTATCAAAAATTCAAGTT
1 GGTAACTAAGTTGCAGCTTTAAGACATAAGTTTCTTTGGGTTAATGGGTATCAAAAATTCAAGTT
19589 TTAAGA
66 TTAAGA
19595 GGTAACTAAGTTGCAGCTTTAAGACATAAGTTTCTTTGGGTTAATGGGTATCAAAAATTCAAGTT
1 GGTAACTAAGTTGCAGCTTTAAGACATAAGTTTCTTTGGGTTAATGGGTATCAAAAATTCAAGTT
19660 TTAAGA
66 TTAAGA
19666 CAGATTTGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (71 bp):
GGTAACTAAGTTGCAGCTTTAAGACATAAGTTTCTTTGGGTTAATGGGTATCAAAAATTCAAGTT
TTAAGA
Found at i:26745 original size:82 final size:81
Alignment explanation
Indices: 26629--26854 Score: 258
Period size: 82 Copynumber: 2.8 Consensus size: 81
26619 AAACGCTGCA
* **
26629 AAAGGT-AAAGCAATAGCGGCGTTTATAGGAAAAACGCCGCTAAAGGTTAGAGCATTAGCGGCGT
1 AAAGGTCAAAGCATTAGCAACGTTTAT-GGAAAAACGCCGCTAAAGGTTA-AGCATTAGCGGCGT
* *
26693 TTATGAGAAAGCACCGCT
64 TTATGAGAAAGCACCACG
* * * * *
26711 AAAGG-CTAGAGCATTAGCAACGTTTATGGGAAAACGCCACTAAAGGTCAAAGCATTAGCGGTGT
1 AAAGGTC-AAAGCATTAGCAACGTTTATGGAAAAACGCCGCTAAAGGT-TAAGCATTAGCGGCGT
*
26775 TTATGAGAAAGCATCACG
64 TTATGAGAAAGCACCACG
* * * *
26793 AAAGGTCAAAGCATTAGCGACATTTATGGAAAAAGCGTCGCTAAAGGTTAAGCAATAGCGGC
1 AAAGGTCAAAGCATTAGCAACGTTTATGGAAAAA-CGCCGCTAAAGGTTAAGCATTAGCGGC
26855 ATTTTCCCTT
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
82 90 0.76
83 29 0.24
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (81 bp):
AAAGGTCAAAGCATTAGCAACGTTTATGGAAAAACGCCGCTAAAGGTTAAGCATTAGCGGCGTTT
ATGAGAAAGCACCACG
Found at i:26858 original size:41 final size:41
Alignment explanation
Indices: 26576--26854 Score: 210
Period size: 41 Copynumber: 6.8 Consensus size: 41
26566 GCGTTTGGAT
* * * **
26576 AAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCGCTTT-TCC
1 AAAAAGCGCCGCTAAAGGTAAAGCATTAGCGGCG-TTTATGG
* * * *
26617 ATAAA-CGCTGCAAAAGGTAAAGCAATAGCGGCGTTTATAGG
1 AAAAAGCGCCGCTAAAGGTAAAGCATTAGCGGCGTTTAT-GG
*
26658 AAAAA-CGCCGCTAAAGGTTAGAGCATTAGCGGCGTTTAT-G
1 AAAAAGCGCCGCTAAAGG-TAAAGCATTAGCGGCGTTTATGG
* * * **
26698 AGAAAGCACCGCTAAAGGCTAGAGCATTAGCAACGTTTATGG
1 AAAAAGCGCCGCTAAAGG-TAAAGCATTAGCGGCGTTTATGG
* * *
26740 GAAAA-CGCCACTAAAGGTCAAAGCATTAGCGGTGTTTAT-G
1 AAAAAGCGCCGCTAAAGGT-AAAGCATTAGCGGCGTTTATGG
* ** * * * *
26780 AGAAAGCATCACGAAAGGTCAAAGCATTAGCGACATTTATGG
1 AAAAAGCGCCGCTAAAGGT-AAAGCATTAGCGGCGTTTATGG
* * *
26822 AAAAAGCGTCGCTAAAGGTTAAGCAATAGCGGC
1 AAAAAGCGCCGCTAAAGGTAAAGCATTAGCGGC
26855 ATTTTCCCTT
Statistics
Matches: 193, Mismatches: 37, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
39 3 0.02
40 38 0.20
41 113 0.59
42 39 0.20
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (41 bp):
AAAAAGCGCCGCTAAAGGTAAAGCATTAGCGGCGTTTATGG
Found at i:28540 original size:42 final size:42
Alignment explanation
Indices: 28478--28577 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
28468 TATGGGAAAG
* * *
28478 AGCATTAGC-AGCATTTTACCCATAAACGCTGATAAAAGTCAA
1 AGCATTAGCGA-CGTTTTACCCATAAACACCGATAAAAGTCAA
* *
28520 AGTATTAGCGACGTTTTACCCATAAACACCGATAAAAGTCAG
1 AGCATTAGCGACGTTTTACCCATAAACACCGATAAAAGTCAA
*
28562 AGCATTAGCGGCGTTT
1 AGCATTAGCGACGTTT
28578 ACGAGAAAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (42 bp):
AGCATTAGCGACGTTTTACCCATAAACACCGATAAAAGTCAA
Found at i:28602 original size:41 final size:41
Alignment explanation
Indices: 28552--28923 Score: 396
Period size: 41 Copynumber: 9.1 Consensus size: 41
28542 TAAACACCGA
* *
28552 TAAAAGTCAGAGCATTAGCGGCGTTTACGAGAAAGCACTGC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACTGC
* * *
28593 TAAAGGTCAGAGCATTAGCGGCGTTTATAAAAAAGCGGC-GC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGC-ACTGC
* * * * * * *
28634 TAAAGCTCACAGCATTAGCAGCGCTTATGAGAAGGTACCGC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACTGC
*
28675 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCGA-AGC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGC-ACTGC
* * * *
28716 TAAAGGTCAGAGCATTAGTGGCATTTATGTGAAA--ACGTCGT
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCAC-T-GC
* * *
28757 TAAAGGTCAGAGCATTAGCGGGGTTTATGAGAAAGCGCCGC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACTGC
* *
28798 TAAAGGTCAGAGCATTAGCGGTGTTTATGAGAAA--ACGTCGT
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCAC-T-GC
* * **
28839 TAAATGTCAGAGCATTAGCGGCGTTTATGAGAAAGCGCCAC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACTGC
* *
28880 TAAAGGTCAGAGCATTAGCGACGTTTATGATAAAGCACTGC
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACTGC
28921 TAA
1 TAA
28924 TGCTCTTTAC
Statistics
Matches: 270, Mismatches: 49, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
40 1 0.00
41 263 0.97
42 2 0.01
43 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (41 bp):
TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGCACTGC
Found at i:28666 original size:82 final size:81
Alignment explanation
Indices: 28552--28923 Score: 451
Period size: 82 Copynumber: 4.5 Consensus size: 81
28542 TAAACACCGA
* *
28552 TAAAAGTCAGAGCATTAGCGGCGTTTACGAGAAAGCACTGCTAAAGGTCAGAGCATTAGCGGCGT
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG-ACTGCTAAAGGTCAGAGCATTAGCGGCGT
* * *
28617 TTATAAAAAAGCGGCGC
65 TTATGAGAAAGCGCCGC
* * * * * *
28634 TAAAGCTCACAGCATTAGCAGCGCTTATGAGAAGGTACCGCTAAAGGTCAGAGCATTAGCGGCGT
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG-ACTGCTAAAGGTCAGAGCATTAGCGGCGT
**
28699 TTATGAGAAAGCGAAGC
65 TTATGAGAAAGCGCCGC
* * * * *
28716 TAAAGGTCAGAGCATTAGTGGCATTTATGTGAAA-ACGTCGTTAAAGGTCAGAGCATTAGCGGGG
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGAC-T-GCTAAAGGTCAGAGCATTAGCGGCG
28780 TTTATGAGAAAGCGCCGC
64 TTTATGAGAAAGCGCCGC
* * *
28798 TAAAGGTCAGAGCATTAGCGGTGTTTATGAGAAA-ACGTCGTTAAATGTCAGAGCATTAGCGGCG
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGAC-T-GCTAAAGGTCAGAGCATTAGCGGCG
*
28862 TTTATGAGAAAGCGCCAC
64 TTTATGAGAAAGCGCCGC
* *
28880 TAAAGGTCAGAGCATTAGCGACGTTTATGATAAAGCACTGCTAA
1 TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG-ACTGCTAA
28924 TGCTCTTTAC
Statistics
Matches: 249, Mismatches: 37, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
80 2 0.01
82 244 0.98
83 1 0.00
84 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (81 bp):
TAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAGACTGCTAAAGGTCAGAGCATTAGCGGCGTT
TATGAGAAAGCGCCGC
Found at i:31764 original size:36 final size:35
Alignment explanation
Indices: 31723--31821 Score: 128
Period size: 36 Copynumber: 2.7 Consensus size: 35
31713 TGGTAACAAG
31723 CATGACCTTTGGATCAATAGGGAGTAAAAT-AAGCAT
1 CATGACCTTTGG-TCAATAGGGAGTAAAATGAA-CAT
* *
31759 CATGACCTTTGGTTTAACAGGGAGTAAAATGAACAT
1 CATGACCTTTGG-TCAATAGGGAGTAAAATGAACAT
*
31795 CATGACTTTTAGGTCAATAGGGAGTAA
1 CATGACCTTT-GGTCAATAGGGAGTAA
31822 GCATGACTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 51 0.93
37 4 0.07
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (35 bp):
CATGACCTTTGGTCAATAGGGAGTAAAATGAACAT
Found at i:31839 original size:28 final size:28
Alignment explanation
Indices: 31795--31849 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
31785 AAATGAACAT
* *
31795 CATGACTTTTAGGTCAATAGGGAGTAAG
1 CATGACTTTTAGGTCAACAAGGAGTAAG
31823 CATGACTTTT-GGATCAACAAGGAGTAA
1 CATGACTTTTAGG-TCAACAAGGAGTAA
31850 ATCAGATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (28 bp):
CATGACTTTTAGGTCAACAAGGAGTAAG
Found at i:50742 original size:26 final size:26
Alignment explanation
Indices: 50702--50758 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
50692 CAAACCAATC
* *
50702 AATTGTCACTGCATG-GACATGTCCAG
1 AATTGTCACTACATGAG-CATGTCCAA
*
50728 AATTGTCGCTACATGAGCATGTCCAA
1 AATTGTCACTACATGAGCATGTCCAA
50754 AATTG
1 AATTG
50759 AGCCCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (26 bp):
AATTGTCACTACATGAGCATGTCCAA
Found at i:65388 original size:13 final size:13
Alignment explanation
Indices: 65370--65396 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65360 AAGTCAAATA
65370 AGAATCAGGAAAC
1 AGAATCAGGAAAC
65383 AGAATCAGGAAAC
1 AGAATCAGGAAAC
65396 A
1 A
65397 AGCAAGAAAT
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:0.56, C:0.15, G:0.22, T:0.07
Consensus pattern (13 bp):
AGAATCAGGAAAC
Found at i:65436 original size:17 final size:18
Alignment explanation
Indices: 65400--65441 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
65390 GGAAACAAGC
*
65400 AAGAAATGAGAAACACAA
1 AAGAAAAGAGAAACACAA
*
65418 AAGAAAAGA-AAAGACAA
1 AAGAAAAGAGAAACACAA
65435 AAGAAAA
1 AAGAAAA
65442 ACAAAGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.74, C:0.07, G:0.17, T:0.02
Consensus pattern (18 bp):
AAGAAAAGAGAAACACAA
Found at i:65697 original size:11 final size:10
Alignment explanation
Indices: 65673--65713 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
65663 TTTTTATAAA
65673 TATTTTGAA-
1 TATTTTGAAT
65682 T-TTTTGAAAT
1 TATTTTG-AAT
65692 TATTTTGAAT
1 TATTTTGAAT
65702 TATTTTGTAAT
1 TATTTTG-AAT
65713 T
1 T
65714 TTTGTTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.18
9 3 0.11
10 11 0.39
11 9 0.32
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (10 bp):
TATTTTGAAT
Found at i:65713 original size:21 final size:20
Alignment explanation
Indices: 65662--65713 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
65652 AAATTATAAT
* *
65662 TTTTTTATAAATATTTTGAA
1 TTTTTTGTAATTATTTTGAA
*
65682 -TTTTTGAAATTATTTTGAA
1 TTTTTTGTAATTATTTTGAA
65701 TTATTTTGTAATT
1 TT-TTTTGTAATT
65714 TTTGTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.62
20 1 0.04
21 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTTGTAATTATTTTGAA
Found at i:81046 original size:15 final size:15
Alignment explanation
Indices: 81028--81058 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
81018 ATATACATAA
81028 AATAAAATGCAAAGG
1 AATAAAATGCAAAGG
81043 AATAAAATGCAAAGG
1 AATAAAATGCAAAGG
81058 A
1 A
81059 TCACAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.19, T:0.13
Consensus pattern (15 bp):
AATAAAATGCAAAGG
Found at i:81550 original size:39 final size:39
Alignment explanation
Indices: 81507--81582 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
81497 AAAGAAAACC
*
81507 TGTTATCTCGAATTAAAAAGTCACATCCAGTAAGTTACT
1 TGTTATCTCGAATTAAAAAGCCACATCCAGTAAGTTACT
81546 TGTTATCTCGAATTAAAAAGCCACATCCAGTAAGTTA
1 TGTTATCTCGAATTAAAAAGCCACATCCAGTAAGTTA
81583 GCACATAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (39 bp):
TGTTATCTCGAATTAAAAAGCCACATCCAGTAAGTTACT
Found at i:82403 original size:94 final size:95
Alignment explanation
Indices: 82282--82454 Score: 248
Period size: 94 Copynumber: 1.8 Consensus size: 95
82272 CAATAAAATG
*
82282 GCATGAAAATAAATAACATCAAGATAAATAAATAAATATAAAAATTAAATGTTAAAAT-AA-AAC
1 GCATGAAAATAAATAAAATCAAGATAAATAAAT-AA-ATAAAAATTAAATGTTAAAATAAACAAC
82345 -AAATATAAACAATAAAAATAATTGAGATTAT
64 TAAATATAAACAATAAAAATAATTGAGATTAT
*
82376 GCATGAAAATAAATGATAAAT-AA-ATAAATAAATAAATGAAAATTAAATGTTAAAATAAACAAC
1 GCATGAAAATAAAT-A-AAATCAAGATAAATAAATAAATAAAAATTAAATGTTAAAATAAACAAC
*
82439 TAAATATAAATAATAA
64 TAAATATAAACAATAA
82455 TGAAAAAGAA
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
92 20 0.28
93 4 0.06
94 27 0.38
95 17 0.24
96 3 0.04
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (95 bp):
GCATGAAAATAAATAAAATCAAGATAAATAAATAAATAAAAATTAAATGTTAAAATAAACAACTA
AATATAAACAATAAAAATAATTGAGATTAT
Found at i:82431 original size:46 final size:46
Alignment explanation
Indices: 82305--82451 Score: 117
Period size: 46 Copynumber: 3.2 Consensus size: 46
82295 TAACATCAAG
*
82305 ATAAATAAATAAAT--ATAAAAATTAAATGTTAAAATAAAACAAAT
1 ATAAATAAATAAATAAATGAAAATTAAATGTTAAAATAAAACAAAT
* * * * * **
82349 ATAAACAATAAAAATAATTG-AGATT--ATGCATGAAAATAAATGATAA-
1 ATAAATAA-ATAAATAAATGAAAATTAAATG--TTAAAATAAAACA-AAT
82395 ATAAATAAATAAATAAATGAAAATTAAATGTTAAAATAAACAACTAAAT
1 ATAAATAAATAAATAAATGAAAATTAAATGTTAAAAT-AA-AAC-AAAT
82444 ATAAATAA
1 ATAAATAA
82452 TAATGAAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 21
0.68 0.14 0.19
Matches are distributed among these distances:
44 10 0.13
45 14 0.19
46 31 0.41
47 5 0.07
48 6 0.08
49 9 0.12
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (46 bp):
ATAAATAAATAAATAAATGAAAATTAAATGTTAAAATAAAACAAAT
Found at i:87540 original size:75 final size:74
Alignment explanation
Indices: 87351--87579 Score: 359
Period size: 75 Copynumber: 3.1 Consensus size: 74
87341 ATGATTTTGA
* * *
87351 TCATTGCGCTCATAATTTGGATAAAATATTGAAGCGGTGTGAAGACACACATCGTGTCCTAAATT
1 TCATTGCGCTGATAATTTGGATAAAGTATTGAAGCGGTGTGAAGACACACATCTTGTCCTAAATT
87416 GGGAAAATG
66 GGGAAAATG
* * **
87425 TCATTACGTTGATAATTTGGATAAAGTATTGAAGCGGTGTGAAGATGCACATCTTGTCCTAAATT
1 TCATTGCGCTGATAATTTGGATAAAGTATTGAAGCGGTGTGAAGACACACATCTTGTCCTAAATT
87490 GGGAAAAATG
66 GGG-AAAATG
* *
87500 TCATTGCGCTGATAATTTGGATAAAGTATTGAAGCGGTGTGAAGACATACATCTTGTCTTAAATT
1 TCATTGCGCTGATAATTTGGATAAAGTATTGAAGCGGTGTGAAGACACACATCTTGTCCTAAA-T
87565 TGGGAAAATG
65 TGGGAAAATG
87575 TCATT
1 TCATT
87580 TCATGGAAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
74 61 0.44
75 74 0.53
76 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (74 bp):
TCATTGCGCTGATAATTTGGATAAAGTATTGAAGCGGTGTGAAGACACACATCTTGTCCTAAATT
GGGAAAATG
Found at i:102761 original size:24 final size:25
Alignment explanation
Indices: 102709--102774 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 25
102699 ATTTTAAAAA
*
102709 ATTTAGTATTTATTAGTAGAATAATAT
1 ATTTAGTATTTATTACT--AATAATAT
102736 ATTTAGTATTTATTACT-ATAATAT
1 ATTTAGTATTTATTACTAATAATAT
102760 ATTT-GATATTTATTA
1 ATTTAG-TATTTATTA
102775 GAATTAGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 1 0.03
24 20 0.54
27 16 0.43
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (25 bp):
ATTTAGTATTTATTACTAATAATAT
Found at i:103321 original size:20 final size:22
Alignment explanation
Indices: 103296--103338 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
103286 CGAAAAATGA
103296 TTTTT-GAAAATAAGTTA-TTT
1 TTTTTGGAAAATAAGTTACTTT
*
103316 TTTTTGGAAAATTAGTTACTTT
1 TTTTTGGAAAATAAGTTACTTT
103338 T
1 T
103339 CTGAAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (22 bp):
TTTTTGGAAAATAAGTTACTTT
Found at i:104546 original size:20 final size:20
Alignment explanation
Indices: 104521--104558 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
104511 ATTATCCTCA
*
104521 GCAATACCTCTTTCAAATCT
1 GCAATACCCCTTTCAAATCT
104541 GCAATACCCCTTTCAAAT
1 GCAATACCCCTTTCAAAT
104559 GCTGAGTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (20 bp):
GCAATACCCCTTTCAAATCT
Found at i:107874 original size:53 final size:53
Alignment explanation
Indices: 107784--108119 Score: 330
Period size: 53 Copynumber: 6.5 Consensus size: 53
107774 TTCACGTTTG
* * *
107784 ATAACTCACAATGACATAGAGTCATTGGAACCTTTAATCTATAATAGGATTCAC
1 ATAACTCACAATGACACAGAGTCATCGG-ACCTTTAATCCATAATAGGATTCAC
* * *
107838 ATAACTCACGATGATACAGATTCATCGGACCTTTAATCCATAATAGGATTCAC
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAC
* * * *
107891 ATAACTCACAATGACAAAGAGTCATTGGACCTTTAATCCGTAATTGG------
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAC
* * * * * * * *
107938 ATAACTCACAATGACATAAAGTCATCGAACCTTTTATCCAAAACAGGATTAAT
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAC
*** *
107991 ATAACTCACAATGACACAGAGTCATAAAACCTTTAATCCGTAATAGGATT--C
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAC
* * * * * *
108042 AT-ACTCACGATAACACAGAGTCATCGGACCTTTAGTCTATAATAGCATTCAT
1 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAC
* *
108094 ATAACTCACGATGACATAGAGTCATC
1 ATAACTCACAATGACACAGAGTCATC
108120 AGACTTTTTT
Statistics
Matches: 230, Mismatches: 43, Indels: 19
0.79 0.15 0.07
Matches are distributed among these distances:
47 38 0.17
50 38 0.17
51 2 0.01
52 2 0.01
53 127 0.55
54 23 0.10
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (53 bp):
ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAC
Found at i:107986 original size:100 final size:100
Alignment explanation
Indices: 107784--108118 Score: 357
Period size: 100 Copynumber: 3.2 Consensus size: 100
107774 TTCACGTTTG
**
107784 ATAACTCACAATGACATAGAGTCATTGGAACCTTTAATCTATAATAGGATTCACATAACTCACGA
1 ATAACTCACAATGACATAGAGTCATTGG-ACCTTTAATCCGTAATAGG------ATAACTCACGA
* * * *
107849 TGATACAGATTCATCGGACCTTTAATCCATAATAGGATTCAC
59 TGACACAGAGTCATCGGACCTTTTATCCATAATAGGATTCAT
* * * *
107891 ATAACTCACAATGACAAAGAGTCATTGGACCTTTAATCCGTAATTGGATAACTCACAATGACATA
1 ATAACTCACAATGACATAGAGTCATTGGACCTTTAATCCGTAATAGGATAACTCACGATGACACA
* * * * *
107956 AAGTCATCGAACCTTTTATCCAAAACAGGATTAAT
66 GAGTCATCGGACCTTTTATCCATAATAGGATTCAT
* *** *
107991 ATAACTCACAATGACACAGAGTCATAAAACCTTTAATCCGTAATAGGATTCATACTCACGATAAC
1 ATAACTCACAATGACATAGAGTCATTGGACCTTTAATCCGTAATAGGA-T-A-ACTCACGATGAC
* *
108056 ACAGAGTCATCGGACC-TTTAGTCTATAATAGCATTCAT
63 ACAGAGTCATCGGACCTTTTA-TCCATAATAGGATTCAT
*
108094 ATAACTCACGATGACATAGAGTCAT
1 ATAACTCACAATGACATAGAGTCAT
108119 CAGACTTTTT
Statistics
Matches: 192, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
100 85 0.44
101 1 0.01
102 5 0.03
103 58 0.30
106 16 0.08
107 27 0.14
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (100 bp):
ATAACTCACAATGACATAGAGTCATTGGACCTTTAATCCGTAATAGGATAACTCACGATGACACA
GAGTCATCGGACCTTTTATCCATAATAGGATTCAT
Found at i:114475 original size:26 final size:25
Alignment explanation
Indices: 114443--114501 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
114433 AAAATTATTA
114443 TATTATAAAATTTTTAAATTTTTTAT
1 TATTATAAAATTTTT-AATTTTTTAT
* * *
114469 TATTAT-ATATTTTTAGTTTTTTTT
1 TATTATAAAATTTTTAATTTTTTAT
114493 TAATTATAA
1 T-ATTATAA
114502 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 9 0.32
25 12 0.43
26 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTATAAAATTTTTAATTTTTTAT
Found at i:114488 original size:23 final size:24
Alignment explanation
Indices: 114437--114506 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
114427 GATTCCAAAA
*
114437 TTATTATATTATAAAATTTTTAAATTTT
1 TTATTA-ATTAT--AATTTTT-AGTTTT
114465 TTATT-ATTATATATTTTTAGTTTT
1 TTATTAATTATA-ATTTTTAGTTTT
*
114489 TTTTTAATTATAATTTTT
1 TTATTAATTATAATTTTT
114507 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 16 0.42
25 12 0.32
26 5 0.13
28 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (24 bp):
TTATTAATTATAATTTTTAGTTTT
Found at i:114549 original size:19 final size:20
Alignment explanation
Indices: 114513--114584 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
114503 TTTTTTTAAA
114513 ATAAA-TATTTTAGAATTTTT
1 ATAAATTATTTT-GAATTTTT
114533 ATAAA-TATTTTGAA-TTTT
1 ATAAATTATTTTGAATTTTT
* *
114551 AAAAATTATTTTTAATTTTT
1 ATAAATTATTTTGAATTTTT
114571 GA-AAATTATTTTGA
1 -ATAAATTATTTTGA
114585 TTATTTTGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.17
19 11 0.24
20 26 0.57
21 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
ATAAATTATTTTGAATTTTT
Found at i:128204 original size:13 final size:13
Alignment explanation
Indices: 128186--128211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128176 AGGAACTTAC
128186 CTCAATTACTAAA
1 CTCAATTACTAAA
128199 CTCAATTACTAAA
1 CTCAATTACTAAA
128212 GTTGGAAAAC
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:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CTCAATTACTAAA
Found at i:138790 original size:102 final size:104
Alignment explanation
Indices: 138684--138879 Score: 326
Period size: 103 Copynumber: 1.9 Consensus size: 104
138674 TGGCCGACAC
* *
138684 CCCTTTTTTGTCAGATAAAAA-ATAATCTTTTT-GTGTTGGCCATACAATGGCCGACACCCCTAT
1 CCCTTTTTTATCAGATAAAAATATAAT-TTTTTGGTGTTGCCCATACAATGGCCGACACCCCTAT
138747 TTATCTGAT-AAAAAATCAAATTTTTGGGTATTGGTCATT
65 TTATCTGATAAAAAAATCAAATTTTTGGGTATTGGTCATT
* *
138786 CCCTTTTTTATCAGATAAAAATTTAATTTTTTGGTGTTGCCCATGCAATGGCCGACACCCCTATT
1 CCCTTTTTTATCAGATAAAAATATAATTTTTTGGTGTTGCCCATACAATGGCCGACACCCCTATT
138851 TATCTGATAAAAAAATCAAATTTTTGGGT
66 TATCTGATAAAAAAATCAAATTTTTGGGT
138880 GTTTACCATG
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
102 25 0.29
103 42 0.48
104 20 0.23
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (104 bp):
CCCTTTTTTATCAGATAAAAATATAATTTTTTGGTGTTGCCCATACAATGGCCGACACCCCTATT
TATCTGATAAAAAAATCAAATTTTTGGGTATTGGTCATT
Found at i:138955 original size:62 final size:61
Alignment explanation
Indices: 138791--139145 Score: 333
Period size: 59 Copynumber: 6.0 Consensus size: 61
138781 TCATTCCCTT
* * *
138791 TTTTATCAGAT--AAAAATT-TAA-TTTTTTGGTGTTGCCCATGCAATGGCCGACA-CCCC
1 TTTTATCAGATAAAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCC
* * **
138847 TATTTATCTGATAAAAAAA-TCAAA-TTTTTGGGTGTTTACCATGCAATGGTCGACACCCCC
1 T-TTTATCAGATAAAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCC
* *
138907 TTTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCTC
1 TTTTATCAGATAAAAAAA-TTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCC
* * * *
138969 TTTTCTCAAATAAAAAAAACTTCAAATTTTTTTGGTGTTAGTCATGCAATGGTCGACA--CCC
1 TTTTATCAGAT-AAAAAAA-TTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCC
* * * * * * *
139030 TTTTTTTAGATAAAAAATTTTC--ATTTTTTTTGTGTTGGTCATGCAATGGTCAACATCCCCT
1 TTTTATCAGATAAAAAA-ATTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACA-CCCCC
** * * *
139091 TTTTATTTGGT-AAAAAATT-AAA-TTTTTTGGTGTTGGCTATGTAATGGTCGACACC
1 TTTTATCAGATAAAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACC
139146 AACTTCCCCT
Statistics
Matches: 250, Mismatches: 34, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.00
57 9 0.04
58 33 0.13
59 77 0.31
60 20 0.08
61 25 0.10
62 42 0.17
63 43 0.17
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (61 bp):
TTTTATCAGATAAAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCC
Found at i:139106 original size:121 final size:116
Alignment explanation
Indices: 138786--139145 Score: 356
Period size: 121 Copynumber: 3.0 Consensus size: 116
138776 ATTGGTCATT
* * * *
138786 CCCTTTTTTATCAGAT-AAAAATTT-AATTTTTTGGTGTTGCCCATGCAATGGCCGACACCCCTA
1 CCCTTTTTT-T-AGATAAAAAATTTCATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCTT
* *
138849 TTTATCTGATAAAAAAA-TCAAATTTTTGGGTGTTTA-CCATGCAATGGTCGACA
64 TTTATATG-TAAAAAAATTCAAATTTTTTGGTG-TTAGCCATGCAATGGTCGACA
* *
138902 CCCCCTTTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCC
1 --CCCTTTTTTTAGAT-AAAAAATTTC--ATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCC
* * *
138967 TCTTTTCTCAAAT-AAAAAAAACTTCAAATTTTTTTGGTGTTAGTCATGCAATGGTCGACA
61 -CTTTT-T-ATATGTAAAAAAA-TTCAAA-TTTTTTGGTGTTAGCCATGCAATGGTCGACA
* * *
139027 CCCTTTTTTTAGATAAAAAATTTTCATTTTTTTTGTGTTGGTCATGCAATGGTCAACATCCCCTT
1 CCCTTTTTTTAGATAAAAAA-TTTCATTTTTTTGGTGTTGGCCATGCAATGGTCGACA-CCCCTT
* * * *
139092 TTTATTTGGT-AAAAAATT-AAATTTTTTGGTGTTGGCTATGTAATGGTCGACA
64 TTTATAT-GTAAAAAAATTCAAATTTTTTGGTGTTAGCCATGCAATGGTCGACA
139144 CC
1 CC
139146 AACTTCCCCT
Statistics
Matches: 203, Mismatches: 23, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
116 4 0.02
117 29 0.14
118 19 0.09
119 4 0.02
120 7 0.03
121 68 0.33
122 20 0.10
123 17 0.08
124 10 0.05
125 25 0.12
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (116 bp):
CCCTTTTTTTAGATAAAAAATTTCATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCTTTT
TATATGTAAAAAAATTCAAATTTTTTGGTGTTAGCCATGCAATGGTCGACA
Found at i:139983 original size:17 final size:17
Alignment explanation
Indices: 139963--140016 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
139953 AAAAAATAAT
139963 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
139980 AATTAGAA-A-A-A--A
1 AATTAGAATATACAGGA
*
139992 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
140009 AATTAGAA
1 AATTAGAA
140017 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 2 0.07
15 2 0.07
16 1 0.03
17 16 0.53
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:139983 original size:34 final size:30
Alignment explanation
Indices: 139953--140012 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
139943 ATAAATTTAA
*
139953 AAAAAATAATAATTAGAATATACAGGAAA-TT
1 AAAAAA-AA-AATTAAAATATACAGGAAATTT
*
139984 AGAAAAAAAATTAAAATATACAGGAAATT
1 AAAAAAAAAATTAAAATATACAGGAAATT
140013 AGAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 18 0.69
30 3 0.12
31 5 0.19
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.23
Consensus pattern (30 bp):
AAAAAAAAAATTAAAATATACAGGAAATTT
Found at i:140023 original size:29 final size:29
Alignment explanation
Indices: 139963--140031 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
139953 AAAAAATAAT
*
139963 AATTAGAATATACAGGAAATTAGAAAAAA
1 AATTAAAATATACAGGAAATTAGAAAAAA
*
139992 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAA-AAA
*
140022 ATTTAAAATA
1 AATTAAAATA
140032 AAAACAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (29 bp):
AATTAAAATATACAGGAAATTAGAAAAAA
Found at i:141207 original size:13 final size:13
Alignment explanation
Indices: 141189--141213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141179 ATTTTGAAAA
141189 TGTAAAAAATATT
1 TGTAAAAAATATT
141202 TGTAAAAAATAT
1 TGTAAAAAATAT
141214 CATATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTAAAAAATATT
Found at i:141272 original size:20 final size:19
Alignment explanation
Indices: 141231--141275 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
141221 TTATTTTTTT
*
141231 AAAAATTTGAAAATATATA
1 AAAAATTTGAAAATAGATA
141250 AAAACATTTCGAAAATAGA-A
1 AAAA-ATTT-GAAAATAGATA
141270 AAAAAT
1 AAAAAT
141276 ATTATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (19 bp):
AAAAATTTGAAAATAGATA
Found at i:142562 original size:84 final size:84
Alignment explanation
Indices: 142424--142815 Score: 574
Period size: 84 Copynumber: 4.6 Consensus size: 84
142414 ATCTAAAATC
* *
142424 TGATAAAAATTGTAATATAATAATAATTGTTTATTTAAATATTTAAAATTAATAAATAATTTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAATAAATAATGTATT
*
142489 GTCAAATCAACATATTATT
66 GTCAAATCAACACATTATT
142508 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAATAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAATAAATAATGTATT
*
142573 GTCAAATCAACATATTATT
66 GTCAAATCAACACATTATT
* * *
142592 TGATAAAAATTATAATATAATAATAATATTTTTATTTAAATATTTAAATTTAGTAAATAATGTAT
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTATTTAAATATTTAAAATTAATAAATAATGTAT
142657 TGTCAAATCAACACATTATT
65 TGTCAAATCAACACATTATT
* * * * *
142677 TGATAAAAATTATAATATAATAATAA-TTTGTACTTTAAATA-TGAAAATTTGATAAATAACGTA
1 TGATAAAAATTGTAATATAATAATAATTTTTTA-TTTAAATATTTAAAA-TTAATAAATAATGTA
* *
142740 TTGTCAAATGAACACAATATT
64 TTGTCAAATCAACACATTATT
*
142761 TGATATAAATTGTAATATAATAATAATTTTTTTATTTAAATAATGTT-AAATTAAT
1 TGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAAT-AT-TTAAAATTAAT
142816 TTTAATTGTA
Statistics
Matches: 281, Mismatches: 19, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
83 9 0.03
84 171 0.61
85 87 0.31
86 10 0.04
87 3 0.01
88 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (84 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAATAAATAATGTATT
GTCAAATCAACACATTATT
Found at i:142702 original size:169 final size:168
Alignment explanation
Indices: 142424--142812 Score: 575
Period size: 169 Copynumber: 2.3 Consensus size: 168
142414 ATCTAAAATC
* * *
142424 TGATAAAAATTGTAATATAATAATAATTGTTTATTTAAATATTTAAAATTAATAAATAATTTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAATAAATAATGTATT
* * * *
142489 GTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTTA-TTTAAATATTTA
66 GTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAA-TTTGTACTTTAAATA-TGA
* * *
142553 AAA-TTAATAAATAATGTATTGTCAAATCAACATATTATT
129 AAATTTAATAAATAACGTATTGTCAAATCAACACAATATT
* *
142592 TGATAAAAATTATAATATAATAATAATATTTTTATTTAAATATTTAAATTTAGTAAATAATGTAT
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTATTTAAATATTTAAATTTAATAAATAATGTAT
142657 TGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATTTGTACTTTAAATATGAA
65 TGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATTTGTACTTTAAATATGAA
* *
142722 AATTTGATAAATAACGTATTGTCAAATGAACACAATATT
130 AATTTAATAAATAACGTATTGTCAAATCAACACAATATT
*
142761 TGATATAAATTGTAATATAATAATAATTTTTTTATTTAAATAATGTTAAATT
1 TGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAAT-AT-TTAAATT
142813 AATTTTAATT
Statistics
Matches: 199, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
168 36 0.18
169 153 0.77
170 3 0.02
171 7 0.04
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (168 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAATAAATAATGTATT
GTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATTTGTACTTTAAATATGAAA
ATTTAATAAATAACGTATTGTCAAATCAACACAATATT
Found at i:146443 original size:29 final size:31
Alignment explanation
Indices: 146385--146445 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
146375 TTGCCTCTTC
* *
146385 ACATGACAGTATATAATTCAACTCCGAAAAT
1 ACATGACAATATATAACTCAACTCCGAAAAT
* *
146416 ACATGACAATATATAGCTCAAC-CCAAAAAT
1 ACATGACAATATATAACTCAACTCCGAAAAT
146446 TCGATTGTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (31 bp):
ACATGACAATATATAACTCAACTCCGAAAAT
Found at i:146965 original size:59 final size:59
Alignment explanation
Indices: 146605--147101 Score: 464
Period size: 61 Copynumber: 8.4 Consensus size: 59
146595 AGGAGAAGTT
** * * * **
146605 GGTGTCGGCCATTATATGGACAACACAAAAAAAAATT-AA-TTTTTACCAAATAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACAC-CAAAAAAATTGAATTTTTTATCTGATAAAAA-GG
* * *
146664 GGTGTCGGCCA-TG-GTGACCAACA--AAAAAAATTGAATTTTTTATCTGATAAGAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGAATTTTTTATCTGATAAAAAGG
* * * *
146719 AGGTGTTGGCCATAGCATGACCAACA-CAAAAAAGTTTTGAAATTTTTTATCTGA-AAAAAGG
1 -GGTGTCGGCCATTGCATGGCCAACACCAAAAAA--ATTG-AATTTTTTATCTGATAAAAAGG
* * *
146780 GGTGTCGACCATTGCATGGCCAACACTAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAA-ATTG-AA-TTTTTTATCTGATAAAAAGG
* * * *
146841 GGTGTCGGCCATTGCACGGCCAACATCGAAAAAATTTGAAATTTTTTTATCTGA-GAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACA-CCAAAAAAATTG-AA-TTTTTTATCTGATAAAAAGG
** * *
146902 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGTTTTTTTTATCAGATAAATAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGAATTTTTTATCTGATAAAAAGG
* *
146961 GGTGTCGGTCATTGCATTGCCAACACC-AAAAAATTGAATTTTTTATCTGATAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGAATTTTTTATCTGAT-AAAAAGG
* * *
147020 AGATGTCGACCATTGCATGGCCAACA-C-AAAAAATT-ATATTTTTTATCTGATAAAAAAGA
1 -GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGA-ATTTTTTATCTGAT-AAAAAGG
* *
147079 GGTGTCGACCATTGCATAGCCAA
1 GGTGTCGGCCATTGCATGGCCAA
147102 AACCCAAATT
Statistics
Matches: 379, Mismatches: 43, Indels: 33
0.83 0.09 0.07
Matches are distributed among these distances:
54 9 0.02
55 4 0.01
56 23 0.06
57 8 0.02
58 64 0.17
59 83 0.22
60 60 0.16
61 107 0.28
62 21 0.06
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGAATTTTTTATCTGATAAAAAGG
Found at i:150850 original size:18 final size:18
Alignment explanation
Indices: 150829--150864 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
150819 ACAAAAAATC
*
150829 AAAATAATTTTTAAAATTA
1 AAAAT-ATTTATAAAATTA
150848 AAAATATTTATAAAATT
1 AAAATATTTATAAAATT
150865 TCTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATTTATAAAATTA
Found at i:150907 original size:18 final size:18
Alignment explanation
Indices: 150867--150908 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
150857 ATAAAATTTC
150867 TAAAATTTGTATTTTTTA
1 TAAAATTTGTATTTTTTA
* * *
150885 AAAAATTTTTATTTTTTT
1 TAAAATTTGTATTTTTTA
150903 TAAAAT
1 TAAAAT
150909 CCAAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TAAAATTTGTATTTTTTA
Found at i:161747 original size:35 final size:37
Alignment explanation
Indices: 161676--161763 Score: 121
Period size: 35 Copynumber: 2.5 Consensus size: 37
161666 AATTTAGGAT
161676 CTCAAACCC-TAAATCTTTAAATTTTAAACTCCAAAC
1 CTCAAACCCTTAAATCTTTAAATTTTAAACTCCAAAC
* *
161712 CTCGAACTCTTAAA-CTTTAAA-TTTAAA-TCCTAAAC
1 CTCAAACCCTTAAATCTTTAAATTTTAAACTCC-AAAC
161747 CTCAAACCCTTAAATCT
1 CTCAAACCCTTAAATCT
161764 CAAACCTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 3 0.07
35 22 0.49
36 16 0.36
37 4 0.09
ACGTcount: A:0.40, C:0.27, G:0.01, T:0.32
Consensus pattern (37 bp):
CTCAAACCCTTAAATCTTTAAATTTTAAACTCCAAAC
Found at i:164837 original size:32 final size:32
Alignment explanation
Indices: 164801--164861 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
164791 AAATACCTCA
*
164801 ATTTGATTTTATTCCAATCAAATTGATTTTCG
1 ATTTGATTTGATTCCAATCAAATTGATTTTCG
***
164833 ATTTGATTTGATTCTGTTCAAATTGATTT
1 ATTTGATTTGATTCCAATCAAATTGATTT
164862 AAAAGGCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.52
Consensus pattern (32 bp):
ATTTGATTTGATTCCAATCAAATTGATTTTCG
Found at i:165619 original size:83 final size:84
Alignment explanation
Indices: 165456--165707 Score: 289
Period size: 83 Copynumber: 3.0 Consensus size: 84
165446 GAATAAAAAT
* * * *
165456 TAAAATTAAATAAATCTA-TTTCAAGATTTATTCTCGTCATTTAACCGATTTTATTTTATTTTGA
1 TAAAATTGAATAAAACTATTTTCAAGATTTATTCTCGTCATTCAACAGATTTTATTTTATTTTGA
165520 TTTTGTTTCCAAAACAAGAA
66 TTTTGTTTCC-AAACAAGAA
* * **
165540 T-AAGTTGAATAAAACTATTTTGAA-ATTTATTCTCGTTGTTCAACAGATTTTATTTTATTTTGG
1 TAAAATTGAATAAAACTATTTTCAAGATTTATTCTCGTCATTCAACAGATTTTATTTTATTTT-G
* *
165603 ATTTAGTTTCCTAACAAGAA
65 ATTTTGTTTCCAAACAAGAA
* * ** * *
165623 TTAAAATTGAAT--AATTTTGTTTCAAGATTTATTCTCACCATTCAACAGATTTGATTTGATTTT
1 -TAAAATTGAATAAAACTAT-TTTCAAGATTTATTCTCGTCATTCAACAGATTTTATTTTATTTT
165686 GATTTTGTTTCCAAACAAGAA
64 GATTTTGTTTCCAAACAAGAA
165707 T
1 T
165708 TAATTAAATT
Statistics
Matches: 140, Mismatches: 22, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
83 59 0.42
84 42 0.30
85 39 0.28
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (84 bp):
TAAAATTGAATAAAACTATTTTCAAGATTTATTCTCGTCATTCAACAGATTTTATTTTATTTTGA
TTTTGTTTCCAAACAAGAA
Found at i:166132 original size:276 final size:276
Alignment explanation
Indices: 165639--166193 Score: 1038
Period size: 276 Copynumber: 2.0 Consensus size: 276
165629 TTGAATAATT
165639 TTGTTTCAAGATTTATTCTCACCATTCAACAGATTTGATTTGATTTTGATTTTGTTTCCAAACAA
1 TTGTTTCAAGATTTATTCTCACCATTCAACAGATTTGATTTGATTTTGATTTTGTTTCCAAACAA
*
165704 GAATTAATTAAATTCTGTTTCAAGATTTAATCCTGTCGCTCAACAAAATTGATTTTGATTTTGTT
66 GAATTAATTAAATTCTGTTTCAAGATTTAATCCTGTCACTCAACAAAATTGATTTTGATTTTGTT
*
165769 TCAGAATTTTAATTCTGCAATTTAACAAAATCAAAGAATGGTATAAACTAAAAATTGATTTGTCT
131 TCAGAATTTTAATTCTGCAATTTAACAAAATCAAAGAATGGTATAAACTAAAAATTGAATTGTCT
*
165834 GTTTATAGTGGCCTTAATTGTGGTTTTAAATTGTGAAAGCTTAAATTGTAGCTTCAAATTGTGAT
196 GTTTATAGTGGCCTTAATTGTGGTCTTAAATTGTGAAAGCTTAAATTGTAGCTTCAAATTGTGAT
165899 ATCAAAGAAAAAGAAA
261 ATCAAAGAAAAAGAAA
* *
165915 TTGTTTCAAGATTTATTCTCGCCATTCAGCAGATTTGATTTGATTTTGATTTTGTTTCCAAACAA
1 TTGTTTCAAGATTTATTCTCACCATTCAACAGATTTGATTTGATTTTGATTTTGTTTCCAAACAA
* *
165980 GAATTAATTAAATTCTGTTTCAAGATTTAATCCTGTCATTCAACAGAATTGATTTTGATTTTGTT
66 GAATTAATTAAATTCTGTTTCAAGATTTAATCCTGTCACTCAACAAAATTGATTTTGATTTTGTT
*
166045 TCAGAATTTTAATTCTGCCATTTAACAAAATCAAAGAATGGTATAAACTAAAAATTGAATTGTCT
131 TCAGAATTTTAATTCTGCAATTTAACAAAATCAAAGAATGGTATAAACTAAAAATTGAATTGTCT
166110 GTTTATAGTGGCCTTAATTGTGGTCTTAAATTGTGAAAGCTTAAATTGTAGCTTCAAATTGTGAT
196 GTTTATAGTGGCCTTAATTGTGGTCTTAAATTGTGAAAGCTTAAATTGTAGCTTCAAATTGTGAT
166175 ATCAAAGAAAAAGAAA
261 ATCAAAGAAAAAGAAA
166191 TTG
1 TTG
166194 ATCGATGGTT
Statistics
Matches: 271, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
276 271 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (276 bp):
TTGTTTCAAGATTTATTCTCACCATTCAACAGATTTGATTTGATTTTGATTTTGTTTCCAAACAA
GAATTAATTAAATTCTGTTTCAAGATTTAATCCTGTCACTCAACAAAATTGATTTTGATTTTGTT
TCAGAATTTTAATTCTGCAATTTAACAAAATCAAAGAATGGTATAAACTAAAAATTGAATTGTCT
GTTTATAGTGGCCTTAATTGTGGTCTTAAATTGTGAAAGCTTAAATTGTAGCTTCAAATTGTGAT
ATCAAAGAAAAAGAAA
Found at i:169482 original size:26 final size:26
Alignment explanation
Indices: 169443--169526 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
169433 TCCAAAATTG
* * * *
169443 TGTCCAAAACTATCGTTGTAGGAACT
1 TGTCCAAAACTATCGCTGCAAGAACA
*
169469 TGTCCAAAATTATCGCTGCAAGAACA
1 TGTCCAAAACTATCGCTGCAAGAACA
** *
169495 TGTCCAAAGTTGTCGCTGCATA-AACA
1 TGTCCAAAACTATCGCTGCA-AGAACA
169521 TGTCCA
1 TGTCCA
169527 GAGTTGTCGC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 49 0.98
27 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (26 bp):
TGTCCAAAACTATCGCTGCAAGAACA
Found at i:169531 original size:26 final size:26
Alignment explanation
Indices: 169464--169537 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
169454 ATCGTTGTAG
* * *
169464 GAACTTGTCCAAAATTATCGCTGCAA
1 GAACATGTCCAAAGTTGTCGCTGCAA
169490 GAACATGTCCAAAGTTGTCGCTGCATA
1 GAACATGTCCAAAGTTGTCGCTGCA-A
*
169517 -AACATGTCCAGAGTTGTCGCT
1 GAACATGTCCAAAGTTGTCGCT
169538 ATATGAGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 42 0.98
27 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (26 bp):
GAACATGTCCAAAGTTGTCGCTGCAA
Found at i:169750 original size:34 final size:34
Alignment explanation
Indices: 169703--169801 Score: 180
Period size: 34 Copynumber: 2.9 Consensus size: 34
169693 GAGGGATATA
* *
169703 AATACTCACAAGGAAAGAGCAAAATACAAACTCT
1 AATACTCATAAGGAAATAGCAAAATACAAACTCT
169737 AATACTCATAAGGAAATAGCAAAATACAAACTCT
1 AATACTCATAAGGAAATAGCAAAATACAAACTCT
169771 AATACTCATAAGGAAATAGCAAAATACAAAC
1 AATACTCATAAGGAAATAGCAAAATACAAAC
169802 ACACACACTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.17
Consensus pattern (34 bp):
AATACTCATAAGGAAATAGCAAAATACAAACTCT
Found at i:171365 original size:12 final size:11
Alignment explanation
Indices: 171343--171399 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
171333 AACATCCAAT
171343 ATAAAGACAAC
1 ATAAAGACAAC
*
171354 ATTAAAGGCAAC
1 A-TAAAGACAAC
171366 ATAAAG-CAGAC
1 ATAAAGACA-AC
* *
171377 ATAAAGTCATC
1 ATAAAGACAAC
*
171388 ATAAAGCCAAC
1 ATAAAGACAAC
171399 A
1 A
171400 AAACACAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 2 0.05
11 25 0.64
12 12 0.31
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.14
Consensus pattern (11 bp):
ATAAAGACAAC
Found at i:171390 original size:22 final size:22
Alignment explanation
Indices: 171343--171399 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
171333 AACATCCAAT
171343 ATAAAGACAACATTAAAGGCAAC
1 ATAAAG-CAACATTAAAGGCAAC
* *
171366 ATAAAGCAGACA-TAAAGTCATC
1 ATAAAGCA-ACATTAAAGGCAAC
171388 ATAAAGCCAACA
1 ATAAAG-CAACA
171400 AAACACAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.14
Consensus pattern (22 bp):
ATAAAGCAACATTAAAGGCAAC
Found at i:171490 original size:24 final size:24
Alignment explanation
Indices: 171438--171493 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
171428 TAGGGTATTA
*
171438 AAAAAACAACATATAAAACAAAAT
1 AAAAAACAACATACAAAACAAAAT
* * *
171462 AAAAAATAACATACAAAATAATAT
1 AAAAAACAACATACAAAACAAAAT
*
171486 TAAAAACA
1 AAAAAACA
171494 TTATACAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (24 bp):
AAAAAACAACATACAAAACAAAAT
Found at i:173746 original size:40 final size:41
Alignment explanation
Indices: 173682--173764 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 41
173672 AAATCATACA
* * *
173682 AATATTTAAATAACCATAAGTC-AAAATAAAAAATGAAAATC
1 AATATTGAAATAACCATAAATCAAAAAT-AAAAATCAAAATC
* *
173723 AATATTGAAA-AACCCTAAATCAAAAATCAAAATCAAAATC
1 AATATTGAAATAACCATAAATCAAAAATAAAAATCAAAATC
173763 AA
1 AA
173765 AATCAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 22 0.61
41 14 0.39
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (41 bp):
AATATTGAAATAACCATAAATCAAAAATAAAAATCAAAATC
Found at i:173755 original size:47 final size:47
Alignment explanation
Indices: 173702--173798 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 47
173692 TAACCATAAG
*
173702 TCAAAATAAAAAATGAAAATC-AATATTGAA-AAACCCTAAATCAAAAA
1 TCAAAAT-AAAAATCAAAATCAAAT-TTGAATAAACCCTAAATCAAAAA
* *
173749 TCAAAATCAAAATCAAAATCAAATTTGAATAAACCCTAAATTAAAAA
1 TCAAAATAAAAATCAAAATCAAATTTGAATAAACCCTAAATCAAAAA
173796 TCA
1 TCA
173799 CAATCCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
46 16 0.36
47 29 0.64
ACGTcount: A:0.61, C:0.14, G:0.03, T:0.22
Consensus pattern (47 bp):
TCAAAATAAAAATCAAAATCAAATTTGAATAAACCCTAAATCAAAAA
Found at i:173756 original size:6 final size:6
Alignment explanation
Indices: 173739--173771 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
173729 GAAAAACCCT
173739 AAATCAA AAATCA AAATCA AAATCA AAATCA AA
1 AAATC-A AAATCA AAATCA AAATCA AAATCA AA
173772 TTTGAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATCA
Found at i:180281 original size:3 final size:3
Alignment explanation
Indices: 180273--180297 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
180263 TCTAAAAATA
180273 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
180298 TTTCTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:180500 original size:20 final size:21
Alignment explanation
Indices: 180477--180518 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
180467 AATATATTCT
180477 AAATCTAAAAAGT-AAAAAAA
1 AAATCTAAAAAGTGAAAAAAA
*
180497 AAATGTAAAAAGTGAAAAAAA
1 AAATCTAAAAAGTGAAAAAAA
180518 A
1 A
180519 TCAATAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (21 bp):
AAATCTAAAAAGTGAAAAAAA
Found at i:180881 original size:21 final size:21
Alignment explanation
Indices: 180855--180900 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
180845 TTTTTAACTT
*
180855 AAACCTTAAA-TCTAAAATCTC
1 AAACCTTAAATTC-AAAACCTC
180876 AAACCTTAAATTCAAAACCTC
1 AAACCTTAAATTCAAAACCTC
180897 AAAC
1 AAAC
180901 TCTAAACTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCTTAAATTCAAAACCTC
Found at i:181377 original size:17 final size:18
Alignment explanation
Indices: 181345--181379 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
181335 TTGTTTTTGA
*
181345 ATTTTTGAATTATTTTTT
1 ATTTTTAAATTATTTTTT
181363 ATTTTTAAATT-TTTTTT
1 ATTTTTAAATTATTTTTT
181380 GAAACTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTTAAATTATTTTTT
Found at i:181398 original size:39 final size:37
Alignment explanation
Indices: 181323--181414 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
181313 CTTTGTATAC
* * *
181323 ATTTTTGAAATTTTGTTTTTGAATTTTTGAATTATTTTTT
1 ATTTTT-AAATTTTG-TTTTGAACTTTTGAAATA-TTTAT
181363 ATTTTTAAATTTT-TTTTGAAACTTTTGATAATATTTAT
1 ATTTTTAAATTTTGTTTTG-AACTTTTGA-AATATTTAT
181401 -TTTTTAAATTTTGT
1 ATTTTTAAATTTTGT
181415 ACAATATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
37 17 0.37
38 13 0.28
39 10 0.22
40 6 0.13
ACGTcount: A:0.26, C:0.01, G:0.08, T:0.65
Consensus pattern (37 bp):
ATTTTTAAATTTTGTTTTGAACTTTTGAAATATTTAT
Found at i:181420 original size:25 final size:26
Alignment explanation
Indices: 181374--181422 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
181364 TTTTTAAATT
*
181374 TTTTTTGAAACTTTTGATAATATTTA
1 TTTTTTGAAACTTTTGACAATATTTA
181400 TTTTTT-AAA-TTTTGTACAATATT
1 TTTTTTGAAACTTTTG-ACAATATT
181423 ATAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (26 bp):
TTTTTTGAAACTTTTGACAATATTTA
Found at i:184127 original size:38 final size:38
Alignment explanation
Indices: 184076--184151 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
184066 ATACCCGGAA
184076 TTGCAAGCCAGCCTATATGAATGTTGAAACTAGACAAT
1 TTGCAAGCCAGCCTATATGAATGTTGAAACTAGACAAT
184114 TTGCAAGCCAGCCTATATGAATGTTGAAACTAGACAAT
1 TTGCAAGCCAGCCTATATGAATGTTGAAACTAGACAAT
184152 CTTTTGAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (38 bp):
TTGCAAGCCAGCCTATATGAATGTTGAAACTAGACAAT
Found at i:194509 original size:22 final size:22
Alignment explanation
Indices: 194481--194548 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
194471 TGCACCAATG
** *
194481 AACGGAGAGCACCGAGGTGCTA
1 AACGGAGAGCACAAACGTGCTA
194503 AACGGAGAGCACAAACGTGCTA
1 AACGGAGAGCACAAACGTGCTA
*
194525 AACGGAGAGCACTACACGTGCTA
1 AACGGAGAGCAC-AAACGTGCTA
194548 A
1 A
194549 TAAACAGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 31 0.76
23 10 0.24
ACGTcount: A:0.37, C:0.24, G:0.29, T:0.10
Consensus pattern (22 bp):
AACGGAGAGCACAAACGTGCTA
Found at i:194788 original size:16 final size:16
Alignment explanation
Indices: 194769--194803 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
194759 ATTTCTATAC
194769 TAAAAATT-ATAACATT
1 TAAAAATTAATAA-ATT
194785 TAAAAATTAATAAATT
1 TAAAAATTAATAAATT
194801 TAA
1 TAA
194804 TCTTAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATTAATAAATT
Found at i:204131 original size:15 final size:14
Alignment explanation
Indices: 204100--204138 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
204090 GTGGCAAAAA
*
204100 GGGAGGGGA-AAGG
1 GGGAAGGGAGAAGG
*
204113 GGAAAGGGAGAAGG
1 GGGAAGGGAGAAGG
204127 GGGAAGGGAGAA
1 GGGAAGGGAGAA
204139 AAACTTTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (14 bp):
GGGAAGGGAGAAGG
Found at i:204433 original size:33 final size:30
Alignment explanation
Indices: 204360--204442 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 30
204350 ATAAAAATTT
* *
204360 AATTTTTTATATAT-TATTTTGACTTTTTA
1 AATTTTTTATTTATATATTTTGAATTTTTA
* *
204389 AAATTTATATTTATATATTTTAGAATTTTATA
1 AATTTTTTATTTATATATTTT-GAATTTT-TA
* *
204421 GAATTTTTTATTTTTAAATTTT
1 -AATTTTTTATTTATATATTTT
204443 TAAAAAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 11 0.26
30 6 0.14
31 6 0.14
32 2 0.05
33 17 0.40
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.63
Consensus pattern (30 bp):
AATTTTTTATTTATATATTTTGAATTTTTA
Found at i:213023 original size:59 final size:59
Alignment explanation
Indices: 212908--213094 Score: 191
Period size: 59 Copynumber: 3.2 Consensus size: 59
212898 TAATAAATTT
** * * *
212908 AGGTACCAAATTAACTCTTAAAAAAAGTCAGATACCAAATTAGAAAAAAATATCAAGTTC
1 AGGTACCAAATTAGGTC-TAAAAAAAATTAGGTACCAAATTAGAAAAAAATATCAAGTTC
* * * *
212968 AGGTACCAAATTAGGTCTAAAAAAAATTAGGTATCAAATTAGGAAAAACTTTCAAGTTC
1 AGGTACCAAATTAGGTCTAAAAAAAATTAGGTACCAAATTAGAAAAAAATATCAAGTTC
* ** * * *
213027 AGGTAACAAATT-GAGTC-AAAAAAGTTTAGGTACCAGATTA-AAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAG-GTCTAAAAAAAATTAGGTACCAAATTAGAAAAAAATATCAAGTTC
*
213084 AGGTATCAAAT
1 AGGTACCAAAT
213095 GTTATATTAA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
57 24 0.22
58 20 0.19
59 49 0.45
60 15 0.14
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (59 bp):
AGGTACCAAATTAGGTCTAAAAAAAATTAGGTACCAAATTAGAAAAAAATATCAAGTTC
Found at i:215753 original size:95 final size:95
Alignment explanation
Indices: 215590--215781 Score: 384
Period size: 95 Copynumber: 2.0 Consensus size: 95
215580 AAGCAGTGCA
215590 TTAGTAATGAAGATCCCTTCCCTAACATGGCATTACAGCAAGGGTTGTCAAAGGTTGGGTGGTTT
1 TTAGTAATGAAGATCCCTTCCCTAACATGGCATTACAGCAAGGGTTGTCAAAGGTTGGGTGGTTT
215655 GGTGGGGGCGGACGAAGACAATAGCAAAGT
66 GGTGGGGGCGGACGAAGACAATAGCAAAGT
215685 TTAGTAATGAAGATCCCTTCCCTAACATGGCATTACAGCAAGGGTTGTCAAAGGTTGGGTGGTTT
1 TTAGTAATGAAGATCCCTTCCCTAACATGGCATTACAGCAAGGGTTGTCAAAGGTTGGGTGGTTT
215750 GGTGGGGGCGGACGAAGACAATAGCAAAGT
66 GGTGGGGGCGGACGAAGACAATAGCAAAGT
215780 TT
1 TT
215782 TTGCTTTATA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (95 bp):
TTAGTAATGAAGATCCCTTCCCTAACATGGCATTACAGCAAGGGTTGTCAAAGGTTGGGTGGTTT
GGTGGGGGCGGACGAAGACAATAGCAAAGT
Found at i:219186 original size:108 final size:108
Alignment explanation
Indices: 218993--219207 Score: 322
Period size: 108 Copynumber: 2.0 Consensus size: 108
218983 ACGAGGGTGC
* *
218993 ATCTTGAGGCTCTTATCAGGTTCTGCATGTACATCATCAGCCAGTTCAGTTTCAGCAGATTTTTT
1 ATCTTGAGGCTCCTATCAGGTTCTGCAAGTACATCATCAGCCAGTTCAGTTTCAGCAGATTTTTT
* *
219058 TTCATTATTCTTCTCAAGAACAGCCGCATCTTTCAAGTTACAT
66 TTCATTATCCTTCTCAAGAACAGCCGCATCTGTCAAGTTACAT
* * * *
219101 ATCTTGAGGCTCCTATCAGGTTCTGCAAGTACATTATCTGCCGGTTCAGTTTTAGCAGATTTTTT
1 ATCTTGAGGCTCCTATCAGGTTCTGCAAGTACATCATCAGCCAGTTCAGTTTCAGCAGATTTTTT
* ** *
219166 TTCATTATCCTTCTCCAGAACAGTTGCATCTGTCAATTTACA
66 TTCATTATCCTTCTCAAGAACAGCCGCATCTGTCAAGTTACA
219208 CAACTTAGTT
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 95 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (108 bp):
ATCTTGAGGCTCCTATCAGGTTCTGCAAGTACATCATCAGCCAGTTCAGTTTCAGCAGATTTTTT
TTCATTATCCTTCTCAAGAACAGCCGCATCTGTCAAGTTACAT
Found at i:221089 original size:19 final size:19
Alignment explanation
Indices: 221038--221089 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
221028 TAATATATAT
*
221038 TATAAATATATTTA-ATAG
1 TATAAATATATTTATTTAG
221056 TAT-AATATA-TTATTTA-
1 TATAAATATATTTATTTAG
221072 TATAAATATGATTTATTT
1 TATAAATAT-ATTTATTT
221090 CTTAATAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.21
17 13 0.45
18 4 0.14
19 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
TATAAATATATTTATTTAG
Found at i:225735 original size:14 final size:14
Alignment explanation
Indices: 225695--225735 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
225685 TTATTTCACT
*
225695 AAAAATAATTTTCG
1 AAAAATAATTTTTG
225709 AAAAATAATTTTTG
1 AAAAATAATTTTTG
225723 AAAAATAATTTTT
1 AAAAATAATTTTT
225736 TTAAAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (14 bp):
AAAAATAATTTTTG
Found at i:226124 original size:38 final size:39
Alignment explanation
Indices: 226049--226124 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 39
226039 AAAATTGAAA
* * *
226049 TATTAAATAATTTATTAAAATAATAAATTTTATTAATTT
1 TATTAAATAATTTATTAAAATAATAAATATAAATAATTT
*
226088 TATT-AATAATTTATT-ATATGAATAAATATAAATAATT
1 TATTAAATAATTTATTAAAAT-AATAAATATAAATAATT
226125 AAATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.09
38 25 0.78
39 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
TATTAAATAATTTATTAAAATAATAAATATAAATAATTT
Found at i:226154 original size:26 final size:26
Alignment explanation
Indices: 226125--226181 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
226115 ATAAATAATT
226125 AAATAT-ATATGTTTAATAATATTGAA
1 AAATATAATAT-TTTAATAATATTGAA
* *
226151 AAATATAATATTTTAATAATTTTTAA
1 AAATATAATATTTTAATAATATTGAA
226177 AAATA
1 AAATA
226182 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AAATATAATATTTTAATAATATTGAA
Found at i:230402 original size:24 final size:23
Alignment explanation
Indices: 230366--230410 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
230356 ATAAATTATC
*
230366 ATAAAAAACTATAATTTTTTTTTT
1 ATAAAAAACTAT-ATTATTTTTTT
* *
230390 ATAAATAAGTATATTATTTTT
1 ATAAAAAACTATATTATTTTT
230411 ATAATATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATAAAAAACTATATTATTTTTTT
Found at i:232953 original size:20 final size:21
Alignment explanation
Indices: 232920--232958 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
232910 TAGAAAAATT
* *
232920 CTTATATAATATTT-TAAAAA
1 CTTATAAAAAATTTATAAAAA
232940 CTTATAAAAAATTTATAAA
1 CTTATAAAAAATTTATAAA
232959 TTATATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
CTTATAAAAAATTTATAAAAA
Found at i:233671 original size:22 final size:22
Alignment explanation
Indices: 233645--233686 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
233635 AGATTGAAAC
* *
233645 CTTGAATTTATTCATTAAATCT
1 CTTGAATTAATCCATTAAATCT
233667 CTTGAATTAATCCATTAAAT
1 CTTGAATTAATCCATTAAAT
233687 TTGTTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (22 bp):
CTTGAATTAATCCATTAAATCT
Found at i:236824 original size:16 final size:17
Alignment explanation
Indices: 236791--236829 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
236781 ACATATTATT
* *
236791 TATTTTAATAATTCAAA
1 TATTTAAATAATTAAAA
236808 TATTTAAATAA-TAAAA
1 TATTTAAATAATTAAAA
236824 TATTTA
1 TATTTA
236830 CCAATTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAAATAATTAAAA
Found at i:236986 original size:3 final size:3
Alignment explanation
Indices: 236978--237013 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
236968 AAGGGCCCAA
236978 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
237014 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:244869 original size:20 final size:20
Alignment explanation
Indices: 244844--244887 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
244834 TGTCAATGCA
244844 TTTTTACATTTACTT-TTATC
1 TTTTTACATTTACTTGTT-TC
*
244864 TTTTTACTTTTACTTGTTTC
1 TTTTTACATTTACTTGTTTC
244884 TTTT
1 TTTT
244888 AAATCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTACATTTACTTGTTTC
Found at i:244888 original size:13 final size:14
Alignment explanation
Indices: 244852--244888 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
244842 CATTTTTACA
244852 TTTACTTTTATCTT
1 TTTACTTTTATCTT
244866 TTTACTTTTA-CTT
1 TTTACTTTTATCTT
244879 GTTT-CTTTTA
1 -TTTACTTTTA
244889 AATCTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTACTTTTATCTT
Found at i:247190 original size:17 final size:18
Alignment explanation
Indices: 247147--247200 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
247137 ATGCATAGCA
*
247147 TTTAGTTGTCATTACATT
1 TTTAGTTGTCACTACATT
* *
247165 TTTAATTGTCACTGCA-T
1 TTTAGTTGTCACTACATT
* *
247182 TTTAGTTGTTAGTACATT
1 TTTAGTTGTCACTACATT
247200 T
1 T
247201 GCATTGTAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (18 bp):
TTTAGTTGTCACTACATT
Found at i:256923 original size:52 final size:50
Alignment explanation
Indices: 256698--256926 Score: 155
Period size: 49 Copynumber: 4.6 Consensus size: 50
256688 AGTAGTGATT
* * **
256698 TTTTAAGAAAAAAGTTTAGATTTTTTTAAAATAAAAATCTATTTTTTAGGTA
1 TTTTAAAAAAAAAGTTTA-A-ATTTTTAAAATAAAAAAGTATTTTTTAGGTA
* *** * **
256750 TTTTAAAAGAAAAAGTTTAAATTTTT-AAACAAAGTTGGATTTTTTAACTA
1 TTTTAAAA-AAAAAGTTTAAATTTTTAAAATAAAAAAGTATTTTTTAGGTA
* * ** * ** *
256800 TTTTGAAATAAAAGTTTTGATTTTT-AAGTAAAGTAGTGATATTTT---T-
1 TTTTAAAAAAAAAGTTTAAATTTTTAAAATAAAAAAGT-ATTTTTTAGGTA
* * *
256846 TTTAAAAAAAGAAACTTTAAATTTTTAAAAATAAAAAAATATTTTTTAGGTA
1 TTTTAAAAAA-AAAGTTTAAATTTTT-AAAATAAAAAAGTATTTTTTAGGTA
256898 TTTTAAAAGAAAAAGTTTAAATTTTTAAA
1 TTTTAAAA-AAAAAGTTTAAATTTTTAAA
256927 CAAATTTTGA
Statistics
Matches: 136, Mismatches: 31, Indels: 21
0.72 0.16 0.11
Matches are distributed among these distances:
46 7 0.05
47 13 0.10
48 6 0.04
49 30 0.22
50 30 0.22
51 9 0.07
52 29 0.21
53 12 0.09
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (50 bp):
TTTTAAAAAAAAAGTTTAAATTTTTAAAATAAAAAAGTATTTTTTAGGTA
Found at i:256952 original size:52 final size:51
Alignment explanation
Indices: 256739--256952 Score: 117
Period size: 52 Copynumber: 4.3 Consensus size: 51
256729 TAAAAATCTA
** *
256739 TTTTTTAGGTATTTTAAAAGAAAAAGTTTAAATTTTTAAACAAAGT-TGGA--
1 TTTTTTAACTATTTTAAAA-AAAAAGTTTAAATTTTTAAACAAA-TATTGATT
* * ** ** *
256789 TTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATAT
1 TTTTTTAACTATTTTAAAAAAAAAGTTTAAATTTTTAAACAAA-TATTGAT-T
* * *** *
256842 TTTTTT---TA----AAAAAAGAAACTTTAAATTTTTAAA-AATAAAAAAATA
1 TTTTTTAACTATTTTAAAAAA-AAAGTTTAAATTTTTAAACAA-ATATTGATT
** *
256887 TTTTTTAGGTATTTTAAAAGAAAAAGTTTAAATTTTTAAACAAATTTTGATT
1 TTTTTTAACTATTTTAAAA-AAAAAGTTTAAATTTTTAAACAAATATTGATT
256939 TTTTTTAACTATTT
1 TTTTTTAACTATTT
256953 CGAAATAAAA
Statistics
Matches: 119, Mismatches: 30, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
45 6 0.05
46 9 0.08
47 15 0.13
48 2 0.02
49 21 0.18
50 20 0.17
52 36 0.30
53 10 0.08
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.46
Consensus pattern (51 bp):
TTTTTTAACTATTTTAAAAAAAAAGTTTAAATTTTTAAACAAATATTGATT
Found at i:257173 original size:25 final size:24
Alignment explanation
Indices: 257126--257173 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
257116 AAAATAGTGA
* *
257126 TTTTGTTTTAAAAAAAGAGAAAAC
1 TTTTGTTTTAAAAAAACAAAAAAC
257150 TTTTGATTTTAAAAAAACAAAAAA
1 TTTTG-TTTTAAAAAAACAAAAAA
257174 AATTTCGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (24 bp):
TTTTGTTTTAAAAAAACAAAAAAC
Found at i:258388 original size:12 final size:12
Alignment explanation
Indices: 258373--258414 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
258363 CAGAAACAAC
258373 ACCAAAAATAGT
1 ACCAAAAATAGT
*
258385 ACC-AAAATAGC
1 ACCAAAAATAGT
258396 ACCAAAAATAGT
1 ACCAAAAATAGT
258408 ACCAAAA
1 ACCAAAA
258415 TTGCATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (12 bp):
ACCAAAAATAGT
Found at i:258393 original size:11 final size:11
Alignment explanation
Indices: 258377--258415 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
258367 AACAACACCA
258377 AAAATAGTACC
1 AAAATAGTACC
*
258388 AAAATAGCACC
1 AAAATAGTACC
258399 AAAAATAGTACC
1 -AAAATAGTACC
258411 AAAAT
1 AAAAT
258416 TGCATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.59, C:0.18, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAATAGTACC
Found at i:258399 original size:23 final size:23
Alignment explanation
Indices: 258372--258437 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
258362 TCAGAAACAA
258372 CACCAAAAATAGTACCAAAATAG
1 CACCAAAAATAGTACCAAAATAG
*
258395 CACCAAAAATAGTACCAAAATTG
1 CACCAAAAATAGTACCAAAATAG
** *
258418 CATAAAAAACAGTACCAAAA
1 CACCAAAAATAGTACCAAAA
258438 ACAACATCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.58, C:0.21, G:0.08, T:0.14
Consensus pattern (23 bp):
CACCAAAAATAGTACCAAAATAG
Found at i:259988 original size:22 final size:22
Alignment explanation
Indices: 259960--260001 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
259950 AATTGAGCCA
259960 ACCCGTTGACCAACCCGACTCG
1 ACCCGTTGACCAACCCGACTCG
*
259982 ACCCGTTGACCAACCTGACT
1 ACCCGTTGACCAACCCGACT
260002 TGAATCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.43, G:0.17, T:0.17
Consensus pattern (22 bp):
ACCCGTTGACCAACCCGACTCG
Found at i:260010 original size:22 final size:22
Alignment explanation
Indices: 259962--260010 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
259952 TTGAGCCAAC
*
259962 CCGTTGACCAACCCGACTCGAC
1 CCGTTGACCAACCCGACTCGAA
* *
259984 CCGTTGACCAACCTGACTTGAA
1 CCGTTGACCAACCCGACTCGAA
*
260006 TCGTT
1 CCGTT
260011 AACTTTGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (22 bp):
CCGTTGACCAACCCGACTCGAA
Found at i:260035 original size:28 final size:28
Alignment explanation
Indices: 260004--260085 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 28
259994 ACCTGACTTG
260004 AATCGTTAACTTTGATCTAACCGAACCA
1 AATCGTTAACTTTGATCTAACCGAACCA
* *
260032 AATCATTGAA-TTTGATCGAACCGAACCA
1 AATCGTT-AACTTTGATCTAACCGAACCA
260060 AA-CTGTTAACTTTGA-CTGAACCGAAC
1 AATC-GTTAACTTTGATCT-AACCGAAC
260086 ATTTGACAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.09
28 40 0.87
29 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (28 bp):
AATCGTTAACTTTGATCTAACCGAACCA
Found at i:265612 original size:21 final size:21
Alignment explanation
Indices: 265562--265612 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
265552 AAGTTTTTTT
*
265562 TATTGGTAGAAGTATGACATG
1 TATTGGTAGAAGTATCACATG
* * *
265583 T-TTCAGTAGAAGTCTCACTTG
1 TATT-GGTAGAAGTATCACATG
265604 TATTGGTAG
1 TATTGGTAG
265613 TACTGCTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (21 bp):
TATTGGTAGAAGTATCACATG
Found at i:270615 original size:22 final size:22
Alignment explanation
Indices: 270573--270615 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
270563 GATTGACCCA
**
270573 ACCCATTGACCAACCCGACTCG
1 ACCCATTGACCAACCAAACTCG
270595 ACCCATTGACCAACCAAACTC
1 ACCCATTGACCAACCAAACTC
270616 AAACCTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.44, G:0.09, T:0.14
Consensus pattern (22 bp):
ACCCATTGACCAACCAAACTCG
Found at i:270669 original size:28 final size:29
Alignment explanation
Indices: 270600--270669 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
270590 ACTCGACCCA
* *
270600 TTGACC-AACCAAACTCAAACCTTTGACT
1 TTGACCAAACCGAACTCAAACCGTTGACT
*
270628 TTGACCAAATCGAAC-CAAACCGTTGACT
1 TTGACCAAACCGAACTCAAACCGTTGACT
* *
270656 TTGATCGAACCGAA
1 TTGACCAAACCGAA
270670 TCATTGATCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 29 0.83
29 6 0.17
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.23
Consensus pattern (29 bp):
TTGACCAAACCGAACTCAAACCGTTGACT
Found at i:271372 original size:6 final size:6
Alignment explanation
Indices: 271337--271361 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
271327 TGATATATCA
271337 TGAGAT TGAGAT TGAGAT TGAGAT T
1 TGAGAT TGAGAT TGAGAT TGAGAT T
271362 AAAATTGAAA
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGAGAT
Found at i:271911 original size:4 final size:4
Alignment explanation
Indices: 271904--271944 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
271894 TATATATATT
271904 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
271945 ATAAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:278500 original size:15 final size:15
Alignment explanation
Indices: 278480--278513 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
278470 TAGCTTGAGT
*
278480 TTTTCTGTCTTTTTG
1 TTTTCTGTCTTATTG
278495 TTTTCTGTCTTATTG
1 TTTTCTGTCTTATTG
278510 TTTT
1 TTTT
278514 GTTCTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.12, G:0.12, T:0.74
Consensus pattern (15 bp):
TTTTCTGTCTTATTG
Found at i:279302 original size:35 final size:35
Alignment explanation
Indices: 279254--279320 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
279244 TGGAGGATAA
279254 GGGTGGTTCTGATGGGAATGGAATTAGGGACGACG
1 GGGTGGTTCTGATGGGAATGGAATTAGGGACGACG
*
279289 GGGTGGTTTTGATGGGAATGGAATTAGGGACG
1 GGGTGGTTCTGATGGGAATGGAATTAGGGACG
279321 GTAGGGTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.22, C:0.06, G:0.46, T:0.25
Consensus pattern (35 bp):
GGGTGGTTCTGATGGGAATGGAATTAGGGACGACG
Found at i:279328 original size:35 final size:35
Alignment explanation
Indices: 279253--279332 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
279243 ATGGAGGATA
279253 AGGGTGGTTCTGATGGGAATGGAATTAGGGACGAC
1 AGGGTGGTTCTGATGGGAATGGAATTAGGGACGAC
* * **
279288 GGGGTGGTTTTGATGGGAATGGAATTAGGGACGGT
1 AGGGTGGTTCTGATGGGAATGGAATTAGGGACGAC
279323 AGGGTGGTTC
1 AGGGTGGTTC
279333 AAGCTGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.21, C:0.06, G:0.46, T:0.26
Consensus pattern (35 bp):
AGGGTGGTTCTGATGGGAATGGAATTAGGGACGAC
Found at i:288103 original size:9 final size:9
Alignment explanation
Indices: 288089--288114 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
288079 TTAGTGTTGG
288089 GTTGATTGT
1 GTTGATTGT
288098 GTTGATTGT
1 GTTGATTGT
288107 GTTGATTG
1 GTTGATTG
288115 CTTGATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.54
Consensus pattern (9 bp):
GTTGATTGT
Found at i:293920 original size:195 final size:194
Alignment explanation
Indices: 293531--293978 Score: 508
Period size: 195 Copynumber: 2.3 Consensus size: 194
293521 TACCAGTACT
* * * * *
293531 CAATGCTGCTCACACGAGCTGTCGAGGACTCGCAACGTATGTGGTACCCCAGCCATCGGTACGGT
1 CAATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATAC-GA
* * * * * * * *
293596 GTTTGTCTGTACTATAAATTGTTCCCTAATGATGCTGCTCACACAAGCTGTCGAGAGTATGCATA
65 GTATCTATGCACTATAAACTGTTCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCATA
* * *
293661 AAGCATAGTCCCAGCCATCGTAAGGCATATAATCCATTTAGGATCCATATCTCTTTCTCGAGTCA
130 AAGCATAATCCCAGCCATCATAAGGCATATAATCCATTTAGGATCCATATCTCTTTCCCGAGTCA
*
293726 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATAC-AG
1 CAATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGAG
* * *
293790 TATCTATGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACACAAGCTATCTATAATATGCACTT
66 TATCTATGCACTATAAACTGTTCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCA-TA
* ** * * * * * * *
293853 ATGCATAAATCTTAGCCATCATAGGGCCTGTAATCCATTCTTGGATTCTTTTCTCATTTCCCGAG
130 AAGCAT-AATCCCAGCCATCATAAGGCATATAATCCATT-TAGGATCCATATCTC-TTTCCCGAG
293918 TCA
192 TCA
* * * *
293921 CAATGTTTCTCACATC-AGCTATCGAGGACTCACAACATATGCGGTACCTCAGCCATCG
1 CAATGCTGCTCACA-CGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
293979 CGTCGGTTTC
Statistics
Matches: 213, Mismatches: 35, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
191 41 0.19
192 9 0.04
193 32 0.15
194 11 0.05
195 119 0.56
196 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (194 bp):
CAATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGAG
TATCTATGCACTATAAACTGTTCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCATAA
AGCATAATCCCAGCCATCATAAGGCATATAATCCATTTAGGATCCATATCTCTTTCCCGAGTCA
Found at i:294475 original size:16 final size:16
Alignment explanation
Indices: 294451--294482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
294441 TCCTTACAAA
*
294451 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
294467 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
294483 AAAAATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:296851 original size:27 final size:27
Alignment explanation
Indices: 296819--296888 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
296809 TAATTTCAAT
296819 TTTTATTTTATTTTTATAATTTAATTA
1 TTTTATTTTATTTTTATAATTTAATTA
*
296846 TTTTATATTATTTTTATAATTTAATTA
1 TTTTATTTTATTTTTATAATTTAATTA
* *
296873 ATTTGTTTATATTTTT
1 TTTTATTT-TATTTTT
296889 TATGTGAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (27 bp):
TTTTATTTTATTTTTATAATTTAATTA
Found at i:299436 original size:20 final size:20
Alignment explanation
Indices: 299404--299455 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
299394 ATACCAAAAC
*
299404 CCTAATCTTAAAAATC-TAAA
1 CCTAAT-TTAAAAACCTTAAA
299424 TCCTAATTTAAAAACCTTAAA
1 -CCTAATTTAAAAACCTTAAA
299445 CCTAA-TTAAAA
1 CCTAATTTAAAA
299456 CAAAAAATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 13 0.45
21 10 0.34
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (20 bp):
CCTAATTTAAAAACCTTAAA
Found at i:300631 original size:21 final size:21
Alignment explanation
Indices: 300605--300644 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
300595 AACTCGTACT
* *
300605 TATATATATATATAATATATG
1 TATATATAGATACAATATATG
300626 TATATATAGATACAATATA
1 TATATATAGATACAATATA
300645 AATATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
TATATATAGATACAATATATG
Found at i:301036 original size:18 final size:18
Alignment explanation
Indices: 301015--301057 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
301005 AGTACGAATG
*
301015 GTTTGATTGGTACGATCA
1 GTTTGATTGGTACAATCA
* * *
301033 GTTTAATTGGTTCAATTA
1 GTTTGATTGGTACAATCA
301051 GTTTGAT
1 GTTTGAT
301058 CGGTTTGATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (18 bp):
GTTTGATTGGTACAATCA
Found at i:311495 original size:24 final size:24
Alignment explanation
Indices: 311468--311527 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
311458 TAGTGACCCT
311468 TTCCTTATCTCTCATTCTCTCACC
1 TTCCTTATCTCTCATTCTCTCACC
*
311492 TTCCTTATCTCTCCTTCTCTCACC
1 TTCCTTATCTCTCATTCTCTCACC
*
311516 ATCCTTATCTCT
1 TTCCTTATCTCT
311528 TCATATAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.12, C:0.42, G:0.00, T:0.47
Consensus pattern (24 bp):
TTCCTTATCTCTCATTCTCTCACC
Found at i:315117 original size:17 final size:17
Alignment explanation
Indices: 315081--315119 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
315071 AGGTGGAGAA
* *
315081 CTTGTTCGTTGAGAGCT
1 CTTGTTCGTAGAGAACT
*
315098 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAACT
315115 CTTGT
1 CTTGT
315120 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (17 bp):
CTTGTTCGTAGAGAACT
Found at i:315166 original size:41 final size:41
Alignment explanation
Indices: 315109--315204 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
315099 TTGTTCGTAG
* *
315109 AGAATTCTTGTCAAGGTGGAGATTTTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
315150 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
*
315191 AGAATTCTTATTAA
1 AGAATTCTTGTTAA
315205 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
Found at i:315899 original size:17 final size:17
Alignment explanation
Indices: 315879--315911 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
315869 GCTCAAGCAC
315879 AAAACAAAATAAAAATA
1 AAAACAAAATAAAAATA
*
315896 AAAACAAAGTAAAAAT
1 AAAACAAAATAAAAAT
315912 TTCTATGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAACAAAATAAAAATA
Found at i:317251 original size:69 final size:69
Alignment explanation
Indices: 317159--317663 Score: 377
Period size: 69 Copynumber: 7.4 Consensus size: 69
317149 AGTTTATAGT
* * * * ** * * * *
317159 TGGGAGCTTGAGCTCGCGTTAACTGTGTTGGAGGTTGTAGTTCTTCACTTGCAAGTCTTACTATG
1 TGGGAGCTT-TGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATG
*
317224 ACAAC
65 ACAGC
* * * * *
317229 TGGGAGCTTTGCTCTCACTAACTATGTTGGAGGCTGCGGCTCTTCACCTGGGAGCCTTAATATAA
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATGA
* *
317294 TAGT
66 CAGC
* * *
317298 TGGGAGCTTTACTCTCGCTAACTATGTTGGAGGCTGTGGCTCTTCAGCTAT--GAGCCTTAATAT
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCA-CT-TGCGAGCCTTAATAT
*
317361 TACAGC
64 GACAGC
* * * * * *
317367 TGAGAACTTTGCTCTCGCTAACTGTGTTAGAGGCTACGGCTTTTCACCTGCGAGCCTTAATATGA
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATGA
*
317432 CAGT
66 CAGC
** * * * ** *
317436 TGATAGCTTT-CTCTCGCTAACTGTCTTGAAGGCTACAACTCTTCACTTGTGAGCCTTAATATGA
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATGA
*
317500 CAGG
66 CAGC
** ** * *
317504 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTATGATTCTTCAC---CTA-CCTTAATGTGA
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATGA
**
317565 CAAT
66 CAGC
* * * * ** * * *
317569 TAGGAGCTTTGCTCTTGTTAACTGTGTTGGAGGCTACGATTTTTCAC---C-TGCCTTAATTTGA
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATGA
317630 CAGC
66 CAGC
* * *
317634 CGGGAGCTTTGCTCTCACTAATTGT-TTGGA
1 TGGGAGCTTTGCTCTCGCTAACTGTGTTGGA
317664 CATCGAAGGT
Statistics
Matches: 355, Mismatches: 74, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
64 5 0.01
65 86 0.24
66 1 0.00
67 1 0.00
68 58 0.16
69 193 0.54
70 10 0.03
71 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (69 bp):
TGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCACTTGCGAGCCTTAATATGA
CAGC
Found at i:317342 original size:138 final size:136
Alignment explanation
Indices: 317154--317663 Score: 446
Period size: 138 Copynumber: 3.8 Consensus size: 136
317144 GCTTGAGTTT
* * * * * *
317154 ATAGTTGGGAGCTTGAGCTCGCGTTAACTGTGTTGGAGGTTGTAGTTCTTCACTTGCAAGTCTTA
1 ATAGTTGGGAGCTTTA-CTCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCACTTG--AGCCTTA
* * * * * *
317219 CTATGACAACTGGGAGCTTTGCTCTCACTAACTATGTTGGAGGCTGCGGCTCTTCACCTGGGAGC
63 ATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTACGGCTCTTCACCTGCGAGC
317284 CTTAATATA
128 CTTAATATA
* *
317293 ATAGTTGGGAGCTTTACTCTCGCTAACTATGTTGGAGGCTGTGGCTCTTCAGCTATGAGCCTTAA
1 ATAGTTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCA-CT-TGAGCCTTAA
* * * * *
317358 TATTACAGCTGAGAACTTTGCTCTCGCTAACTGTGTTAGAGGCTACGGCTTTTCACCTGCGAGCC
64 TATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTACGGCTCTTCACCTGCGAGCC
*
317423 TTAATATG
129 TTAATATA
* ** * * ** *
317431 ACAGTTGATAGCTTT-CTCTCGCTAACTGTCTTGAAGGCTACAACTCTTCACTTGTGAGCCTTAA
1 ATAGTTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCAC-T-TGAGCCTTAA
* * **
317495 TATGACAGGTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTATGATTCTTCACCT---A-CC
64 TATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTACGGCTCTTCACCTGCGAGCC
* *
317556 TTAATGTG
129 TTAATATA
* * * * * * * * *
317564 ACAATTAGGAGCTTTGCTCTTGTTAACTGTGTTGGAGGC--TACGATTTTTCACCT--GCCTTAA
1 ATAGTTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGCTGTA-G-CTCTTCACTTGAGCCTTAA
* * * *
317625 TTTGACAGCCGGGAGCTTTGCTCTCACTAATTGT-TTGGA
64 TATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGA
317664 CATCGAAGGT
Statistics
Matches: 306, Mismatches: 59, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
129 5 0.02
130 36 0.12
132 2 0.01
133 20 0.07
134 26 0.08
136 1 0.00
137 88 0.29
138 109 0.36
139 17 0.06
140 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (136 bp):
ATAGTTGGGAGCTTTACTCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCACTTGAGCCTTAATA
TGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTACGGCTCTTCACCTGCGAGCCTT
AATATA
Found at i:317550 original size:137 final size:138
Alignment explanation
Indices: 317200--317552 Score: 397
Period size: 137 Copynumber: 2.6 Consensus size: 138
317190 AGGTTGTAGT
** * * * * * *
317200 TCTTCACTTGCAAGTCTTACTATGACAACTGGGAGCTTTGCTCTCACTAACTATGTTGGAGGCTG
1 TCTTCACTTGTGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTA
** * * * * *
317265 CGGCTCTTCACCTGGGAGCCTTAATATAATAGTTGGGAGCTTTACTCTCGCTAACTATGTTGGAG
66 CGATTCTTCACCTGCGAGCCTTAATATAACAGTTGAGAGCTTTACTCTCGCTAACTATCTTGAAG
****
317330 GCTGTGGC
131 GCTACAAC
* * * * *
317338 TCTTCAGC-TATGAGCCTTAATATTACAGCTGAGAACTTTGCTCTCGCTAACTGTGTTAGAGGCT
1 TCTTCA-CTTGTGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCT
* * * *
317402 ACGGCTT-TTCACCTGCGAGCCTTAATATGACAGTTGATAGCTTT-CTCTCGCTAACTGTCTTGA
65 AC-GATTCTTCACCTGCGAGCCTTAATATAACAGTTGAGAGCTTTACTCTCGCTAACTATCTTGA
317465 AGGCTACAAC
129 AGGCTACAAC
*
317475 TCTTCACTTGTGAGCCTTAATATGACAGGTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTA
1 TCTTCACTTGTGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTA
*
317540 TGATTCTTCACCT
66 CGATTCTTCACCT
317553 ACCTTAATGT
Statistics
Matches: 176, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
136 4 0.02
137 86 0.49
138 83 0.47
139 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (138 bp):
TCTTCACTTGTGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTA
CGATTCTTCACCTGCGAGCCTTAATATAACAGTTGAGAGCTTTACTCTCGCTAACTATCTTGAAG
GCTACAAC
Found at i:317591 original size:65 final size:65
Alignment explanation
Indices: 317373--317663 Score: 230
Period size: 65 Copynumber: 4.4 Consensus size: 65
317363 CAGCTGAGAA
* * * *
317373 CTTTGCTCTCGCTAACTGTGTTAGAGGCTACGGCTT-TTCACCTGCGAGCCTTAATATGACAGTT
1 CTTTGCTCTCGCTAACTGTGTTGGAGGCTAC-GATTCTTCACCT---A-CCTTAATGTGACAATT
*
317437 -GATAG
61 AG-GAG
* * * * * * ** *
317442 CTTT-CTCTCGCTAACTGTCTTGAAGGCTACAACTCTTCACTTGTGAGCCTTAATATGACAGGTG
1 CTTTGCTCTCGCTAACTGTGTTGGAGGCTACGATTCTTCAC--CT-A-CCTTAATGTGACAATTA
317506 GGAG
62 GGAG
*
317510 CTTTGCTCTCGCTAACTGTGTTGGAGGCTATGATTCTTCACCTACCTTAATGTGACAATTAGGAG
1 CTTTGCTCTCGCTAACTGTGTTGGAGGCTACGATTCTTCACCTACCTTAATGTGACAATTAGGAG
* * * * * ****
317575 CTTTGCTCTTGTTAACTGTGTTGGAGGCTACGATTTTTCACCTGCCTTAATTTGACAGCCGGGAG
1 CTTTGCTCTCGCTAACTGTGTTGGAGGCTACGATTCTTCACCTACCTTAATGTGACAATTAGGAG
* *
317640 CTTTGCTCTCACTAATTGT-TTGGA
1 CTTTGCTCTCGCTAACTGTGTTGGA
317664 CATCGAAGGT
Statistics
Matches: 184, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
64 5 0.03
65 87 0.47
66 1 0.01
67 2 0.01
68 52 0.28
69 36 0.20
70 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (65 bp):
CTTTGCTCTCGCTAACTGTGTTGGAGGCTACGATTCTTCACCTACCTTAATGTGACAATTAGGAG
Found at i:319751 original size:16 final size:14
Alignment explanation
Indices: 319738--319799 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
319728 AAAGAGAATG
*
319738 AAAAAAAA-AAAGA
1 AAAAAAAAGAAAAA
319751 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
319765 AAAAGAAAAGCTAAAAGA
1 AAAA-AAAAG--AAAA-A
* *
319783 ACATAAAAGAAAAA
1 AAAAAAAAGAAAAA
319797 AAA
1 AAA
319800 TTAAATTGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.20
14 11 0.28
15 9 0.22
17 9 0.22
18 3 0.08
ACGTcount: A:0.84, C:0.03, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:319755 original size:10 final size:10
Alignment explanation
Indices: 319740--319799 Score: 75
Period size: 10 Copynumber: 5.8 Consensus size: 10
319730 AGAGAATGAA
319740 AAAAAAAAAG
1 AAAAAAAAAG
319750 AAAAAAAAAG
1 AAAAAAAAAG
319760 AAAAAAAAAG
1 AAAAAAAAAG
*
319770 AAAAGCTAAAAG
1 AAAA--AAAAAG
* *
319782 AACATAAAAG
1 AAAAAAAAAG
319792 AAAAAAAA
1 AAAAAAAA
319800 TTAAATTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
10 36 0.82
12 8 0.18
ACGTcount: A:0.83, C:0.03, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:320272 original size:2 final size:2
Alignment explanation
Indices: 320265--320292 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
320255 CCTTTGTTTA
320265 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
320293 GCCTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321249 original size:5 final size:5
Alignment explanation
Indices: 321241--321294 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
321231 AAGAAAAAAC
* * * *
321241 AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAA AGAAA AGAAA AGAAA
1 AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT
321291 AGAA
1 AGAA
321295 AAAAAATCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (5 bp):
AGAAT
Found at i:321295 original size:5 final size:5
Alignment explanation
Indices: 321229--321300 Score: 67
Period size: 5 Copynumber: 14.8 Consensus size: 5
321219 TCGATCTTGA
* * * * * * *
321229 AAAAG AAAA- AACAG AATAG AATAG AATAG AATAG AATAG AATAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
321278 AAAAG AAAAG AAAAG AAAA- AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAA
321301 TCCTCACATA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
4 7 0.11
5 56 0.89
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (5 bp):
AAAAG
Found at i:323713 original size:255 final size:255
Alignment explanation
Indices: 323260--323764 Score: 920
Period size: 255 Copynumber: 2.0 Consensus size: 255
323250 AGGCCATATC
323260 GACTTCAATGGCTTAATAATGGAGTCGAAGTTAAGGTAAATAGACAAATTCTCGTTTCTTTTAAA
1 GACTTCAATGGCTTAATAATGGAGTCGAAGTTAAGGTAAATAGACAAATTCTCGTTTCTTTTAAA
* * *
323325 ATTGGGAAGTATAAGGATGAAATTTGTTGTGATGTGCTGCCCATGCAAGTTGCCCATTTGTTATT
66 ATTAGGAACTATAAGGATGAAATTTGTTGTGATGTGCTGCCCATGCAAGCTGCCCATTTGTTATT
323390 TGGCCGTCCATGGCAATATGATAGAGATGTGCAACACCATGGCAAGCTAAATCGATATTCCCTCA
131 TGGCCGTCCATGGCAATATGATAGAGATGTGCAACACCATGGCAAGCTAAATCGATATTCCCTCA
*
323455 TCTTCAAAGGGAAAATGTACACTTTAATACCGTTGACACCCAAAGAAGTTCATGAAAATT
196 TCTTCAAAGAGAAAATGTACACTTTAATACCGTTGACACCCAAAGAAGTTCATGAAAATT
* *
323515 GACTTCAATGGCTTAATGATGGCGTCGAAGTTAAGGTAAATAGACAAATTCTCGTTTCTTTTAAA
1 GACTTCAATGGCTTAATAATGGAGTCGAAGTTAAGGTAAATAGACAAATTCTCGTTTCTTTTAAA
* * *
323580 ATTAGGAACTATAAGGTTGAAATTTGTTGTGATGTGGTGCCCATGCCAGCTGCCCATTTGTTATT
66 ATTAGGAACTATAAGGATGAAATTTGTTGTGATGTGCTGCCCATGCAAGCTGCCCATTTGTTATT
*
323645 TGGCCGTCCATGGCAATATGATAGAGATGTGCAACACCATGGCAAGCTAAATCGATATTCCTTCA
131 TGGCCGTCCATGGCAATATGATAGAGATGTGCAACACCATGGCAAGCTAAATCGATATTCCCTCA
323710 TCTTCAAAGAGAAAATGTACACTTTAATACCGTTGACACCCAAAGAAGTTCATGA
196 TCTTCAAAGAGAAAATGTACACTTTAATACCGTTGACACCCAAAGAAGTTCATGA
323765 CAAACAACTC
Statistics
Matches: 240, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
255 240 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (255 bp):
GACTTCAATGGCTTAATAATGGAGTCGAAGTTAAGGTAAATAGACAAATTCTCGTTTCTTTTAAA
ATTAGGAACTATAAGGATGAAATTTGTTGTGATGTGCTGCCCATGCAAGCTGCCCATTTGTTATT
TGGCCGTCCATGGCAATATGATAGAGATGTGCAACACCATGGCAAGCTAAATCGATATTCCCTCA
TCTTCAAAGAGAAAATGTACACTTTAATACCGTTGACACCCAAAGAAGTTCATGAAAATT
Found at i:326811 original size:48 final size:45
Alignment explanation
Indices: 326759--326955 Score: 189
Period size: 48 Copynumber: 4.1 Consensus size: 45
326749 ATAAATAAAG
*
326759 TTGTTTATTAATGCTTCATTAAGTGTTTTTTTTTTGTTAAATGCATCT
1 TTGTTTATTAATGCTT-ATTAAGTG--TTTTGTTTGTTAAATGCATCT
* *
326807 TTGTTTAATAATCTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCT
1 TTGTTTATTAA--TGC-TTATTAAGTGTTTTGTTTGTTAAATGCATCT
* * *
326855 TTGTTTAGTAAT-CTATATTATTAACTATTTTGTTTGTTAAATGCATCT
1 TTGTTTATTAATGC----TTATTAAGTGTTTTGTTTGTTAAATGCATCT
* * *
326903 TTGTTTAGTAATATGCATTATTAACTGTTTTGTTTGTTAAATGCACCT
1 TTGTTTA-TTA-ATGC-TTATTAAGTGTTTTGTTTGTTAAATGCATCT
326951 TTGTT
1 TTGTT
326956 AAATGCCTTG
Statistics
Matches: 129, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
45 1 0.01
46 1 0.01
48 111 0.86
49 1 0.01
50 13 0.10
51 2 0.02
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (45 bp):
TTGTTTATTAATGCTTATTAAGTGTTTTGTTTGTTAAATGCATCT
Found at i:326970 original size:48 final size:48
Alignment explanation
Indices: 326786--326959 Score: 222
Period size: 48 Copynumber: 3.6 Consensus size: 48
326776 ATTAAGTGTT
* * * * *
326786 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAGTG
1 TTTTGTTTGTTAAATGCATCTTTGTTAAATAATATGCATTATTAACTG
* * * ** *
326834 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTATATTATTAACTA
1 TTTTGTTTGTTAAATGCATCTTTGTTAAATAATATGCATTATTAACTG
* *
326882 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTG
1 TTTTGTTTGTTAAATGCATCTTTGTTAAATAATATGCATTATTAACTG
*
326930 TTTTGTTTGTTAAATGCACCTTTGTTAAAT
1 TTTTGTTTGTTAAATGCATCTTTGTTAAAT
326960 GCCTTGCATT
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 112 1.00
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (48 bp):
TTTTGTTTGTTAAATGCATCTTTGTTAAATAATATGCATTATTAACTG
Done.