Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009007.1 Hibiscus syriacus cultivar Beakdansim tig00112392_pilon, 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: 93860
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5204 original size:5 final size:5
Alignment explanation
Indices: 5194--5290 Score: 77
Period size: 5 Copynumber: 17.8 Consensus size: 5
5184 AACGGTCAAC
* * *
5194 GGTCG GGTCG GGTCG GGTCAAC GATCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
* *
5243 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
5291 AGACCGGTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
5 59 0.80
7 15 0.20
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:5221 original size:17 final size:17
Alignment explanation
Indices: 5221--5291 Score: 97
Period size: 17 Copynumber: 3.9 Consensus size: 17
5211 TCAACGATCG
5221 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA----C
5242 GGGTCGGGTCGGGTCAAC
1 G-GTCGGGTCGGGTCAAC
5260 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
5277 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
5292 GACCGGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 31 0.63
18 2 0.04
21 1 0.02
22 15 0.31
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:5236 original size:44 final size:39
Alignment explanation
Indices: 5187--5290 Score: 163
Period size: 39 Copynumber: 2.5 Consensus size: 39
5177 AACGGTTAAC
5187 GGTCAACGGTCGGGTCGGGTCGGGTCAACGATCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTC-A--A-C-GGTCGGGTCG
5231 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
5270 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
5291 AGACCGGTCA
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
39 31 0.52
40 1 0.02
41 1 0.02
43 1 0.02
44 26 0.43
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (39 bp):
GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
Found at i:5286 original size:22 final size:22
Alignment explanation
Indices: 5187--5273 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
5177 AACGGTTAAC
5187 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
5209 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5231 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5253 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
5274 AACGGTCGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:5311 original size:19 final size:19
Alignment explanation
Indices: 5289--5386 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
5279 TCGGGTCGGG
5289 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
5308 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
5327 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
5346 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
5366 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
5386 T
1 T
5387 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:5317 original size:10 final size:9
Alignment explanation
Indices: 5287--5385 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
5277 GGTCGGGTCG
*
5287 GGTCAGACC
1 GGTCAAACC
5296 GGTCAAACC
1 GGTCAAACC
*
5305 GGTTCAGACC
1 GG-TCAAACC
5315 GGTCAAACC
1 GGTCAAACC
*
5324 GGTTCGAACC
1 GG-TCAAACC
*
5334 GGTTGAAACC
1 GG-TCAAACC
5344 GGTCAAACC
1 GGTCAAACC
5353 GGTCAGAACC
1 GGTCA-AACC
*
5363 GGTTGAAAACC
1 GG-T-CAAACC
*
5374 GGTTAAACC
1 GGTCAAACC
5383 GGT
1 GGT
5386 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:5344 original size:29 final size:28
Alignment explanation
Indices: 5288--5385 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
5278 GTCGGGTCGG
* * *
5288 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
5316 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
5345 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
5375 GTTAAACCGGT
1 GTCAAACCGGT
5386 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:6317 original size:26 final size:26
Alignment explanation
Indices: 6281--6331 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
6271 GGTTTGAATC
6281 CTGACCTTACTTAAAAGATCTAGTAT
1 CTGACCTTACTTAAAAGATCTAGTAT
* **
6307 CTGATCTTACTTAAGGGATCTAGTA
1 CTGACCTTACTTAAAAGATCTAGTA
6332 CCTCATCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (26 bp):
CTGACCTTACTTAAAAGATCTAGTAT
Found at i:8951 original size:20 final size:20
Alignment explanation
Indices: 8926--8987 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
8916 CTTCTGGATC
*
8926 CTCCCCTATAACCATCGGCT
1 CTCCCCTATATCCATCGGCT
8946 CTCCCCTATATCCATCGGCT
1 CTCCCCTATATCCATCGGCT
8966 CTCCCCTATATCCATCGGCT
1 CTCCCCTATATCCATCGGCT
8986 CT
1 CT
8988 ATTCTCATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.45, G:0.10, T:0.29
Consensus pattern (20 bp):
CTCCCCTATATCCATCGGCT
Found at i:10571 original size:13 final size:13
Alignment explanation
Indices: 10555--10599 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
10545 TTAAATTTAA
10555 ATTTAAAATATTT
1 ATTTAAAATATTT
*
10568 ATTT-AAAT-TTAA
1 ATTTAAAATATT-T
10580 ATTTAAAATATTT
1 ATTTAAAATATTT
10593 ATTTAAA
1 ATTTAAA
10600 TTTATTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 2 0.07
12 8 0.30
13 15 0.56
14 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTAAAATATTT
Found at i:10572 original size:25 final size:25
Alignment explanation
Indices: 10543--10603 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
10533 TTTTTCTTAA
10543 ATTTAAATTTAAATTTAAAATATTT
1 ATTTAAATTTAAATTTAAAATATTT
10568 ATTTAAATTTAAATTTAAAATATTT
1 ATTTAAATTTAAATTTAAAATATTT
10593 ATTTAAATTTA
1 ATTTAAATTTA
10604 TTGTAAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAAATTTAAATTTAAAATATTT
Found at i:10603 original size:6 final size:6
Alignment explanation
Indices: 10539--10586 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
10529 CTATTTTTTC
*
10539 TTAAAT TTAAAT TTAAAT TTAAAAT ATT-TAT TTAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT -TTAAAT TTAAAT TTAAAT TTAAA
10587 ATATTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 2 0.05
6 29 0.78
7 4 0.11
8 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:11797 original size:21 final size:21
Alignment explanation
Indices: 11749--11797 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
11739 TTTATTTTTA
*
11749 ATTTTTAAAGCTACATGATTG
1 ATTTTTGAAGCTACATGATTG
11770 ATTTTTGAAGCTACATGATTG
1 ATTTTTGAAGCTACATGATTG
11791 ATTTTTG
1 ATTTTTG
11798 GACTAAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (21 bp):
ATTTTTGAAGCTACATGATTG
Found at i:14144 original size:588 final size:585
Alignment explanation
Indices: 13206--14356 Score: 2239
Period size: 588 Copynumber: 2.0 Consensus size: 585
13196 TGTTTTCTAC
13206 TTTAATTATGGATTATTTCCATAATATTTATAAATATTTTATGGATGATTTAGGGTATAAACTGC
1 TTTAATTATGGATTATTTCCATAATATTTATAAATATTTTATGGATGATTTAGGGTATAAACTGC
13271 CCAAGTACGAGTTTTATGAGAATGAATATTAAATGTTTATGATTTTCAAATGTTGATTAATAAAT
66 CCAAGTACGAGTTTTATGAGAATGAATATTAAATGTTTATGATTTTCAAATGTTGATTAATAAAT
13336 TATTATATTGTGAATTAAAAGCCCATTGTATGTCGCATTGAGAGTCATAGGTACATTTGTCATGC
131 TATTATATTGTGAATTAAAAGCCCATTGTATGTCGCATTGAGAGTCATAGGTACATTTGTCATGC
* *
13401 CATTAAGTTGAGTACTTTCAAGTCAAGTTATGGTATATTTGTGTACATTATGATTAGCACCGTTG
196 CATTAAGTTGAATACTTTCAAGTCAAGTTATGGTACATTTGTGTACATTATGATTAGCACCGTTG
13466 GTACATATATTACGATCTGCACTTCAAGTGCATCTTATGATATGATATTTTATGATTGGCGTCGT
261 GTACATATATTACGATCTGCACTTCAAGTGCATCTTATGATATGATATTTTATGATTGGCGTCGT
13531 GATGTGCCTAGTGTGCACCTTATATTTTACTCACGTGCCTTATATTCACTTAAATATACTTTGGG
326 GATGTGCCTAGTGTGCACCTTATATTTTACTCACGTGCCTTATATTCACTTAAATATACTTTGGG
13596 CTATGAAAATGAAATATTAGCTACGAACGTGTTAAGTTGACACGGAATATGTTATGTTTATGTTA
391 CTATGAAAATGAAATATTAGCTACGAACGTGTTAAGTTGACACGGAATATGTTATGTTTATGTTA
*
13661 TCTGATATGATTTTATAAGAAAATGGAACAAGTTGATTTTCAGGTTACGGTGAAGTATTGGACTT
456 TCTGATATGATTTTATAAGAAAATGGAACAAGTTGATCTTCAGGTTACGGTGAAGTATTGGACTT
13726 GAATAAGTCGGTTTGAAAGTTTAATATTTTATTCAAAATTTATATAAATATTTCCATAATATGAG
521 GAATAAGTCGGTTTGAAAGTTTAATATTTTATTCAAAATTTATATAAATATTTCCATAATATGAG
13791 TTTAATTATGGATTATTTCCATAATATTTATATAAATATTTTATGGATGATTTAGGGTATAAACT
1 TTTAATTATGGATTATTTCCATAATA-TT-TATAAATATTTTATGGATGATTTAGGGTATAAACT
13856 GCCCAAGTACGAGTTTTATGAGAATGAATATTAAATGTTTATGATTTTCAAATGTTGATTAATAA
64 GCCCAAGTACGAGTTTTATGAGAATGAATATTAAATGTTTATGATTTTCAAATGTTGATTAATAA
13921 ATTATTATATTTGTGAATTAAAAGCCCATTGTATGTCGCATTGAGAGTCATAGGTACATTTGTCA
129 ATTATTATA-TTGTGAATTAAAAGCCCATTGTATGTCGCATTGAGAGTCATAGGTACATTTGTCA
*
13986 TGCCATTAAGTTGAATACTTTCAAGTCAAGTTATGGTACATTTGTGTACATTATGATTAGCATCG
193 TGCCATTAAGTTGAATACTTTCAAGTCAAGTTATGGTACATTTGTGTACATTATGATTAGCACCG
14051 TTGGTACATATATTACGATCTGCACTTCAAGTGCATCTTATGATATGATATTTTATGATTGGCGT
258 TTGGTACATATATTACGATCTGCACTTCAAGTGCATCTTATGATATGATATTTTATGATTGGCGT
14116 CGTGATGTGCCTAGTGTGCACCTTATATTTTACTCACGTGCCTTATATTCACTTAAATATACTTT
323 CGTGATGTGCCTAGTGTGCACCTTATATTTTACTCACGTGCCTTATATTCACTTAAATATACTTT
14181 GGGCTATGAAAATGAAATATTAGCTACGAACGTGTTAAGTTGACACGGAATATGTTATGTTTATG
388 GGGCTATGAAAATGAAATATTAGCTACGAACGTGTTAAGTTGACACGGAATATGTTATGTTTATG
14246 TTATCTGATATGATTTTATAAGAAAATGGAACAAGTTGATCTTCAGGTTACGGTGAAGTATTGGA
453 TTATCTGATATGATTTTATAAGAAAATGGAACAAGTTGATCTTCAGGTTACGGTGAAGTATTGGA
14311 CTTGAATAAGTCGGTTTGAAAGTTTAATATTTTATTCAAAATTTAT
518 CTTGAATAAGTCGGTTTGAAAGTTTAATATTTTATTCAAAATTTAT
14357 TTTTAATGCT
Statistics
Matches: 559, Mismatches: 4, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
585 26 0.05
586 2 0.00
587 109 0.19
588 422 0.75
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (585 bp):
TTTAATTATGGATTATTTCCATAATATTTATAAATATTTTATGGATGATTTAGGGTATAAACTGC
CCAAGTACGAGTTTTATGAGAATGAATATTAAATGTTTATGATTTTCAAATGTTGATTAATAAAT
TATTATATTGTGAATTAAAAGCCCATTGTATGTCGCATTGAGAGTCATAGGTACATTTGTCATGC
CATTAAGTTGAATACTTTCAAGTCAAGTTATGGTACATTTGTGTACATTATGATTAGCACCGTTG
GTACATATATTACGATCTGCACTTCAAGTGCATCTTATGATATGATATTTTATGATTGGCGTCGT
GATGTGCCTAGTGTGCACCTTATATTTTACTCACGTGCCTTATATTCACTTAAATATACTTTGGG
CTATGAAAATGAAATATTAGCTACGAACGTGTTAAGTTGACACGGAATATGTTATGTTTATGTTA
TCTGATATGATTTTATAAGAAAATGGAACAAGTTGATCTTCAGGTTACGGTGAAGTATTGGACTT
GAATAAGTCGGTTTGAAAGTTTAATATTTTATTCAAAATTTATATAAATATTTCCATAATATGAG
Found at i:16089 original size:20 final size:20
Alignment explanation
Indices: 16064--16101 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16054 TTTGATTCAC
*
16064 AGAATAGAAGATTACCAGTA
1 AGAATAAAAGATTACCAGTA
16084 AGAATAAAAGATTACCAG
1 AGAATAAAAGATTACCAG
16102 AGAATAAGAT
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:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (20 bp):
AGAATAAAAGATTACCAGTA
Found at i:16112 original size:16 final size:17
Alignment explanation
Indices: 16064--16121 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 17
16054 TTTGATTCAC
16064 AGAATAGAAGATTACCAG
1 AGAATA-AAGATTACCAG
16082 TAAGAATAAAAGATTACCAG
1 --AGAAT-AAAGATTACCAG
16102 AGAAT-AAGATTA-CAG
1 AGAATAAAGATTACCAG
16117 AGAAT
1 AGAAT
16122 GTTGTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.22
16 7 0.19
18 5 0.14
20 16 0.43
21 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (17 bp):
AGAATAAAGATTACCAG
Found at i:17426 original size:3 final size:3
Alignment explanation
Indices: 17420--17493 Score: 114
Period size: 3 Copynumber: 24.7 Consensus size: 3
17410 CTCCATTTAC
*
17420 TAT TAT TAT TATT TAT TAT TAT TAT TAT GAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
17466 TAT TAT TTT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17494 CAAACGGGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17934 original size:31 final size:31
Alignment explanation
Indices: 17896--18004 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
17886 TCTGCGAGAA
17896 AAAAAAACAGAGAACAACGGAGAGAGACGAG
1 AAAAAAACAGAGAACAACGGAGAGAGACGAG
17927 AAAAAAACAGAGAACAACGGAGAGAGACGAG
1 AAAAAAACAGAGAACAACGGAGAGAGACGAG
*
17958 AAAAAAACAGAGAACAACGGAGAGAGACCAG
1 AAAAAAACAGAGAACAACGGAGAGAGACGAG
*
17989 -CAAAAACAGAGAACAA
1 AAAAAAACAGAGAACAA
18005 AAACAAGGAA
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 15 0.20
31 61 0.80
ACGTcount: A:0.60, C:0.15, G:0.26, T:0.00
Consensus pattern (31 bp):
AAAAAAACAGAGAACAACGGAGAGAGACGAG
Found at i:18118 original size:19 final size:19
Alignment explanation
Indices: 18096--18140 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
18086 CCTTGACCAC
18096 CGCCGGAAGCACTAAACAT
1 CGCCGGAAGCACTAAACAT
18115 CGCCGGAAGCACTAAACAT
1 CGCCGGAAGCACTAAACAT
18134 CGCCGGA
1 CGCCGGA
18141 GAACAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.09
Consensus pattern (19 bp):
CGCCGGAAGCACTAAACAT
Found at i:19014 original size:22 final size:21
Alignment explanation
Indices: 18955--19015 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
18945 TTATGTAGTC
* **
18955 ATAAATATATATATATAATAA
1 ATAAATATTTATATATTTTAA
*
18976 ATAAATATTTATTTATTTTAA
1 ATAAATATTTATATATTTTAA
18997 ATAAATTATTT-TAATATTT
1 ATAAA-TATTTAT-ATATTT
19016 ATTTTTCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAATATTTATATATTTTAA
Found at i:23007 original size:15 final size:16
Alignment explanation
Indices: 22982--23014 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22972 GATCAATACC
22982 TTTTCGCATACATGCA
1 TTTTCGCATACATGCA
*
22998 TTTT-GCATACATTCA
1 TTTTCGCATACATGCA
23013 TT
1 TT
23015 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.45
Consensus pattern (16 bp):
TTTTCGCATACATGCA
Found at i:30369 original size:23 final size:23
Alignment explanation
Indices: 30343--30405 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
30333 TATTATGCTT
30343 GAAAAAAAAGAAGAA-GAAAGAAA
1 GAAAAAAAAGAAGAAGGAAA-AAA
30366 GAAAGAAAAA-AAGAAGGAAAAAA
1 GAAA-AAAAAGAAGAAGGAAAAAA
*
30389 GAAAAAAAAGAAAAAGG
1 GAAAAAAAAGAAGAAGG
30406 GGGGTCAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 5 0.14
23 22 0.61
24 9 0.25
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
GAAAAAAAAGAAGAAGGAAAAAA
Found at i:30373 original size:12 final size:11
Alignment explanation
Indices: 30346--30401 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
30336 TATGCTTGAA
30346 AAAAAAGAAGAAG
1 AAAAAAG-A-AAG
30359 AAAGAAAGAAAG
1 AAA-AAAGAAAG
*
30371 AAAAAAAGAAGG
1 -AAAAAAGAAAG
30383 AAAAAAG-AA-
1 AAAAAAGAAAG
30392 AAAAAAGAAA
1 AAAAAAGAAA
30402 AAGGGGGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 7 0.18
10 3 0.08
11 7 0.18
12 10 0.26
13 7 0.18
14 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:30394 original size:8 final size:8
Alignment explanation
Indices: 30345--30403 Score: 55
Period size: 8 Copynumber: 6.6 Consensus size: 8
30335 TTATGCTTGA
30345 AAAAAAAG
1 AAAAAAAG
30353 AAGAAGAAAG
1 AA-AA-AAAG
*
30363 AAAGAAAG
1 AAAAAAAG
30371 AAAAAAAG
1 AAAAAAAG
30379 AAGGAAAAAAG
1 -A--AAAAAAG
30390 AAAAAAAAG
1 -AAAAAAAG
30399 AAAAA
1 AAAAA
30404 GGGGGGTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
8 18 0.41
9 11 0.25
10 6 0.14
11 9 0.20
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:30404 original size:26 final size:26
Alignment explanation
Indices: 30345--30403 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 26
30335 TTATGCTTGA
*
30345 AAAAAAAGAAGAAGAAAGAAAGAAAG
1 AAAAAAAGAAGAAAAAAGAAAGAAAG
*
30371 AAAAAAAGAAGGAAAAAAGAAAAAAAAG
1 AAAAAAAGAA-GAAAAAAG-AAAGAAAG
30399 AAAAA
1 AAAAA
30404 GGGGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 10 0.34
27 7 0.24
28 12 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAGAAAAAAGAAAGAAAG
Found at i:30742 original size:16 final size:16
Alignment explanation
Indices: 30716--30760 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
30706 TTTGAATACA
*
30716 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
30733 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
30748 ATTCAATTTATTT
1 ATTCAATTTATTT
30761 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:31688 original size:83 final size:83
Alignment explanation
Indices: 31549--32100 Score: 1050
Period size: 83 Copynumber: 6.7 Consensus size: 83
31539 TGGAAAGATG
31549 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
31614 CATTGAATTTGGAAGAAT
66 CATTGAATTTGGAAGAAT
31632 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
31697 CATTGAATTTGGAAGAAT
66 CATTGAATTTGGAAGAAT
31715 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
31780 CATTGAATTTGGAAGAAT
66 CATTGAATTTGGAAGAAT
*
31798 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTGAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
31863 CATTGAATTTGGAAGAAT
66 CATTGAATTTGGAAGAAT
31881 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
31946 CATTGAATTTGGAAGAAT
66 CATTGAATTTGGAAGAAT
31964 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
**
32029 CATTGAATTTGGAAGAGG
66 CATTGAATTTGGAAGAAT
* * *
32047 AATGGGCTAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTTG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
32101 ATATGAAACC
Statistics
Matches: 462, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 462 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.38
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGGAAGAAT
Found at i:33141 original size:113 final size:113
Alignment explanation
Indices: 32979--33503 Score: 729
Period size: 113 Copynumber: 4.7 Consensus size: 113
32969 TTCCAGTTCG
* *
32979 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAATAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
33044 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
* * *
33092 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
** * * *
33157 AACCTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
33205 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * * * *
33270 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAG-AA
* *
33318 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* *
33383 TTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCCAGAG-A
63 TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
* **
33433 AGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTTCATAATAAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
33494 AACTTTTTGC
66 AACCTTTTGC
33504 ATAATTCTAT
Statistics
Matches: 369, Mismatches: 38, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
108 38 0.10
109 3 0.01
112 7 0.02
113 222 0.60
115 19 0.05
116 79 0.21
117 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
Found at i:33484 original size:17 final size:17
Alignment explanation
Indices: 33430--33485 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
33420 GCTTTTCCAG
*
33430 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATAAGA
* *
33447 AGAA-CTCATCTGAAGAAGA
1 AGAAGTTCA--T-AATAAGA
33466 AGAAGTTCATAATAAGA
1 AGAAGTTCATAATAAGA
33483 AGA
1 AGA
33486 GCTTGTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 2 0.07
19 9 0.30
20 3 0.10
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (17 bp):
AGAAGTTCATAATAAGA
Found at i:33622 original size:84 final size:84
Alignment explanation
Indices: 33468--33622 Score: 202
Period size: 84 Copynumber: 1.8 Consensus size: 84
33458 GAAGAAGAAG
* * * * * *
33468 AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAAATTA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAAATCA
*
33533 GCATCAGCCTTTCCAGAGA
66 ACATCAGCCTTTCCAGAGA
* * * **
33552 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAAATCA
33617 ACATCA
66 ACATCA
33623 TCCCCAGCAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 59 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (84 bp):
AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAAATCA
ACATCAGCCTTTCCAGAGA
Found at i:33822 original size:3 final size:3
Alignment explanation
Indices: 33816--33876 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
33806 CTCCATTTAC
*
33816 TAT TAT TAT TAT TAT TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33864 TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TA
33877 CAAACGGGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:34316 original size:31 final size:31
Alignment explanation
Indices: 34273--34355 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
34263 ACCCCATCTG
34273 CGAGAAAAAAAACAGAGAACAACGGAGAGAGA
1 CGAG-AAAAAAACAGAGAACAACGGAGAGAGA
34305 CGAGAAAAAAACAGAGAACAACGGAGAGAGA
1 CGAGAAAAAAACAGAGAACAACGGAGAGAGA
* *
34336 CCA-ACAAAAACAGAGAACAA
1 CGAGAAAAAAACAGAGAACAA
34356 AAACAAGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 16 0.33
31 29 0.59
32 4 0.08
ACGTcount: A:0.60, C:0.16, G:0.24, T:0.00
Consensus pattern (31 bp):
CGAGAAAAAAACAGAGAACAACGGAGAGAGA
Found at i:35328 original size:13 final size:13
Alignment explanation
Indices: 35312--35351 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
35302 ATATAATAAA
35312 TAAATATTTATTT
1 TAAATATTTATTT
*
35325 TAAATAAATTATTT
1 TAAAT-ATTTATTT
35339 T-AATATTTATTT
1 TAAATATTTATTT
35351 T
1 T
35352 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:42870 original size:13 final size:13
Alignment explanation
Indices: 42854--42880 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42844 TTACAGACGC
42854 GCATATGAAGACT
1 GCATATGAAGACT
42867 GCATATGAAGACT
1 GCATATGAAGACT
42880 G
1 G
42881 TTCAACTATG
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:51437 original size:19 final size:19
Alignment explanation
Indices: 51413--51450 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
51403 AGATAATTAC
51413 ACTATTGTCTAAGATCTTT
1 ACTATTGTCTAAGATCTTT
51432 ACTATTGTCTAAGATCTTT
1 ACTATTGTCTAAGATCTTT
51451 GGACATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (19 bp):
ACTATTGTCTAAGATCTTT
Found at i:52253 original size:23 final size:23
Alignment explanation
Indices: 52227--52274 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
52217 ATAAAGTACA
*
52227 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
52250 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
52273 AT
1 AT
52275 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:52717 original size:21 final size:22
Alignment explanation
Indices: 52692--52743 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
52682 ACACTTTACA
*
52692 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
52715 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
52738 ATATAA
1 ATATAA
52744 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:52728 original size:23 final size:23
Alignment explanation
Indices: 52702--52764 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
52692 ATATAACCAC
52702 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
52725 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
52748 TACCTATTACATCATAT
1 TACCTATTACATTATAT
52765 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:53108 original size:25 final size:25
Alignment explanation
Indices: 53051--53116 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
53041 CACTCAAAAG
*
53051 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
53076 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
53101 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
53117 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:56096 original size:182 final size:183
Alignment explanation
Indices: 55577--56469 Score: 1621
Period size: 183 Copynumber: 4.9 Consensus size: 183
55567 TTAAAATTAC
* *
55577 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
55642 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
55707 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
55760 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
55825 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
55890 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
55943 CGATACTTTTTTAAATCGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
56007 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
56072 ATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
56125 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
56190 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
56255 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
56308 CGACACTTTTTTAAATCGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
56372 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
56437 ATATTGCAAATTTACCTATTTTATTAT-AATATG
131 ATATTACAAAATTATCTATTACATTATAAATATG
56470 TTGAAAGTGT
Statistics
Matches: 694, Mismatches: 15, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
181 5 0.01
182 300 0.43
183 389 0.56
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:56276 original size:365 final size:365
Alignment explanation
Indices: 55577--56469 Score: 1626
Period size: 365 Copynumber: 2.4 Consensus size: 365
55567 TTAAAATTAC
* *
55577 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
55642 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
55707 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACTTTTTT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
*
55772 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAAAGTGT
195 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
55837 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
260 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
*
55902 TATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
325 TATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
55943 CGATACTTTTTTAAATCGTATCGACACATTTTCTTCCAATATGGACATAAAGTACCGACACAATA
1 CGACACTTTTTTAAATCGTATCGACACATTTTCTTCCAATATGGACATAAAGTACCGACACAATA
56008 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
66 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
* *
56073 TATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
131 TATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
56138 AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
196 AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
56203 GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATT
261 GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATT
*
56268 ATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
326 ATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
56308 CGACACTTTTTTAAATCGTATCGACACATTTTCTTCCAATATGGACATAAAGTACCGACACAATA
1 CGACACTTTTTTAAATCGTATCGACACATTTTCTTCCAATATGGACATAAAGTACCGACACAATA
56373 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
66 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
* * * **
56438 TATTGCAAATTTACCTATTTTATTAT-AATATG
131 TATTACAAAATTATCTATTACATTATAAATATG
56470 TTGAAAGTGT
Statistics
Matches: 508, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
364 5 0.01
365 477 0.94
366 26 0.05
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (365 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTCTTCCAATATGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATT
ATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:57892 original size:3 final size:3
Alignment explanation
Indices: 57884--57925 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
57874 ACTTGTTTGG
* * *
57884 ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
57926 GTCAGCTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:57901 original size:12 final size:12
Alignment explanation
Indices: 57884--57929 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
57874 ACTTGTTTGG
*
57884 ATCATCATCATC
1 ATCATCGTCATC
57896 ATCATCGTCATC
1 ATCATCGTCATC
57908 ATCATCGTCATC
1 ATCATCGTCATC
*
57920 TTCATCGTCA
1 ATCATCGTCA
57930 GCTTCATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.26, C:0.33, G:0.07, T:0.35
Consensus pattern (12 bp):
ATCATCGTCATC
Found at i:57934 original size:12 final size:12
Alignment explanation
Indices: 57885--57937 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
57875 CTTGTTTGGA
* *
57885 TCATCATCATCA
1 TCATCGTCATCT
*
57897 TCATCGTCATCA
1 TCATCGTCATCT
57909 TCATCGTCATCT
1 TCATCGTCATCT
*
57921 TCATCGTCAGCT
1 TCATCGTCATCT
57933 TCATC
1 TCATC
57938 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:59798 original size:197 final size:198
Alignment explanation
Indices: 59401--60747 Score: 2124
Period size: 197 Copynumber: 6.9 Consensus size: 198
59391 TTTAAATTAG
* *
59401 TATCGACACTAACTATATTAGTGTCGACACATTTTTTAGACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
59465 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
59529 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
59594 CAAA
196 -AAA
59598 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
59663 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
59728 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
59792 AAA
196 AAA
***
59795 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
59860 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
59924 CGACAC-TTTTATATATGGATAGACAC-TTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
59987 CAA
196 AAA
59990 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
60055 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
60119 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
60184 ACAA
196 A-AA
*
60188 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* **
60253 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGATCGACACTTTTTTATA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG--A--TGATT-T-
* * * * *
60317 TATGGATCGACAC------T-TATGGGT-GCACCCTGT-T--G-G---CC---ATT-CATTC--T
125 T-GGGATCGACACTTTTTATATATGGATCG-ACACTTTATGGGTGCACCCTGTTTTCCATTCATT
**** *
60361 GGAAAAAACAA
188 CTGGAAAAAAA
60372 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
60437 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
** *
60502 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCGTTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAA
60567 AAAAA
194 AAAAA
60572 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
60637 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
60702 CGACACTTTGTTATATATGGATCGACACTTTATGGGTGCA-CCTGTT
131 CGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCCTGTT
60748 GGCCATATTG
Statistics
Matches: 1063, Mismatches: 48, Indels: 76
0.90 0.04 0.06
Matches are distributed among these distances:
178 10 0.01
179 1 0.00
180 1 0.00
181 3 0.00
183 1 0.00
184 84 0.08
185 38 0.04
186 11 0.01
187 7 0.01
189 1 0.00
190 1 0.00
191 2 0.00
193 2 0.00
194 1 0.00
195 171 0.16
196 67 0.06
197 221 0.21
198 178 0.17
199 75 0.07
200 173 0.16
202 3 0.00
203 1 0.00
204 1 0.00
205 10 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:60418 original size:184 final size:184
Alignment explanation
Indices: 60110--60489 Score: 710
Period size: 184 Copynumber: 2.1 Consensus size: 184
60100 GGTTCGATGA
60110 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCAT
*
60175 TCTGGAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCA
66 TCTGGAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCA
60240 TAAAACCGGTATAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATAC
131 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
60293 TTTTGGGATCGACACTTTTTTATATATGGATCGACAC-TTATGGGTGCACCCTGTTGGCCATTCA
1 TTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCA
60357 TTCTGGAAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
65 TTCTGG-AAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
60422 CATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
129 CATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
*
60478 TTTTGGGTTCGA
1 TTTTGGGATCGA
60490 TGATTTTGGG
Statistics
Matches: 192, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 48 0.25
184 111 0.58
185 33 0.17
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (184 bp):
TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCAT
TCTGGAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCA
TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
Found at i:60530 original size:200 final size:200
Alignment explanation
Indices: 60293--60753 Score: 872
Period size: 200 Copynumber: 2.3 Consensus size: 200
60283 TACATTATAC
60293 TTTTGGGATCGACACTTTTTTATATATGGATCGACAC-TTATGGGTGCACCCTGTTGGCCATTCA
1 TTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCA
60357 TTCTGGAAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
66 TTCTGGAAAAAA-AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
60422 CATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTT
130 CATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTT
60487 CGATGA
195 CGATGA
*
60493 TTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCG
1 TTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCA
*
60558 TTCTGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
66 TTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
60623 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
131 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
60688 GATGA
196 GATGA
*
60693 TTTTGGGATCGACACTTTGTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTGGCCAT
1 TTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCAT
60754 ATTGTAAATT
Statistics
Matches: 257, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
199 12 0.05
200 208 0.81
201 37 0.14
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (200 bp):
TTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCA
TTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
GATGA
Found at i:60898 original size:19 final size:19
Alignment explanation
Indices: 60866--60913 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
60856 TTATATTCAC
60866 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
60884 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
60903 ATACAAAATTA
1 ATACAAAATTA
60914 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:62736 original size:33 final size:33
Alignment explanation
Indices: 62690--62755 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
62680 CCATCTAATA
* *
62690 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
62723 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
62756 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:62828 original size:21 final size:21
Alignment explanation
Indices: 62788--62829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62778 CCCCTTATGC
*
62788 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTGTATCTACGACT
* *
62809 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTGTATCTACGACT
62830 TGATCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.31, G:0.17, T:0.38
Consensus pattern (21 bp):
CTCTCGAGTGTATCTACGACT
Found at i:65081 original size:17 final size:18
Alignment explanation
Indices: 65059--65101 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
65049 ATATATCCGG
65059 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
65076 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
65096 TATCAT
1 TATCAT
65102 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:65119 original size:20 final size:19
Alignment explanation
Indices: 65064--65110 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
65054 TCCGGTATCA
65064 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
65083 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
65104 TTTTACC
1 TTTTACC
65111 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:65258 original size:20 final size:20
Alignment explanation
Indices: 65233--65292 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
65223 ACTTTTAAAT
65233 TTACCGGTTTTATCATTTTG
1 TTACCGGTTTTATCATTTTG
65253 TTACCGGTTTTATCATATTT-
1 TTACCGGTTTTATCAT-TTTG
*
65273 TTACCTGG-TATATCATTTTG
1 TTACC-GGTTTTATCATTTTG
65293 GATCGATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.08
20 28 0.78
21 5 0.14
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.53
Consensus pattern (20 bp):
TTACCGGTTTTATCATTTTG
Found at i:68386 original size:2 final size:2
Alignment explanation
Indices: 68379--68412 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
68369 CCAACATAAA
68379 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
68413 CAATAATTGA
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:68755 original size:3 final size:3
Alignment explanation
Indices: 68747--68771 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
68737 ATTATAAGTA
68747 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
68772 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:69392 original size:60 final size:60
Alignment explanation
Indices: 69281--69394 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
69271 ATAGTCGAGT
* * * *
69281 GATCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGCAAAATTCTATAATTAGAG
1 GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAAAACTCTATAATTAGAG
* * * *
69341 GATCATTTTATAACTTTTAATAGTCGAGGGACTTAATAAAACAATACTCTATAA
1 GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAAAACTCTATAA
69395 CTGGGAGATC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAAAACTCTATAATTAGAG
Found at i:69405 original size:60 final size:60
Alignment explanation
Indices: 69281--69417 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
69271 ATAGTCGAGT
* * * * *
69281 GATCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGCAAAATTCTATAATTAGAG
1 GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAAAACTCTATAATGAGAG
* * * * *
69341 GATCATTTTATAACTTTTAATAGTCGAGGGACTTAATAAAACAATACTCTATAACTGGGA-
1 GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAAAACTCTATAA-TGAGAG
69401 GATCATTTGTAT-ACTTT
1 GATCATTT-TATAACTTT
69418 ATCATTATGT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 59 0.91
61 6 0.09
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAAAACTCTATAATGAGAG
Found at i:70366 original size:5 final size:5
Alignment explanation
Indices: 70356--70495 Score: 280
Period size: 5 Copynumber: 28.0 Consensus size: 5
70346 GTCAGTGGGA
70356 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
70406 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
70456 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
70496 GTGTGTGCAC
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 135 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:72551 original size:22 final size:22
Alignment explanation
Indices: 72523--72574 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
72513 TTGATCACAG
* * *
72523 AAGTGCCTGAGCACTAATACTA
1 AAGTGCCTCAGAACTAATACAA
72545 AAGTGCCTCAGAACTAATACAA
1 AAGTGCCTCAGAACTAATACAA
72567 AAGTGCCT
1 AAGTGCCT
72575 TAACACTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (22 bp):
AAGTGCCTCAGAACTAATACAA
Found at i:72582 original size:22 final size:22
Alignment explanation
Indices: 72523--72582 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
72513 TTGATCACAG
* * *
72523 AAGTGCCTGAGCACTAATACTA
1 AAGTGCCTCAACACTAATACAA
72545 AAGTGCCTCAGA-ACTAATACAA
1 AAGTGCCTCA-ACACTAATACAA
*
72567 AAGTGCCTTAACACTA
1 AAGTGCCTCAACACTA
72583 GGGGAGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (22 bp):
AAGTGCCTCAACACTAATACAA
Found at i:73134 original size:32 final size:31
Alignment explanation
Indices: 73098--73190 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 31
73088 ACACTAACTC
* *
73098 TGCTATGCATTATCTGAACGAGATACTGAATA
1 TGCTATGCACTATCTGAATGA-ATACTGAATA
* *
73130 TGCTACGCACTATCTGAATGCAATACTGAATT
1 TGCTATGCACTATCTGAATG-AATACTGAATA
*
73162 TGCTATGCACTATATGAATGAAATACTGA
1 TGCTATGCACTATCTGAATG-AATACTGA
73191 TACTATTATA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
32 52 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (31 bp):
TGCTATGCACTATCTGAATGAATACTGAATA
Found at i:74978 original size:25 final size:25
Alignment explanation
Indices: 74935--74985 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
74925 ATGGAGTTTT
*
74935 AAAAGGAAGAAGGAAGAAATGGGAAA
1 AAAAGGAAGAA-GAAGAAATGAGAAA
74961 AAAAGGAAGAA-AATGAAATGAGAAA
1 AAAAGGAAGAAGAA-GAAATGAGAAA
74986 TATAAAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 10 0.43
26 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (25 bp):
AAAAGGAAGAAGAAGAAATGAGAAA
Found at i:76887 original size:19 final size:20
Alignment explanation
Indices: 76844--76888 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
76834 TACTATTCTG
* *
76844 AAAATTAATGTTAGAGTGTT
1 AAAATTAATGTCAGAATGTT
76864 AAAATTAATGTCAGAATG-T
1 AAAATTAATGTCAGAATGTT
76883 AAAATT
1 AAAATT
76889 GGATCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.36
Consensus pattern (20 bp):
AAAATTAATGTCAGAATGTT
Found at i:77024 original size:90 final size:90
Alignment explanation
Indices: 76866--77042 Score: 318
Period size: 90 Copynumber: 2.0 Consensus size: 90
76856 AGAGTGTTAA
*
76866 AATTAATGTCAGAATGTAAAATTGGATCGTTTTGGAAACTTGGTAAGTTTGGTGAGTAGTTTGGA
1 AATTAATGTCAGAATGTAAAATTGGATCATTTTGGAAACTTGGTAAGTTTGGTGAGTAGTTTGGA
76931 AAGTTTGTAGGGTTTAAAGGTAATT
66 AAGTTTGTAGGGTTTAAAGGTAATT
* * *
76956 AATTGATGTCAGAATGTGAAATTGGATCATTTTGTAAACTTGGTAAGTTTGGTGAGTAGTTTGGA
1 AATTAATGTCAGAATGTAAAATTGGATCATTTTGGAAACTTGGTAAGTTTGGTGAGTAGTTTGGA
77021 AAGTTTGTAGGGTTTAAAGGTA
66 AAGTTTGTAGGGTTTAAAGGTA
77043 TTTATGAAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (90 bp):
AATTAATGTCAGAATGTAAAATTGGATCATTTTGGAAACTTGGTAAGTTTGGTGAGTAGTTTGGA
AAGTTTGTAGGGTTTAAAGGTAATT
Found at i:78852 original size:20 final size:20
Alignment explanation
Indices: 78819--78977 Score: 221
Period size: 20 Copynumber: 8.0 Consensus size: 20
78809 TATACATTGG
78819 GCTATGAATCTGAAAGTAAA
1 GCTATGAATCTGAAAGTAAA
* * *
78839 GTTATGGATATGAAAGTAAA
1 GCTATGAATCTGAAAGTAAA
*
78859 GCTATGAATATGAAAGTAAA
1 GCTATGAATCTGAAAGTAAA
*
78879 GTTATGAATCTGAAAGTAAA
1 GCTATGAATCTGAAAGTAAA
*
78899 ACTATGAATCTGAAAGTAAA
1 GCTATGAATCTGAAAGTAAA
* *
78919 GCTATGAATATGAAAATAAA
1 GCTATGAATCTGAAAGTAAA
**
78939 TTTATGAATCTGAAAGTAAA
1 GCTATGAATCTGAAAGTAAA
78959 GCTATGAATCTGAAA-TAAA
1 GCTATGAATCTGAAAGTAAA
78978 TTTTGAATTT
Statistics
Matches: 121, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 4 0.03
20 117 0.97
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (20 bp):
GCTATGAATCTGAAAGTAAA
Found at i:78914 original size:60 final size:60
Alignment explanation
Indices: 78821--78977 Score: 253
Period size: 60 Copynumber: 2.6 Consensus size: 60
78811 TACATTGGGC
* * * *
78821 TATGAATCTGAAAGTAAAGTTATGGATATGAAAGTAAAGCTATGAATATGAAAGTAAAGT
1 TATGAATCTGAAAGTAAAGCTATGAATCTGAAAGTAAAGCTATGAATATGAAAATAAAGT
* *
78881 TATGAATCTGAAAGTAAAACTATGAATCTGAAAGTAAAGCTATGAATATGAAAATAAATT
1 TATGAATCTGAAAGTAAAGCTATGAATCTGAAAGTAAAGCTATGAATATGAAAATAAAGT
78941 TATGAATCTGAAAGTAAAGCTATGAATCTGAAA-TAAA
1 TATGAATCTGAAAGTAAAGCTATGAATCTGAAAGTAAA
78978 TTTTGAATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 4 0.04
60 86 0.96
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (60 bp):
TATGAATCTGAAAGTAAAGCTATGAATCTGAAAGTAAAGCTATGAATATGAAAATAAAGT
Found at i:87242 original size:18 final size:19
Alignment explanation
Indices: 87202--87239 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
87192 TGGTTCACGA
87202 AATGTAAGATTACCAGTGGG
1 AATGTAAGATTACCAG-GGG
87222 AATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
87240 AATAGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:88497 original size:16 final size:16
Alignment explanation
Indices: 88476--88508 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
88466 TAAAAGAAAC
88476 TAGACTGGTATACAAA
1 TAGACTGGTATACAAA
88492 TAGACTGGTATACAAA
1 TAGACTGGTATACAAA
88508 T
1 T
88509 CCAACGGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (16 bp):
TAGACTGGTATACAAA
Found at i:90067 original size:29 final size:28
Alignment explanation
Indices: 89992--90069 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
89982 ATATATAACT
* *
89992 TTTCAAAATCATATTTTGGTCCTTAAAC
1 TTTCAAAATTATATTTTAGTCCTTAAAC
* *
90020 TTTTATAAAGTT-TACTTTAG-CCATTAAAC
1 TTTCA-AAA-TTATATTTTAGTCC-TTAAAC
90049 TTTCAAAACTTATATTTTAGT
1 TTTCAAAA-TTATATTTTAGT
90070 TACTAACCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
28 11 0.29
29 26 0.68
30 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.46
Consensus pattern (28 bp):
TTTCAAAATTATATTTTAGTCCTTAAAC
Found at i:93271 original size:31 final size:31
Alignment explanation
Indices: 93236--93345 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
93226 ACTGACGTTC
* *
93236 ATGTGCATTATCTGAATGTAACA-TAACTCGG
1 ATGTGCA-TATCTGAATGCAACACTAACTCTG
* * *
93267 ATGTGC-CATCTAAATGCAACACTGACTCTG
1 ATGTGCATATCTGAATGCAACACTAACTCTG
*
93297 TTGTGCATATCTGAATGCAACACTAACTCTG
1 ATGTGCATATCTGAATGCAACACTAACTCTG
* *
93328 CTATGCATTATCTGAATG
1 ATGTGCA-TATCTGAATG
93346 TGATATTGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 12 0.18
30 11 0.17
31 32 0.49
32 10 0.15
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (31 bp):
ATGTGCATATCTGAATGCAACACTAACTCTG
Found at i:93385 original size:31 final size:31
Alignment explanation
Indices: 93328--93406 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
93318 ACTAACTCTG
* ** *
93328 CTATGCATTATCTGAATGTGATATTGAATCTT
1 CTATGCACTATCTGAA-GCAATATTGAATCTA
*
93360 CTATGCACTATTTGAAGCAATATTGAATCTA
1 CTATGCACTATCTGAAGCAATATTGAATCTA
93391 CTATGCACTATCTGAA
1 CTATGCACTATCTGAA
93407 TAAAATGCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 27 0.66
32 14 0.34
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (31 bp):
CTATGCACTATCTGAAGCAATATTGAATCTA
Done.