Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 6 of 31
Found at i:2908259 original size:2 final size:2
Alignment explanation
Indices: 2908252--2908289 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2908242 TTTAAAGCCT
*
2908252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2908290 TTAAATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2911137 original size:14 final size:15
Alignment explanation
Indices: 2911104--2911137 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2911094 TTGATTTAAA
*
2911104 AAATTATTATTTTAT
1 AAATTATAATTTTAT
2911119 AAATTATAATTTT-T
1 AAATTATAATTTTAT
2911133 AAATT
1 AAATT
2911138 TTTTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATTATAATTTTAT
Found at i:2913734 original size:2 final size:2
Alignment explanation
Indices: 2913727--2913753 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2913717 TTTCTTATTT
2913727 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2913754 TCTAGGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2921923 original size:2 final size:2
Alignment explanation
Indices: 2921885--2921915 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2921875 GATGGGCACA
*
2921885 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2921916 AGTATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2922849 original size:19 final size:19
Alignment explanation
Indices: 2922827--2922865 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2922817 TAATAATGTA
2922827 ATATATA-TT-ATATATAC
1 ATATATATTTAATATATAC
*
2922844 ATATATATTTAATTTATAC
1 ATATATATTTAATATATAC
2922863 ATA
1 ATA
2922866 AGAATTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATTTAATATATAC
Found at i:2923071 original size:218 final size:216
Alignment explanation
Indices: 2922626--2923084 Score: 597
Period size: 218 Copynumber: 2.1 Consensus size: 216
2922616 TGTAAACATT
* *
2922626 ATATTTATTTATTTTATACATAAACATTATAATAACTTATAATAAATTTTATTTATATGATTACA
1 ATATATATTTAATTTATACATAAACATTATAATAACTTATAATAAATTTTATTTATATGATTACA
* *
2922691 CTTAATAATTTTATTAATTATCACCTTAGTGTTTATAACATTTTGTTTATAATTAGTTATTATTT
66 CTTAATAATTTTATTAATTATCACCTTAATGTTTATAACATATTGTTTATAATTAGTTATTATTT
* *
2922756 ATACAAACTTTGATATAAAACATTATAACATATAAGTTGTATCATTAATTTCATATATACATAAT
131 ATACAAACTTTGATATAAAACATTATAACATATAAATTGTATCATAAATTT-ATATATACATAAT
*
2922821 AATGTAATATATATTATATATA
195 AAAGTAATATATATTATATATA
** *
2922843 CATATATATTTAATTTATACATAAGA-ATTATTGTAACTTATAATAGATTTTATTTATATGATTA
1 -ATATATATTTAATTTATACATAA-ACATTATAATAACTTATAATAAATTTTATTTATATGATTA
* * * * * *
2922907 TACTTAATAATTTTTTTAGTTGTCGCCTTAATTTTTATAACATATTGTTTATAATTAGTTATTAT
64 CACTTAATAATTTTATTAATTATCACCTTAATGTTTATAACATATTGTTTATAATTAGTTATTAT
* *
2922972 TTATACAAACTTTGATATAAAAATTAAAATATTATAACATATAAATTGTGT-ATAAATTT-TATA
129 TTATACAAACTTTG--AT----A-TAAAACATTATAACATATAAATTGTATCATAAATTTATATA
*
2923035 TATATAATAAAGT-A-ATATATTATATAT-
187 TACATAATAAAGTAATATATATTATATATA
* *
2923062 ATCTATATTTAATTGATACATAA
1 ATATATATTTAATTTATACATAA
2923085 TTTGTATCTA
Statistics
Matches: 212, Mismatches: 21, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
218 148 0.70
219 1 0.00
220 15 0.07
221 1 0.00
222 15 0.07
224 8 0.04
225 24 0.11
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (216 bp):
ATATATATTTAATTTATACATAAACATTATAATAACTTATAATAAATTTTATTTATATGATTACA
CTTAATAATTTTATTAATTATCACCTTAATGTTTATAACATATTGTTTATAATTAGTTATTATTT
ATACAAACTTTGATATAAAACATTATAACATATAAATTGTATCATAAATTTATATATACATAATA
AAGTAATATATATTATATATA
Found at i:2927538 original size:49 final size:49
Alignment explanation
Indices: 2927461--2927562 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
2927451 TATCTACATC
2927461 TCATCCAGCAAAACATGTCCTGTCGGATGTAGTGCATTCGAAGATAATT
1 TCATCCAGCAAAACATGTCCTGTCGGATGTAGTGCATTCGAAGATAATT
* *
2927510 TCATCCAGCAAAACATGTCCTGTTGGATGTAGTGCATTCGAAGTTAATT
1 TCATCCAGCAAAACATGTCCTGTCGGATGTAGTGCATTCGAAGATAATT
2927559 TCAT
1 TCAT
2927563 GACTTAGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (49 bp):
TCATCCAGCAAAACATGTCCTGTCGGATGTAGTGCATTCGAAGATAATT
Found at i:2938762 original size:24 final size:23
Alignment explanation
Indices: 2938718--2938766 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2938708 CCTTCTCCTA
* *
2938718 TCTCCTCCTCCGCTTCCCCCCTT
1 TCTCCTCCTCCCCCTCCCCCCTT
*
2938741 TCTCCTACCTCCCCCTCTCCCCTT
1 TCTCCT-CCTCCCCCTCCCCCCTT
2938765 TC
1 TC
2938767 CTTCATCCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.02, C:0.61, G:0.02, T:0.35
Consensus pattern (23 bp):
TCTCCTCCTCCCCCTCCCCCCTT
Found at i:2945070 original size:2 final size:2
Alignment explanation
Indices: 2945063--2945095 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2945053 AAGGTGCAAA
2945063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2945096 ATAATTGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2947818 original size:15 final size:15
Alignment explanation
Indices: 2947800--2947829 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2947790 CTCTTTTCCT
2947800 TTTTTTTGTTTTTGG
1 TTTTTTTGTTTTTGG
*
2947815 TTTTTTTTTTTTTGG
1 TTTTTTTGTTTTTGG
2947830 GTATTGATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (15 bp):
TTTTTTTGTTTTTGG
Found at i:2953741 original size:15 final size:15
Alignment explanation
Indices: 2953709--2953740 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2953699 GTAAAAAGTG
2953709 TTTTCTTTCATTTTT
1 TTTTCTTTCATTTTT
2953724 TTTTCTTT--TTTTT
1 TTTTCTTTCATTTTT
2953737 TTTT
1 TTTT
2953741 TAAAATACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
15 8 0.47
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTCTTTCATTTTT
Found at i:2966398 original size:10 final size:10
Alignment explanation
Indices: 2966385--2966410 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2966375 CTCTCTCTCT
2966385 CTCTCTACAC
1 CTCTCTACAC
2966395 CTCTCTACAC
1 CTCTCTACAC
2966405 CTCTCT
1 CTCTCT
2966411 TTCATCTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (10 bp):
CTCTCTACAC
Found at i:2966410 original size:2 final size:2
Alignment explanation
Indices: 2966365--2966390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2966355 AATGTTCCCA
2966365 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2966391 ACACCTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2968224 original size:31 final size:28
Alignment explanation
Indices: 2968136--2968228 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
2968126 CATTAAAGTA
* * * *
2968136 TAACAA-AATGTTTTTGAATATGACGTG
1 TAACAACAATATTTTTCAACATGGCGTG
**
2968163 TAACAACAATATTTTTCAACATGGTATG
1 TAACAACAATATTTTTCAACATGGCGTG
*
2968191 TAATAACAATATTTTTTTTCAACATGGCGTG
1 TAACAACAATA---TTTTTCAACATGGCGTG
2968222 TAACAAC
1 TAACAAC
2968229 TTTTTTTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 6 0.12
28 25 0.48
31 21 0.40
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (28 bp):
TAACAACAATATTTTTCAACATGGCGTG
Found at i:2968333 original size:21 final size:21
Alignment explanation
Indices: 2968264--2968333 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
2968254 TGTTTTTGTA
*
2968264 CATGACGTGTAACAACCTAAT
1 CATGACGTGTAACAACTTAAT
* * * ** **
2968285 AATAACTTGTAACATGTTTGT
1 CATGACGTGTAACAACTTAAT
2968306 ACATGACGTGTAACAACTTAAT
1 -CATGACGTGTAACAACTTAAT
2968328 CATGAC
1 CATGAC
2968334 ATATCATACG
Statistics
Matches: 33, Mismatches: 15, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (21 bp):
CATGACGTGTAACAACTTAAT
Found at i:2968583 original size:13 final size:13
Alignment explanation
Indices: 2968565--2968613 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
2968555 TAAAATTATA
2968565 AAAAATTATTTTT
1 AAAAATTATTTTT
2968578 AAAAATATCTTATTTTT
1 -AAAA-A--TTATTTTT
2968595 AAAAATTATTTTT
1 AAAAATTATTTTT
*
2968608 TAAAAT
1 AAAAAT
2968614 ACCTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.42
14 4 0.13
15 2 0.06
16 4 0.13
17 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:2973959 original size:72 final size:72
Alignment explanation
Indices: 2973818--2973959 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 72
2973808 AGTAGAAACT
* * *
2973818 CTTTTTATCCTCATCCTCCTAGTTAGGACAAAGAATTTATGAAACCATTGCTATAAATCAACAAG
1 CTTTTTATCCTCATCCTCCTAGTTAGGACAAAGAATTTATGAAACCATTACTACAAATCAACAAC
2973883 TTTTTCC
66 TTTTTCC
* * * *
2973890 CTTTTTATCCTCATCCTCTTAGTTAGGACAAAGAATTTCATGAGACCATTACTACAAGTCAA-TA
1 CTTTTTATCCTCATCCTCCTAGTTAGGACAAAGAATTT-ATGAAACCATTACTACAAATCAACAA
2973954 CTTTTT
65 CTTTTT
2973960 TTCTTTTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 43 0.69
73 19 0.31
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (72 bp):
CTTTTTATCCTCATCCTCCTAGTTAGGACAAAGAATTTATGAAACCATTACTACAAATCAACAAC
TTTTTCC
Found at i:2977655 original size:13 final size:13
Alignment explanation
Indices: 2977633--2977676 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2977623 GAGTGAAAAA
*
2977633 ATTATAATATCAT
1 ATTATCATATCAT
2977646 ATTATCATATCAT
1 ATTATCATATCAT
** *
2977659 AAAAACATATCAT
1 ATTATCATATCAT
2977672 ATTAT
1 ATTAT
2977677 TATTTATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTATCATATCAT
Found at i:2981438 original size:30 final size:30
Alignment explanation
Indices: 2981404--2981490 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 30
2981394 TGGAGCAATG
* *
2981404 GGGAAGGAAAATGGTGGTGGAGAACCATTA
1 GGGAAGGAAACTGGTGGTGGAGAACCACTA
*
2981434 GGGAAGGAAACTGGAGGTGGTGAAGAACCACTA
1 GGGAAGGAAACT---GGTGGTGGAGAACCACTA
*
2981467 GGGAAGGAAACTGGAGGTGGAGAA
1 GGGAAGGAAACTGGTGGTGGAGAA
2981491 GTAGGGTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 21 0.43
33 28 0.57
ACGTcount: A:0.37, C:0.08, G:0.43, T:0.13
Consensus pattern (30 bp):
GGGAAGGAAACTGGTGGTGGAGAACCACTA
Found at i:2981461 original size:33 final size:33
Alignment explanation
Indices: 2981416--2981491 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
2981406 GAAGGAAAAT
* *
2981416 GGTGGTGGAGAACCATTAGGGAAGGAAACTGGA
1 GGTGGTGAAGAACCACTAGGGAAGGAAACTGGA
2981449 GGTGGTGAAGAACCACTAGGGAAGGAAACTGGA
1 GGTGGTGAAGAACCACTAGGGAAGGAAACTGGA
*
2981482 GGTGGAGAAG
1 GGTGGTGAAG
2981492 TAGGGTATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.34, C:0.09, G:0.43, T:0.13
Consensus pattern (33 bp):
GGTGGTGAAGAACCACTAGGGAAGGAAACTGGA
Found at i:2986142 original size:2 final size:2
Alignment explanation
Indices: 2986135--2986189 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
2986125 TCTTTTCCTC
2986135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2986177 AT -T AT AC AT AT AT
1 AT AT AT AT AT AT AT
2986190 TTGGGTCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2989968 original size:21 final size:20
Alignment explanation
Indices: 2989930--2989969 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2989920 ACCTCCACCT
*
2989930 CCCCTCCACCGCCGCCAGCG
1 CCCCTCCACCGCCACCAGCG
*
2989950 CCCCGTCCGCCGCCACCAGC
1 CCCC-TCCACCGCCACCAGC
2989970 AGCACTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.10, C:0.65, G:0.20, T:0.05
Consensus pattern (20 bp):
CCCCTCCACCGCCACCAGCG
Found at i:2994053 original size:2 final size:2
Alignment explanation
Indices: 2994046--2994072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2994036 AGAAAGTTAC
2994046 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2994073 TGAGTTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2995754 original size:108 final size:108
Alignment explanation
Indices: 2995635--2995844 Score: 350
Period size: 108 Copynumber: 1.9 Consensus size: 108
2995625 TATAAGAAAT
* *
2995635 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAGTTGAATAATTGT-AAAAGAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAATTGAATAATT-TCAAAAGAATATGTAT
2995699 TTGGAAATTATGAAAATTATAACTAAATCAACATATTTTGCTAA
65 TTGGAAATTATGAAAATTATAACTAAATCAACATATTTTGCTAA
2995743 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAATTGAATAATTTCAAAAGAATATGTATT
1 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAATTGAATAATTTCAAAAGAATATGTATT
* * * *
2995808 TGTAAATTGTGAAAATTGTAATTAAATCAACATATTT
66 TGGAAATTATGAAAATTATAACTAAATCAACATATTT
2995845 AGTCATTTTA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
107 1 0.01
108 94 0.99
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAATTGAATAATTTCAAAAGAATATGTATT
TGGAAATTATGAAAATTATAACTAAATCAACATATTTTGCTAA
Found at i:2996065 original size:15 final size:17
Alignment explanation
Indices: 2996023--2996065 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2996013 AATATTTATA
*
2996023 TATATATTTTTTAACAC
1 TATATATATTTTAACAC
*
2996040 TATAAATATTTT-ACAC
1 TATATATATTTTAACAC
2996056 T-TATATATTT
1 TATATATATTT
2996066 GGCTTATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 5 0.22
17 10 0.43
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATTTTAACAC
Found at i:3007880 original size:42 final size:42
Alignment explanation
Indices: 3007815--3007899 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
3007805 TTGAGATGAA
* * *
3007815 ATGTAGACTTTCTCTTTAGCTTTTTGGATTCAAACAGTTTCT
1 ATGTAGACTTTCTCATTAGCTTTTTGAACTCAAACAGTTTCT
*
3007857 ATGTAGACTTTCTCATTATCTTTTTGAACTCAAACAGTTTCT
1 ATGTAGACTTTCTCATTAGCTTTTTGAACTCAAACAGTTTCT
3007899 A
1 A
3007900 ACTTTGTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (42 bp):
ATGTAGACTTTCTCATTAGCTTTTTGAACTCAAACAGTTTCT
Found at i:3027389 original size:4 final size:4
Alignment explanation
Indices: 3027382--3027408 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3027372 GCGCATTCCT
3027382 TCCC TCCC TCCC TCCC TCCC TCCC TCC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCC
3027409 TTTATTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (4 bp):
TCCC
Found at i:3029898 original size:103 final size:101
Alignment explanation
Indices: 3029684--3029918 Score: 353
Period size: 102 Copynumber: 2.3 Consensus size: 101
3029674 ACCCCAATTG
* *
3029684 CTCAATGCATTTGTAAGATAGGGTTTTGGCTTTGTATGCTCAATGAAGATACCTGCAAACACTTA
1 CTCAATGCAATTGTAAGATA-GGTTTTGGCTATGTATGCTCAATGAAGATACCTGCAAACACTTA
*
3029749 TGCACATCTTTCCCCCATTACCCTTTGATTTATCTTT
65 AGCACATCTTTCCCCCATTACCCTTTGATTTATCTTT
* * * *
3029786 CTCAATGCAATTGCAAGATAGGATTTTGGCTATGTATGCTCAATGGAGATGCCTTCAAACACTTA
1 CTCAATGCAATTGTAAGATAGG-TTTTGGCTATGTATGCTCAATGAAGATACCTGCAAACACTTA
*
3029851 GAGCACATCTTTCCCCCATTATCCTTTGATTTATCTTT
65 -AGCACATCTTTCCCCCATTACCCTTTGATTTATCTTT
* *
3029889 CTCATTGCAATTGTAAGATAGGGTTTGGCT
1 CTCAATGCAATTGTAAGATAGGTTTTGGCT
3029919 TTTTTTTTTG
Statistics
Matches: 120, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
101 2 0.02
102 63 0.52
103 55 0.46
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (101 bp):
CTCAATGCAATTGTAAGATAGGTTTTGGCTATGTATGCTCAATGAAGATACCTGCAAACACTTAA
GCACATCTTTCCCCCATTACCCTTTGATTTATCTTT
Found at i:3030040 original size:132 final size:134
Alignment explanation
Indices: 3029802--3030052 Score: 398
Period size: 132 Copynumber: 1.9 Consensus size: 134
3029792 GCAATTGCAA
** *
3029802 GATAGGATTTTGGCTATGTATGCTCAATGGAGATGCCTTCAAACACTTAGAGCACATCTTTCCCC
1 GATAGGATTTTGGCTATGTATGCTCAATAAAGATGCCTGCAAACACTTAGAGCACATCTTTCCCC
* *
3029867 CATTATCCTTTGATTTATCTTTCTCATTGCAATTGTAAGATAGGG-TTTGGCTTTTTTTTTTGGT
66 CATTACCCTTTGATTTATCTTTCTCAATGCAATTGTAAGATAGGGTTTTGGCTTTTTTTTTTGGT
3029931 ACAT
131 ACAT
* * * * *
3029935 GATAGGGTTTTGGCTTTGTATGCTCAATAAAGATGCCTGCAAACACTTA-TGCAGATCTTTCCCT
1 GATAGGATTTTGGCTATGTATGCTCAATAAAGATGCCTGCAAACACTTAGAGCACATCTTTCCCC
3029999 CATTACCCTTTGATTTATCTTTCTCAATGCAATTGTAAGATAGGGTTTTGGCTT
66 CATTACCCTTTGATTTATCTTTCTCAATGCAATTGTAAGATAGGGTTTTGGCTT
3030053 ATGTATGCTC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
132 55 0.51
133 52 0.49
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (134 bp):
GATAGGATTTTGGCTATGTATGCTCAATAAAGATGCCTGCAAACACTTAGAGCACATCTTTCCCC
CATTACCCTTTGATTTATCTTTCTCAATGCAATTGTAAGATAGGGTTTTGGCTTTTTTTTTTGGT
ACAT
Found at i:3030074 original size:103 final size:103
Alignment explanation
Indices: 3029935--3030229 Score: 466
Period size: 103 Copynumber: 2.9 Consensus size: 103
3029925 TTTGGTACAT
** * *
3029935 GATAGGGTTTTGGCTTTGTATGCTCAATAAAGATGCCTGCAAACACTT-ATGCAGATCTTTCCCT
1 GATAGGGTTTTGGCTTTGTATGCTCAATGGAGATGCCTGCAAACACTTAATGCACATCTTTCCCC
*
3029999 CATTACCCTTTGATTTATCTTTCTCAATGCAATTGTAA
66 CATTACCCTTTGATTTATCTTTCTCAATGCAACTGTAA
* * *
3030037 GATAGGGTTTTGGCTTATGTATGCTCGATGGAGATGCCCGCAAACACTTAATGTACATCTTTCCC
1 GATAGGGTTTTGGCTT-TGTATGCTCAATGGAGATGCCTGCAAACACTTAATGCACATCTTTCCC
* * *
3030102 CCACTATCCTTTGATTTATCTTGCTCAATGCAACTGTAA
65 CCATTACCCTTTGATTTATCTTTCTCAATGCAACTGTAA
*
3030141 GATAGGGTTTTGGCTTTGTATGCTCAATGGAGATGCCTGCAAACATTTAATGCACATCTTTCCCC
1 GATAGGGTTTTGGCTTTGTATGCTCAATGGAGATGCCTGCAAACACTTAATGCACATCTTTCCCC
3030206 CATTACCCTTTGATTTATCTTTCT
66 CATTACCCTTTGATTTATCTTTCT
3030230 TGGTAGTAAA
Statistics
Matches: 173, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
102 16 0.09
103 94 0.54
104 63 0.36
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (103 bp):
GATAGGGTTTTGGCTTTGTATGCTCAATGGAGATGCCTGCAAACACTTAATGCACATCTTTCCCC
CATTACCCTTTGATTTATCTTTCTCAATGCAACTGTAA
Found at i:3037182 original size:22 final size:20
Alignment explanation
Indices: 3037156--3037195 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3037146 TTTTGAAATA
3037156 AATTTTAATAAAAATAATTACC
1 AATTTT-ATAAAAA-AATTACC
*
3037178 AATTTTTTAAAAAAATTA
1 AATTTTATAAAAAAATTA
3037196 TATGATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTTATAAAAAAATTACC
Found at i:3060158 original size:2 final size:2
Alignment explanation
Indices: 3060151--3060187 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3060141 CCTATAACAT
3060151 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3060188 GCATGAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3065912 original size:201 final size:202
Alignment explanation
Indices: 3065561--3065956 Score: 731
Period size: 201 Copynumber: 2.0 Consensus size: 202
3065551 CATTTACTAT
3065561 CCTCAAAGCTAATATTAACATTACCTACAGAAGAGATTTTTGTAAGTTCACCGGCAGTGCAAAAG
1 CCTCAAAGCTAATATTAACATTACCTACAGAAGAGATTTTTGTAAGTTCACCGGCAGTGCAAAAG
*
3065626 ATTGAACATTTTCACCAAATTATTGAGGTGTGTGAGCTCAAAAAAGGCTTTGCAAATCAGAGACA
66 ATCGAACATTTTCACCAAATTATTGAGGTGTGTGAGCTCAAAAAAGGCTTTGCAAATCAGAGACA
3065691 AGGACGCAAACCAATGAAAGAATAAGTGAAGAGCCTTAATATACATAAGAGTACACCAAAAACTA
131 AGGACGCAAACCAATGAAAGAATAAGTGAAGAGCCTTAATATACATAAGAGTACACCAAAAACTA
3065756 ATGATCA
196 ATGATCA
* *
3065763 CCTCAAAGCTAATTTTAACATTACCTACAG-AGAGATTTTTGTAAGTTCACCGGCAGTGTAAAAG
1 CCTCAAAGCTAATATTAACATTACCTACAGAAGAGATTTTTGTAAGTTCACCGGCAGTGCAAAAG
*
3065827 ATCGAACATTTTTACCAAATTATTGAGGTGTGTGAGCTCAAAAAAGGCTTTGCAAATCAGAGACA
66 ATCGAACATTTTCACCAAATTATTGAGGTGTGTGAGCTCAAAAAAGGCTTTGCAAATCAGAGACA
* *
3065892 AGGATGCAAACCAGTGAAAGAATAAGTGAAGAGCCTTAATATACATAAGAGTACACCAAAAACTA
131 AGGACGCAAACCAATGAAAGAATAAGTGAAGAGCCTTAATATACATAAGAGTACACCAAAAACTA
3065957 TGTATTTGAA
Statistics
Matches: 188, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
201 159 0.85
202 29 0.15
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (202 bp):
CCTCAAAGCTAATATTAACATTACCTACAGAAGAGATTTTTGTAAGTTCACCGGCAGTGCAAAAG
ATCGAACATTTTCACCAAATTATTGAGGTGTGTGAGCTCAAAAAAGGCTTTGCAAATCAGAGACA
AGGACGCAAACCAATGAAAGAATAAGTGAAGAGCCTTAATATACATAAGAGTACACCAAAAACTA
ATGATCA
Found at i:3080127 original size:27 final size:28
Alignment explanation
Indices: 3080082--3080134 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
3080072 AATTTTTTAT
*
3080082 TTATAAATAAAATAAATTTTACTAATAA
1 TTATAAATAAAATAAATTTTAATAATAA
3080110 TTAT-AATAAAA-AATATTTTAATAAT
1 TTATAAATAAAATAA-ATTTTAATAAT
3080135 CATTCCTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 17 0.74
28 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TTATAAATAAAATAAATTTTAATAATAA
Found at i:3080372 original size:5 final size:6
Alignment explanation
Indices: 3080354--3080379 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3080344 GAAAATATCA
3080354 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
3080380 GATCTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:3080494 original size:33 final size:33
Alignment explanation
Indices: 3080449--3080511 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
3080439 TTATAACACC
* *
3080449 TAAAAAACTTCAACATGATAAAAA-TATTTTTCA
1 TAAAAAACTTCAA-ATAACAAAAATTATTTTTCA
3080482 TAAAATAA-TTCAAATAACAAAAATTATTTT
1 TAAAA-AACTTCAAATAACAAAAATTATTTT
3080512 CAACAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 8 0.31
33 16 0.62
34 2 0.08
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (33 bp):
TAAAAAACTTCAAATAACAAAAATTATTTTTCA
Found at i:3103427 original size:17 final size:17
Alignment explanation
Indices: 3103405--3103437 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3103395 TATTTTAATT
3103405 AATTA-TTAATTATAAAA
1 AATTATTTAATT-TAAAA
3103422 AATTATTTAATTTAAA
1 AATTATTTAATTTAAA
3103438 TAAAACTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATTTAATTTAAAA
Found at i:3106142 original size:24 final size:24
Alignment explanation
Indices: 3106115--3106160 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3106105 ACAAATGAAC
3106115 CAAAAGGCTT-TTCTCAATTATTCT
1 CAAAAGGCTTCTT-TCAATTATTCT
**
3106139 CAAAATTCTTCTTTCAATTATT
1 CAAAAGGCTTCTTTCAATTATT
3106161 TTCTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (24 bp):
CAAAAGGCTTCTTTCAATTATTCT
Found at i:3106894 original size:8 final size:8
Alignment explanation
Indices: 3106881--3106923 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3106871 TATTTATTAA
3106881 TTATTTTT
1 TTATTTTT
3106889 TTATTTTT
1 TTATTTTT
*
3106897 ATATTTTT
1 TTATTTTT
* *
3106905 TTATTATA
1 TTATTTTT
*
3106913 TGATTTTT
1 TTATTTTT
3106921 TTA
1 TTA
3106924 AATTAAGGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (8 bp):
TTATTTTT
Found at i:3106903 original size:16 final size:15
Alignment explanation
Indices: 3106873--3106923 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
3106863 GTTAATTATA
3106873 TTTATTA-ATTATTTT
1 TTTATTATA-TATTTT
*
3106888 TTTATTTTTATATTTT
1 TTTA-TTATATATTTT
3106904 TTTATTATATGATTTT
1 TTTATTATAT-ATTTT
3106920 TTTA
1 TTTA
3106924 AATTAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 9 0.29
16 21 0.68
17 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTATTATATATTTT
Found at i:3107338 original size:23 final size:22
Alignment explanation
Indices: 3107292--3107336 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3107282 TTAAAATAAA
* * *
3107292 TATTTTTAAAATTATGAATATT
1 TATTTTTAAAAATATCAAAATT
3107314 TATTTTTAAAAATATCAAAATT
1 TATTTTTAAAAATATCAAAATT
3107336 T
1 T
3107337 TAAATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTTAAAAATATCAAAATT
Found at i:3107846 original size:23 final size:21
Alignment explanation
Indices: 3107798--3107838 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3107788 ATGGAATTAT
*
3107798 GAAATTAGCATTTTTTTTAAG
1 GAAATTAGCATTTTTATTAAG
3107819 GAAATTAGCATATTTTATTA
1 GAAATTAGCAT-TTTTATTA
3107839 TATTAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
GAAATTAGCATTTTTATTAAG
Found at i:3132649 original size:2 final size:2
Alignment explanation
Indices: 3132642--3132669 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3132632 ACATAAAGTA
3132642 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
3132670 GCTCATTTTA
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:3145499 original size:21 final size:21
Alignment explanation
Indices: 3145475--3145527 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
3145465 TATGCTCTCG
3145475 ATTTCTCTTTCGCGCTTTTAA
1 ATTTCTCTTTCGCGCTTTTAA
3145496 ATTTCTCTTTCGCGCTTTTAA
1 ATTTCTCTTTCGCGCTTTTAA
3145517 ATTTCTCTTTC
1 ATTTCTCTTTC
3145528 CAGTACTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.13, C:0.25, G:0.08, T:0.55
Consensus pattern (21 bp):
ATTTCTCTTTCGCGCTTTTAA
Found at i:3146097 original size:45 final size:45
Alignment explanation
Indices: 3146047--3146262 Score: 263
Period size: 45 Copynumber: 4.8 Consensus size: 45
3146037 TTTTTTTTTA
* *
3146047 ATATGACTTGTAACAACTTAACCATGACGTGTCACACGTTTTTGT
1 ATATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGT
* * * * *
3146092 ATATGACGTGTAACAATCTAATCATGATGTGTAACATGTTTTTGT
1 ATATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGT
* * * * * *
3146137 ACATGACATGTAACAACCTAATCATGACATGTAACATGTTTTTGT
1 ATATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGT
* * *
3146182 ACATGACGTGTAATATCCTAACCATGACGTGTCACACGTTTTTGT
1 ATATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGT
*
3146227 ATATGAAGTGTAACAACCTAACCAT-AGCGTGTCACA
1 ATATGACGTGTAACAACCTAACCATGA-CGTGTCACA
3146263 ACCTAACCAT
Statistics
Matches: 147, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
44 1 0.01
45 146 0.99
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (45 bp):
ATATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGT
Found at i:3146148 original size:24 final size:24
Alignment explanation
Indices: 3146121--3146194 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
3146111 AATCATGATG
3146121 TGTAACATGTTTTTGTACATGACA
1 TGTAACATGTTTTTGTACATGACA
*** **
3146145 TGTAACA--ACCTAAT-CATGACA
1 TGTAACATGTTTTTGTACATGACA
*
3146166 TGTAACATGTTTTTGTACATGACG
1 TGTAACATGTTTTTGTACATGACA
3146190 TGTAA
1 TGTAA
3146195 TATCCTAACC
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 2 0.06
24 18 0.50
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (24 bp):
TGTAACATGTTTTTGTACATGACA
Found at i:3146278 original size:21 final size:21
Alignment explanation
Indices: 3146229--3146283 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
3146219 GTTTTTGTAT
* *
3146229 ATGAAGTGTAACAACCTAACC
1 ATGACGTGTCACAACCTAACC
3146250 AT-AGCGTGTCACAACCTAACC
1 ATGA-CGTGTCACAACCTAACC
3146271 ATGACGTGTCACA
1 ATGACGTGTCACA
3146284 CGTTTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (21 bp):
ATGACGTGTCACAACCTAACC
Found at i:3146303 original size:45 final size:45
Alignment explanation
Indices: 3146254--3146340 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
3146244 CTAACCATAG
* * *
3146254 CGTGTCACAACCTAACCATGACGTGTCACACGTTTTTGTACATGA
1 CGTGTAACAACCTAACCATGACGTGTAACACGTTTCTGTACATGA
*
3146299 CGTGTAACAACCTAACCATGACGTGTAACATGTTTCTGTACA
1 CGTGTAACAACCTAACCATGACGTGTAACACGTTTCTGTACA
3146341 CAATGTGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (45 bp):
CGTGTAACAACCTAACCATGACGTGTAACACGTTTCTGTACATGA
Found at i:3146324 original size:66 final size:66
Alignment explanation
Indices: 3146183--3146328 Score: 231
Period size: 66 Copynumber: 2.2 Consensus size: 66
3146173 TGTTTTTGTA
* * *
3146183 CATGACGTGTAATATCCTAACCATGACGTGTCACACGTTTTTGTATATGAAGTGTAACAACCTAA
1 CATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGTACATGAAGTGTAACAACCTAA
3146248 C
66 C
* *
3146249 CAT-AGCGTGTCACAACCTAACCATGACGTGTCACACGTTTTTGTACATGACGTGTAACAACCTA
1 CATGA-CGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGTACATGAAGTGTAACAACCTA
3146313 AC
65 AC
3146315 CATGACGTGTAACA
1 CATGACGTGTAACA
3146329 TGTTTCTGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 1 0.01
66 70 0.97
67 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (66 bp):
CATGACGTGTAACAACCTAACCATGACGTGTCACACGTTTTTGTACATGAAGTGTAACAACCTAA
C
Found at i:3165067 original size:18 final size:19
Alignment explanation
Indices: 3165046--3165084 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3165036 CGTCAATTAT
*
3165046 AAATAATATACAT-TTAAA
1 AAATAATATAAATATTAAA
3165064 AAATAATATAAATATTAAA
1 AAATAATATAAATATTAAA
3165083 AA
1 AA
3165085 TTCATTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAATATAAATATTAAA
Found at i:3165085 original size:18 final size:18
Alignment explanation
Indices: 3165041--3165085 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3165031 TAATACGTCA
* *
3165041 ATTATAAATAATATACAT
1 ATTAAAAATAATATAAAT
3165059 -TTAAAAAATAATATAAAT
1 ATT-AAAAATAATATAAAT
3165077 ATTAAAAAT
1 ATTAAAAAT
3165086 TCATTATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAATAATATAAAT
Found at i:3186097 original size:2 final size:2
Alignment explanation
Indices: 3186090--3186127 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3186080 ATCAACGTAC
3186090 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3186128 CCTGAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3188689 original size:24 final size:22
Alignment explanation
Indices: 3188658--3188706 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
3188648 TAAAAAAATT
* *
3188658 AAAATATTTTTTTATTAATTTAA
1 AAAATATTATTATATT-ATTTAA
*
3188681 AAAATTATTATTATATTTTTTAA
1 AAAA-TATTATTATATTATTTAA
3188704 AAA
1 AAA
3188707 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAAATATTATTATATTATTTAA
Found at i:3200239 original size:2 final size:2
Alignment explanation
Indices: 3200232--3200273 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3200222 TTTCACAATA
3200232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3200274 GGAACAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3201999 original size:84 final size:84
Alignment explanation
Indices: 3201858--3202025 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
3201848 GTACACCCGC
* *
3201858 TTTTAAAGAGCCTAAAACCTCCCATTCCTGTTCTATGTCGATGTGGGATAGAGGCATTTTCTTTG
1 TTTTAAAGAGCCTAAAACCTCCCATTCATGTTCGATGTCGATGTGGGATAGAGGCATTTTCTTTG
*
3201923 TGATACTCTCTCCCACCCA
66 TGACACTCTCTCCCACCCA
*
3201942 TTTTAAAGAGCCTAAGACCTCCCATTCATGTTCGATGTCGATGTGGGATAGAGGCATTTTCTTTG
1 TTTTAAAGAGCCTAAAACCTCCCATTCATGTTCGATGTCGATGTGGGATAGAGGCATTTTCTTTG
3202007 TGACACTCTCTCCCACCCA
66 TGACACTCTCTCCCACCCA
3202026 ATTCCGACAA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (84 bp):
TTTTAAAGAGCCTAAAACCTCCCATTCATGTTCGATGTCGATGTGGGATAGAGGCATTTTCTTTG
TGACACTCTCTCCCACCCA
Found at i:3202052 original size:14 final size:14
Alignment explanation
Indices: 3202033--3202059 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3202023 CCAATTCCGA
3202033 CAACGTCACGTTGC
1 CAACGTCACGTTGC
3202047 CAACGTCACGTTG
1 CAACGTCACGTTG
3202060 TTGCTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (14 bp):
CAACGTCACGTTGC
Found at i:3202494 original size:84 final size:88
Alignment explanation
Indices: 3202406--3202588 Score: 206
Period size: 87 Copynumber: 2.1 Consensus size: 88
3202396 TATTTTTATT
* * **
3202406 TTTTAAAGAGCCTTAATCCTATT-TTTGTCACGGTGAAT-TTTA-TAT-ACT-TTAT-AACGCTC
1 TTTTAAAGAGCCTTAATCCTATTCGTTGTCACGG-G-ATCATTACTATCACTCCCATAAACGCTC
3202465 TTATGAGGGTGTGCAG-TACACCTGC
64 TTATGAGGGTGTGCAGCTACA-CTGC
* *
3202490 TTTT-AAGCAGCC-TAATCCTATTCGTTGTCACGGGGTCATTACTCTCACTCCCATAAACGCTCT
1 TTTTAAAG-AGCCTTAATCCTATTCGTTGTCACGGGATCATTACTATCACTCCCATAAACGCTCT
3202553 TATGAGGGTGTGCAGCTACACTGC
65 TATGAGGGTGTGCAGCTACACTGC
3202577 -TTTAAAGAGCCT
1 TTTTAAAGAGCCT
3202589 AAGACCTCCC
Statistics
Matches: 83, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
82 1 0.01
83 17 0.20
84 19 0.23
85 3 0.04
86 9 0.11
87 30 0.36
88 4 0.05
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (88 bp):
TTTTAAAGAGCCTTAATCCTATTCGTTGTCACGGGATCATTACTATCACTCCCATAAACGCTCTT
ATGAGGGTGTGCAGCTACACTGC
Found at i:3202714 original size:103 final size:102
Alignment explanation
Indices: 3202577--3202881 Score: 484
Period size: 102 Copynumber: 3.0 Consensus size: 102
3202567 GCTACACTGC
* * *
3202577 TTTAAAGAGCCTAAGACCTCCCGTTCCTGTTCGATGTGGGATAGAGACACTTTCCTCGTGACACT
1 TTTAAAGAGCCCAAGACCTCCCATTCCTGTTCGATGTGGGATAGAGACACTTTCCTAGTGACACT
3202642 CTCTCCCACCCGATTCCTGACAACGTCACGTTGCCGCT
66 CTCTCCCACCCGATTCC-GACAACGTCACGTTGCCGCT
* *
3202680 TTTAAAGAGCCCAAGACCTCCCATTCCTGTTCGATGTGGGATAGAGACACTTTTCTTGTGACACT
1 TTTAAAGAGCCCAAGACCTCCCATTCCTGTTCGATGTGGGATAGAGACACTTTCCTAGTGACACT
* * *
3202745 CTCTCTCACCCGATTCAGACAACGTCACGTTGTCGCT
66 CTCTCCCACCCGATTCCGACAACGTCACGTTGCCGCT
* * * * *
3202782 TTTAAAAAGCCCAGGACCTCCCATTCCTGTTCAATATGGGATAGAGACACTTTCCTAGTGACGCT
1 TTTAAAGAGCCCAAGACCTCCCATTCCTGTTCGATGTGGGATAGAGACACTTTCCTAGTGACACT
3202847 CTCTCCCACCCGATTCCGACAACGTCACGTTGCCG
66 CTCTCCCACCCGATTCCGACAACGTCACGTTGCCG
3202882 TTGGCCACCC
Statistics
Matches: 185, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
102 109 0.59
103 76 0.41
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (102 bp):
TTTAAAGAGCCCAAGACCTCCCATTCCTGTTCGATGTGGGATAGAGACACTTTCCTAGTGACACT
CTCTCCCACCCGATTCCGACAACGTCACGTTGCCGCT
Found at i:3207036 original size:3 final size:3
Alignment explanation
Indices: 3207028--3207061 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3207018 TATCATTAAG
3207028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3207062 GACATTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3244866 original size:6 final size:6
Alignment explanation
Indices: 3244855--3244884 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3244845 GGTCAGGGAT
3244855 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG
1 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG
3244885 GGCATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
ATGGAG
Found at i:3258377 original size:24 final size:24
Alignment explanation
Indices: 3258350--3258397 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3258340 TATAATGCGT
* *
3258350 TTTTATCTTTTAAACATTTTATAA
1 TTTTATCTTTCAAAAATTTTATAA
3258374 TTTTATCTTTCAAAAATTTTATAA
1 TTTTATCTTTCAAAAATTTTATAA
3258398 CATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATCTTTCAAAAATTTTATAA
Found at i:3262494 original size:1 final size:1
Alignment explanation
Indices: 3262488--3262514 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3262478 TTGGGCCGGA
3262488 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
3262515 TGTGGGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3267230 original size:20 final size:21
Alignment explanation
Indices: 3267202--3267241 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3267192 CATTTCAGCT
*
3267202 CTTTTTTCTAAT-AAATTTTC
1 CTTTGTTCTAATGAAATTTTC
*
3267222 CTTTGTTCTATTGAAATTTT
1 CTTTGTTCTAATGAAATTTT
3267242 GAGCAGACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (21 bp):
CTTTGTTCTAATGAAATTTTC
Found at i:3285799 original size:49 final size:50
Alignment explanation
Indices: 3285704--3285839 Score: 186
Period size: 50 Copynumber: 2.8 Consensus size: 50
3285694 GAGTCTCGAC
3285704 TCCCGATTCCCCCCTACGGCCCTGCCCGCCCCCCTCCGGCTCCCCACGAG
1 TCCCGATTCCCCCCTACGGCCCTGCCCGCCCCCCTCCGGCTCCCCACGAG
* *
3285754 TCCCGATTCCCCCCTGCGGCCCTGCTCGCCCCCCTCCGGCT-CCCACGAG
1 TCCCGATTCCCCCCTACGGCCCTGCCCGCCCCCCTCCGGCTCCCCACGAG
* ** * **
3285803 TCTCGGCTCCCCCTTA-AACCCTGCCCGCCCCCCTCCG
1 TCCCGATTCCCCCCTACGGCCCTGCCCGCCCCCCTCCG
3285840 TCTAAATATG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
48 18 0.24
49 19 0.25
50 39 0.51
ACGTcount: A:0.07, C:0.59, G:0.18, T:0.16
Consensus pattern (50 bp):
TCCCGATTCCCCCCTACGGCCCTGCCCGCCCCCCTCCGGCTCCCCACGAG
Found at i:3288754 original size:24 final size:24
Alignment explanation
Indices: 3288725--3288786 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
3288715 AAATTGATCA
3288725 TTCAAATTTTGTAACCAAATTTAT
1 TTCAAATTTTGTAACCAAATTTAT
3288749 TTCAAATTTTGTAACCAAATTTAT
1 TTCAAATTTTGTAACCAAATTTAT
3288773 TTCAAATTTTGTAA
1 TTCAAATTTTGTAA
3288787 TGACTAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (24 bp):
TTCAAATTTTGTAACCAAATTTAT
Found at i:3291638 original size:24 final size:25
Alignment explanation
Indices: 3291611--3291657 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
3291601 TTATTTGAAA
*
3291611 TTTTTTAATTTTTTTTA-AAAATCG
1 TTTTTTAAATTTTTTTATAAAATCG
3291635 TTTTTTAAATTTTTTTATAAAAT
1 TTTTTTAAATTTTTTTATAAAAT
3291658 ATTATTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTTAAATTTTTTTATAAAATCG
Found at i:3328875 original size:11 final size:10
Alignment explanation
Indices: 3328861--3328901 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
3328851 GCTTCCCATA
*
3328861 CCCCTCCCCG
1 CCCCCCCCCG
3328871 CCCCCCCCC-
1 CCCCCCCCCG
*
3328880 CGCCCCCCC-
1 CCCCCCCCCG
3328889 CCCCCCCCCG
1 CCCCCCCCCG
3328899 CCC
1 CCC
3328902 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 16 0.59
10 11 0.41
ACGTcount: A:0.00, C:0.90, G:0.07, T:0.02
Consensus pattern (10 bp):
CCCCCCCCCG
Found at i:3328885 original size:9 final size:9
Alignment explanation
Indices: 3328873--3328901 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3328863 CCTCCCCGCC
3328873 CCCCCCCCG
1 CCCCCCCCG
3328882 CCCCCCCC-
1 CCCCCCCCG
3328890 CCCCCCCCG
1 CCCCCCCCG
3328899 CCC
1 CCC
3328902 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.00, C:0.93, G:0.07, T:0.00
Consensus pattern (9 bp):
CCCCCCCCG
Found at i:3328891 original size:17 final size:17
Alignment explanation
Indices: 3328866--3328901 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3328856 CCATACCCCT
*
3328866 CCCCGCCCCCCCCCCGC
1 CCCCCCCCCCCCCCCGC
3328883 CCCCCCCCCCCCCCCGC
1 CCCCCCCCCCCCCCCGC
3328900 CC
1 CC
3328902 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.92, G:0.08, T:0.00
Consensus pattern (17 bp):
CCCCCCCCCCCCCCCGC
Found at i:3340796 original size:13 final size:13
Alignment explanation
Indices: 3340743--3340796 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
3340733 TTCATACTTT
3340743 AATATATATTATA
1 AATATATATTATA
*
3340756 AATA-A-ACTATA
1 AATATATATTATA
*
3340767 AAT-TACATATATA
1 AATATATAT-TATA
3340780 AATATATATTATA
1 AATATATATTATA
3340793 AATA
1 AATA
3340797 ATAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 9 0.26
12 2 0.06
13 19 0.56
14 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (13 bp):
AATATATATTATA
Found at i:3343020 original size:2 final size:2
Alignment explanation
Indices: 3343013--3343101 Score: 88
Period size: 2 Copynumber: 44.5 Consensus size: 2
3343003 AACGATGCTT
*
3343013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TN
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** ** ** ** *
3343055 NN NN NN NN NA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3343097 TA TA T
1 TA TA T
3343102 CTTAGGTATA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3343318 original size:11 final size:11
Alignment explanation
Indices: 3343302--3343331 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3343292 AAAATCTCAA
3343302 AATGATGGGAT
1 AATGATGGGAT
*
3343313 AATGATGAGAT
1 AATGATGGGAT
3343324 AATGATGG
1 AATGATGG
3343332 CATTTGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (11 bp):
AATGATGGGAT
Found at i:3351373 original size:2 final size:2
Alignment explanation
Indices: 3351366--3351397 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3351356 ACATCATGAA
3351366 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3351398 TTGAGGTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3352870 original size:15 final size:15
Alignment explanation
Indices: 3352850--3352880 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3352840 AACGCCAAAC
3352850 ACACTTGCTAATGAT
1 ACACTTGCTAATGAT
3352865 ACACTTGCTAATGAT
1 ACACTTGCTAATGAT
3352880 A
1 A
3352881 TCCTTTCTTT
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:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
ACACTTGCTAATGAT
Found at i:3354460 original size:25 final size:26
Alignment explanation
Indices: 3354400--3354464 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
3354390 AAATTTATTC
3354400 AACATGGCATGTAACAATATATTTTG
1 AACATGGCATGTAACAATATATTTTG
* *
3354426 AACATAGCATGTAGCAA-A-ATTTTAG
1 AACATGGCATGTAACAATATATTTT-G
*
3354451 AACACGGCATGTAA
1 AACATGGCATGTAA
3354465 TGTGTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 5 0.15
25 13 0.39
26 15 0.45
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (26 bp):
AACATGGCATGTAACAATATATTTTG
Found at i:3359444 original size:21 final size:22
Alignment explanation
Indices: 3359420--3359460 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3359410 TGAGATTTGA
*
3359420 CTTCTCAGC-CACATCCTTGTC
1 CTTCTCAGCTAACATCCTTGTC
*
3359441 CTTCTCCGCTAACATCCTTG
1 CTTCTCAGCTAACATCCTTG
3359461 ATCGAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.15, C:0.41, G:0.10, T:0.34
Consensus pattern (22 bp):
CTTCTCAGCTAACATCCTTGTC
Found at i:3364891 original size:31 final size:32
Alignment explanation
Indices: 3364856--3364919 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
3364846 ACATGCTCAA
* *
3364856 TATCCTTCACATAACAAC-AATGCTTGTTCAT
1 TATCCTCCACATAACAACAAATGCTTATTCAT
* *
3364887 TATCCTCCATATATCAACAAATGCTTATTCAT
1 TATCCTCCACATAACAACAAATGCTTATTCAT
3364919 T
1 T
3364920 TAAACCATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (32 bp):
TATCCTCCACATAACAACAAATGCTTATTCAT
Found at i:3365615 original size:21 final size:22
Alignment explanation
Indices: 3365575--3365617 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3365565 TGTAAAACCC
*
3365575 TAAAAAGAAAGAAAGAGGCATT
1 TAAAAACAAAGAAAGAGGCATT
*
3365597 TAAAAACAAAG-AAGGGGCATT
1 TAAAAACAAAGAAAGAGGCATT
3365618 CTCACTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.56, C:0.07, G:0.23, T:0.14
Consensus pattern (22 bp):
TAAAAACAAAGAAAGAGGCATT
Found at i:3366580 original size:78 final size:78
Alignment explanation
Indices: 3366481--3366637 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
3366471 TTCAAACTAG
3366481 ATCAAAACCCAAAAATTTGTGTCCCAGTTGATTAGAACATGCATATATACAAATTTCTTCCTTTG
1 ATCAAAACCCAAAAATTTGTGTCCCAGTTGATTAGAACATGCATATATACAAATTTCTTCCTTTG
3366546 TCCTTACCGACAC
66 TCCTTACCGACAC
* *
3366559 ATCAAAACCCAAAAATTTGTGTCCCTGTTGATTAGAACATGCATATATACAAATTTCTTCTTTTG
1 ATCAAAACCCAAAAATTTGTGTCCCAGTTGATTAGAACATGCATATATACAAATTTCTTCCTTTG
3366624 TCCTTACCGACAC
66 TCCTTACCGACAC
3366637 A
1 A
3366638 AATGAAAAGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (78 bp):
ATCAAAACCCAAAAATTTGTGTCCCAGTTGATTAGAACATGCATATATACAAATTTCTTCCTTTG
TCCTTACCGACAC
Found at i:3366614 original size:38 final size:38
Alignment explanation
Indices: 3366493--3366614 Score: 92
Period size: 38 Copynumber: 3.2 Consensus size: 38
3366483 CAAAACCCAA
*
3366493 AAATTTGTGTCCCAGTTGATTAGAACATGCATATATAC
1 AAATTTGTGTCCCTGTTGATTAGAACATGCATATATAC
* * * * *
3366531 AAATTTCT-T-CCT-TTGTCCTTACCGACACAT-CA-AAACCCAA
1 AAATTTGTGTCCCTGTTG--ATTA--GA-ACATGCATATA--TAC
3366571 AAATTTGTGTCCCTGTTGATTAGAACATGCATATATAC
1 AAATTTGTGTCCCTGTTGATTAGAACATGCATATATAC
3366609 AAATTT
1 AAATTT
3366615 CTTCTTTTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 24
0.64 0.11 0.25
Matches are distributed among these distances:
35 3 0.05
36 2 0.03
37 4 0.07
38 20 0.33
39 8 0.13
40 14 0.23
41 4 0.07
42 3 0.05
43 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (38 bp):
AAATTTGTGTCCCTGTTGATTAGAACATGCATATATAC
Found at i:3378496 original size:23 final size:25
Alignment explanation
Indices: 3378453--3378499 Score: 71
Period size: 23 Copynumber: 1.9 Consensus size: 25
3378443 TTTGCAGCCA
3378453 AATATTATATTTCATAAATTAATCTT
1 AATATTATATTT-ATAAATTAATCTT
3378479 AATATTA-ATTT-TAAATTAATC
1 AATATTATATTTATAAATTAATC
3378500 ACACATAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
25 4 0.19
26 7 0.33
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATTATATTTATAAATTAATCTT
Found at i:3382943 original size:2 final size:2
Alignment explanation
Indices: 3382936--3382974 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3382926 ATCCTGTAAG
*
3382936 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3382975 CAATTCTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3385524 original size:3 final size:3
Alignment explanation
Indices: 3385516--3385546 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3385506 TAATGTGTAC
*
3385516 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3385547 TTTTCCTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3400424 original size:2 final size:2
Alignment explanation
Indices: 3400412--3400448 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3400402 ATGATAGATA
*
3400412 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3400449 TTCTTTCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3404732 original size:4 final size:4
Alignment explanation
Indices: 3404711--3404761 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
3404701 ATGGATCTGC
* * * *
3404711 ATAT ACAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
3404759 ATA
1 ATA
3404762 ACTATCACTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:3404738 original size:10 final size:10
Alignment explanation
Indices: 3404711--3404761 Score: 66
Period size: 10 Copynumber: 5.1 Consensus size: 10
3404701 ATGGATCTGC
* *
3404711 ATATACATAC
1 ATATATATAT
*
3404721 ATACATATAT
1 ATATATATAT
3404731 ATATATATAT
1 ATATATATAT
3404741 ATATATATAT
1 ATATATATAT
*
3404751 ATATGTATAT
1 ATATATATAT
3404761 A
1 A
3404762 ACTATCACTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATATATAT
Found at i:3421294 original size:2 final size:2
Alignment explanation
Indices: 3421287--3421311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3421277 AAAAGCAATA
3421287 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3421312 AATAAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3421374 original size:18 final size:19
Alignment explanation
Indices: 3421342--3421385 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
3421332 AAAATTTACA
3421342 TAAATATTTATTTTTTATTT
1 TAAAT-TTTATTTTTTATTT
*
3421362 TGAATTTTA-TTTTTATTT
1 TAAATTTTATTTTTTATTT
3421380 TAAATT
1 TAAATT
3421386 AAATTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TAAATTTTATTTTTTATTT
Found at i:3421464 original size:35 final size:35
Alignment explanation
Indices: 3421423--3421543 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
3421413 TTAATTAAAA
*
3421423 TAATATTTATTATTTTATATAATATAATATTGATG
1 TAATATTTATTATTTTATATAATATAATATTGATT
* *
3421458 TGATATTTAATATTATAATTAATAATAATATATAGTATT-ATTT
1 TAATA-TT--TATTAT--TTTAT-ATAATATA-A-TATTGA-TT
*
3421501 TAATATTTATTATTTTATGTAATATAATATTGATT
1 TAATATTTATTATTTTATATAATATAATATTGATT
*
3421536 TTATATTT
1 TAATATTT
3421544 TAATAAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
35 17 0.25
36 4 0.06
37 7 0.10
38 10 0.14
40 10 0.14
41 8 0.12
42 4 0.06
43 9 0.13
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (35 bp):
TAATATTTATTATTTTATATAATATAATATTGATT
Found at i:3421509 original size:78 final size:79
Alignment explanation
Indices: 3421423--3421569 Score: 226
Period size: 78 Copynumber: 1.9 Consensus size: 79
3421413 TTAATTAAAA
3421423 TAATATTTATTATTTTATATAATATAATATTGATGTGATA-TTTAAT-ATTATAATTAATAATAA
1 TAATATTTATTATTTTATATAATATAATATTGATGTGATATTTTAATAATTATAATT-ATAATAA
3421486 TATATAGTATTATTT
65 TATATAGTATTATTT
* * * *
3421501 TAATATTTATTATTTTATGTAATATAATATTGATTTTATATTTTAATAAATTTTAATTATAATAA
1 TAATATTTATTATTTTATATAATATAATATTGATGTGATATTTTAAT-AATTATAATTATAATAA
3421566 TATA
65 TATA
3421570 ACATGTCAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
78 37 0.60
79 6 0.10
80 11 0.18
81 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (79 bp):
TAATATTTATTATTTTATATAATATAATATTGATGTGATATTTTAATAATTATAATTATAATAAT
ATATAGTATTATTT
Found at i:3421565 original size:16 final size:17
Alignment explanation
Indices: 3421533--3421565 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3421523 TATAATATTG
*
3421533 ATTTTATATTTTAATAA
1 ATTTTATATTATAATAA
3421550 ATTTTA-ATTATAATAA
1 ATTTTATATTATAATAA
3421566 TATAACATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATATTATAATAA
Found at i:3422828 original size:89 final size:90
Alignment explanation
Indices: 3422677--3422878 Score: 300
Period size: 89 Copynumber: 2.3 Consensus size: 90
3422667 AAGTGGTGTC
* * *
3422677 ATTAATGTCTTTAGCCATATTTTGTCATCCTTCTTCTTCATCTTTTCTCTTTCCTTTGGATTAGG
1 ATTAGTGTCTTTAACCATATTTTGTCATCCTTCTTCTTCATCGTTTCTCTTTCCTTTGGATTA-G
3422742 T-TAGTATAATTAGTATTATACCATT
65 TCTAGTATAATTAGTATTATACCATT
3422767 ATTAGTGTCTTTAACCATATTTTGTCATCCTTC-TCTTCATCGTTTCTCTTTCCTTTGGATTAGT
1 ATTAGTGTCTTTAACCATATTTTGTCATCCTTCTTCTTCATCGTTTCTCTTTCCTTTGGATTAGT
* * *
3422831 CTAGTATAATTGGTATTATGCTATT
66 CTAGTATAATTAGTATTATACCATT
* * *
3422856 GTTAGTCTCTTTAATCATATTTT
1 ATTAGTGTCTTTAACCATATTTT
3422879 CCTATGGAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 2 0.02
89 69 0.68
90 31 0.30
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.51
Consensus pattern (90 bp):
ATTAGTGTCTTTAACCATATTTTGTCATCCTTCTTCTTCATCGTTTCTCTTTCCTTTGGATTAGT
CTAGTATAATTAGTATTATACCATT
Found at i:3423647 original size:9 final size:9
Alignment explanation
Indices: 3423633--3423663 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3423623 TGAAGAGAAG
*
3423633 GAGACTGAA
1 GAGACTAAA
3423642 GAGACTAAA
1 GAGACTAAA
3423651 GAGACTAAA
1 GAGACTAAA
3423660 GAGA
1 GAGA
3423664 AGGAAGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.29, T:0.10
Consensus pattern (9 bp):
GAGACTAAA
Found at i:3423714 original size:24 final size:24
Alignment explanation
Indices: 3423675--3423749 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
3423665 GGAAGGTGAG
* * *
3423675 GAGAAAGAAAGTGAAGAGAGTAAA
1 GAGAAGGAAAATGAAGAGAGCAAA
*
3423699 GAGAAGG-AGATAGAAGAGAGCAAA
1 GAGAAGGAAAAT-GAAGAGAGCAAA
* *
3423723 GAAAAGGAAAATGAAGAGAGGAAA
1 GAGAAGGAAAATGAAGAGAGCAAA
3423747 GAG
1 GAG
3423750 GAAAATGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.88
25 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.36, T:0.05
Consensus pattern (24 bp):
GAGAAGGAAAATGAAGAGAGCAAA
Found at i:3423797 original size:27 final size:27
Alignment explanation
Indices: 3423736--3423797 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
3423726 AAGGAAAATG
*
3423736 AAGAGAGGAAAGAGGAAAATGAAAACA
1 AAGAGAGTAAAGAGGAAAATGAAAACA
* *
3423763 AAGAGAGTAAAGAGGACAGTGAAAACA
1 AAGAGAGTAAAGAGGAAAATGAAAACA
3423790 AAGAGAGT
1 AAGAGAGT
3423798 GAAGTCAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.58, C:0.05, G:0.31, T:0.06
Consensus pattern (27 bp):
AAGAGAGTAAAGAGGAAAATGAAAACA
Found at i:3425034 original size:51 final size:51
Alignment explanation
Indices: 3424965--3425110 Score: 215
Period size: 51 Copynumber: 2.9 Consensus size: 51
3424955 CACCAACAAT
** * * *
3424965 AATGAAAATGTTGATCAGAGTGTGAACAATGTCT-CTGAGAGCAATACCAAC
1 AATGAAAATGCAGGTCAGAGTGAGAACAATG-CTGCTCAGAGCAATACCAAC
3425016 AATGAAAATGCAGGTCAGAGTGAGAACAATGCTGCTCAGAGCAATACCAAC
1 AATGAAAATGCAGGTCAGAGTGAGAACAATGCTGCTCAGAGCAATACCAAC
3425067 AATGAAAATGCAGGTCAGAAG-GAGAACAATGCTGCTCAGAGCAA
1 AATGAAAATGCAGGTCAG-AGTGAGAACAATGCTGCTCAGAGCAA
3425111 CAATGAAAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
50 2 0.02
51 84 0.95
52 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (51 bp):
AATGAAAATGCAGGTCAGAGTGAGAACAATGCTGCTCAGAGCAATACCAAC
Found at i:3425129 original size:45 final size:46
Alignment explanation
Indices: 3425012--3425147 Score: 159
Period size: 51 Copynumber: 2.9 Consensus size: 46
3425002 AGAGCAATAC
3425012 CAACAATGAAAATGCAGGTCAG-AGTGAGAACAATGCTGCTCAGAGCAATA
1 CAACAATGAAAATGCAGGTCAGAAG-GAGAACAATGCTGCTCAGAG----A
3425062 CCAACAATGAAAATGCAGGTCAGAAGGAGAACAATGCTGCTCAGAG-
1 -CAACAATGAAAATGCAGGTCAGAAGGAGAACAATGCTGCTCAGAGA
* * * * *
3425108 CAACAATGAAAGTGCACGTCAGAATGAGAGCAATGATGCT
1 CAACAATGAAAATGCAGGTCAGAAGGAGAACAATGCTGCT
3425148 GTTCAGAGCA
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
45 35 0.44
51 42 0.53
52 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.15
Consensus pattern (46 bp):
CAACAATGAAAATGCAGGTCAGAAGGAGAACAATGCTGCTCAGAGA
Found at i:3438520 original size:12 final size:12
Alignment explanation
Indices: 3438502--3438548 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
3438492 AATTTAACAA
3438502 ATATATAATATT
1 ATATATAATATT
*
3438514 GTATAT-ATA-T
1 ATATATAATATT
* *
3438524 ATATATATTAAT
1 ATATATAATATT
3438536 ATATATAATATT
1 ATATATAATATT
3438548 A
1 A
3438549 GTTTTGTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
10 6 0.21
11 5 0.18
12 17 0.61
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
ATATATAATATT
Found at i:3440429 original size:15 final size:16
Alignment explanation
Indices: 3440398--3440431 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3440388 ATTTAAATAA
*
3440398 TATCAAAAAGTAGATT
1 TATCAAAAAATAGATT
3440414 TATCAAAAAATA-ATT
1 TATCAAAAAATAGATT
3440429 TAT
1 TAT
3440432 ATATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
TATCAAAAAATAGATT
Found at i:3443050 original size:15 final size:15
Alignment explanation
Indices: 3443020--3443086 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
3443010 CGTTTGATAC
*
3443020 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
3443036 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
*
3443051 ATTACAAGTAACGTG
1 ATTACAAGTAATGTG
* *
3443066 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
3443081 ATTACA
1 ATTACA
3443087 GGGAAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 37 0.86
16 6 0.14
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:3443325 original size:30 final size:30
Alignment explanation
Indices: 3443291--3443498 Score: 87
Period size: 26 Copynumber: 7.4 Consensus size: 30
3443281 AATATATTTT
3443291 TAATATCATATATTTTATTTATTATTATTA
1 TAATATCATATATTTTATTTATTATTATTA
** *
3443321 TAATATTTTATATTTTATTT-TTAATA-TA
1 TAATATCATATATTTTATTTATTATTATTA
* * * *
3443349 T-TTAT-AT-TTTTATTATTAATTTTTA-TA
1 TAATATCATATATT-TTATTTATTATTATTA
* **
3443376 TAATATCAT-T-TCTTAAATA-TATT-TT-
1 TAATATCATATATTTTATTTATTATTATTA
*
3443401 TAATGTCATATATTTTATTT-TTATTTATTA
1 TAATATCATATATTTTATTTATTA-TTATTA
*
3443431 T--TAT-A-ATATTTTATAT-TTATT-TT-
1 TAATATCATATATTTTATTTATTATTATTA
* *
3443454 TAATAT-ATTTATATTTATATTATTAATTTTATA
1 TAATATCATATAT-TTTAT-TTATT-ATTAT-TA
3443487 TTAATATCATAT
1 -TAATATCATAT
3443499 TTTAAATATA
Statistics
Matches: 131, Mismatches: 24, Indels: 41
0.67 0.12 0.21
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 17 0.13
26 27 0.21
27 27 0.21
28 12 0.09
29 12 0.09
30 22 0.17
31 1 0.01
32 1 0.01
34 6 0.05
35 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TAATATCATATATTTTATTTATTATTATTA
Found at i:3443326 original size:23 final size:23
Alignment explanation
Indices: 3443300--3443478 Score: 78
Period size: 23 Copynumber: 7.9 Consensus size: 23
3443290 TTAATATCAT
3443300 ATATTTTATTTATTATTATTATA
1 ATATTTTATTTATTATTATTATA
3443323 ATATTTTATATT-TTATT-TT-TA
1 ATATTTTAT-TTATTATTATTATA
*
3443344 ATATATTTA--TATTTTTATTATTA
1 ATAT-TTTATTTATTATTATTA-TA
* * * *
3443367 AT-TTTTATATAATATCATTTCTTA
1 ATATTTTATTTATTATTA-TT-ATA
* * * *
3443391 A-A-TATATTT-TTAATGTCAT-
1 ATATTTTATTTATTATTATTATA
3443410 ATATTTTATTTTTATTTATTATTATA
1 ATATTTTA--TTTA-TTATTATTATA
* *
3443436 ATATTTTATAT-TTATTTTTA-A
1 ATATTTTATTTATTATTATTATA
3443457 TATATTTATATTTA-TATTATTA
1 -ATATTT-TATTTATTATTATTA
3443479 ATTTTATATT
Statistics
Matches: 114, Mismatches: 21, Indels: 42
0.64 0.12 0.24
Matches are distributed among these distances:
19 2 0.02
20 6 0.05
21 17 0.15
22 23 0.20
23 42 0.37
24 9 0.08
25 7 0.06
26 8 0.07
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATTTTATTTATTATTATTATA
Found at i:3443444 original size:20 final size:20
Alignment explanation
Indices: 3443419--3443502 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 20
3443409 TATATTTTAT
3443419 TTTTATTTATTATTATAATA
1 TTTTATTTATTATTATAATA
*
3443439 TTTTATATTTATTTTTA-ATATA
1 -TTT-TATTTATTATTATA-ATA
*
3443461 TTTATATTTA-TATTATTA-A
1 TTT-TATTTATTATTATAATA
* *
3443480 TTTTA--TATTAATATCATA
1 TTTTATTTATTATTATAATA
3443498 TTTTA
1 TTTTA
3443503 AATATATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
16 2 0.04
17 6 0.11
18 8 0.15
19 4 0.08
20 5 0.09
21 14 0.26
22 14 0.26
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTTATTATTATAATA
Found at i:3443466 original size:6 final size:6
Alignment explanation
Indices: 3443409--3443474 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
3443399 TTTAATGTCA
* *
3443409 TATATT T-TATT TTTATT TATTATT ATAATATTT TATATT TAT-TT T-TA-A
1 TATATT TATATT TATATT TA-TATT -T-ATA-TT TATATT TATATT TATATT
3443457 TATATT TATATT TATATT
1 TATATT TATATT TATATT
3443475 ATTAATTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 23 0.47
7 7 0.14
8 4 0.08
9 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:3443488 original size:48 final size:48
Alignment explanation
Indices: 3443408--3443513 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
3443398 TTTTAATGTC
* * * *
3443408 ATATATTTTATTTTTATTTATTATTATAATATTTTATAT-TTATTTTTA
1 ATATATTTTATTTATATTTATTATTATAATA-TTAATATCATATTTTAA
*
3443456 ATATATTTATATTTATA-TTATTAATT-TTATATTAATATCATATTTTAA
1 ATATATTT-TATTTATATTTATT-ATTATAATATTAATATCATATTTTAA
3443504 ATATATTTTA
1 ATATATTTTA
3443514 ATGTCAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
47 8 0.16
48 32 0.64
49 10 0.20
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (48 bp):
ATATATTTTATTTATATTTATTATTATAATATTAATATCATATTTTAA
Found at i:3443492 original size:112 final size:112
Alignment explanation
Indices: 3443233--3443548 Score: 499
Period size: 110 Copynumber: 2.9 Consensus size: 112
3443223 AAAATATAAG
* *
3443233 TTTAATATA-TTATATTTTATTATTAATTTTTATATAATATCA-TTCTTTAATATATTTTTAATA
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATG
3443296 TCATATATTTTA--TTTA-TTATTATTATAATATTTTATATTTTATT
66 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
3443340 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATA-TTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
3443405 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATA-TTTATT
65 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
3443452 TTTAATATATTTATATTTATATTATTAA-TTTTATATTAATATCATATT-TTAAATATA-TTTTA
1 TTTAATATATTTATATTT-TATTATTAATTTTTATA-TAATATCAT-TTCTTAAATATATTTTTA
3443514 ATGTCA-ATATTTTATTTTTATTTATTATCTATAAT
63 ATGTCATATATTTTATTTTTATTTATTAT-TATAAT
3443549 TATATAGTTA
Statistics
Matches: 197, Mismatches: 2, Indels: 16
0.92 0.01 0.07
Matches are distributed among these distances:
107 9 0.05
108 5 0.03
109 28 0.14
110 53 0.27
111 27 0.14
112 52 0.26
113 23 0.12
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (112 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATG
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:3443513 original size:11 final size:11
Alignment explanation
Indices: 3443436--3443514 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
3443426 TATTATTATA
*
3443436 ATATTTTATAT
1 ATATTTTAAAT
* *
3443447 TTATTTTTAAT
1 ATATTTTAAAT
**
3443458 ATATTTATATTT
1 ATATTT-TAAAT
*
3443470 ATATTATTAATT
1 ATATT-TTAAAT
* *
3443482 TTATATTAATAT
1 ATATTTTAA-AT
3443494 CATATTTTAAAT
1 -ATATTTTAAAT
3443506 ATATTTTAA
1 ATATTTTAA
3443515 TGTCAATATT
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
11 26 0.51
12 17 0.33
13 8 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTTTAAAT
Found at i:3443535 original size:25 final size:24
Alignment explanation
Indices: 3443470--3443536 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
3443460 ATTTATATTT
*
3443470 ATATTATTAATTTTATATTAATATC
1 ATATT-TTAATTTTATTTTAATATC
* * *
3443495 ATATTTTAAATATATTTTAATGTC
1 ATATTTTAATTTTATTTTAATATC
*
3443519 AATATTTTATTTTTATTT
1 -ATATTTTAATTTTATTT
3443537 ATTATCTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (24 bp):
ATATTTTAATTTTATTTTAATATC
Found at i:3443537 original size:24 final size:23
Alignment explanation
Indices: 3443470--3443542 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
3443460 ATTTATATTT
3443470 ATATTATTAATTTTATATTAATATC
1 ATATT-TTAATTTTAT-TTAATATC
* * *
3443495 ATATTTTAAATATATTTTAATGTC
1 ATATTTTAATTTTA-TTTAATATC
* *
3443519 AATATTTTATTTTTATTTATTATC
1 -ATATTTTAATTTTATTTAATATC
3443543 TATAATTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
24 21 0.55
25 17 0.45
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
ATATTTTAATTTTATTTAATATC
Found at i:3443579 original size:112 final size:109
Alignment explanation
Indices: 3443243--3443586 Score: 445
Period size: 110 Copynumber: 3.1 Consensus size: 109
3443233 TTTAATATAT
*
3443243 TATATTTTATTATTAATTTTTATATAATATCATTCTTT-AATATATTTTTAATATCATATATTTT
1 TATATTTTATTATTAATTTTTATATAATATCATT-TTTAAATATATTTTTAATGTCATATATTTT
*
3443307 ATTTATTA-TTATTATAAT-ATTTTATATTTTATTTTTAATATATTTA
65 ATTT-TTATTTATTATTATAATTTTATA-TTTATTTTTAATAT-TTTA
3443353 TAT-TTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTT
1 TATATTTTATTATTAATTTTTATATAATATCATTT-TTAAATATATTTTTAATGTCATATATTTT
3443417 ATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATATTTA
65 ATTTTTATTTATTATTAT-A-ATTTTATATTTATTTTTAATAT-TTTA
*
3443465 TAT-TTATATTATTAA-TTTTATATTAATATCATATTTTAAATATA-TTTTAATGTCA-ATATTT
1 TATATTTTATTATTAATTTTTATA-TAATATCAT-TTTTAAATATATTTTTAATGTCATATATTT
* * * *
3443526 TATTTTTATTTATTATCTATAATTATATAGTTATTTTTCATTTCTTTAA
64 TATTTTTATTTATTAT-TATAATTTTATATTTATTTTTAATAT-TTT-A
3443575 TATATTTT-TTAT
1 TATATTTTATTAT
3443587 ATTATATATG
Statistics
Matches: 214, Mismatches: 9, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
108 1 0.00
109 56 0.26
110 72 0.34
111 24 0.11
112 51 0.24
113 10 0.05
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (109 bp):
TATATTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATGTCATATATTTTA
TTTTTATTTATTATTATAATTTTATATTTATTTTTAATATTTTA
Found at i:3443628 original size:24 final size:22
Alignment explanation
Indices: 3443578--3443635 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
3443568 TCTTTAATAT
*
3443578 ATTTTTTATATTATATATGTT-
1 ATTTTTTATATTATATATATTA
3443599 ATTTTTATATATTATATAAATATTA
1 ATTTTT-TATATTATAT--ATATTA
3443624 ATTTTTTATATT
1 ATTTTTTATATT
3443636 TTATTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.19
22 10 0.31
24 10 0.31
25 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTTTATATTATATATATTA
Found at i:3443636 original size:221 final size:217
Alignment explanation
Indices: 3443233--3443646 Score: 461
Period size: 221 Copynumber: 1.9 Consensus size: 217
3443223 AAAATATAAG
3443233 TTTAATATATTATATTTTATTATTAATTTTTATATAATATCATTCTTTAATATATTTTTAATATC
1 TTTAATATATTATATTTTATTATTAATTTTTATATAATATCATTCTTTAATATATTTTTAATATC
* *
3443298 ATATATTTTATTTATTATTATTATAATATTTTATATTTTATTTTTAATATATTTATATTTTTATT
66 ATATATTTTATTTATTATTATTATAATATTATATATGTTATTTTTAATATATTTATATTTTTATT
* * * * *
3443363 ATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTTATTTA
131 ATTAATTGTTATAT-ATATCATATATTAAATATAATATTAATGTCATATATTTTA-TTTTATTTA
3443428 TTATTATAATATTTTATATTTATT
194 TTATTATAATATTTTATATTTATT
3443452 TTTAATATATTTATATTTATATTATTAA-TTTTATATTAATATCATAT-TTTAA-ATATATTTTA
1 TTTAATATA-TTATATTT-TATTATTAATTTTTATA-TAATATCAT-TCTTTAATATAT-TTTTA
* * * * *
3443514 ATGTCA-ATATTTTATTT-TTATTTATTATCTATAATTATATA-GTTATTTTTCATTTCTTTAAT
61 ATATCATATATTTTATTTATTA-TTATTAT-AAT-ATTATATATGTTATTTTTAATATATTT-AT
* * * * **
3443576 ATATTTTTTATATTATATATGTTAT-T-T-TTATATATTATATA-AATATTAATTTTTTATATTT
122 AT-TTTTAT-TATTA-AT-TGTTATATATATCATATATTAAATATAATATTAATGTCATATATTT
3443637 TATTTTATTT
183 TATTTTATTT
3443647 TAANNNNNNN
Statistics
Matches: 164, Mismatches: 18, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
219 12 0.07
220 45 0.27
221 66 0.40
222 22 0.13
223 6 0.04
224 5 0.03
225 3 0.02
226 5 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (217 bp):
TTTAATATATTATATTTTATTATTAATTTTTATATAATATCATTCTTTAATATATTTTTAATATC
ATATATTTTATTTATTATTATTATAATATTATATATGTTATTTTTAATATATTTATATTTTTATT
ATTAATTGTTATATATATCATATATTAAATATAATATTAATGTCATATATTTTATTTTATTTATT
ATTATAATATTTTATATTTATT
Found at i:3444552 original size:37 final size:37
Alignment explanation
Indices: 3444499--3444575 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
3444489 TCAAGGGCGC
* *
3444499 TTGATTTCTTTGTATGGG-CCTGGAAAGTAATGGAAGA
1 TTGATTTCTTTATATGGGTCCT-GAAAGTAATGAAAGA
*
3444536 TTGATTTCTTTATATGGGTCCTGAAAGTGATGAAAGA
1 TTGATTTCTTTATATGGGTCCTGAAAGTAATGAAAGA
3444573 TTG
1 TTG
3444576 CAGCATTCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 33 0.92
38 3 0.08
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (37 bp):
TTGATTTCTTTATATGGGTCCTGAAAGTAATGAAAGA
Found at i:3444956 original size:21 final size:21
Alignment explanation
Indices: 3444917--3444958 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3444907 AATACTTTTT
3444917 ATTATAATATTTAATTTTTAA
1 ATTATAATATTTAATTTTTAA
*
3444938 ATTA-AATATTTATTATTTTAA
1 ATTATAATATTTAAT-TTTTAA
3444959 TAATTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATAATATTTAATTTTTAA
Found at i:3445036 original size:22 final size:22
Alignment explanation
Indices: 3445011--3445062 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3445001 ATTATTATTT
*
3445011 ATTATATATTTTAT-TTTAAAAC
1 ATTA-ATATTTTATAATTAAAAC
* *
3445033 ATTAATAATTTATAATTAAAAT
1 ATTAATATTTTATAATTAAAAC
3445055 ATTAATAT
1 ATTAATAT
3445063 CGATATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAATATTTTATAATTAAAAC
Found at i:3445700 original size:4 final size:4
Alignment explanation
Indices: 3445691--3445716 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3445681 CTTTCAGGAG
3445691 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
3445717 GAAATCAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3453149 original size:30 final size:31
Alignment explanation
Indices: 3453113--3453181 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
3453103 ATCAAAAATT
* * *
3453113 TTTTTATATTAAATTAAATATATTTTTA-TA
1 TTTTTATATTAAATCAAATAAATTTATATTA
*
3453143 TTTTTATTTTAAATCAAATAAATTTATATTA
1 TTTTTATATTAAATCAAATAAATTTATATTA
3453174 TTTGTTAT
1 TTT-TTAT
3453182 TTTATGTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 24 0.73
31 5 0.15
32 4 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTTTATATTAAATCAAATAAATTTATATTA
Found at i:3453258 original size:33 final size:33
Alignment explanation
Indices: 3453211--3453281 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
3453201 ATAAGAAATA
* * *
3453211 TTAATATATCATAATTAATGATGATGTGATATG
1 TTAATATATCATAATTAATAATAATATGATATG
*
3453244 TTAATATATTATAATTAATAATAATATGATATG
1 TTAATATATCATAATTAATAATAATATGATATG
*
3453277 ATAAT
1 TTAAT
3453282 GTAATATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (33 bp):
TTAATATATCATAATTAATAATAATATGATATG
Found at i:3453304 original size:24 final size:23
Alignment explanation
Indices: 3453251--3453304 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3453241 ATGTTAATAT
*
3453251 ATTATAATTAATAATAATATGAT
1 ATTATAATTAATAATAATATGAC
* *
3453274 ATGATAATGTAAT-ATACATGTGAC
1 ATTATAAT-TAATAATA-ATATGAC
3453298 ATTATAA
1 ATTATAA
3453305 CATGCTGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
ATTATAATTAATAATAATATGAC
Found at i:3456010 original size:20 final size:20
Alignment explanation
Indices: 3455957--3455995 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3455947 TTTTGAAATC
*
3455957 ATGAAAATTTA-TTAATTAA
1 ATGAAATTTTATTTAATTAA
3455976 ATGAAATTTTATTTAATTAA
1 ATGAAATTTTATTTAATTAA
3455996 TAAATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATGAAATTTTATTTAATTAA
Done.