Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 314 of 325
Found at i:95154414 original size:127 final size:127
Alignment explanation
Indices: 95154279--95154590 Score: 464
Period size: 127 Copynumber: 2.5 Consensus size: 127
95154269 AACGAAAAAC
* * * * * * *
95154279 CGAAACCCAACACGGTAAGGCACGATTCCTCGAATTTCCAAACATTGAATATTGTCTTGCTTTAG
1 CGAAACCCAGCACGATAGGGCACGGTTCCTCGAATTTCCAAACATTGAACATTGCCTTACTTTAG
* *
95154344 AATTTATAAAACATGAGTGGAATTCTAAAGGAATATTCAATTATTTGGAACAAACCGGAAAT
66 AATTTATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTGGAACAAACCGGAAAT
* *
95154406 CGAAACCCAGCACGATAGGGCACGGTT-CTCCGAATTTCCAAATATTGAACATTGCCTTATTTTA
1 CGAAACCCAGCACGATAGGGCACGGTTCCT-CGAATTTCCAAACATTGAACATTGCCTTACTTTA
95154470 GAATTTATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTGGAACAAACCGGAAAT
65 GAATTTATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTGGAACAAACCGGAAAT
* * * * *
95154533 CAAAACCCAGCGCGATAGGGCACGGTTCCCCGAATTTCCAAACATTAAACATTACCTT
1 CGAAACCCAGCACGATAGGGCACGGTTCCTCGAATTTCCAAACATTGAACATTGCCTT
95154591 CATTTTAAGG
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
126 2 0.01
127 163 0.98
128 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (127 bp):
CGAAACCCAGCACGATAGGGCACGGTTCCTCGAATTTCCAAACATTGAACATTGCCTTACTTTAG
AATTTATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTGGAACAAACCGGAAAT
Found at i:95161620 original size:24 final size:24
Alignment explanation
Indices: 95161591--95161642 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
95161581 AACCAACACA
95161591 AACAAACTTAAAAATAAACAAACG
1 AACAAACTTAAAAATAAACAAACG
95161615 AACAAACTTAAAAATAAACAAACG
1 AACAAACTTAAAAATAAACAAACG
95161639 AACA
1 AACA
95161643 TAAAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.12
Consensus pattern (24 bp):
AACAAACTTAAAAATAAACAAACG
Found at i:95161651 original size:24 final size:24
Alignment explanation
Indices: 95161591--95161651 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
95161581 AACCAACACA
**
95161591 AACAAACTTAAAAATAAACAAACG
1 AACAAACAAAAAAATAAACAAACG
**
95161615 AACAAACTTAAAAATAAACAAACG
1 AACAAACAAAAAAATAAACAAACG
*
95161639 AACATA-AAAAAAA
1 AACAAACAAAAAAA
95161652 GTTTGTTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.11
Consensus pattern (24 bp):
AACAAACAAAAAAATAAACAAACG
Found at i:95164000 original size:22 final size:20
Alignment explanation
Indices: 95163954--95164000 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
95163944 ACAGCCGTAA
95163954 AAAAG-AAAGAAAAATAAGG
1 AAAAGAAAAGAAAAATAAGG
* *
95163973 AGAAGAAAAGAGAGAAATAGGG
1 AAAAGAAAAGA-A-AAATAAGG
95163995 AAAAGA
1 AAAAGA
95164001 CTTGTGTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 1 0.05
22 12 0.55
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATAAGG
Found at i:95171182 original size:20 final size:20
Alignment explanation
Indices: 95171159--95171199 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
95171149 ATTTTGAAGT
95171159 ATATCTTTAGATCTGAACAA
1 ATATCTTTAGATCTGAACAA
95171179 ATATCTTTAGATCTGAACAA
1 ATATCTTTAGATCTGAACAA
95171199 A
1 A
95171200 ACTCTAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (20 bp):
ATATCTTTAGATCTGAACAA
Found at i:95172885 original size:7 final size:7
Alignment explanation
Indices: 95172863--95172897 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
95172853 TACAAATAAG
*
95172863 TAAAATA
1 TAAAAAA
*
95172870 TATAAAA
1 TAAAAAA
95172877 TAAAAAA
1 TAAAAAA
95172884 TAAAAAA
1 TAAAAAA
95172891 TAAAAAA
1 TAAAAAA
95172898 ACTACTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAAAAA
Found at i:95175009 original size:25 final size:25
Alignment explanation
Indices: 95174962--95175009 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
95174952 TTCCTTATAA
**
95174962 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
95174987 ACTTTAAATTAGGAATTAGATTA
1 ACTTTAAATTAGGAATTAGATTA
95175010 TGATTTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:95179660 original size:25 final size:25
Alignment explanation
Indices: 95179626--95179676 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
95179616 TTCCTTATAA
**
95179626 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
95179651 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
95179676 A
1 A
95179677 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:95179675 original size:12 final size:12
Alignment explanation
Indices: 95179629--95179676 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
95179619 CTTATAAACT
95179629 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
95179641 TTCTATTAGGACT
1 TTAAATTAGGA-A
95179654 TTAAATTAGGAA
1 TTAAATTAGGAA
*
95179666 TTAGATTAGGA
1 TTAAATTAGGA
95179677 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:95180812 original size:21 final size:21
Alignment explanation
Indices: 95180786--95180826 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
95180776 TCCAGCAACC
*
95180786 AAACACTCTCATTCCAGCTCT
1 AAACACTCCCATTCCAGCTCT
*
95180807 AAACACTCCCATTCCGGCTC
1 AAACACTCCCATTCCAGCTC
95180827 CTGTCCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.41, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACACTCCCATTCCAGCTCT
Found at i:95185268 original size:100 final size:100
Alignment explanation
Indices: 95185095--95185294 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
95185085 AAAAGTATGC
*
95185095 TCTTTAAGGAACTGGCAATAGATAGAGAATCCAAACTTGAATGTAAAGATAGAACCACAAATTCA
1 TCTTTAAGGAACTGGCAATAGATAGAGAATCCAAACTTGAATGTAAAGATAAAACCACAAATTCA
95185160 AGTAAAATTGATGTGGAATAAAATCTTTCAACATA
66 AGTAAAATTGATGTGGAATAAAATCTTTCAACATA
*
95185195 TCTTTGAGGAACTGGCAATAGATAGAGAATCCAAACTTGAATGTAAAGATAAAACCACAAATTCA
1 TCTTTAAGGAACTGGCAATAGATAGAGAATCCAAACTTGAATGTAAAGATAAAACCACAAATTCA
95185260 AGTAAAATTGATGTGGAATAAAATCTTTCAACATA
66 AGTAAAATTGATGTGGAATAAAATCTTTCAACATA
95185295 AAGATGGCAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (100 bp):
TCTTTAAGGAACTGGCAATAGATAGAGAATCCAAACTTGAATGTAAAGATAAAACCACAAATTCA
AGTAAAATTGATGTGGAATAAAATCTTTCAACATA
Found at i:95190259 original size:1 final size:1
Alignment explanation
Indices: 95190253--95190285 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
95190243 CTGAAAAGCC
95190253 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
95190286 GCGAAATACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:95213083 original size:138 final size:138
Alignment explanation
Indices: 95212914--95213330 Score: 771
Period size: 138 Copynumber: 3.0 Consensus size: 138
95212904 TTTTAAAATT
95212914 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACGTAAAAACAAT
1 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACGTAAAAACAAT
95212979 TTAATGCCAATTTTTAAAGAAATTACATATGGTTCTAAAATTCAAAACAGGGACTCCTGAAAGCA
66 TTAATGCCAATTTTTAAAGAAATTACATATGGTTCTAAAATTCAAAACAGGGACTCCTGAAAGCA
95213044 TTCAGACG
131 TTCAGACG
95213052 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACGTAAAAACAAT
1 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACGTAAAAACAAT
*
95213117 TTAATGCCAATTTTTAAAGAAATTACATATGGTTCTAAAGTTCAAAACAGGGACTCCTGAAAGCA
66 TTAATGCCAATTTTTAAAGAAATTACATATGGTTCTAAAATTCAAAACAGGGACTCCTGAAAGCA
95213182 TTCAGACG
131 TTCAGACG
* *
95213190 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTATTATAAAACCTAAAAACAAT
1 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACGTAAAAACAAT
* *
95213255 TTAATGCCAATTTTTAAAGAAATTACATATGATTCTAAAATTCAAAACAGGGACTCCTCAAAGCA
66 TTAATGCCAATTTTTAAAGAAATTACATATGGTTCTAAAATTCAAAACAGGGACTCCTGAAAGCA
* *
95213320 TCCATACG
131 TTCAGACG
95213328 TTA
1 TTA
95213331 TTAAGCCTCC
Statistics
Matches: 271, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 271 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (138 bp):
TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACGTAAAAACAAT
TTAATGCCAATTTTTAAAGAAATTACATATGGTTCTAAAATTCAAAACAGGGACTCCTGAAAGCA
TTCAGACG
Found at i:95217295 original size:26 final size:26
Alignment explanation
Indices: 95217261--95217314 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
95217251 CTCCAATAAT
95217261 AGAGACAAGAGATTTGACAATGAACA
1 AGAGACAAGAGATTTGACAATGAACA
95217287 AGAGACAAGAGATTTGACAATGAACA
1 AGAGACAAGAGATTTGACAATGAACA
95217313 AG
1 AG
95217315 GGCAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.15
Consensus pattern (26 bp):
AGAGACAAGAGATTTGACAATGAACA
Found at i:95220237 original size:12 final size:10
Alignment explanation
Indices: 95220215--95220270 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
95220205 AAACTATCTA
95220215 AAATAATATT
1 AAATAATATT
95220225 AAATATTATATT
1 AAATA--ATATT
95220237 -AATAATATT
1 AAATAATATT
95220246 AAATATTATATT
1 AAATA--ATATT
95220258 -AATAATATT
1 AAATAATATT
95220267 AAAT
1 AAAT
95220271 TTTAAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 10 0.25
10 12 0.30
11 8 0.20
12 10 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATAATATT
Found at i:95220241 original size:21 final size:21
Alignment explanation
Indices: 95220216--95220270 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
95220206 AACTATCTAA
95220216 AATAATATTAAATATTATATT
1 AATAATATTAAATATTATATT
95220237 AATAATATTAAATATTATATT
1 AATAATATTAAATATTATATT
95220258 AATAATATTAAAT
1 AATAATATTAAAT
95220271 TTTAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATATTAAATATTATATT
Found at i:95220246 original size:9 final size:9
Alignment explanation
Indices: 95220216--95220268 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 9
95220206 AACTATCTAA
95220216 AATAATATT
1 AATAATATT
95220225 AAATATTATATT
1 -AATA--ATATT
95220237 AATAATATT
1 AATAATATT
95220246 AAATATTATATT
1 -AATA--ATATT
95220258 AATAATATT
1 AATAATATT
95220267 AA
1 AA
95220269 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 12 0.32
10 8 0.21
11 8 0.21
12 10 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATAATATT
Found at i:95223804 original size:93 final size:93
Alignment explanation
Indices: 95223630--95223903 Score: 340
Period size: 93 Copynumber: 2.9 Consensus size: 93
95223620 GCACCTAATC
* * * *
95223630 ATATTATAAAAGTAGATGAAAATTTTGTGTCAAATTAAATTAT-AGGACTAAATCTCATAT-ATG
1 ATATTATAAAAGTTGATGAAAA-ATTATGTCAAATTAAATTATAAGGACTAAATCTCA-ATCAAG
*
95223693 AGTATAATAAAAGGACCAAAATCACAATTTG
64 -GTATAATAAAAGGACCAAAACCACAATTTG
* **
95223724 ATATTATAAAAGTTGATGAAAAATTATGTCAAATTAAATTATAAGGACT-AATATCAACTCCCGG
1 ATATTATAAAAGTTGATGAAAAATTATGTCAAATTAAATTATAAGGACTAAATCTCAA-TCAAGG
* *
95223788 TATAATAAAAAGACCAAAACCATAATTTG
65 TATAATAAAAGGACCAAAACCACAATTTG
* * *
95223817 ATATTATAAAAG-TAATAGAAAAATTATGTCAAATTAAATTATAAGGACTGAATCTCAAATCTAG
1 ATATTATAAAAGTTGAT-GAAAAATTATGTCAAATTAAATTATAAGGACTAAATCTC-AATCAAG
*
95223881 ATATAATAAAAGGACCAAAACCA
64 GTATAATAAAAGGACCAAAACCA
95223904 TAAATTGACA
Statistics
Matches: 159, Mismatches: 15, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
92 4 0.03
93 96 0.60
94 57 0.36
95 2 0.01
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.29
Consensus pattern (93 bp):
ATATTATAAAAGTTGATGAAAAATTATGTCAAATTAAATTATAAGGACTAAATCTCAATCAAGGT
ATAATAAAAGGACCAAAACCACAATTTG
Found at i:95224836 original size:30 final size:30
Alignment explanation
Indices: 95224800--95224896 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
95224790 CTAGCCTTTG
*
95224800 CCACCACCAACTTCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
95224830 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
95224860 CCACTACCTACTCCAATAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
95224890 CCACCAC
1 CCACCAC
95224897 TACTTGTACC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.27, C:0.48, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:95224863 original size:18 final size:18
Alignment explanation
Indices: 95224813--95224865 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
95224803 CCACCAACTT
95224813 CACTAGCCACACTTGCTC
1 CACTAGCCACACTTGCTC
*
95224831 CACCA-CCA-A----CTC
1 CACTAGCCACACTTGCTC
95224843 CACTAGCCACACTTGCTC
1 CACTAGCCACACTTGCTC
95224861 CACTA
1 CACTA
95224866 CCTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 12 0.44
ACGTcount: A:0.26, C:0.47, G:0.08, T:0.19
Consensus pattern (18 bp):
CACTAGCCACACTTGCTC
Found at i:95225071 original size:16 final size:16
Alignment explanation
Indices: 95225038--95225067 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
95225028 GAAAGGTTTT
95225038 TTTTTAGGGGGAGAAG
1 TTTTTAGGGGGAGAAG
95225054 TTTTT-GGGGGAGAA
1 TTTTTAGGGGGAGAA
95225068 AGTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.33
Consensus pattern (16 bp):
TTTTTAGGGGGAGAAG
Found at i:95225491 original size:22 final size:23
Alignment explanation
Indices: 95225443--95225488 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
95225433 CCTTTTTTGT
95225443 TATTATTATATTTTTTAATATTA
1 TATTATTATATTTTTTAATATTA
95225466 TATTATATATATTCTTTTAATAT
1 TATTAT-TATATT-TTTTAATAT
95225489 ATTGGGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTATATTTTTTAATATTA
Found at i:95225843 original size:16 final size:15
Alignment explanation
Indices: 95225819--95225866 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
95225809 TAATTATTAT
*
95225819 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
95225835 TATTTTAATATTTTA
1 TATTTTAATATTTTA
95225850 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
95225866 T
1 T
95225867 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:95225854 original size:7 final size:8
Alignment explanation
Indices: 95225819--95225870 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
95225809 TAATTATTAT
*
95225819 TATTCTAA
1 TATTTTAA
*
95225827 TATTTTGA
1 TATTTTAA
95225835 TATTTTAA
1 TATTTTAA
95225843 TATTTT-A
1 TATTTTAA
95225850 TATTTTATA
1 TATTTTA-A
*
95225859 TATTTTAT
1 TATTTTAA
95225867 TATT
1 TATT
95225871 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:95229384 original size:68 final size:70
Alignment explanation
Indices: 95229239--95229374 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 70
95229229 CAAACTCCTT
*** *
95229239 TTTCTCTACAATTTCTCAACACTGTGCAACAAACAAACAAACAAAAAAGTCAAAAAGTTTTAATC
1 TTTCTCTACAATTTCTCAACACCACGCAAC--ACAAACAAACAAAAAAGTCAAAAAGTTTAAATC
95229304 TCTTCAA
64 TCTTCAA
* *
95229311 TTTCTCTACAATTTCTCAATACCACGCAAC-CAAACAAA-AAAAATGTCAAAAAGTTTAAATCTC
1 TTTCTCTACAATTTCTCAACACCACGCAACACAAACAAACAAAAAAGTCAAAAAGTTTAAATCTC
95229374 T
66 T
95229375 ATGATTTCTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 24 0.41
69 8 0.14
72 26 0.45
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.28
Consensus pattern (70 bp):
TTTCTCTACAATTTCTCAACACCACGCAACACAAACAAACAAAAAAGTCAAAAAGTTTAAATCTC
TTCAA
Found at i:95229691 original size:2 final size:2
Alignment explanation
Indices: 95229684--95229732 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
95229674 CCCTATTAGT
95229684 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
95229726 TT TA TA T
1 TA TA TA T
95229733 TAATATTGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:95232664 original size:9 final size:9
Alignment explanation
Indices: 95232650--95232712 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
95232640 TAGTGTCAAA
95232650 TAATATTTT
1 TAATATTTT
95232659 TAATA-TTT
1 TAATATTTT
**
95232667 TAATAAATT
1 TAATATTTT
95232676 TATATATTTT
1 TA-ATATTTT
95232686 TAAGT-TTTT
1 TAA-TATTTT
*
95232695 T-ATAATTT
1 TAATATTTT
95232703 TATATATTTT
1 TA-ATATTTT
95232713 AAATTTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
7 1 0.02
8 13 0.30
9 15 0.35
10 14 0.33
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TAATATTTT
Found at i:95232682 original size:27 final size:27
Alignment explanation
Indices: 95232652--95232712 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
95232642 GTGTCAAATA
95232652 ATATTTTTAA-TATTTTAATAAATTTAT
1 ATATTTTTAAGT-TTTTAATAAATTTAT
* *
95232679 ATATTTTTAAGTTTTTTATAATTTTAT
1 ATATTTTTAAGTTTTTAATAAATTTAT
95232706 ATATTTT
1 ATATTTT
95232713 AAATTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
ATATTTTTAAGTTTTTAATAAATTTAT
Found at i:95233607 original size:10 final size:10
Alignment explanation
Indices: 95233592--95233616 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
95233582 AATGTAAAGA
95233592 AAAAAGAATT
1 AAAAAGAATT
95233602 AAAAAGAATT
1 AAAAAGAATT
95233612 AAAAA
1 AAAAA
95233617 AATAGTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAAAAGAATT
Found at i:95236312 original size:9 final size:9
Alignment explanation
Indices: 95236298--95236329 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
95236288 ATAAGTATAA
95236298 AATTAACCG
1 AATTAACCG
*
95236307 AATTAATCG
1 AATTAACCG
95236316 AATTAACCG
1 AATTAACCG
95236325 AATTA
1 AATTA
95236330 TTTGTTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:95236367 original size:5 final size:6
Alignment explanation
Indices: 95236352--95236392 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
95236342 AATTATATGT
*
95236352 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
95236393 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:95236433 original size:13 final size:13
Alignment explanation
Indices: 95236417--95236441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95236407 AATTTTTATG
95236417 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
95236430 ATTGGGTTGGGT
1 ATTGGGTTGGGT
95236442 TGGGTACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:95236441 original size:18 final size:18
Alignment explanation
Indices: 95236418--95236452 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
95236408 ATTTTTATGA
95236418 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
95236436 TTGGGTTGGGTACTTGG
1 TTGGGTTGGGTAATTGG
95236453 ATTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.03, G:0.49, T:0.40
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:95239708 original size:30 final size:32
Alignment explanation
Indices: 95239649--95239715 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
95239639 TAAAATTTTA
95239649 AAATTCAAAAAGTACAAACACTAAAATTGAT-
1 AAATTCAAAAAGTACAAACACTAAAATTGATC
* *
95239680 AAATTCGAAAAGTACAGGA-ACT-AAATTGATC
1 AAATTCAAAAAGTACA-AACACTAAAATTGATC
95239711 AAATT
1 AAATT
95239716 AAGCACATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 8 0.25
31 23 0.72
32 1 0.03
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (32 bp):
AAATTCAAAAAGTACAAACACTAAAATTGATC
Found at i:95240227 original size:33 final size:33
Alignment explanation
Indices: 95240180--95240243 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
95240170 ACAAGCTAAC
* *
95240180 ATAATATTAGACATATGATAATATGTTTGCCCT
1 ATAACATTAAACATATGATAATATGTTTGCCCT
95240213 ATAACATTAAACATATGATAATATGTTTGCC
1 ATAACATTAAACATATGATAATATGTTTGCC
95240244 TTATCATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (33 bp):
ATAACATTAAACATATGATAATATGTTTGCCCT
Found at i:95247608 original size:7 final size:7
Alignment explanation
Indices: 95247592--95247623 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
95247582 AGGAAAGTAC
95247592 AAAAAA-
1 AAAAAAG
95247598 AAAAAAG
1 AAAAAAG
95247605 -AAAAAG
1 AAAAAAG
95247611 AAAAAAG
1 AAAAAAG
95247618 AAAAAA
1 AAAAAA
95247624 ATTGAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:95247614 original size:13 final size:13
Alignment explanation
Indices: 95247592--95247624 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
95247582 AGGAAAGTAC
95247592 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
95247605 AAAAAGAAAAAAG
1 AAAAAAAAAAAAG
95247618 AAAAAAA
1 AAAAAAA
95247625 TTGAACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:95248634 original size:26 final size:26
Alignment explanation
Indices: 95248597--95248706 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
95248587 TGATACAAAT
95248597 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
95248623 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
95248649 TGATAATAGGTTATGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
95248675 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
95248701 TGATAA
1 TGATAA
95248707 GAATATCATG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:95248653 original size:52 final size:52
Alignment explanation
Indices: 95248597--95248706 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
95248587 TGATACAAAT
95248597 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
*
95248649 TGATAATAGGTTATGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
95248701 TGATAA
1 TGATAA
95248707 GAATATCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:95252606 original size:4 final size:4
Alignment explanation
Indices: 95252591--95252624 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
95252581 GTTTGACTCG
*
95252591 AGAA AAAA AGAA AGAA AGAA AGAA AGAAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AG-AA AGAA A
95252625 CTAACATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:95255889 original size:2 final size:2
Alignment explanation
Indices: 95255882--95255922 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
95255872 TCATACATAC
95255882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
95255923 CGAGTTTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95257362 original size:18 final size:19
Alignment explanation
Indices: 95257339--95257375 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
95257329 GGTTAGATAG
*
95257339 TTAAATG-TTAGTGATTTT
1 TTAAATGTTTAGTAATTTT
95257357 TTAAATGTTTAGTAATTTT
1 TTAAATGTTTAGTAATTTT
95257376 GAACTACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (19 bp):
TTAAATGTTTAGTAATTTT
Found at i:95259518 original size:23 final size:23
Alignment explanation
Indices: 95259492--95259537 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
95259482 CATTTGAGTG
95259492 ACAAAACACTTTAGGAAATTATA
1 ACAAAACACTTTAGGAAATTATA
95259515 ACAAAACACTTTAGGAAATTATA
1 ACAAAACACTTTAGGAAATTATA
95259538 CTTAGTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (23 bp):
ACAAAACACTTTAGGAAATTATA
Found at i:95260239 original size:7 final size:7
Alignment explanation
Indices: 95260220--95260262 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
95260210 AACACAAATG
95260220 TATCATA
1 TATCATA
95260227 -ATCATA
1 TATCATA
95260233 TATCATA
1 TATCATA
*
95260240 TATACATG
1 TAT-CATA
95260248 TATCATA
1 TATCATA
*
95260255 AATCATA
1 TATCATA
95260262 T
1 T
95260263 GGCATACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (7 bp):
TATCATA
Found at i:95260253 original size:15 final size:13
Alignment explanation
Indices: 95260217--95260260 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
95260207 TAGAACACAA
95260217 ATGTATCATAATC
1 ATGTATCATAATC
*
95260230 ATATATCATATATAC
1 ATGTATCATA-AT-C
95260245 ATGTATCATAAATC
1 ATGTATCAT-AATC
95260259 AT
1 AT
95260261 ATGGCATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.35
14 5 0.19
15 11 0.42
16 1 0.04
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (13 bp):
ATGTATCATAATC
Found at i:95263217 original size:47 final size:47
Alignment explanation
Indices: 95263108--95263218 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
95263098 CCGGGATAAG
* *
95263108 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * * *
95263155 CATAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
95263202 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
95263219 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:95266800 original size:18 final size:17
Alignment explanation
Indices: 95266767--95266803 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
95266757 CATTATGATA
95266767 AACCTAAAACTTTTTTT
1 AACCTAAAACTTTTTTT
95266784 AACCTAAAACTTTTTTT
1 AACCTAAAACTTTTTTT
95266801 AAC
1 AAC
95266804 ATAAGTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (17 bp):
AACCTAAAACTTTTTTT
Found at i:95271784 original size:6 final size:6
Alignment explanation
Indices: 95271769--95271806 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
95271759 CATCTCGCTT
95271769 CCCC-C CCCCTC CCCCTC CCCCTTC CCCCTTC CCCCTC C
1 CCCCTC CCCCTC CCCCTC CCCC-TC CCCC-TC CCCCTC C
95271807 TCTCTCGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 4 0.13
6 14 0.45
7 13 0.42
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (6 bp):
CCCCTC
Found at i:95271794 original size:13 final size:12
Alignment explanation
Indices: 95271769--95271806 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
95271759 CATCTCGCTT
95271769 CCCC-CCCCCTC
1 CCCCTCCCCCTC
95271780 CCCCTCCCCCTTC
1 CCCCTCCCCC-TC
95271793 CCCCTTCCCCCTC
1 CCCC-TCCCCCTC
95271806 C
1 C
95271807 TCTCTCGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 5 0.21
13 9 0.38
14 6 0.25
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (12 bp):
CCCCTCCCCCTC
Found at i:95271804 original size:7 final size:7
Alignment explanation
Indices: 95271772--95271804 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
95271762 CTCGCTTCCC
*
95271772 CCCCCCT
1 CCCCCTT
95271779 CCCCC-T
1 CCCCCTT
95271785 CCCCCTT
1 CCCCCTT
95271792 CCCCCTT
1 CCCCCTT
95271799 CCCCCT
1 CCCCCT
95271805 CCTCTCTCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.79, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCCCTT
Found at i:95277631 original size:14 final size:14
Alignment explanation
Indices: 95277612--95277641 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
95277602 TAAAAATTAT
95277612 AAATAATAATAGTA
1 AAATAATAATAGTA
*
95277626 AAATAATAGTAGTA
1 AAATAATAATAGTA
95277640 AA
1 AA
95277642 CGGTAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (14 bp):
AAATAATAATAGTA
Found at i:95277808 original size:20 final size:20
Alignment explanation
Indices: 95277785--95277823 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
95277775 AATATAACAA
95277785 ACAATGTA-ATAAATATAATG
1 ACAATGTACATAAA-ATAATG
*
95277805 ACAATTTACATAAAATAAT
1 ACAATGTACATAAAATAAT
95277824 TAGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (20 bp):
ACAATGTACATAAAATAATG
Found at i:95277974 original size:30 final size:28
Alignment explanation
Indices: 95277927--95278008 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 28
95277917 TGATTAAATT
95277927 AAATGAAAATAAATATAAAAAATAATGA
1 AAATGAAAATAAATATAAAAAATAATGA
*
95277955 AAATGATATAATAAGTATAAAAAATAAT-A
1 AAATGA-A-AATAAATATAAAAAATAATGA
* * *
95277984 TAATAAAAAT-AATATAATAAATAAT
1 AAATGAAAATAAATATAAAAAATAAT
95278009 AGGAAAGTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
26 13 0.28
27 3 0.06
28 7 0.15
29 6 0.13
30 18 0.38
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
AAATGAAAATAAATATAAAAAATAATGA
Found at i:95277993 original size:14 final size:14
Alignment explanation
Indices: 95277974--95278009 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
95277964 AATAAGTATA
95277974 AAAAATAATATAAT
1 AAAAATAATATAAT
95277988 AAAAATAATATAAT
1 AAAAATAATATAAT
95278002 AAATAATA
1 AAA-AATA
95278010 GGAAAGTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATAATATAAT
Found at i:95277995 original size:21 final size:21
Alignment explanation
Indices: 95277932--95278009 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
95277922 AAATTAAATG
95277932 AAAATAAAT-ATAAAAAATAAT
1 AAAATAAATAAT-AAAAATAAT
* **
95277953 GAAAATGATATAATAAGTATAA-
1 -AAAAT-AAATAATAAAAATAAT
95277975 AAAATAATATAATAAAAATAAT
1 AAAATAA-ATAATAAAAATAAT
*
95277997 ATAATAAATAATA
1 AAAATAAATAATA
95278010 GGAAAGTAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 22 0.49
22 11 0.24
23 9 0.20
24 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAATAAATAATAAAAATAAT
Found at i:95286156 original size:15 final size:15
Alignment explanation
Indices: 95286138--95286180 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
95286128 TCATCCTCCG
95286138 GCTCATTGACCTCTT
1 GCTCATTGACCTCTT
**
95286153 GCTCATTGACCGGTT
1 GCTCATTGACCTCTT
*
95286168 GCTCATCGACCTC
1 GCTCATTGACCTC
95286181 GCAAGATCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.19, T:0.33
Consensus pattern (15 bp):
GCTCATTGACCTCTT
Found at i:95287221 original size:32 final size:32
Alignment explanation
Indices: 95287181--95287263 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
95287171 AGGTGTGTAA
95287181 AATATTGATTAAATAAATTAAACCGAATTAAT
1 AATATTGATTAAATAAATTAAACCGAATTAAT
95287213 AATATTGATTAAATAAATTAAACCGAATTAAT
1 AATATTGATTAAATAAATTAAACCGAATTAAT
** *
95287245 AATATCAAATAAATAAATT
1 AATATTGATTAAATAAATT
95287264 TTTTGATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (32 bp):
AATATTGATTAAATAAATTAAACCGAATTAAT
Found at i:95290331 original size:16 final size:18
Alignment explanation
Indices: 95290310--95290347 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
95290300 TTAGGGGAGA
*
95290310 GAATAAAA-AGTTGG-AT
1 GAATAAAATACTTGGAAT
95290326 GAATAAAATACTTGGAAT
1 GAATAAAATACTTGGAAT
95290344 GAAT
1 GAAT
95290348 TATCAGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (18 bp):
GAATAAAATACTTGGAAT
Found at i:95292718 original size:16 final size:16
Alignment explanation
Indices: 95292697--95292729 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
95292687 ATGTTGGTCC
95292697 TTAATGCTTTGTAACT
1 TTAATGCTTTGTAACT
95292713 TTAATGCTTTGTAACT
1 TTAATGCTTTGTAACT
95292729 T
1 T
95292730 ATGGTACTTG
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:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (16 bp):
TTAATGCTTTGTAACT
Found at i:95311533 original size:15 final size:15
Alignment explanation
Indices: 95311513--95311545 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
95311503 TCTTCACCAA
95311513 CAATTTTGAAGCCTT
1 CAATTTTGAAGCCTT
95311528 CAATTTTGAAGCCTT
1 CAATTTTGAAGCCTT
95311543 CAA
1 CAA
95311546 GCTGCTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (15 bp):
CAATTTTGAAGCCTT
Found at i:95314911 original size:146 final size:146
Alignment explanation
Indices: 95314647--95314934 Score: 540
Period size: 146 Copynumber: 2.0 Consensus size: 146
95314637 TGGTCAGCTT
95314647 TAACATATTTACTATTTTTAGACTTCATTGAAACTTACACCGCTTGACATTGCAACTTGCAAATC
1 TAACATATTTACTATTTTTAGACTTCATTGAAACTTACACCGCTTGACATTGCAACTTGCAAATC
*
95314712 ACAACTTGCACAATTAGGTAAGCTGATTTATCGATCTTATCAACATCGAATGCATTAAATATGCT
66 ACAACTTGCACAATTAGGTAAGCTGATCTATCGATCTTATCAACATCGAATGCATTAAATATGCT
95314777 ACCTACTTAGTTATAG
131 ACCTACTTAGTTATAG
* *
95314793 TAACATATTTACTATTTTTAGACTTCATTGTAACTTGCACCGCTTGACATTGCAACTTGCAAATC
1 TAACATATTTACTATTTTTAGACTTCATTGAAACTTACACCGCTTGACATTGCAACTTGCAAATC
*
95314858 ACAACTTGCACAATTAGGTAAGTTGATCTATCGATCTTATCAACATCGAATGCATTAAATATGCT
66 ACAACTTGCACAATTAGGTAAGCTGATCTATCGATCTTATCAACATCGAATGCATTAAATATGCT
95314923 ACCTACTTAGTT
131 ACCTACTTAGTT
95314935 TTAATTTAAC
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 138 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (146 bp):
TAACATATTTACTATTTTTAGACTTCATTGAAACTTACACCGCTTGACATTGCAACTTGCAAATC
ACAACTTGCACAATTAGGTAAGCTGATCTATCGATCTTATCAACATCGAATGCATTAAATATGCT
ACCTACTTAGTTATAG
Found at i:95314972 original size:146 final size:145
Alignment explanation
Indices: 95314678--95314972 Score: 425
Period size: 146 Copynumber: 2.0 Consensus size: 145
95314668 ACTTCATTGA
*
95314678 AACTTACACCGCTTGACATTGCAACTTGCAAATCACAACTTGCACAATTAGGTAAGCTGATTTAT
1 AACTTACACCGCTTGACATTGCAACTTGCAAATCACAACTTGCACAATTAGGTAAGCTGATCTAT
* * *
95314743 CGATCTTATCAACATCGAATGCATTAAATATGCTACCTACTTAGTTATAGTAACATATTTACTAT
66 CGATCTTATCAACATCGAATGCATTAAATATGCTACCTACTTAGTTATAGTAACATAGTTACAAA
* **
95314808 TTTTAGACTTCATTGT
131 TATTA-ACTTCAAAGT
* *
95314824 AACTTGCACCGCTTGACATTGCAACTTGCAAATCACAACTTGCACAATTAGGTAAGTTGATCTAT
1 AACTTACACCGCTTGACATTGCAACTTGCAAATCACAACTTGCACAATTAGGTAAGCTGATCTAT
* *
95314889 CGATCTTATCAACATCGAATGCATTAAATATGCTACCTACTTAGTTTTAATTTAAC-TAAGTTAC
66 CGATCTTATCAACATCGAATGCATTAAATATGCTACCTACTTAGTTAT-A-GTAACAT-AGTTAC
95314953 AAAATATT-AC-TCAAAGT
128 -AAATATTAACTTCAAAGT
95314970 AAC
1 AAC
95314973 AAAATGAAAC
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
146 117 0.87
147 4 0.03
148 9 0.07
149 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (145 bp):
AACTTACACCGCTTGACATTGCAACTTGCAAATCACAACTTGCACAATTAGGTAAGCTGATCTAT
CGATCTTATCAACATCGAATGCATTAAATATGCTACCTACTTAGTTATAGTAACATAGTTACAAA
TATTAACTTCAAAGT
Found at i:95315777 original size:14 final size:14
Alignment explanation
Indices: 95315758--95315828 Score: 78
Period size: 12 Copynumber: 5.2 Consensus size: 14
95315748 TATGCAAACC
95315758 CCCATGTATGCGAA
1 CCCATGTATGCGAA
95315772 CCCATGTATGCG--
1 CCCATGTATGCGAA
*
95315784 CCCATATATGCG--
1 CCCATGTATGCGAA
95315796 CCCATGTATGCGAA
1 CCCATGTATGCGAA
*
95315810 CCCCTATGTATGCAAA
1 -CCC-ATGTATGCGAA
95315826 CCC
1 CCC
95315829 TAAGTGAACT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
12 22 0.44
14 12 0.24
15 6 0.12
16 10 0.20
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (14 bp):
CCCATGTATGCGAA
Found at i:95316046 original size:22 final size:22
Alignment explanation
Indices: 95316021--95316111 Score: 74
Period size: 22 Copynumber: 4.1 Consensus size: 22
95316011 ATGTGTAAAT
*
95316021 CCTAGATGAAATATTATACGAA
1 CCTAGATGAATTATTATACGAA
* * *
95316043 CCTATATGAATTATTATGCAAA
1 CCTAGATGAATTATTATACGAA
* * * *
95316065 CCCTAGATGAAGTACTCTAAGAA
1 -CCTAGATGAATTATTATACGAA
* * *
95316088 CCTATATGAATTGTTATGCGAA
1 CCTAGATGAATTATTATACGAA
95316110 CC
1 CC
95316112 CTTATGCTAA
Statistics
Matches: 50, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
22 35 0.70
23 15 0.30
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (22 bp):
CCTAGATGAATTATTATACGAA
Found at i:95316072 original size:45 final size:45
Alignment explanation
Indices: 95316021--95316113 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 45
95316011 ATGTGTAAAT
* *
95316021 CCTAGATGAAATATTATACGAACCTATATGAATTATTATGCAAAC
1 CCTAGATGAAATACTATAAGAACCTATATGAATTATTATGCAAAC
* * * *
95316066 CCTAGATGAAGTACTCTAAGAACCTATATGAATTGTTATGCGAAC
1 CCTAGATGAAATACTATAAGAACCTATATGAATTATTATGCAAAC
95316111 CCT
1 CCT
95316114 TATGCTAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (45 bp):
CCTAGATGAAATACTATAAGAACCTATATGAATTATTATGCAAAC
Found at i:95316190 original size:44 final size:43
Alignment explanation
Indices: 95316123--95316212 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 43
95316113 TTATGCTAAC
*
95316123 TATATTGCGAACCCCTAGAACATGATATGCAAACCCTTAAGGGAA
1 TATATTGCGAACCCCTAGAACATG-TAGGCAAACCCTT-AGGGAA
* * * *
95316168 TATA-TGCGAACCCTTAGTACATGTAGGCAATCCCTTAGTGAA
1 TATATTGCGAACCCCTAGAACATGTAGGCAAACCCTTAGGGAA
95316210 TAT
1 TAT
95316213 GTCTGTGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 8 0.20
43 11 0.28
44 17 0.43
45 4 0.10
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (43 bp):
TATATTGCGAACCCCTAGAACATGTAGGCAAACCCTTAGGGAA
Found at i:95316430 original size:15 final size:15
Alignment explanation
Indices: 95316406--95316480 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
95316396 AATATTATGC
* *
95316406 GAACCCTATATGTAT
1 GAACCTTATATGTGT
*
95316421 GAACCTTATATGTGC
1 GAACCTTATATGTGT
* *
95316436 AAACCTTGTATGTGT
1 GAACCTTATATGTGT
**
95316451 GAACCCTTTATACATGT
1 GAA-CC-TTATATGTGT
*
95316468 GAACCTAATATGT
1 GAACCTTATATGT
95316481 ATGTGGTAGT
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
15 31 0.69
16 4 0.09
17 10 0.22
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (15 bp):
GAACCTTATATGTGT
Found at i:95317914 original size:19 final size:19
Alignment explanation
Indices: 95317876--95317911 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
95317866 GGCATGCCTA
*
95317876 GAACATTCAAGGTATGTTG
1 GAACATTCAAGATATGTTG
95317895 GAACATTCAA-ATATGTT
1 GAACATTCAAGATATGTT
95317912 TGGGGTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (19 bp):
GAACATTCAAGATATGTTG
Found at i:95320418 original size:10 final size:10
Alignment explanation
Indices: 95320405--95320433 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
95320395 ACGTATACGT
95320405 TTATATATTA
1 TTATATATTA
95320415 TTATATATTA
1 TTATATATTA
95320425 TTAT-TATTA
1 TTATATATTA
95320434 GTTTTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATATATTA
Found at i:95320588 original size:19 final size:19
Alignment explanation
Indices: 95320564--95320606 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
95320554 TATAGTTTTA
*
95320564 TATGTTGTA-AATATCATAT
1 TATGTTCTATAATAT-ATAT
*
95320583 TATGTTCTATCATATATAT
1 TATGTTCTATAATATATAT
95320602 TATGT
1 TATGT
95320607 AGATCATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (19 bp):
TATGTTCTATAATATATAT
Found at i:95327814 original size:38 final size:39
Alignment explanation
Indices: 95327767--95327842 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
95327757 TAATACAACC
* *
95327767 AAACGTTTATTATATTTAT-TCGTATTTTTAATATAATA
1 AAACATTTATTATATTTATGTAGTATTTTTAATATAATA
*
95327805 AAACATTTATTATATTTATGGTAGTGTTTTTAATATAA
1 AAACATTTATTATATTTAT-GTAGTATTTTTAATATAA
95327843 ATACTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 18 0.55
40 15 0.45
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (39 bp):
AAACATTTATTATATTTATGTAGTATTTTTAATATAATA
Found at i:95332049 original size:22 final size:22
Alignment explanation
Indices: 95332023--95332074 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
95332013 ACTCATCCTA
95332023 ATTAAAATGATAA-TTTTTCTT
1 ATTAAAATGATAACTTTTTCTT
*
95332044 ATTTAAATGATAACTTTTTCTT
1 ATTAAAATGATAACTTTTTCTT
*
95332066 AGTAAAATG
1 ATTAAAATG
95332075 TTAGGGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTAAAATGATAACTTTTTCTT
Found at i:95332071 original size:21 final size:21
Alignment explanation
Indices: 95332027--95332071 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
95332017 ATCCTAATTA
*
95332027 AAATGATAATTTTTCTTATTT
1 AAATGATAATTTTTCTTATGT
95332048 AAATGATAACTTTTTCTTA-GT
1 AAATGATAA-TTTTTCTTATGT
95332069 AAA
1 AAA
95332072 ATGTTAGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
AAATGATAATTTTTCTTATGT
Found at i:95347482 original size:4 final size:4
Alignment explanation
Indices: 95347473--95347497 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
95347463 ACAATGATAA
95347473 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
95347498 AACAGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:95347826 original size:13 final size:14
Alignment explanation
Indices: 95347803--95347832 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
95347793 TTGTTTTTTT
95347803 AAAAAACACACAAC
1 AAAAAACACACAAC
95347817 AAAAAA-ACACAAC
1 AAAAAACACACAAC
95347830 AAA
1 AAA
95347833 GATGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAACACACAAC
Found at i:95350322 original size:13 final size:13
Alignment explanation
Indices: 95350304--95350331 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
95350294 ATTCAACCTT
95350304 TTACAAGTATTCG
1 TTACAAGTATTCG
95350317 TTACAAGTATTCG
1 TTACAAGTATTCG
95350330 TT
1 TT
95350332 GGACCTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTACAAGTATTCG
Found at i:95362674 original size:18 final size:18
Alignment explanation
Indices: 95362651--95362693 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
95362641 TTAAGGTATT
95362651 TTTCATATCCGTTTTATA
1 TTTCATATCCGTTTTATA
95362669 TTTCATATCCGTTTTATA
1 TTTCATATCCGTTTTATA
*
95362687 ATTCATA
1 TTTCATA
95362694 AAGATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTCATATCCGTTTTATA
Found at i:95365165 original size:21 final size:24
Alignment explanation
Indices: 95365141--95365185 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
95365131 AATAGAAGAT
95365141 AAAAG-AGAAA-GTAG-GTGAAAA
1 AAAAGAAGAAAGGTAGAGTGAAAA
95365162 AAAAGATAGAAAGGTAGAGTGAAA
1 AAAAGA-AGAAAGGTAGAGTGAAA
95365186 GTCTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
23 5 0.25
24 4 0.20
25 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (24 bp):
AAAAGAAGAAAGGTAGAGTGAAAA
Found at i:95367594 original size:326 final size:326
Alignment explanation
Indices: 95367133--95367779 Score: 1123
Period size: 326 Copynumber: 2.0 Consensus size: 326
95367123 CACAAGTATC
* * * *
95367133 GATATGGGCTGGGACACGGCCGTGTGCCTCACATCGAATGTCCACGCGGCCTGGGACATGGGCAT
1 GATATGGGCTGGGACACGGCCGTGTGCCTCACATCAAATGTCCACACGGCCTAGGACATAGGCAT
* * *
95367198 ATCGCTTGGCTGTGTGGATGGCCACACGGGCGTGTGTCCCCTGCATCTTTGAAAAATTTCTATGT
66 ATCGCTTGGCCGTGTGGATGGCCACACGGGCGTGTGTCCCCTGCATATTTGAAAAATTTCTATAT
* *
95367263 TTTTTGAAAAAATTTCTTGAGTACTTGGTTTAGCCCCAACTAATTTTAATGATTATTTTGGACTT
131 TTTTTGAAAAAATTTCTTGAGTACCTAGTTTAGCCCCAACTAATTTTAATGATTATTTTGGACTT
*
95367328 CGAGGGCTTATATTAAGGACCATATGAATGTTTATGAATAATTTGTTAATTGAATGAAATATGTG
196 CGAGGGCTTATATTAAGGACCATATGAATGTTTATGAATAATTTGTGAATTGAATGAAATATGTG
* * *
95367393 TATAAAATGTTGATTGATTGAGTTATAAGTCCGGTAATTCTCTGTAACCCTGTTCCGGCGATGAT
261 CATAAAATGTTGATTGATTGAGTTATAAGTCCAGTAATACTCTGTAACCCTGTTCCGGCGATGAT
95367458 G
326 G
* *
95367459 GATATGGGCTGGGACACGGTCGTGTGCCTCACATCAAATGTCCACACGGCCTAGGACATAGGCGT
1 GATATGGGCTGGGACACGGCCGTGTGCCTCACATCAAATGTCCACACGGCCTAGGACATAGGCAT
* *
95367524 ATCGCTTGGCCGTGTGGATGGCCACACGGGCGTGTGTCGCCTGTATATTTGAAAAATTTCTATAT
66 ATCGCTTGGCCGTGTGGATGGCCACACGGGCGTGTGTCCCCTGCATATTTGAAAAATTTCTATAT
95367589 TTTTTGAAAAAATTTCTTGAGTACCTAGTTTAGCCCCAACTAATTTTAATGATTATTTTGGACTT
131 TTTTTGAAAAAATTTCTTGAGTACCTAGTTTAGCCCCAACTAATTTTAATGATTATTTTGGACTT
95367654 CGAGGGCTTATATTAAGGACCATATGAATGTTTATGAATAATTTGTGAATTGAATGAAATATGTG
196 CGAGGGCTTATATTAAGGACCATATGAATGTTTATGAATAATTTGTGAATTGAATGAAATATGTG
* *
95367719 CATGAAATGTTGATTGATTGAGTTATAAGTCTAGTAATACTCTGTAACCCTGTTCCGGCGA
261 CATAAAATGTTGATTGATTGAGTTATAAGTCCAGTAATACTCTGTAACCCTGTTCCGGCGA
95367780 CGGATATGGG
Statistics
Matches: 302, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
326 302 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (326 bp):
GATATGGGCTGGGACACGGCCGTGTGCCTCACATCAAATGTCCACACGGCCTAGGACATAGGCAT
ATCGCTTGGCCGTGTGGATGGCCACACGGGCGTGTGTCCCCTGCATATTTGAAAAATTTCTATAT
TTTTTGAAAAAATTTCTTGAGTACCTAGTTTAGCCCCAACTAATTTTAATGATTATTTTGGACTT
CGAGGGCTTATATTAAGGACCATATGAATGTTTATGAATAATTTGTGAATTGAATGAAATATGTG
CATAAAATGTTGATTGATTGAGTTATAAGTCCAGTAATACTCTGTAACCCTGTTCCGGCGATGAT
G
Found at i:95370154 original size:27 final size:26
Alignment explanation
Indices: 95370081--95370174 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 26
95370071 TATGTCATTC
* * * **
95370081 TTTAATTTGCTTTGTGTATTATAGAT
1 TTTAAATTGTTTTATGTATTATTCAT
* * ** *
95370107 TTTAAAATGCTTTATACATTATTTAT
1 TTTAAATTGTTTTATGTATTATTCAT
95370133 TTTAAACTTGTTTTATGTATTATTCAT
1 TTTAAA-TTGTTTTATGTATTATTCAT
95370160 TTTAAATTGTTTTAT
1 TTTAAATTGTTTTAT
95370175 TGTTTACTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 34 0.62
27 21 0.38
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.59
Consensus pattern (26 bp):
TTTAAATTGTTTTATGTATTATTCAT
Found at i:95372850 original size:24 final size:25
Alignment explanation
Indices: 95372823--95372870 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
95372813 TTTCTCATTG
* *
95372823 TTTTGCTACAATTTT-TTTTTATTA
1 TTTTACTACAATTTTGTTGTTATTA
*
95372847 TTTTACTACTATTTTGTTGTTATT
1 TTTTACTACAATTTTGTTGTTATT
95372871 GTTTGGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTTACTACAATTTTGTTGTTATTA
Found at i:95380415 original size:19 final size:20
Alignment explanation
Indices: 95380374--95380425 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
95380364 TATTAATTCT
*
95380374 TTTTACAAATAAATAATAAAA
1 TTTTA-AAATTAATAATAAAA
*
95380395 TTTTAAAATTAA-AATATAA
1 TTTTAAAATTAATAATAAAA
95380414 -TTTAAAATTAAT
1 TTTTAAAATTAAT
95380426 TTTTTTGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.39
19 6 0.21
20 6 0.21
21 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAATTAATAATAAAA
Found at i:95383730 original size:56 final size:54
Alignment explanation
Indices: 95383635--95383756 Score: 154
Period size: 56 Copynumber: 2.2 Consensus size: 54
95383625 GTGTATACTC
** * * *
95383635 TACAGAGTATATGCAACAATTGACATAGCCAAAATTTTATAATAGAGGTACATATA
1 TACAGAGTATACCCAACAATTGACATAGACAAAAGTTTATAATAGA--TACACATA
* * *
95383691 TACAGAGTATACCCAACAATTGACATAGATAAAAGTTTATGATAGATACACATG
1 TACAGAGTATACCCAACAATTGACATAGACAAAAGTTTATAATAGATACACATA
95383745 TACAGAGTATAC
1 TACAGAGTATAC
95383757 ACATAAAAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 18 0.31
56 40 0.69
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (54 bp):
TACAGAGTATACCCAACAATTGACATAGACAAAAGTTTATAATAGATACACATA
Found at i:95385089 original size:28 final size:28
Alignment explanation
Indices: 95385049--95385105 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
95385039 TTTCAATCAA
*
95385049 ACACTATTCAGAAACAGGTATAACTGTC
1 ACACTATTCAGAAACAGGTACAACTGTC
95385077 ACACTATTCAGAAACAGGTACAACTGTC
1 ACACTATTCAGAAACAGGTACAACTGTC
95385105 A
1 A
95385106 AAATAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (28 bp):
ACACTATTCAGAAACAGGTACAACTGTC
Found at i:95386497 original size:65 final size:65
Alignment explanation
Indices: 95386383--95386517 Score: 243
Period size: 65 Copynumber: 2.1 Consensus size: 65
95386373 GACATGTTCT
*
95386383 TAAAAAATTATACAAAAGCCCAATAAGGAATTGCAAGAAGAAGACGAAGAAGAAACCCCATATGA
1 TAAATAATTATACAAAAGCCCAATAAGGAATTGCAAGAAGAAGACGAAGAAGAAACCCCATATGA
*
95386448 TAAATAATTATACAAAAGCCCAATAAGGAATTGCAAGAAGAAGAGGAAGAAGAAACCCCATATGA
1 TAAATAATTATACAAAAGCCCAATAAGGAATTGCAAGAAGAAGACGAAGAAGAAACCCCATATGA
*
95386513 AAAAT
1 TAAAT
95386518 TTTGACAATA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.15
Consensus pattern (65 bp):
TAAATAATTATACAAAAGCCCAATAAGGAATTGCAAGAAGAAGACGAAGAAGAAACCCCATATGA
Found at i:95392011 original size:12 final size:12
Alignment explanation
Indices: 95391994--95392036 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
95391984 GATATAATGA
95391994 GGTTAAATAAAT
1 GGTTAAATAAAT
95392006 GGTTAAAT-AAT
1 GGTTAAATAAAT
95392017 GAGGTTAAATAAAT
1 --GGTTAAATAAAT
95392031 GGTTAA
1 GGTTAA
95392037 CATGTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.11
12 14 0.50
13 8 0.29
14 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.33
Consensus pattern (12 bp):
GGTTAAATAAAT
Found at i:95392017 original size:25 final size:25
Alignment explanation
Indices: 95391987--95392036 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
95391977 ACTAAATGAT
95391987 ATAATGAGGTTAAATAAATGGTTAA
1 ATAATGAGGTTAAATAAATGGTTAA
95392012 ATAATGAGGTTAAATAAATGGTTAA
1 ATAATGAGGTTAAATAAATGGTTAA
95392037 CATGTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (25 bp):
ATAATGAGGTTAAATAAATGGTTAA
Found at i:95392022 original size:13 final size:13
Alignment explanation
Indices: 95391987--95392028 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
95391977 ACTAAATGAT
95391987 ATAATGAGGTTAA
1 ATAATGAGGTTAA
95392000 ATAA--ATGGTTAA
1 ATAATGA-GGTTAA
95392012 ATAATGAGGTTAA
1 ATAATGAGGTTAA
95392025 ATAA
1 ATAA
95392029 ATGGTTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 10 0.38
13 14 0.54
14 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (13 bp):
ATAATGAGGTTAA
Found at i:95395754 original size:110 final size:110
Alignment explanation
Indices: 95395560--95395780 Score: 316
Period size: 110 Copynumber: 2.0 Consensus size: 110
95395550 TTGAGACCAT
* * * * * * *
95395560 GCTCATAGTGTGCAGTTTTAAAGGAGCTGATTATGAATTCAGTGGGGACCACGATCTCTGTTCCA
1 GCTCATAGTATGCAGTTTTAAAAGAGATGATTAGGAATTCAGTGGAGACCACGACCTCTCTTCCA
* *
95395625 AATATTAGATCAAAAGGAGTTTCCATTGTTCCAGTATGTGAAGTG
66 AACATTAGATCAAAAGGAGTTTCCACTGTTCCAGTATGTGAAGTG
*
95395670 GCTCATAGTATGCAGTTTTAAAAGAGATGATTAGGATTTCAGTGGAGACCACGACCTCTCTTCCA
1 GCTCATAGTATGCAGTTTTAAAAGAGATGATTAGGAATTCAGTGGAGACCACGACCTCTCTTCCA
* * * *
95395735 AACATTAGATTAAAGGGAGTTTCCCCTGTTCTAGTATGTGAAGTG
66 AACATTAGATCAAAAGGAGTTTCCACTGTTCCAGTATGTGAAGTG
95395780 G
1 G
95395781 TTCAAAAGGC
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 97 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (110 bp):
GCTCATAGTATGCAGTTTTAAAAGAGATGATTAGGAATTCAGTGGAGACCACGACCTCTCTTCCA
AACATTAGATCAAAAGGAGTTTCCACTGTTCCAGTATGTGAAGTG
Found at i:95399397 original size:11 final size:11
Alignment explanation
Indices: 95399374--95399418 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
95399364 TCTGTTTTTG
95399374 ATTAAATAAATT
1 ATTAAA-AAATT
95399386 ATTAAAAAATT
1 ATTAAAAAATT
95399397 ATTAAAAAATT
1 ATTAAAAAATT
95399408 A-TAAAAAATT
1 ATTAAAAAATT
95399418 A
1 A
95399419 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.30
11 17 0.52
12 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:95399429 original size:7 final size:8
Alignment explanation
Indices: 95399397--95399431 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
95399387 TTAAAAAATT
95399397 ATTAAAAA
1 ATTAAAAA
95399405 ATTATAAAAA
1 A-T-TAAAAA
95399415 ATTAAAAA
1 ATTAAAAA
95399423 ATTAAAAA
1 ATTAAAAA
95399431 A
1 A
95399432 ATAGAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.64
9 2 0.08
10 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
ATTAAAAA
Found at i:95399432 original size:11 final size:11
Alignment explanation
Indices: 95399376--95399423 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
95399366 TGTTTTTGAT
*
95399376 TAAATAAATTAT
1 TAAA-AAATTAA
*
95399388 TAAAAAATTAT
1 TAAAAAATTAA
95399399 TAAAAAATT-A
1 TAAAAAATTAA
95399409 TAAAAAATTAA
1 TAAAAAATTAA
95399420 -AAAA
1 TAAAA
95399424 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
10 13 0.38
11 17 0.50
12 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAAAATTAA
Found at i:95399443 original size:18 final size:18
Alignment explanation
Indices: 95399374--95399433 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 18
95399364 TCTGTTTTTG
95399374 ATTAAATAAATTATTAAAAAA
1 ATTAAA-AAATTA-T-AAAAA
95399395 TTATTAAAAAATTATAAAAA
1 --ATTAAAAAATTATAAAAA
95399415 ATTAAAAAATTA-AAAAA
1 ATTAAAAAATTATAAAAA
95399432 AT
1 AT
95399434 AGAGAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.19
18 12 0.32
20 5 0.14
21 1 0.03
22 6 0.16
23 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAAAATTATAAAAA
Found at i:95400332 original size:22 final size:22
Alignment explanation
Indices: 95400304--95400345 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
95400294 GAGTGGCAAC
95400304 AATAATTAATACCTCAATTTGG
1 AATAATTAATACCTCAATTTGG
95400326 AATAATTAATACCTCAATTT
1 AATAATTAATACCTCAATTT
95400346 TAGCTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (22 bp):
AATAATTAATACCTCAATTTGG
Found at i:95411698 original size:123 final size:123
Alignment explanation
Indices: 95411470--95411716 Score: 359
Period size: 123 Copynumber: 2.0 Consensus size: 123
95411460 CCACCCCGTC
* * *
95411470 CACCACCTCTGCCTCTTCCACTAGCTGATCCTGTTGATGCACCCCTACCACCACGACCCCTTCCA
1 CACCACCTCTGCCTCTTCCACCAGCTGAGCCTGTTGATGCACCCCTACCACCACGAACCCTTCCA
* * * *
95411535 CCAGACTTCACAGGAGACTCCAAATCTTTAATATCCTCTTCATCACTTTCGTCAATAT
66 CCAGACTTCACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
* * * * *
95411593 CACCACCTCTGCCTCTTCCGCCAGCTGGGCCTTTTGATGCACCCCTGCCACCACGAACCTTTCCA
1 CACCACCTCTGCCTCTTCCACCAGCTGAGCCTGTTGATGCACCCCTACCACCACGAACCCTTCCA
* * *
95411658 CCTGACTTTACAGGAGACTTCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
66 CCAGACTTCACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
95411716 C
1 C
95411717 TACAGCTTTT
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 109 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (123 bp):
CACCACCTCTGCCTCTTCCACCAGCTGAGCCTGTTGATGCACCCCTACCACCACGAACCCTTCCA
CCAGACTTCACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
Found at i:95421056 original size:19 final size:18
Alignment explanation
Indices: 95421023--95421058 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
95421013 ACTCAATTGT
*
95421023 TTTTTTTTATAAAATTTG
1 TTTTTTTTAAAAAATTTG
95421041 TTTTTTTTAAACAAATTT
1 TTTTTTTTAAA-AAATTT
95421059 AATTCCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTTTTTAAAAAATTTG
Found at i:95421246 original size:19 final size:18
Alignment explanation
Indices: 95421205--95421248 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
95421195 AAGTGATTGC
*
95421205 AATACTAACCATAATTATA
1 AATA-TAACCATAATAATA
*
95421224 AATATAACCATATATAATT
1 AATATAACCATA-ATAATA
95421243 AATATA
1 AATATA
95421249 TTAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAACCATAATAATA
Found at i:95423301 original size:105 final size:105
Alignment explanation
Indices: 95423119--95423434 Score: 587
Period size: 105 Copynumber: 3.0 Consensus size: 105
95423109 AGGAAGGTTG
* *
95423119 CAGATTGTTTTGGGGCATGGATGACGTGGACGAATATTCCTTGCCATTCTTATTGCTTTCATCTG
1 CAGATTGTTTTGGGGCATGGATGGCGTGGACGAATATTCCTTGCCATTCTCATTGCTTTCATCTG
95423184 CTGCTCTCTTGTTGGCATCATCAGTCTGATTTTTCTTTTC
66 CTGCTCTCTTGTTGGCATCATCAGTCTGATTTTTCTTTTC
95423224 CAGATTGTTTTGGGGCATGGATGGCGTGGACGAATATTCCTTGCCATTCTCATTGCTTTCATCTG
1 CAGATTGTTTTGGGGCATGGATGGCGTGGACGAATATTCCTTGCCATTCTCATTGCTTTCATCTG
95423289 CTGCTCTCTTGTTGGCATCATCAGTCTGATTTTTCTTTTC
66 CTGCTCTCTTGTTGGCATCATCAGTCTGATTTTTCTTTTC
95423329 CAGATTGTTTTGGGGCATGGATGGCGTGGACGAATATTCCTTGCCATTCTCATTGCTTTCATCTG
1 CAGATTGTTTTGGGGCATGGATGGCGTGGACGAATATTCCTTGCCATTCTCATTGCTTTCATCTG
* * *
95423394 CTGCTTTCTTGTTGGCATCATCAGTTTGATCTTTCTTTTC
66 CTGCTCTCTTGTTGGCATCATCAGTCTGATTTTTCTTTTC
95423434 C
1 C
95423435 TCTTCATCAC
Statistics
Matches: 206, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 206 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (105 bp):
CAGATTGTTTTGGGGCATGGATGGCGTGGACGAATATTCCTTGCCATTCTCATTGCTTTCATCTG
CTGCTCTCTTGTTGGCATCATCAGTCTGATTTTTCTTTTC
Found at i:95428401 original size:17 final size:17
Alignment explanation
Indices: 95428379--95428414 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
95428369 AAATCAACAT
* *
95428379 AAATATATAAACGAATA
1 AAATATACAAACAAATA
95428396 AAATATACAAACAAATA
1 AAATATACAAACAAATA
95428413 AA
1 AA
95428415 TAAATGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATATACAAACAAATA
Found at i:95432745 original size:259 final size:259
Alignment explanation
Indices: 95432286--95432804 Score: 975
Period size: 259 Copynumber: 2.0 Consensus size: 259
95432276 CATCTCAGGG
* * *
95432286 TGCTTGGGAGCAAAAGAGAATTTCTGGCTCTACACAAGGGTTACTTATTCATGATCTTTGTATTT
1 TGCTTGGGACCAAAACAGAATTTCTGGCTCTACACAAGGGTTACTTATTCAGGATCTTTGTATTT
95432351 CTCCCTTTGAGGGTGTTTTTTCCTCTTTCTGTCTAGAGAGTACCATTCAGTGGATATTTTCTTTT
66 CTCCCTTTGAGGGTGTTTTTTCCTCTTTCTGTCTAGAGAGTACCATTCAGTGGATATTTTCTTTT
95432416 CTTAGCAGGTTTTAAAGCGCAGGAGTTCAGTATTAGACAATGATATAGGATCAGTTGATCAGCAT
131 CTTAGCAGGTTTTAAAGCGCAGGAGTTCAGTATTAGACAATGATATAGGATCAGTTGATCAGCAT
*
95432481 GATATAGGTTTTAAAGCGCATGATATTGGATAGAGGAGGGATATCCATAAGCTTTACTTTTGGA
196 GATATAGGTTTTAAAGCGCATGATATTGGATAGAGGAGGGATATCCATAAGCTTCACTTTTGGA
*
95432545 TGCTTGGGACCAAAACAGAATTTCTGGCTCTTCACAAGGGTTACTTATTCAGGATCTTTGTATTT
1 TGCTTGGGACCAAAACAGAATTTCTGGCTCTACACAAGGGTTACTTATTCAGGATCTTTGTATTT
*
95432610 CTTCCTTTGAGGGTGTTTTTTCCTCTTTCTGTCTAGAGAGTACCATTCAGTGGATATTTTCTTTT
66 CTCCCTTTGAGGGTGTTTTTTCCTCTTTCTGTCTAGAGAGTACCATTCAGTGGATATTTTCTTTT
95432675 CTTAGCAGGTTTTAAAGCGCAGGAGTTCAGTATTAGACAATGATATAGGATCAGTTGATCAGCAT
131 CTTAGCAGGTTTTAAAGCGCAGGAGTTCAGTATTAGACAATGATATAGGATCAGTTGATCAGCAT
*
95432740 GATATAGGTTTTAAAGCGCATGATATTGGATTGAGGAGGGATATCCATAAGCTTCACTTTTGGA
196 GATATAGGTTTTAAAGCGCATGATATTGGATAGAGGAGGGATATCCATAAGCTTCACTTTTGGA
95432804 T
1 T
95432805 CAGTTGGTTG
Statistics
Matches: 253, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
259 253 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (259 bp):
TGCTTGGGACCAAAACAGAATTTCTGGCTCTACACAAGGGTTACTTATTCAGGATCTTTGTATTT
CTCCCTTTGAGGGTGTTTTTTCCTCTTTCTGTCTAGAGAGTACCATTCAGTGGATATTTTCTTTT
CTTAGCAGGTTTTAAAGCGCAGGAGTTCAGTATTAGACAATGATATAGGATCAGTTGATCAGCAT
GATATAGGTTTTAAAGCGCATGATATTGGATAGAGGAGGGATATCCATAAGCTTCACTTTTGGA
Found at i:95433712 original size:42 final size:42
Alignment explanation
Indices: 95433625--95433820 Score: 204
Period size: 42 Copynumber: 4.8 Consensus size: 42
95433615 TTCCCCAGTG
* * * **
95433625 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGTAGGT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
95433667 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
* * * *
95433709 ACAAGCAC-GGCCACTGGTTTATTTGGCGGTACATCTGCAACT
1 ACAAGCACAGG-CAATGGTATCTTTGGTGGTACATCTGCAACT
* * *
95433751 ACAAGCACTGGC-ATGGCATCTCTGGTGGTACATCTGC-A--
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
* * * *
95433789 ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTAC
95433821 GTCTTTGCCA
Statistics
Matches: 129, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
38 10 0.08
39 14 0.11
40 1 0.01
41 21 0.16
42 81 0.63
43 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
Found at i:95437755 original size:42 final size:42
Alignment explanation
Indices: 95437667--95437863 Score: 233
Period size: 42 Copynumber: 4.8 Consensus size: 42
95437657 TGGCAAAGAC
* * * *
95437667 GTACCACCAAAAATACTACTACCTGTGCTTGT---TGCAGAT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGTAGCTGCAGAT
*
95437706 GTACCACCAAAGATGA-CATTGCCTGTGCTTGTAGCTGCTGAT
1 GTACCACCAAAGAT-ACCATTGCCTGTGCTTGTAGCTGCAGAT
* * * *
95437748 GTACCACCAAATAAACCAGTGGCC-GTGCTTGTAGTTGCAGAT
1 GTACCACCAAAGATACCA-TTGCCTGTGCTTGTAGCTGCAGAT
*
95437790 GTACCACCAAAGATACCATTGCCTGTGCTTGTACCTGCAGAT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGTAGCTGCAGAT
* *
95437832 GTACCACCGAAGATACCATTGCTTGTGCTTGT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGT
95437864 CACTGGGGAA
Statistics
Matches: 134, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
39 26 0.19
40 1 0.01
41 5 0.04
42 98 0.73
43 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (42 bp):
GTACCACCAAAGATACCATTGCCTGTGCTTGTAGCTGCAGAT
Found at i:95438718 original size:19 final size:20
Alignment explanation
Indices: 95438684--95438721 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
95438674 TATGATCTTT
95438684 AAATTATTAGATAATTAAAA
1 AAATTATTAGATAATTAAAA
95438704 AAATTATTA-ATAATTAAA
1 AAATTATTAGATAATTAAA
95438722 TGACTAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTATTAGATAATTAAAA
Found at i:95445085 original size:14 final size:14
Alignment explanation
Indices: 95445066--95445109 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
95445056 CATAACTTAT
95445066 ATTATATACATATA
1 ATTATATACATATA
* *
95445080 ATTATATACATTTT
1 ATTATATACATATA
95445094 ATTATTATAACATATA
1 ATTA-TAT-ACATATA
95445110 TATATTGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 16 0.67
15 3 0.12
16 5 0.21
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATATACATATA
Found at i:95453824 original size:42 final size:42
Alignment explanation
Indices: 95453733--95453869 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 42
95453723 AATACTACTA
* * * * *
95453733 CCTGTGCTTGTAGCTGCTGATGTACCACCAAATAAACCAGTG
1 CCTGTGCTTGTAGTTGCAGATGTACCACCAAAGATACCATTG
* * *
95453775 CCCGTGCTTGTAGTTGCAGATGTAACACCAAAGATAGCATTG
1 CCTGTGCTTGTAGTTGCAGATGTACCACCAAAGATACCATTG
* * * * *
95453817 CCTGTGCTTGCACTTGCAGAGGTACCACCGAAGGTACCATTG
1 CCTGTGCTTGTAGTTGCAGATGTACCACCAAAGATACCATTG
*
95453859 CTTGTGCTTGT
1 CCTGTGCTTGT
95453870 CACTGGGGAA
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (42 bp):
CCTGTGCTTGTAGTTGCAGATGTACCACCAAAGATACCATTG
Found at i:95456016 original size:116 final size:116
Alignment explanation
Indices: 95455812--95456046 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 116
95455802 TATAAGAACT
95455812 CCTGACCAGGTATCCTTTTACACCCTGCCAATTAACTAACTACTAGCCTACTCCATTCAACCAGA
1 CCTGACCAGGTATCCTTTTACACCCTGCCAATTAACTAACTACTAGCCTACTCCATTCAACCAGA
95455877 TATTAGTGACCCTATGCACAAGGGTTAGATTCACCACCAAAATCCCCAACC
66 TATTAGTGACCCTATGCACAAGGGTTAGATTCACCACCAAAATCCCCAACC
95455928 CCTGACCAGGTATCCTTTTACACCCTGCCAATTAACTAACTACTAGCCTACTCCATTCAACCAGA
1 CCTGACCAGGTATCCTTTTACACCCTGCCAATTAACTAACTACTAGCCTACTCCATTCAACCAGA
*
95455993 TATTAGTGACCCTATGCACAAGGGTTAGATTCACCTCCAAAATCCCCAACC
66 TATTAGTGACCCTATGCACAAGGGTTAGATTCACCACCAAAATCCCCAACC
95456044 CCT
1 CCT
95456047 TCCATCCTTT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (116 bp):
CCTGACCAGGTATCCTTTTACACCCTGCCAATTAACTAACTACTAGCCTACTCCATTCAACCAGA
TATTAGTGACCCTATGCACAAGGGTTAGATTCACCACCAAAATCCCCAACC
Found at i:95466103 original size:17 final size:16
Alignment explanation
Indices: 95466078--95466112 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
95466068 ATTTTATTAA
95466078 ATAAAAAATTCAAAAAT
1 ATAAAAAA-TCAAAAAT
*
95466095 ATAATAAATCAAAAAT
1 ATAAAAAATCAAAAAT
95466111 AT
1 AT
95466113 TTAAAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAATCAAAAAT
Found at i:95466134 original size:22 final size:22
Alignment explanation
Indices: 95466107--95466163 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
95466097 AATAAATCAA
*
95466107 AAATATTTAAAA-ACATAAAAAC
1 AAATA-TTAAAACAAATAAAAAC
95466129 AAATATTAAAACAAATAAAAA-
1 AAATATTAAAACAAATAAAAAC
* *
95466150 TAATACTAAAACAA
1 AAATATTAAAACAA
95466164 TTCTTAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (22 bp):
AAATATTAAAACAAATAAAAAC
Found at i:95466154 original size:21 final size:21
Alignment explanation
Indices: 95466100--95466163 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
95466090 AAAATATAAT
95466100 AAATCAAAAAT-AT-TTAAAA-
1 AAAT-AAAAATAATATTAAAAC
* *
95466119 ACATAAAAACAAATATTAAAAC
1 AAATAAAAA-TAATATTAAAAC
*
95466141 AAATAAAAATAATACTAAAAC
1 AAATAAAAATAATATTAAAAC
95466162 AA
1 AA
95466164 TTCTTAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 2 0.06
21 18 0.50
22 8 0.22
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATAAAAATAATATTAAAAC
Found at i:95474887 original size:30 final size:30
Alignment explanation
Indices: 95474851--95474911 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
95474841 TAAAATGTGC
95474851 TTCATTTCTATGAGTGATGATCGGATTTTG
1 TTCATTTCTATGAGTGATGATCGGATTTTG
95474881 TTCATTTCTATGAGTGATGATCGGATTTTG
1 TTCATTTCTATGAGTGATGATCGGATTTTG
95474911 T
1 T
95474912 GCTCGAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.48
Consensus pattern (30 bp):
TTCATTTCTATGAGTGATGATCGGATTTTG
Found at i:95478266 original size:4 final size:4
Alignment explanation
Indices: 95478257--95478282 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
95478247 TTGGAGGTAT
95478257 AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AG
95478283 GGGAAGAGAA
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:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:95484625 original size:33 final size:33
Alignment explanation
Indices: 95484588--95484711 Score: 230
Period size: 33 Copynumber: 3.8 Consensus size: 33
95484578 CTCTGTTTCA
95484588 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
*
95484621 GGTTGCTGGACGGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
95484654 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
*
95484687 GGTTGCTGGACAGTAGCTGGAATGT
1 GGTTGCTGGACAGGAGCTGGAATGT
95484712 CAAGAAGAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.18, C:0.10, G:0.43, T:0.30
Consensus pattern (33 bp):
GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
Found at i:95488713 original size:26 final size:25
Alignment explanation
Indices: 95488684--95488739 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
95488674 GCTATTCTCA
*
95488684 AATTTAAAAT-TTAATTTCTATATTTT
1 AATTTAAAATATT-ATTT-GATATTTT
**
95488710 AATTTTTAATATTATTTGATATTTT
1 AATTTAAAATATTATTTGATATTTT
95488735 AATTT
1 AATTT
95488740 TTTAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.46
26 12 0.46
27 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
AATTTAAAATATTATTTGATATTTT
Found at i:95488734 original size:18 final size:16
Alignment explanation
Indices: 95488706--95488755 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
95488696 AATTTCTATA
95488706 TTTTAAT-TTTTAATAT
1 TTTTAATATTTTAAT-T
*
95488722 TATTTGATATTTTAATT
1 T-TTTAATATTTTAATT
95488739 TTTTAATATATTTAATT
1 TTTTAATAT-TTTAATT
95488756 AATATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 8 0.28
17 14 0.48
18 7 0.24
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTAATATTTTAATT
Found at i:95488736 original size:25 final size:25
Alignment explanation
Indices: 95488703--95488751 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
95488693 TTTAATTTCT
95488703 ATATTTTAA-TTTTTAATATTATTTG
1 ATATTTTAATTTTTTAATA-TATTTG
95488728 ATATTTTAATTTTTTAATATATTT
1 ATATTTTAATTTTTTAATATATTT
95488752 AATTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATTTTAATTTTTTAATATATTTG
Found at i:95489030 original size:17 final size:15
Alignment explanation
Indices: 95489008--95489046 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
95488998 TATAAAAATA
95489008 AAATATTTTAATATTTT
1 AAATATTTT-ATA-TTT
95489025 AAATATTTTATATTT
1 AAATATTTTATATTT
95489040 AAATATT
1 AAATATT
95489047 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.45
16 3 0.14
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATATTTTATATTT
Found at i:95489055 original size:20 final size:20
Alignment explanation
Indices: 95489030--95489082 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
95489020 ATTTTAAATA
95489030 TTTTATATTTAAATATTATT
1 TTTTATATTTAAATATTATT
**
95489050 TTTTATA-GGAAATATTATT
1 TTTTATATTTAAATATTATT
*
95489069 CTTTA-ATATTAAAT
1 TTTTATAT-TTAAAT
95489083 TAATGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 11 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTTATATTTAAATATTATT
Found at i:95492580 original size:6 final size:6
Alignment explanation
Indices: 95492571--95492596 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
95492561 CAGCATCGGA
95492571 ATGACC ATGACC ATGACC ATGACC AT
1 ATGACC ATGACC ATGACC ATGACC AT
95492597 AATCAGGAAC
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:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (6 bp):
ATGACC
Found at i:95504407 original size:10 final size:10
Alignment explanation
Indices: 95504365--95504409 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
95504355 AAATTCAAAG
95504365 AAATATATAA
1 AAATATATAA
*
95504375 AATTATATAA
1 AAATATATAA
* * *
95504385 ATATTTTTAA
1 AAATATATAA
95504395 AAATATATAA
1 AAATATATAA
95504405 AAATA
1 AAATA
95504410 AAAAATATTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATATATAA
Found at i:95504454 original size:23 final size:23
Alignment explanation
Indices: 95504428--95504478 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
95504418 TGATCACAAG
*
95504428 AAATAATAATATATA-TAATTTAA
1 AAATAATAAAATA-AGTAATTTAA
* *
95504451 AAATACTAAAATAAGTAATTTCA
1 AAATAATAAAATAAGTAATTTAA
95504474 AAATA
1 AAATA
95504479 TATATGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATAAAATAAGTAATTTAA
Done.