Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 36 of 66
Found at i:12582296 original size:20 final size:21
Alignment explanation
Indices: 12582258--12582299 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
12582248 CGCCCATAAC
12582258 AAAGTGAGAAGAGAAAAAAAG
1 AAAGTGAGAAGAGAAAAAAAG
12582279 AAAG-GAGAA-AGAAGAAAAAG
1 AAAGTGAGAAGAGAA-AAAAAG
12582299 A
1 A
12582300 GAAAGGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (21 bp):
AAAGTGAGAAGAGAAAAAAAG
Found at i:12583269 original size:2 final size:2
Alignment explanation
Indices: 12583262--12583348 Score: 156
Period size: 2 Copynumber: 43.5 Consensus size: 2
12583252 TTTGTGTAGA
* *
12583262 AT AT AT AT AT AT AT AT AT AT AT AN NT 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
12583304 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
12583346 AT A
1 AT A
12583349 CACATATGTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12587747 original size:38 final size:38
Alignment explanation
Indices: 12587612--12587750 Score: 120
Period size: 36 Copynumber: 3.7 Consensus size: 38
12587602 ACCCAGTTCA
** *
12587612 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACA-A-CTAGAGACATCG
* *** * *
12587652 CGTGCATCCCCCCACATCGTGCACTGGTACAGACATCA
1 TGTGCATCCCCCCACATCGTGCACAACTAGAGACATCG
* * * * *
12587690 TGTGC-T-TCCACACATCGTGCACAATTAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAACTAGAGACATCG
12587726 TGTGCATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
12587751 CGGGCAATAT
Statistics
Matches: 76, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
36 26 0.34
37 2 0.03
38 25 0.33
40 23 0.30
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAACTAGAGACATCG
Found at i:12587869 original size:2 final size:2
Alignment explanation
Indices: 12587862--12587888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12587852 TATGACATAG
12587862 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
12587889 CAACATTATA
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:12589265 original size:2 final size:2
Alignment explanation
Indices: 12589260--12589287 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12589250 GTGTGTGTNT
12589260 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
12589288 ATCAAACATT
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):
TA
Found at i:12590065 original size:18 final size:18
Alignment explanation
Indices: 12590042--12590104 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
12590032 CGAACCTTCA
12590042 TTTCTTTCTATCTTTTTC
1 TTTCTTTCTATCTTTTTC
*
12590060 TTTCTTTCTATC-TTTCC
1 TTTCTTTCTATCTTTTTC
*
12590077 TTTCCTTTCTCT-TTTCTTC
1 TTT-CTTTCTATCTTT-TTC
*
12590096 TTTCCTTCT
1 TTTCTTTCT
12590105 TCACCTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.18
18 26 0.68
19 5 0.13
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCTTTCTATCTTTTTC
Found at i:12590096 original size:28 final size:27
Alignment explanation
Indices: 12590053--12590123 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
12590043 TTCTTTCTAT
* * *
12590053 CTTTTTCTTTCTTTCTATCTTTCCTT-TC
1 CTTTCTCTTTC-TTCTATCCTT-CTTCAC
*
12590081 CTTTCTCTTTTCTTCTTTCCTTCTTCAC
1 CTTTCTC-TTTCTTCTATCCTTCTTCAC
12590109 CTTTCTCTTTCTTCT
1 CTTTCTCTTTCTTCT
12590124 TTGGCTATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 11 0.30
28 22 0.59
29 4 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (27 bp):
CTTTCTCTTTCTTCTATCCTTCTTCAC
Found at i:12590097 original size:24 final size:26
Alignment explanation
Indices: 12590062--12590125 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
12590052 TCTTTTTCTT
12590062 TCTTTCTATCTTTCC-T-TT-CCTTTC
1 TCTTTCT-TCTTTCCTTCTTACCTTTC
12590086 TCTTTTCTTCTTTCCTTCTTCACCTTTC
1 TC-TTTCTTCTTTCCTTCTT-ACCTTTC
12590114 TCTTTCTTCTTT
1 TCTTTCTTCTTT
12590126 GGCTATGGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 9 0.26
25 6 0.17
26 2 0.06
27 10 0.29
28 8 0.23
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (26 bp):
TCTTTCTTCTTTCCTTCTTACCTTTC
Found at i:12595008 original size:38 final size:38
Alignment explanation
Indices: 12594906--12595009 Score: 131
Period size: 38 Copynumber: 2.7 Consensus size: 38
12594896 TAATTGTGTG
* *
12594906 TGTGCATGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
* *
12594944 TATGCACGATGTGGGGGGATGCACATGATGGCAGGCT-A-
1 TGTGCACGATGTGGGGGGATGTACATGATGGCA--CTGAT
*
12594982 TGTGCACGATGTGGGGTGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
12595010 GCCGGGTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 54 0.95
39 1 0.02
40 2 0.04
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
Found at i:12596411 original size:20 final size:20
Alignment explanation
Indices: 12596386--12596434 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
12596376 AGATTTTTCT
12596386 TCCTTTCTTTCTTTCCCTTC
1 TCCTTTCTTTCTTTCCCTTC
*
12596406 TCCTTTCTTTCTTTCCTTTC
1 TCCTTTCTTTCTTTCCCTTC
12596426 TCCTTTCTT
1 TCCTTTCTT
12596435 CCAAATGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (20 bp):
TCCTTTCTTTCTTTCCCTTC
Found at i:12601968 original size:21 final size:22
Alignment explanation
Indices: 12601942--12601983 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
12601932 ACCCTAGGTG
*
12601942 GAAAATTCAAGGGAA-AAGTGT
1 GAAAATTCAAGGAAACAAGTGT
12601963 GAAAATTCAAGGAAACAAGTG
1 GAAAATTCAAGGAAACAAGTG
12601984 ACAAAAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (22 bp):
GAAAATTCAAGGAAACAAGTGT
Found at i:12601989 original size:22 final size:21
Alignment explanation
Indices: 12601943--12601989 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12601933 CCCTAGGTGG
* **
12601943 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGAC
12601964 AAAATTCAAGGAAACAAGTGAC
1 AAAATTCAAGGAAA-AAGTGAC
12601986 AAAA
1 AAAA
12601990 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGAC
Found at i:12604335 original size:19 final size:19
Alignment explanation
Indices: 12604311--12604349 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12604301 ACAAGTGAAA
12604311 AATTTTAGAATAAAATAAT
1 AATTTTAGAATAAAATAAT
* * *
12604330 AATTTTTGGATAAAGTAAT
1 AATTTTAGAATAAAATAAT
12604349 A
1 A
12604350 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
AATTTTAGAATAAAATAAT
Found at i:12615033 original size:35 final size:35
Alignment explanation
Indices: 12614983--12615101 Score: 166
Period size: 35 Copynumber: 3.4 Consensus size: 35
12614973 GGAGCCAAAT
**
12614983 GGGAGTGCATGTGATGATATTGAAATGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
12615018 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
* * ***
12615053 GGGACTACACATGATGATATTGCCTTGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
*
12615088 AGGAGTGCACATGA
1 GGGAGTGCACATGA
12615102 GCTGAGTAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.27, C:0.11, G:0.34, T:0.29
Consensus pattern (35 bp):
GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
Found at i:12615137 original size:2 final size:2
Alignment explanation
Indices: 12615130--12615172 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12615120 GGTGTACATG
12615130 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
12615172 T
1 T
12615173 GCTATAGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12618713 original size:2 final size:2
Alignment explanation
Indices: 12618706--12618746 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12618696 ATTCCTAATG
12618706 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
12618747 GTANNNNNNN
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:12624765 original size:170 final size:169
Alignment explanation
Indices: 12624159--12625440 Score: 1216
Period size: 171 Copynumber: 7.5 Consensus size: 169
12624149 TTCTTAACCA
* * * * *
12624159 AAAATGTAAAAAAATTCAACCTAAAATCAATTATAAGATTATAGAACCATTTAAAGCAAGTAATT
1 AAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * *
12624224 AGGCTTCCGAAGGCATGAGTGACTATAAATGGGCTTTTCTTGTCAATGGATGGCTTTCGCTTCAC
66 AGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTCAC
* * * *
12624289 GTTTCT-TGAAGCAAACATTCAATTATAATCT-TGTTTAACCT
131 GTTTCTCT-AGGTAAATATTCAATTATAATCTAT-TTTAA--G
** * ** *** *
12624330 AAAATTTAAAAAAAAAT-AA-TGTAAAATCAATTACAAGATTATAAAACCATTTAAAATGATTAA
1 AAAAGGT-AAAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAA
* * ** *
12624393 TAAGGCTTTCGAAGGCATGAGTGACTATAAATGGGCTTTTCTTCACAATGGATGGCTTTTGCTTC
64 TAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTC
* ** * *
12624458 ACGTTTCCCTAGACAAATATTCAACTATAATCTCTTTTAACCG
129 ACGTTTCTCTAGGTAAATATTCAATTATAATCTATTTTAA--G
** **
12624501 AAAACGCAAAAAAAATTCAACTTAAAATCAATTA-GAAGATTATAAAACCATTTAAAGTGAGTAA
1 AAAA-GGTAAAAAAATTCAACTTAAAATCAATTATG-AGATTATAAAACCATTTAAAGCAAGTAA
* * * * * * * ** *
12624565 TAAGTCTTTTAAAGGCATGAGTGCCTATAAATGAACTTTTTTTCTCAATGAATAACTTTCCCTTC
64 TAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTC
* *
12624630 ATGTTTCTCTAGGTAAATATTCAATTATGATCTATTTTATAG
129 ACGTTTCTCTAGGTAAATATTCAATTATAATCTATTTTA-AG
* * * * *
12624672 AAAAGGTAAAAATATTCAATTTAAAACCAATTATGAGATTATAAAACCACTTAAAGCAAGTGATA
1 AAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * ** * *
12624737 GGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATAAATAGCTTTTGCTTCAC
66 AGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTCAC
* * * *
12624802 ATTTCTCAAGGTAAATATTCAATTATAATCTTTTTTAACAA
131 GTTTCTCTAGGTAAATATTCAATTATAATCTATTTT-A-AG
** * * *
12624843 AAAATTTTAAAAAATTGAACTTAAAATCAATTATGAGATTATAATACCATTTAAAGCAAGTAATA
1 AAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * * * * * * * *
12624908 AGGCTTTCGAAGGCATAAGTGGCTATGAATGGACATTTCTTGGCAATAGATGGCTTTTGCTTTAT
66 AGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTCAC
* * * * *
12624973 GTGTCCCGAGGTAAACATTCAATTATAATCTACTTTCACCA-
131 GTTTCTCTAGGTAAATATTCAATTATAATCTA-TTTTA--AG
* * *** *
12625014 AAAAGG--AAACAATATCAACTTAAAATCAATTCTGAGATTATAAAACCATTTAAAATGAGCAAT
1 AAAAGGTAAAAAAAT-TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAAT
* * *
12625077 AAGACTTTCAAAGGCATGAGTGACTATGAAA-GGACTTTTCCTGACAATGGATGGCTTTCGCTTC
65 AAGGCTTTCAAAGGCATGAGTGACTAT-AAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTC
* * * *
12625141 ACGTTTCCCCAGGTAAATATTTAATTATAATCTGTTTTAAG
129 ACGTTTCTCTAGGTAAATATTCAATTATAATCTATTTTAAG
* ** *
12625182 CAAAAAGGTAAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACTTTTTAAAGCGAGTAA
1 --AAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAA
* * * * * * * *
12625247 TAATGCTTTCGAAGGTAGGAGTGATTATAAATGGACTTTTCTTGTCAACGGATGACTTTCACTTC
64 TAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTC
* * * * *
12625312 ACGTTTCTCGAGATAAACATTCAATTATCAA-CTGTTTTAACCA
129 ACGTTTCTCTAGGTAAATATTCAATTAT-AATCTATTTTAA--G
** * * *
12625355 AAAAGGTAAAAAAATTCTGCTAAAAATCAATTATGAGATCATAAAACCATTTAAAGTAAGTAATA
1 AAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* *
12625420 GGGCTTTCAAAGGTATGAGTG
66 AGGCTTTCAAAGGCATGAGTG
12625441 GCTANNNNNN
Statistics
Matches: 918, Mismatches: 169, Indels: 48
0.81 0.15 0.04
Matches are distributed among these distances:
167 1 0.00
169 10 0.01
170 263 0.29
171 495 0.54
172 147 0.16
173 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (169 bp):
AAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
AGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTCGCTTCAC
GTTTCTCTAGGTAAATATTCAATTATAATCTATTTTAAG
Found at i:12625058 original size:341 final size:341
Alignment explanation
Indices: 12624138--12625440 Score: 1427
Period size: 341 Copynumber: 3.8 Consensus size: 341
12624128 GGCAAAATTT
* * * * *
12624138 AATTATAATCTTTCTTAACCAAAAATGTAAAAAAATTCAACCTAAAATCAATTATAAGATTATAG
1 AATTATAATCTTTTTTAACCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * *
12624203 AACCATTTAAAGCAAGTAATTAGGCTTCCGAAGGCATGAGTGACTATAAATGGGCTTTTCTTGTC
66 AACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTGTC
* * * * * *
12624268 AATGGATGGCTTTCGCTTCACGTTTCTTGAAGCAAACATTCAATTATAATCTTGTTTAACCTAAA
131 AATGGATGACTTTCGCTTCACGTTTCTCGAGGTAAACATTCAATTATAATC-TATTTAACCAAAA
** * ** * *
12624333 ATTTAAAAAAAAAT-AA-TGTAAAATCAATTACAAGATTATAAAACCATTTAAAATGATTAATAA
195 AGGT-AAAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAACCATTTAAAATAAGTAATAA
* *
12624396 GGCTTTCGAAGGCATGAGTGACTATAAATGGGCTTTTCTT-CACAATGGATGGCTTTTGCTTCAC
258 GGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGC-CAATGGATGGCTTTTGCTTCAC
* **
12624460 GTTTCCCTAGACAAATATTC
322 GTTTCCCAAGGTAAATATTC
* * * **
12624480 AACTATAATCTCTTTTAACCGAAAACGCAAAAAAAATTCAACTTAAAATCAATTA-GAAGATTAT
1 AATTATAATCTTTTTTAACC-AAAAAGGTAAAAAAATTCAACTTAAAATCAATTATG-AGATTAT
** * ** * * * *
12624544 AAAACCATTTAAAGTGAGTAATAAGTCTTTTAAAGGCATGAGTGCCTATAAATGAACTTTTTTTC
64 AAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * * *
12624609 TCAATGAATAACTTTCCCTTCATGTTTCTCTAGGTAAATATTCAATTATGATCTATTTTA-TAGA
129 TCAATGGATGACTTTCGCTTCACGTTTCTCGAGGTAAACATTCAATTATAATCTATTTAACCA-A
* * * * ** * *
12624673 AAAGGTAAAAATATTCAATTTAAAACCAATTATGAGATTATAAAACCACTTAAAGCAAGTGATAG
193 AAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAATAAGTAATAA
** * *
12624738 GGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATAAATAGCTTTTGCTTCACA
258 GGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCACG
*
12624803 TTTCTCAAGGTAAATATTC
323 TTTCCCAAGGTAAATATTC
* ** * *
12624822 AATTATAATCTTTTTTAACAAAAAATTTTAAAAAATTGAACTTAAAATCAATTATGAGATTATAA
1 AATTATAATCTTTTTTAACCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * *
12624887 TACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAAGTGGCTATGAATGGACATTTCTTGGC
66 AACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTGTC
* * * * * * * *
12624952 AATAGATGGCTTTTGCTTTATGTGTCCCGAGGTAAACATTCAATTATAATCTACTTTCACCAAAA
131 AATGGATGACTTTCGCTTCACGTTTCTCGAGGTAAACATTCAATTATAATCTA-TTTAACCAAAA
* * * *
12625017 AGG--AAACAATATCAACTTAAAATCAATTCTGAGATTATAAAACCATTTAAAATGAGCAATAAG
195 AGGTAAAAAAAT-TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAATAAGTAATAAG
* * * *
12625080 ACTTTCAAAGGCATGAGTGACTATGAAA-GGACTTTTCCTGACAATGGATGGCTTTCGCTTCACG
259 GCTTTCAAAGGCATGAGTGACTAT-AAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCACG
* *
12625144 TTTCCCCAGGTAAATATTT
323 TTTCCCAAGGTAAATATTC
* * *
12625163 AATTATAATCTGTTTTAAGCAAAAAGGTAAAAAAATTCAAATTAAAATCAATTATGAGATTATAA
1 AATTATAATCTTTTTTAACCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
** * * * * *
12625228 AACTTTTTAAAGCGAGTAATAATGCTTTCGAAGGTAGGAGTGATTATAAATGGACTTTTCTTGTC
66 AACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTGTC
* * * *
12625293 AACGGATGACTTTCACTTCACGTTTCTCGAGATAAACATTCAATTATCAA-CTGTTTTAACCAAA
131 AATGGATGACTTTCGCTTCACGTTTCTCGAGGTAAACATTCAATTAT-AATCT-ATTTAACCAAA
** * * * *
12625357 AAGGTAAAAAAATTCTGCTAAAAATCAATTATGAGATCATAAAACCATTTAAAGTAAGTAATAGG
194 AAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAATAAGTAATAAG
*
12625422 GCTTTCAAAGGTATGAGTG
259 GCTTTCAAAGGCATGAGTG
12625441 GCTANNNNNN
Statistics
Matches: 780, Mismatches: 166, Indels: 30
0.80 0.17 0.03
Matches are distributed among these distances:
340 5 0.01
341 407 0.52
342 229 0.29
343 139 0.18
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (341 bp):
AATTATAATCTTTTTTAACCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTGTC
AATGGATGACTTTCGCTTCACGTTTCTCGAGGTAAACATTCAATTATAATCTATTTAACCAAAAA
GGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAATAAGTAATAAGGC
TTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCACGTTT
CCCAAGGTAAATATTC
Found at i:12627762 original size:15 final size:15
Alignment explanation
Indices: 12627714--12627762 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12627704 AGATCAGAGA
*
12627714 TTTTCGTTTTAAAGC
1 TTTTAGTTTTAAAGC
* *
12627729 -TTTGGATTTTAAAGT
1 TTTTAG-TTTTAAAGC
12627744 TTTTAGTTTTAAAGC
1 TTTTAGTTTTAAAGC
12627759 TTTT
1 TTTT
12627763 TTAAGAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTTAGTTTTAAAGC
Found at i:12627841 original size:5 final size:5
Alignment explanation
Indices: 12627801--12627840 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
12627791 CCCCAAGTCC
** *
12627801 AGTTA AGTTA AAATA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
12627841 GATTTAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (5 bp):
AGTTA
Found at i:12633182 original size:55 final size:55
Alignment explanation
Indices: 12633122--12633246 Score: 139
Period size: 55 Copynumber: 2.3 Consensus size: 55
12633112 TGGTAATATT
* *
12633122 TTTCCAACGGAAATTTTCGTTGGAAA-TGCCAA-ATG-TTTTTCCGTTGGAAATAGGA
1 TTTCCAACGGAAATTCT-GTTGGAAATTGCCAACA-GATTTTT-CATTGGAAATAGGA
* * * *
12633177 TTTCCAGCGAAAATTCTGTTGGAAATTTCCAACAGATTTTTCATTGGAAATAGGC
1 TTTCCAACGGAAATTCTGTTGGAAATTGCCAACAGATTTTTCATTGGAAATAGGA
*
12633232 TTTCCAACGGGAATT
1 TTTCCAACGGAAATT
12633247 GTTTGAATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
54 8 0.14
55 44 0.76
56 6 0.10
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (55 bp):
TTTCCAACGGAAATTCTGTTGGAAATTGCCAACAGATTTTTCATTGGAAATAGGA
Found at i:12638344 original size:20 final size:21
Alignment explanation
Indices: 12638311--12638350 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12638301 ATAGGCTCCA
*
12638311 TAATTTTATAAT-AATATAAT
1 TAATTATATAATAAATATAAT
*
12638331 TAATTATATTATAAATATAA
1 TAATTATATAATAAATATAA
12638351 AAAATTTAAC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTATATAATAAATATAAT
Found at i:12657514 original size:23 final size:23
Alignment explanation
Indices: 12657454--12657518 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
12657444 ATTGAAAAGT
*
12657454 TGTGTTTGTTATGTTTCAACAAA
1 TGTGTCTGTTATGTTTCAACAAA
* *
12657477 -GAAGTCTATTATGTTTCAACAAA
1 TG-TGTCTGTTATGTTTCAACAAA
*
12657500 TGTGTCTGTTGTGTTTCAA
1 TGTGTCTGTTATGTTTCAA
12657519 TAGTTGTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (23 bp):
TGTGTCTGTTATGTTTCAACAAA
Found at i:12658380 original size:3 final size:3
Alignment explanation
Indices: 12658372--12658403 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12658362 AGGAAATTGG
12658372 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12658404 GAGTAAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12660816 original size:134 final size:135
Alignment explanation
Indices: 12660659--12660928 Score: 497
Period size: 135 Copynumber: 2.0 Consensus size: 135
12660649 CAAAAGTTAA
*
12660659 TCAATAGTTAGTGAGAGAGTCAACAGTTAGTAAGAGGAGCTTATTTGAC-TTAAAATAAAAGTTA
1 TCAATAGTTAGTGAGAAAGTCAACAGTTAGTAAGAGGAGCTTATTTGACTTTAAAATAAAAGTTA
12660723 TGGGGCTTATTTGAACGCAAAAAAATGATAAGGACTTAATTGATTTTTTTGACATAGTTTAGGGC
66 TGGGGCTTATTTGAACGCAAAAAAATGATAAGGACTTAATTGATTTTTTTGACATAGTTTAGGGC
12660788 TTATT
131 TTATT
*
12660793 TCAATAGTTAGTGAGAAAGTCAACAGTTAGTAAGAGGAGTTTATTTGACTTTAAAATAAAAGTTA
1 TCAATAGTTAGTGAGAAAGTCAACAGTTAGTAAGAGGAGCTTATTTGACTTTAAAATAAAAGTTA
* *
12660858 TGTGGCTTATTTGAACGCAAGAAAATGATAAGGACTTAATTGATTTTTTTGACATAGTTTAGGGC
66 TGGGGCTTATTTGAACGCAAAAAAATGATAAGGACTTAATTGATTTTTTTGACATAGTTTAGGGC
12660923 TTATT
131 TTATT
12660928 T
1 T
12660929 AGGTATTTAG
Statistics
Matches: 131, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
134 47 0.36
135 84 0.64
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (135 bp):
TCAATAGTTAGTGAGAAAGTCAACAGTTAGTAAGAGGAGCTTATTTGACTTTAAAATAAAAGTTA
TGGGGCTTATTTGAACGCAAAAAAATGATAAGGACTTAATTGATTTTTTTGACATAGTTTAGGGC
TTATT
Found at i:12661317 original size:39 final size:39
Alignment explanation
Indices: 12661263--12661340 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
12661253 ATTCCAATAG
12661263 AAGAAATGTGCAATTGTTACTTATAATATATTAGCTGGC
1 AAGAAATGTGCAATTGTTACTTATAATATATTAGCTGGC
12661302 AAGAAATGTGCAATTGTTACTTATAATATATTAGCTGGC
1 AAGAAATGTGCAATTGTTACTTATAATATATTAGCTGGC
12661341 TTGGTGGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (39 bp):
AAGAAATGTGCAATTGTTACTTATAATATATTAGCTGGC
Found at i:12661583 original size:15 final size:16
Alignment explanation
Indices: 12661563--12661592 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12661553 AACTTAATCA
12661563 ATAATAAAAA-AATTG
1 ATAATAAAAATAATTG
12661578 ATAATAAAAATAATT
1 ATAATAAAAATAATT
12661593 TTATATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAATAAAAATAATTG
Found at i:12665752 original size:20 final size:22
Alignment explanation
Indices: 12665729--12665768 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12665719 TATTTAAATT
12665729 TATAATAC-T-AAATATAAAAC
1 TATAATACATAAAATATAAAAC
*
12665749 TATAATTCATAAAATATAAA
1 TATAATACATAAAATATAAA
12665769 TAATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 1 0.06
22 9 0.53
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TATAATACATAAAATATAAAAC
Found at i:12667936 original size:47 final size:47
Alignment explanation
Indices: 12667859--12668113 Score: 298
Period size: 47 Copynumber: 5.4 Consensus size: 47
12667849 ATACTCTAGT
* * *
12667859 GTTCAGAGTTGGTGAGACGCCATGGAGGGAAACTATGACACACCAGA
1 GTTCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAGA
* * * *
12667906 GTTAAGAGTTGGTGACACGCCATGGTGGGAATCTGTGACACGCCAGC
1 GTTCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAGA
* * * ** *
12667953 GTTCAGAGTTGATGAGACACCATGGAGGGAATCTGTGACAGGCTAGCA
1 GTTCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAG-A
* * * * * *
12668001 -TTCAAAGTTGCTGAGACACTATGGAGGGAATCTGTGACACACTAGA
1 GTTCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAGA
*
12668047 GTTCAGAGTTGGTGACACGCCATGGAGGGAAGCTGTGACA-AGCCAGA
1 GTTCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACA-CCAGA
12668094 GTTCAGAGTTGGTGACACGC
1 GTTCAGAGTTGGTGACACGC
12668114 TATGTTTAGA
Statistics
Matches: 178, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
46 2 0.01
47 176 0.99
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (47 bp):
GTTCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAGA
Found at i:12668168 original size:47 final size:46
Alignment explanation
Indices: 12668106--12668261 Score: 206
Period size: 47 Copynumber: 3.3 Consensus size: 46
12668096 TCAGAGTTGG
* *
12668106 TGACACGCTAT-GTTTAGAGTGTGTGACACGACATTGCTTGTTAAGC
1 TGACACGCCATGGTTTAGAGTGTGTGACACGACATTGCTTG-AAAGC
* * *
12668152 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTGAAAAGT
1 TGACACGCCATGGTTTAGAGTGTGTGACACGACATTGCTTG-AAAGC
*
12668199 TGACACGCCATGGTTTAAAGTGTGTGACACGACATTGCTTGAACAGC
1 TGACACGCCATGGTTTAGAGTGTGTGACACGACATTGCTTGAA-AGC
* *
12668246 TAACACGTCATGGTTT
1 TGACACGCCATGGTTT
12668262 GAAATAGAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
46 12 0.12
47 84 0.88
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (46 bp):
TGACACGCCATGGTTTAGAGTGTGTGACACGACATTGCTTGAAAGC
Found at i:12668227 original size:24 final size:24
Alignment explanation
Indices: 12668152--12668229 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
12668142 CTTGTTAAGC
*
12668152 TGACACGCCATGGTTTAGAGTGTG
1 TGACACGCCATGGTTTAAAGTGTG
* * * * *
12668176 TGACATGGCATTGCTTGAAA-AGT-
1 TGACACGCCA-TGGTTTAAAGTGTG
12668199 TGACACGCCATGGTTTAAAGTGTG
1 TGACACGCCATGGTTTAAAGTGTG
12668223 TGACACG
1 TGACACG
12668230 ACATTGCTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 7 0.17
23 10 0.25
24 17 0.43
25 6 0.15
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (24 bp):
TGACACGCCATGGTTTAAAGTGTG
Found at i:12668766 original size:31 final size:31
Alignment explanation
Indices: 12668731--12668994 Score: 331
Period size: 31 Copynumber: 8.5 Consensus size: 31
12668721 TCAGCGTTAA
* *
12668731 CGTGTGACAACATTTGACTCGATATGCATGG
1 CGTGTCACAACATTTGACTTGATATGCATGG
*
12668762 CGTGTGACAACATTTGACTTGATATGCATGG
1 CGTGTCACAACATTTGACTTGATATGCATGG
12668793 CGTGTCACAACATTTGACTTGATATGCATGG
1 CGTGTCACAACATTTGACTTGATATGCATGG
* *
12668824 CGTGTGAACAACATTTTACTTGATATGCATGG
1 CGTGT-CACAACATTTGACTTGATATGCATGG
* * *
12668856 CGTGTCACAAGATTTTACTTGTTATGCATGG
1 CGTGTCACAACATTTGACTTGATATGCATGG
*
12668887 CGTGTCACAACATTTTACTTG-TCATGCATGG
1 CGTGTCACAACATTTGACTTGAT-ATGCATGG
*
12668918 TGTGTCACAACATTTTG-CTTG-TCATGCATGG
1 CGTGTCACAACA-TTTGACTTGAT-ATGCATGG
12668949 CGTGTCACAACATTTTG-CTTG-TCATGCATGG
1 CGTGTCACAACA-TTTGACTTGAT-ATGCATGG
* *
12668980 TGTTTCACAACATTT
1 CGTGTCACAACATTT
12668995 ATTCCTTAAT
Statistics
Matches: 217, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.02
31 181 0.83
32 32 0.15
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
CGTGTCACAACATTTGACTTGATATGCATGG
Found at i:12668953 original size:125 final size:124
Alignment explanation
Indices: 12668731--12668994 Score: 347
Period size: 125 Copynumber: 2.1 Consensus size: 124
12668721 TCAGCGTTAA
* * * * *
12668731 CGTGTGACAACATTTGACTCGATATGCATGGCGTGTGACAACATTTGACTTGATATGCATGGCGT
1 CGTGTCACAACATTTTACTTGTTATGCATGGCGTGTCACAACATTTGACTTGATATGCATGGCGT
12668796 GTCACAACATTTGACTTGATATGCATGGCGTGTGAACAACATTTTACTTGAT-ATGCATGG
66 GTCACAACATTTGACTTGATATGCATGGCGTGT-AACAACATTTTACTTG-TCATGCATGG
* * *
12668856 CGTGTCACAAGATTTTACTTGTTATGCATGGCGTGTCACAACATTTTACTTG-TCATGCATGGTG
1 CGTGTCACAACATTTTACTTGTTATGCATGGCGTGTCACAACATTTGACTTGAT-ATGCATGGCG
* *
12668920 TGTCACAACATTTTG-CTTG-TCATGCATGGCGTGTCACAACATTTTGCTTGTCATGCATGG
65 TGTCACAACA-TTTGACTTGAT-ATGCATGGCGTGTAACAACATTTTACTTGTCATGCATGG
* *
12668980 TGTTTCACAACATTT
1 CGTGTCACAACATTT
12668995 ATTCCTTAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
123 1 0.01
124 36 0.30
125 81 0.66
126 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (124 bp):
CGTGTCACAACATTTTACTTGTTATGCATGGCGTGTCACAACATTTGACTTGATATGCATGGCGT
GTCACAACATTTGACTTGATATGCATGGCGTGTAACAACATTTTACTTGTCATGCATGG
Found at i:12670040 original size:14 final size:14
Alignment explanation
Indices: 12670021--12670136 Score: 142
Period size: 14 Copynumber: 7.8 Consensus size: 14
12670011 CAGAAGCCAA
12670021 AAGAAATTTGCAAT
1 AAGAAATTTGCAAT
*
12670035 AAGAAATTTGCTAAAAGA
1 AAGAAATTTGC---AA-T
12670053 ATAGAAATGTTGTCAAT
1 A-AGAAAT-TTG-CAAT
12670070 AAGAAATTTGCAAT
1 AAGAAATTTGCAAT
*
12670084 AAGAAGTTTGCAAT
1 AAGAAATTTGCAAT
12670098 AAGAAATTTGCAAT
1 AAGAAATTTGCAAT
12670112 AAGAAATTTGCAAT
1 AAGAAATTTGCAAT
*
12670126 AAAAAATTTGC
1 AAGAAATTTGC
12670137 CATCAGTTTC
Statistics
Matches: 90, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
14 65 0.72
15 3 0.03
16 6 0.07
17 3 0.03
18 3 0.03
19 6 0.07
20 3 0.03
21 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (14 bp):
AAGAAATTTGCAAT
Found at i:12670778 original size:18 final size:18
Alignment explanation
Indices: 12670732--12670790 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
12670722 ACAATTACAC
* *
12670732 ATCCACTTTTGGTGGGTG
1 ATCCACTTATGGTGGGTT
* * *
12670750 ATCCCCATATGATGGGTT
1 ATCCACTTATGGTGGGTT
*
12670768 ATCCACTTATGGTGGATT
1 ATCCACTTATGGTGGGTT
12670786 ATCCA
1 ATCCA
12670791 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (18 bp):
ATCCACTTATGGTGGGTT
Found at i:12671138 original size:53 final size:54
Alignment explanation
Indices: 12671027--12671179 Score: 182
Period size: 53 Copynumber: 2.8 Consensus size: 54
12671017 TATTAAATAA
* *
12671027 TGTCACATTCACTTCAAGGAATGGACGTATTTATAATTTTTCATTAGTAGTTCATT
1 TGTCACATTCACTTCAAGGAATGGAC--ATTCATAATTTTTCATTAGTAGCTCATT
** * * * *
12671083 TGTTGCATTTACTTCAGGGAATGAACATTCATAATTTTT-ATTAGTAGCTCGTT
1 TGTCACATTCACTTCAAGGAATGGACATTCATAATTTTTCATTAGTAGCTCATT
* **
12671136 TGTCACATTCATTTCAAGGAATGGACATTCATGGTTTTTCATTA
1 TGTCACATTCACTTCAAGGAATGGACATTCATAATTTTTCATTA
12671180 ATAACTATAT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
53 43 0.54
54 16 0.20
56 21 0.26
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (54 bp):
TGTCACATTCACTTCAAGGAATGGACATTCATAATTTTTCATTAGTAGCTCATT
Found at i:12673739 original size:11 final size:11
Alignment explanation
Indices: 12673723--12673748 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12673713 TCAAGCAGAA
12673723 CCTTTACAATG
1 CCTTTACAATG
12673734 CCTTTACAATG
1 CCTTTACAATG
12673745 CCTT
1 CCTT
12673749 GCTATGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (11 bp):
CCTTTACAATG
Found at i:12678634 original size:15 final size:15
Alignment explanation
Indices: 12678614--12678643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12678604 CATTGAGCTA
12678614 TTTAGATATTTTTAT
1 TTTAGATATTTTTAT
*
12678629 TTTAGATTTTTTTAT
1 TTTAGATATTTTTAT
12678644 GGATATATTA
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:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTAGATATTTTTAT
Found at i:12683215 original size:22 final size:23
Alignment explanation
Indices: 12683166--12683215 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
12683156 TAAGTGGGTC
** *
12683166 TTATATGTTTTTTTTTTATGGGTC
1 TTATATGTTTTTTTTAAAT-GGTA
12683190 TTATATGTTTTTTTTAAAT-GTA
1 TTATATGTTTTTTTTAAATGGTA
12683212 TTAT
1 TTAT
12683216 CTTATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
24 17 0.74
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (23 bp):
TTATATGTTTTTTTTAAATGGTA
Found at i:12689815 original size:28 final size:26
Alignment explanation
Indices: 12689781--12689861 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
12689771 AAAATTTTTA
*
12689781 TTATAAATATTTTTAATTATCATCAATG
1 TTATAAA-ATTTTTAATTAT-ATAAATG
12689809 TTATAAAATTTATCTAATT-TATAAATG
1 TTATAAAATTT-T-TAATTATATAAATG
* *
12689836 -TATAAAAATTTTAATTAAATCAAATG
1 TTATAAAATTTTTAATTATAT-AAATG
12689862 ACTCTCATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 5 0.11
25 3 0.07
26 14 0.30
27 10 0.22
28 9 0.20
29 5 0.11
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (26 bp):
TTATAAAATTTTTAATTATATAAATG
Found at i:12690686 original size:11 final size:11
Alignment explanation
Indices: 12690669--12690698 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12690659 CTTTGTATTC
12690669 CCAACGGATTT
1 CCAACGGATTT
*
12690680 GCAACGGATTT
1 CCAACGGATTT
12690691 CCAACGGA
1 CCAACGGA
12690699 ATTTAATTAA
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:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (11 bp):
CCAACGGATTT
Found at i:12694597 original size:36 final size:35
Alignment explanation
Indices: 12694528--12694597 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
12694518 GATTCCCCAT
* *
12694528 ATATTTGTTTTTAGTTATTTAATTTTAAGTTTAAG
1 ATATTTGTTTTTAGTTATTTAACTTAAAGTTTAAG
*
12694563 ATATTTGTTTTTTA-TTATTTAAACTTAAATTTTAA
1 ATATTTG-TTTTTAGTTATTT-AACTTAAAGTTTAA
12694598 TTTTTTTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.60
Consensus pattern (35 bp):
ATATTTGTTTTTAGTTATTTAACTTAAAGTTTAAG
Found at i:12696164 original size:19 final size:19
Alignment explanation
Indices: 12696140--12696177 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12696130 CCATTTGACT
12696140 TATTGGAATATGATTTGAG
1 TATTGGAATATGATTTGAG
*
12696159 TATTGGAGTATGATTTGAG
1 TATTGGAATATGATTTGAG
12696178 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAATATGATTTGAG
Found at i:12697429 original size:13 final size:13
Alignment explanation
Indices: 12697411--12697435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12697401 GGAGAAATTG
12697411 TGATTTTATAAAA
1 TGATTTTATAAAA
12697424 TGATTTTATAAA
1 TGATTTTATAAA
12697436 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12702117 original size:6 final size:6
Alignment explanation
Indices: 12702108--12702163 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
12702098 GGAGAAGATA
* * *
12702108 ATGAAG ATGATG AAGAAG ATGAAG ATGAAG ATGAAT ATGAAG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
12702156 ATGAAG AT
1 ATGAAG AT
12702164 CATGTGGAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:12707630 original size:29 final size:30
Alignment explanation
Indices: 12707598--12707669 Score: 110
Period size: 32 Copynumber: 2.4 Consensus size: 30
12707588 TGAATATAGT
12707598 GTGTAACAACAATA-TTTTTTCAACATGGC
1 GTGTAACAACAATATTTTTTTCAACATGGC
*
12707627 GTGTAACAACAATATTTTTTTTTCAACATGGT
1 GTGTAACAACAATA--TTTTTTTCAACATGGC
12707659 GTGTAACAACA
1 GTGTAACAACA
12707670 TTTTTTAACC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 14 0.36
32 25 0.64
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (30 bp):
GTGTAACAACAATATTTTTTTCAACATGGC
Found at i:12707672 original size:29 final size:29
Alignment explanation
Indices: 12707571--12707675 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
12707561 AGGCATTAAA
* * * *
12707571 GTGTAACAA-A-TTATTTTTGAATATAGT
1 GTGTAACAACATTTTTTTTTCAACATGGT
* * *
12707598 GTGTAACAACAATATTTTTTCAACATGGC
1 GTGTAACAACATTTTTTTTTCAACATGGT
12707627 GTGTAACAACAATATTTTTTTTTCAACATGGT
1 GTGTAACAAC---ATTTTTTTTTCAACATGGT
12707659 GTGTAACAACATTTTTT
1 GTGTAACAACATTTTTT
12707676 AACCATGGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
27 9 0.14
28 1 0.02
29 28 0.44
32 26 0.41
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (29 bp):
GTGTAACAACATTTTTTTTTCAACATGGT
Found at i:12707706 original size:24 final size:25
Alignment explanation
Indices: 12707644--12707719 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
12707634 AACAATATTT
*
12707644 TTTTTTCAACATGGTGTGTAACAACA
1 TTTTTT-AACATGGTATGTAACAACA
*
12707670 TTTTTTAACCATGGTATGTAAC-ATA
1 TTTTTTAA-CATGGTATGTAACAACA
* *
12707695 TTTTTGT-ACATGGCATGTAATAACA
1 TTTTT-TAACATGGTATGTAACAACA
12707720 GTATTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 11 0.26
25 12 0.29
26 19 0.45
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (25 bp):
TTTTTTAACATGGTATGTAACAACA
Found at i:12707714 original size:82 final size:77
Alignment explanation
Indices: 12707620--12707834 Score: 229
Period size: 75 Copynumber: 2.8 Consensus size: 77
12707610 TATTTTTTCA
* * **
12707620 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGGTGTGTAACAACATTTTTTAACCATGGT
1 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGGCGTGTAACAAC-----CTAACCATGAC
12707685 ATGT-AACATATTTTTGT
61 AT-TAAACATATTTTTGT
* * * * *
12707702 ACATGGCATGTAATAACAGTA-TTTTTTTT-AATATAGCGTGTAACAACCTAACCATGACATTAA
1 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGGCGTGTAACAACCTAACCATGACATTAA
*
12707765 ACATGTTTTTGT
66 ACATATTTTTGT
* * * *
12707777 ACATGACGTGTAACAATAATATTTTTTTTTCAACATGACGTGTAATAACCTAACCATG
1 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGGCGTGTAACAACCTAACCATG
12707835 GCGTGTCACA
Statistics
Matches: 111, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
74 1 0.01
75 38 0.34
76 8 0.07
77 23 0.21
80 15 0.14
81 8 0.07
82 18 0.16
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (77 bp):
ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGGCGTGTAACAACCTAACCATGACATTAA
ACATATTTTTGT
Found at i:12707846 original size:77 final size:77
Alignment explanation
Indices: 12707620--12707870 Score: 249
Period size: 77 Copynumber: 3.2 Consensus size: 77
12707610 TATTTTTTCA
** * *
12707620 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGGTGTGTAACAACATTTTTTAACCATGGT
1 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGACGTGTAACAAC-----CTAACCATGGC
*
12707685 ATGTAACATATTTTTGT
61 ATGTAACATGTTTTTGT
* * * * *
12707702 ACATGGCATGTAATAACAGTA-TTTTTTTT-AATAT-AGCGTGTAACAACCTAACCATGACAT-T
1 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGA-CGTGTAACAACCTAACCATGGCATGT
12707763 AAACATGTTTTTGT
65 -AACATGTTTTTGT
* * * * *
12707777 ACATGACGTGTAACAATAATATTTTTTTTTCAACATGACGTGTAATAACCTAACCATGGCGTGTC
1 ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGACGTGTAACAACCTAACCATGGCATGTA
12707842 ACATGTTTTTGT
66 ACATGTTTTTGT
* * *
12707854 ATATAGCATGTAACAAC
1 ACATGGCGTGTAACAAC
12707871 CTAACCATGA
Statistics
Matches: 138, Mismatches: 25, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
74 1 0.01
75 38 0.28
76 8 0.06
77 49 0.36
78 2 0.01
80 14 0.10
81 8 0.06
82 18 0.13
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (77 bp):
ACATGGCGTGTAACAACAATATTTTTTTTTCAACATGACGTGTAACAACCTAACCATGGCATGTA
ACATGTTTTTGT
Found at i:12707866 original size:45 final size:45
Alignment explanation
Indices: 12707817--12707989 Score: 213
Period size: 45 Copynumber: 3.8 Consensus size: 45
12707807 CAACATGACG
*
12707817 TGTAATAACCTAACCATGGCGTGTCACATGTTTTTGTATATAGCA
1 TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTATATAGCA
* * * *
12707862 TGTAACAACCTAACCATGAG-GTGTAACATATTTTTGTACATGGCA
1 TGTAACAACCTAACCATG-GCGTGTCACATGTTTTTGTATATAGCA
* * **
12707907 TGTAACAACTTAACCATGACGTGTCACATGTTTTTGTATATAGTG
1 TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTATATAGCA
* * * *
12707952 TATAACAACTTAATCATGGCGTGTCACATGGTTTTGTA
1 TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTA
12707990 CATGACGTGT
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 108 0.99
46 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (45 bp):
TGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTATATAGCA
Found at i:12707911 original size:90 final size:90
Alignment explanation
Indices: 12707809--12708003 Score: 248
Period size: 90 Copynumber: 2.2 Consensus size: 90
12707799 TTTTTTTTCA
* * *
12707809 ACATGACGTGTAATAACCTAACCATGGCGTGTCACATGTTTTTGTATATAGCATGTAACAACCTA
1 ACATGACATGTAATAACCTAACCATGACGTGTCACATGTTTTTGTATATAGCATATAACAACCTA
*
12707874 ACCATGAG-GTGTAACATATTTTTGT
66 ACCATG-GCGTGTAACATAGTTTTGT
* * * ** *
12707899 ACATGGCATGTAACAACTTAACCATGACGTGTCACATGTTTTTGTATATAGTGTATAACAACTTA
1 ACATGACATGTAATAACCTAACCATGACGTGTCACATGTTTTTGTATATAGCATATAACAACCTA
* * *
12707964 ATCATGGCGTGTCACATGGTTTTGT
66 ACCATGGCGTGTAACATAGTTTTGT
*
12707989 ACATGACGTGTAATA
1 ACATGACATGTAATA
12708004 TCATAACGTG
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 87 0.99
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (90 bp):
ACATGACATGTAATAACCTAACCATGACGTGTCACATGTTTTTGTATATAGCATATAACAACCTA
ACCATGGCGTGTAACATAGTTTTGT
Found at i:12708515 original size:20 final size:20
Alignment explanation
Indices: 12708490--12708528 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12708480 TCCATATATT
12708490 AATTGAACAAATTCATATCA
1 AATTGAACAAATTCATATCA
12708510 AATTGAACAAATTCATATC
1 AATTGAACAAATTCATATC
12708529 CAGTTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (20 bp):
AATTGAACAAATTCATATCA
Found at i:12711713 original size:21 final size:23
Alignment explanation
Indices: 12711672--12711720 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
12711662 ACCTTTTTTT
12711672 ATAATAATATAAAAATATTAATAA
1 ATAATAATATAAAAATATTAA-AA
12711696 ATAATAA-A-AAAAAT-TTAAAA
1 ATAATAATATAAAAATATTAAAA
12711716 A-AATA
1 ATAATA
12711721 GAGAAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 4 0.16
22 6 0.24
23 1 0.04
24 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAATAATATAAAAATATTAAAA
Found at i:12712232 original size:25 final size:25
Alignment explanation
Indices: 12712210--12712278 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
12712200 AGAAGAGATT
12712210 TGAGCGGCGCAGA-AAAGGGGAGAG
1 TGAGCGGCGCAGAGAAAGGGGAGAG
* *
12712234 TGAGCGGCGTAGAGAAA-GAGAGAG
1 TGAGCGGCGCAGAGAAAGGGGAGAG
* *
12712258 TGAGCGACGTCAGAGCAAGGG
1 TGAGCGGCG-CAGAGAAAGGG
12712279 CGAAGAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 26 0.72
25 9 0.25
26 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.46, T:0.07
Consensus pattern (25 bp):
TGAGCGGCGCAGAGAAAGGGGAGAG
Found at i:12712676 original size:21 final size:21
Alignment explanation
Indices: 12712635--12712698 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
12712625 TGAACAATAT
12712635 AAATATT-AT-AATAAT-ATAA
1 AAATATTAATAAATAATGA-AA
12712654 AAATATTAATAAATAATGAAA
1 AAATATTAATAAATAATGAAA
*
12712675 AAAAATTTAA-AAATGAA-GAAA
1 AAATA-TTAATAAAT-AATGAAA
12712696 AAA
1 AAA
12712699 ACAAAGAGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 7 0.18
20 2 0.05
21 23 0.59
22 7 0.18
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
AAATATTAATAAATAATGAAA
Found at i:12712699 original size:21 final size:23
Alignment explanation
Indices: 12712652--12712699 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
12712642 ATAATAATAT
12712652 AAAAATATTAATAAATAATGAAA
1 AAAAATATTAATAAATAATGAAA
12712675 AAAAAT-TTAA-AAATGAA-GAAA
1 AAAAATATTAATAAAT-AATGAAA
12712696 AAAA
1 AAAA
12712700 CAAAGAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.50
22 6 0.25
23 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (23 bp):
AAAAATATTAATAAATAATGAAA
Found at i:12713246 original size:2 final size:2
Alignment explanation
Indices: 12713239--12713271 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12713229 TGAGCTGCAT
12713239 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12713272 CTAGCATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12713379 original size:13 final size:13
Alignment explanation
Indices: 12713361--12713386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12713351 AAACATTTTT
12713361 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
12713374 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
12713387 CTAGNCCGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Found at i:12714662 original size:267 final size:268
Alignment explanation
Indices: 12714186--12714706 Score: 733
Period size: 267 Copynumber: 1.9 Consensus size: 268
12714176 AAGGGAAAAA
* * *
12714186 ATTTATAGTATAAATGTATTTAAATACCTGTAAGTATAGTAAAATACATGATGCAAATATAAAGA
1 ATTTATAGTATAAATATATTTAAATACCTGTAAGTATAATAAAATACATGACGCAAATATAAAGA
* *
12714251 CCATAAAAAAATGAAATGATTATTTTGAGTGATCCAATGATAGAATTTCACCTAAAAAGGGGCAA
66 CCATAAAAAAATGAAATGATTATTTTAAGTGATCCAAGGATAGAATTTCACCTAAAAAGGGGCAA
* * * * * * * *
12714316 AGAGTTGCTTCTTTCGAGTGGATTTCTTAGGTGCTAGGTTTGAGACGAATTTTCACTGAATCGTC
131 AAAGTTGCCTCTTTCGAGTGGATTCCTTAAGTGCTAGGTTCGAAACAAATTTTCACTGAAGCGTC
* * *
12714381 GGGATAAGTCCGAACTCTATACTCCAATA-CCATTAACTCAAATAATCGTTGTTTAAAATGGGAG
196 GGGATAAATCCGAACTCCATACTCCAATATCCATTAACTCAAATAATCATTGTTTAAAATGGGAG
12714445 AAGGAAAT
261 AAGGAAAT
* * *
12714453 ATTTATAGTATAAATATATTTAGATACTTGTAAGTATAATAAAATATATGACGCAAATATAAAGA
1 ATTTATAGTATAAATATATTTAAATACCTGTAAGTATAATAAAATACATGACGCAAATATAAAGA
** * * * *
12714518 TTATAAAAAAATGGAATGATTATTTTAAGTGATCCGAGGATAGAATTTCACCTACAAAGTGGCAA
66 CCATAAAAAAATGAAATGATTATTTTAAGTGATCCAAGGATAGAATTTCACCTAAAAAGGGGCAA
*
12714583 AAAGTTGCCTCTTTC-AGGTGGATTCCTTAAGTG-TGGAGTTCGAAACAAATTTTCACTGAAGCG
131 AAAGTTGCCTCTTTCGA-GTGGATTCCTTAAGTGCTAG-GTTCGAAACAAATTTTCACTGAAGCG
* * * *
12714646 TTGGGATAAATCCGAACTCCATGCTTCAATATTCATTAACTCAAATAATCATTGTTTAAAA
194 TCGGGATAAATCCGAACTCCATACTCCAATATCCATTAACTCAAATAATCATTGTTTAAAA
12714707 ACTATACATT
Statistics
Matches: 221, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
266 3 0.01
267 191 0.86
268 27 0.12
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (268 bp):
ATTTATAGTATAAATATATTTAAATACCTGTAAGTATAATAAAATACATGACGCAAATATAAAGA
CCATAAAAAAATGAAATGATTATTTTAAGTGATCCAAGGATAGAATTTCACCTAAAAAGGGGCAA
AAAGTTGCCTCTTTCGAGTGGATTCCTTAAGTGCTAGGTTCGAAACAAATTTTCACTGAAGCGTC
GGGATAAATCCGAACTCCATACTCCAATATCCATTAACTCAAATAATCATTGTTTAAAATGGGAG
AAGGAAAT
Found at i:12715975 original size:21 final size:21
Alignment explanation
Indices: 12715949--12715988 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12715939 ACTTTATTTA
12715949 TAAAAAAAATA-TTGTTACAAT
1 TAAAAAAAA-AGTTGTTACAAT
12715970 TAAAAAAAAAGTTGTTACA
1 TAAAAAAAAAGTTGTTACA
12715989 CGTTTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAAAAAAAAGTTGTTACAAT
Found at i:12716177 original size:34 final size:34
Alignment explanation
Indices: 12716139--12716231 Score: 141
Period size: 34 Copynumber: 2.7 Consensus size: 34
12716129 CTAAAACTTT
*
12716139 AGCACTAGATGTTACATGCCAATGCCAAAGCTTC
1 AGCACTAGATGTTACATGCCAAAGCCAAAGCTTC
*
12716173 AGCACTAGATGTTACATGCCAAAGTCAAAGCTTC
1 AGCACTAGATGTTACATGCCAAAGCCAAAGCTTC
* * *
12716207 AGCACCAGATATTAAATGCCAAAGC
1 AGCACTAGATGTTACATGCCAAAGC
12716232 TTCCTTCTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (34 bp):
AGCACTAGATGTTACATGCCAAAGCCAAAGCTTC
Found at i:12717507 original size:2 final size:2
Alignment explanation
Indices: 12717500--12717538 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12717490 TTCATCAAAC
12717500 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 A
12717539 ATGTAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12782274 original size:69 final size:67
Alignment explanation
Indices: 12782186--12782337 Score: 171
Period size: 68 Copynumber: 2.2 Consensus size: 67
12782176 TTCATCCTTA
* * *
12782186 TGGTACTCTTACCCACACACCGA-GCTTTAGAAGGGGAAAATATGGGTACATTCGCCTAACTTGA
1 TGGTATTCTTACCC-CACA-CGAGGCTTTAGAAGGGGAAAAGAT-GGTACATTCGCCAAACTTGA
12782250 CCATG
63 CCATG
* * * * *
12782255 TGGTATTCTTATCCCCACACTAGGTTTTAGGAGGGGAAAAGATGGTACATTTGTCAAACTTGACC
1 TGGTATTCTTA-CCCCACACGAGGCTTTAGAAGGGGAAAAGATGGTACATTCGCCAAACTTGACC
*
12782320 TTG
65 ATG
*
12782323 TAGTATTCTTACCCC
1 TGGTATTCTTACCCC
12782338 CACATCATGT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
67 4 0.06
68 33 0.46
69 31 0.44
70 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (67 bp):
TGGTATTCTTACCCCACACGAGGCTTTAGAAGGGGAAAAGATGGTACATTCGCCAAACTTGACCA
TG
Found at i:12782331 original size:68 final size:67
Alignment explanation
Indices: 12782211--12782419 Score: 222
Period size: 68 Copynumber: 3.1 Consensus size: 67
12782201 CACACCGAGC
* * * * *
12782211 TTTAGAAGGGGAAAATATGGGTACATTCGCCTAACTTGACCATGTGGTATTCTTATCCCCACA-C
1 TTTAGGAGGGGAAAA-AT-GGTACATTTGCCAAACTTGACCTTGTGGTATTCTTACCCCCACATC
12782275 TAGGT
64 -AGGT
* *
12782280 TTTAGGAGGGGAAAAGATGGTACATTTGTCAAACTTGACCTTGTAGTATTCTTACCCCCACATCA
1 TTTAGGAGGGGAAAA-ATGGTACATTTGCCAAACTTGACCTTGTGGTATTCTTACCCCCACATCA
*
12782345 TGT
65 GGT
* * * * * * * *
12782348 TTTAAGTGGGGAAAATTGGTACGTTTGCCCAACTTGACTTTGGGGTATTCTTACCCCCTACATCG
1 TTTAGGAGGGGAAAAATGGTACATTTGCCAAACTTGACCTTGTGGTATTCTTACCCCC-ACATCA
12782413 GGT
65 GGT
12782416 TTTA
1 TTTA
12782420 TTCAATTCAT
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
67 36 0.31
68 65 0.55
69 17 0.14
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (67 bp):
TTTAGGAGGGGAAAAATGGTACATTTGCCAAACTTGACCTTGTGGTATTCTTACCCCCACATCAG
GT
Found at i:12785103 original size:14 final size:14
Alignment explanation
Indices: 12785077--12785118 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
12785067 AAATTAGTTG
12785077 AAAAATAATAAATTA
1 AAAAATAA-AAATTA
12785092 AAAAATAAAAATTA
1 AAAAATAAAAATTA
*
12785106 AATATATAAAAAT
1 AA-AAATAAAAAT
12785119 AGATGCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAAAAATTA
Found at i:12786877 original size:17 final size:17
Alignment explanation
Indices: 12786852--12786891 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
12786842 AAAAATTATG
*
12786852 AAAATAAAAAGAAAGAA
1 AAAAGAAAAAGAAAGAA
12786869 AAAAGAAAAAGAAAGAA
1 AAAAGAAAAAGAAAGAA
*
12786886 TAAAGA
1 AAAAGA
12786892 GTAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAGAAAGAA
Found at i:12788436 original size:5 final size:5
Alignment explanation
Indices: 12788426--12788469 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
12788416 ATTTCTCAAA
* *
12788426 AAAAT AAAAT AAAAT AAAAT ACAA- AAAAT AAAAA ATAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAA
12788470 AAACAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 26 0.79
6 4 0.12
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:12788450 original size:25 final size:27
Alignment explanation
Indices: 12788422--12788481 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 27
12788412 GAGGATTTCT
* *
12788422 CAAAAAAATAAAATA-AAAT-AAAATA
1 CAAAAAAATAAAAAATAAATAAAAAAA
12788447 C-AAAAAATAAAAAATAAATAAAAAAA
1 CAAAAAAATAAAAAATAAATAAAAAAA
12788473 CAAAAAAAT
1 CAAAAAAAT
12788482 GATGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 12 0.40
25 5 0.17
26 6 0.20
27 7 0.23
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (27 bp):
CAAAAAAATAAAAAATAAATAAAAAAA
Found at i:12788460 original size:26 final size:25
Alignment explanation
Indices: 12788422--12788480 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
12788412 GAGGATTTCT
* *
12788422 CAAAAAAATAAAATAAA-ATAAAATA
1 CAAAAAAAAAAAATAAATA-AAAAAA
12788447 CAAAAAATAAAAAATAAATAAAAAAA
1 CAAAAAA-AAAAAATAAATAAAAAAA
12788473 CAAAAAAA
1 CAAAAAAA
12788481 TGATGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.27
26 21 0.70
27 1 0.03
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (25 bp):
CAAAAAAAAAAAATAAATAAAAAAA
Found at i:12788465 original size:20 final size:18
Alignment explanation
Indices: 12788431--12788480 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
12788421 TCAAAAAAAT
*
12788431 AAAATAAAATAAAATACAA
1 AAAATAAAAAAAAATA-AA
12788450 AAAATAAAAAATAAATAAA
1 AAAATAAAAAA-AAATAAA
*
12788469 AAAACAAAAAAA
1 AAAATAAAAAAA
12788481 TGATGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 22 0.79
20 5 0.18
ACGTcount: A:0.84, C:0.04, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAATAAAAAAAAATAAA
Found at i:12788481 original size:20 final size:21
Alignment explanation
Indices: 12788425--12788481 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
12788415 GATTTCTCAA
12788425 AAAAATAAAATAAAATAAAATAC
1 AAAAA-AAAA-AAAATAAAATAC
*
12788448 AAAAAATAAAAAAT-AAATA-
1 AAAAAAAAAAAAATAAAATAC
12788467 AAAAAACAAAAAAAT
1 AAAAAA-AAAAAAAT
12788482 GATGAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 12 0.39
21 5 0.16
22 3 0.10
23 5 0.16
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAAAAAAAAAATAAAATAC
Found at i:12791880 original size:18 final size:18
Alignment explanation
Indices: 12791835--12791882 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
12791825 AAAGAATAAA
** *
12791835 AAAAAAGAAATCAAAATG
1 AAAAAAGAAAAAAAAAGG
**
12791853 AAAATTGAAAAAAAAAGG
1 AAAAAAGAAAAAAAAAGG
12791871 AAAAAAGAAAAA
1 AAAAAAGAAAAA
12791883 GCATAGAAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.08
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAGG
Found at i:12800842 original size:142 final size:141
Alignment explanation
Indices: 12800588--12801150 Score: 794
Period size: 142 Copynumber: 4.0 Consensus size: 141
12800578 GGTCGTGACA
* * *
12800588 TCCTAAATCCTCCGGGTACATTTTGAAGACCTCCGAGCACATTATTCTCTTAAATCC-CAG-GTG
1 TCCTAAATCCTCCGGGTACATTCTGAAGACCTTCGAGCACATTATTCTCTTAAATCCTCCGAGTG
*
12800651 CATCTTTTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCG
66 CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTT-AAGTTACGTTGCCTCAGTTTTCG
*
12800716 AAGAGCCACATT
130 AGGAGCCACATT
** * *
12800728 TCCTAAATCCTTTGGGTACATTCTGAAGACCTTCGAGTACATTATTCTCTTAAATCCTTCGAGTG
1 TCCTAAATCCTCCGGGTACATTCTGAAGACCTTCGAGCACATTATTCTCTTAAATCCTCCGAGTG
* * *
12800793 CATCTTTTAAAACCTCCTGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTTAGTTTTCG
66 CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTT-AAGTTACGTTGCCTCAGTTTTCG
12800858 AGGAGCCACATT
130 AGGAGCCACATT
*
12800870 TCCTAAATCCTCCGGGTACATTCTGAAGACCTTCGGGCACATTATTCTCTTAAATCCTCCGAGTG
1 TCCTAAATCCTCCGGGTACATTCTGAAGACCTTCGAGCACATTATTCTCTTAAATCCTCCGAGTG
* * * * * *
12800935 CATCTTCTCAAACTTCCGGGTAATTAGTTTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTTGG
66 CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGA
*
12801000 GGAGCCACATG
131 GGAGCCACATT
* * * * *
12801011 TCCTAAATCCTCTGGGTACATTCTCAAGACC-TCTGGGCACATTATTCTCTTAAAACCTCCGGGT
1 TCCTAAATCCTCCGGGTACATTCTGAAGACCTTC-GAGCACATTATTCTCTTAAATCCTCCGAGT
* * * * *
12801075 ACAT-TTCCAAAACCTCCGGGTAATTAGTTTCAAGA-TTTTTAAGTTGCGTTGCCTCAGTTTTCG
65 GCATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCG
12801138 AGGAGCCACATT
130 AGGAGCCACATT
12801150 T
1 T
12801151 TTTTCTTAAA
Statistics
Matches: 383, Mismatches: 37, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
139 37 0.10
140 82 0.21
141 92 0.24
142 172 0.45
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (141 bp):
TCCTAAATCCTCCGGGTACATTCTGAAGACCTTCGAGCACATTATTCTCTTAAATCCTCCGAGTG
CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGA
GGAGCCACATT
Found at i:12801049 original size:141 final size:142
Alignment explanation
Indices: 12800588--12801217 Score: 783
Period size: 142 Copynumber: 4.5 Consensus size: 142
12800578 GGTCGTGACA
* * * * *
12800588 TCCTAAATCCTCCGGGTACATTTTGAAGACCTCCGAGCACATTATTCTCTTAAATCC-CAG-GTG
1 TCCTAAATCCTCTGGGTACATTCTGAAGACCTCTGGGCACATTATTCTCTTAAATCCTCCGAGTG
*
12800651 CATCTTTTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCG
66 CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCG
*
12800716 AAGAGCCACATT
131 AGGAGCCACATT
* * * *
12800728 TCCTAAATCCTTTGGGTACATTCTGAAGACCT-TCGAGTACATTATTCTCTTAAATCCTTCGAGT
1 TCCTAAATCCTCTGGGTACATTCTGAAGACCTCT-GGGCACATTATTCTCTTAAATCCTCCGAGT
* * *
12800792 GCATCTTTTAAAACCTCCTGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTTAGTTTTC
65 GCATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTC
12800857 GAGGAGCCACATT
130 GAGGAGCCACATT
*
12800870 TCCTAAATCCTCCGGGTACATTCTGAAGACCT-TCGGGCACATTATTCTCTTAAATCCTCCGAGT
1 TCCTAAATCCTCTGGGTACATTCTGAAGACCTCT-GGGCACATTATTCTCTTAAATCCTCCGAGT
* * * * *
12800934 GCATCTTCTCAAACTTCCGGGTAATTAGTTTCAAGATTTTTT-AAGTTACGTTGCCTCAGTTTTT
65 GCATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTC
* *
12800998 GGGGAGCCACATG
130 GAGGAGCCACATT
* * * *
12801011 TCCTAAATCCTCTGGGTACATTCTCAAGACCTCTGGGCACATTATTCTCTTAAAACCTCCGGGTA
1 TCCTAAATCCTCTGGGTACATTCTGAAGACCTCTGGGCACATTATTCTCTTAAATCCTCCGAGTG
* * * *
12801076 CAT-TTCCAAAACCTCCGGGTAATTAGTTTCAAGA-TTTTT-AAGTTGCGTTGCCTCAGTTTTCG
66 CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCG
12801138 AGGAGCCACATTTTTT
131 AGGAGCCACA----TT
* * * * * * * * *
12801154 TCTTAAAACCT-TCGAGTACATTTTCAAAACCTCTGGGCACATTTTTCTCTCAAAACCTCCGAGT
1 TCCTAAATCCTCT-GGGTACATTCTGAAGACCTCTGGGCACATTATTCTCTTAAATCCTCCGAGT
12801218 AATCAGTTTC
Statistics
Matches: 436, Mismatches: 45, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
139 35 0.08
140 79 0.18
141 93 0.21
142 174 0.40
143 55 0.13
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (142 bp):
TCCTAAATCCTCTGGGTACATTCTGAAGACCTCTGGGCACATTATTCTCTTAAATCCTCCGAGTG
CATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCG
AGGAGCCACATT
Found at i:12801078 original size:26 final size:23
Alignment explanation
Indices: 12801030--12801100 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 23
12801020 CTCTGGGTAC
* * *
12801030 ATTCTCAAGACCTCTGGGCACATT
1 ATTC-CAAAACCTCCGGGTACATT
12801054 ATTCTCTTAAAACCTCCGGGTACA-T
1 ATTC-C--AAAACCTCCGGGTACATT
12801079 -TTCCAAAACCTCCGGGTA-ATT
1 ATTCCAAAACCTCCGGGTACATT
12801100 A
1 A
12801101 GTTTCAAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
23 1 0.03
24 9 0.22
25 1 0.03
26 13 0.32
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (23 bp):
ATTCCAAAACCTCCGGGTACATT
Found at i:12801492 original size:8 final size:8
Alignment explanation
Indices: 12801458--12801506 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
12801448 TAAACATTAT
12801458 AAAA-GAA
1 AAAATGAA
12801465 AAAATGAGA
1 AAAATGA-A
*
12801474 AAAAAGCAA
1 AAAATG-AA
12801483 AAAATG--
1 AAAATGAA
12801489 AAAATGAA
1 AAAATGAA
12801497 AAAATGAA
1 AAAATGAA
12801505 AA
1 AA
12801507 TGTACGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
6 6 0.17
7 4 0.11
8 12 0.34
9 12 0.34
10 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAATGAA
Found at i:12801498 original size:14 final size:14
Alignment explanation
Indices: 12801481--12801508 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12801471 AGAAAAAAGC
12801481 AAAAAATGAAAATG
1 AAAAAATGAAAATG
12801495 AAAAAATGAAAATG
1 AAAAAATGAAAATG
12801509 TACGATTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAATGAAAATG
Found at i:12803091 original size:15 final size:15
Alignment explanation
Indices: 12803053--12803092 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
12803043 AATTAGTTGA
12803053 AAAATA-AT-AAATT
1 AAAATATATAAAATT
*
12803066 AAAAAAT-TAAAATT
1 AAAATATATAAAATT
12803080 AAAATATATAAAA
1 AAAATATATAAAA
12803093 ATAGATGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.27
14 11 0.50
15 5 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATATATAAAATT
Found at i:12803426 original size:213 final size:210
Alignment explanation
Indices: 12803205--12803628 Score: 586
Period size: 213 Copynumber: 2.0 Consensus size: 210
12803195 GCATATAGAT
12803205 TTTTTTTTTTTACGAGTTAAGTCCCGATGATGAGATTTTACGAAGATCTTGCGAAGGCGAGTACT
1 TTTTTTTTTTTACGAGTTAAGTCCCGATGATGAGATTTTACGAAGATCTTGCGAAGGCGAGT--T
* * * *
12803270 TC-TCGAAAAGTTTCCTAGGTGAAA-GATGTCCCCGGGTCGCACCAGTATGATGGGAGGGCTCAA
64 TCGTCGAAAAGCTCCCTAGGTGAAATGATGTCCCCGGGTCCCACCAGTATGATGAGAGGGCTC--
* * * * * *
12803333 GG-AAATATCTTTAAT-AAAAGGTTTTTGTTCGTATTAGGTTTATTATTCATGAAAATATTATTT
127 GGAAAACATCTTTAATAAAAAGGTTTTTGCTCGTAATAGGTTCA-TATTCACGAAAACATTA-TT
*
12803396 TTTAAAGAAAAACGTACGATA
190 TTTAAAGAAAAACATACGATA
* * *
12803417 NTTTTTTTTTTTACGAGTTAAGTCCCGATGATGGGATTTTTCGAAGATCTTGCGAAGGTGAGTTT
1 -TTTTTTTTTTTACGAGTTAAGTCCCGATGATGAGATTTTACGAAGATCTTGCGAAGGCGAGTTT
* ** *
12803482 CTGTCGGAAAGCTCCCTAGGTGAAATGATGTCTTCGGGTCCCACCAGTATGATGAGAGGGGTCGG
65 C-GTCGAAAAGCTCCCTAGGTGAAATGATGTCCCCGGGTCCCACCAGTATGATGAGAGGGCTCGG
12803547 AAAACATCTTTAATAAAAAGGTTTTTGCTCGTAATAGGTTCATATTCACGAAAACATTATTTTTA
129 AAAACATCTTTAATAAAAAGGTTTTTGCTCGTAATAGGTTCATATTCACGAAAACATTATTTTTA
12803612 AAGAAAAACATACGATA
194 AAGAAAAACATACGATA
12803629 ACCCCGATGA
Statistics
Matches: 188, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
211 3 0.02
212 24 0.13
213 105 0.56
214 56 0.30
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (210 bp):
TTTTTTTTTTTACGAGTTAAGTCCCGATGATGAGATTTTACGAAGATCTTGCGAAGGCGAGTTTC
GTCGAAAAGCTCCCTAGGTGAAATGATGTCCCCGGGTCCCACCAGTATGATGAGAGGGCTCGGAA
AACATCTTTAATAAAAAGGTTTTTGCTCGTAATAGGTTCATATTCACGAAAACATTATTTTTAAA
GAAAAACATACGATA
Found at i:12804313 original size:20 final size:20
Alignment explanation
Indices: 12804288--12804333 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12804278 AGTTAGTGTA
*
12804288 ATCTATTGATAGATTTTGCC
1 ATCTATTGATAGATTTGGCC
*
12804308 ATCTATTGATAGATTTGGTC
1 ATCTATTGATAGATTTGGCC
12804328 ATCTAT
1 ATCTAT
12804334 CGAATCTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (20 bp):
ATCTATTGATAGATTTGGCC
Found at i:12805986 original size:27 final size:31
Alignment explanation
Indices: 12805955--12806015 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
12805945 ATTTAATTAT
12805955 TTATATAAGT-GTAC-TA-CT-TTATTTTTA
1 TTATATAAGTAGTACATATCTGTTATTTTTA
*
12805982 TTATATAAGTAGTACATATTTGTTATTTTTA
1 TTATATAAGTAGTACATATCTGTTATTTTTA
12806013 TTA
1 TTA
12806016 ATTATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.34
28 4 0.14
29 2 0.07
30 1 0.03
31 12 0.41
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (31 bp):
TTATATAAGTAGTACATATCTGTTATTTTTA
Found at i:12809098 original size:16 final size:17
Alignment explanation
Indices: 12809074--12809117 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
12809064 ATATTTACCA
12809074 AATAT-AATAAAAT-TT
1 AATATCAATAAAATCTT
12809089 AATATCAAT-AAATCTT
1 AATATCAATAAAATCTT
12809105 AATTATC-ATAAAA
1 AA-TATCAATAAAA
12809118 ATATTAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.36
16 9 0.36
17 7 0.28
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATCAATAAAATCTT
Found at i:12813718 original size:16 final size:15
Alignment explanation
Indices: 12813676--12813730 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12813666 AGATATTATT
*
12813676 TAATTAATAAATTAA
1 TAATTAATTAATTAA
* *
12813691 TAATTTATTAATTTA
1 TAATTAATTAATTAA
*
12813706 TACATTAATTAATAAA
1 TA-ATTAATTAATTAA
*
12813722 AAATTAATT
1 TAATTAATT
12813731 TATCAAGGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTAATTAATTAA
Found at i:12831655 original size:15 final size:15
Alignment explanation
Indices: 12831632--12831661 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12831622 AATGACTCTC
12831632 ATCAAAAATATTTTT
1 ATCAAAAATATTTTT
*
12831647 ATCATAAATATTTTT
1 ATCAAAAATATTTTT
12831662 TTTGAATTTT
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:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCAAAAATATTTTT
Found at i:12831741 original size:34 final size:34
Alignment explanation
Indices: 12831694--12831781 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
12831684 TTCAGGAATT
* *
12831694 TAATTACTTAATTATTGACATTTTAATAATTTAA
1 TAATTACTTAATTAATGAAATTTTAATAATTTAA
*
12831728 TAATTA-TTCAATTAATGAAATTTTGATAATTTAA
1 TAATTACTT-AATTAATGAAATTTTAATAATTTAA
* * *
12831762 TAATTAGTAAATTTATGAAA
1 TAATTACTTAATTAATGAAA
12831782 CCATTCTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 2 0.04
34 44 0.94
35 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (34 bp):
TAATTACTTAATTAATGAAATTTTAATAATTTAA
Found at i:12840400 original size:2 final size:2
Alignment explanation
Indices: 12840393--12840423 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12840383 GTACAGTATC
12840393 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12840424 TCATTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12841229 original size:23 final size:23
Alignment explanation
Indices: 12841203--12841248 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
12841193 ATACAATAAC
*
12841203 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
12841226 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
12841249 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:12846416 original size:24 final size:26
Alignment explanation
Indices: 12846362--12846418 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
12846352 ATTAATATTT
* * *
12846362 AAATTATCTATTATTAATATTTTAAC
1 AAATAATCAATTATTAATATTTCAAC
12846388 TAAATAATCAATTATTAAT-TTTCAA-
1 -AAATAATCAATTATTAATATTTCAAC
12846413 AAATAA
1 AAATAA
12846419 AATAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.22
26 5 0.19
27 16 0.59
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATAATCAATTATTAATATTTCAAC
Found at i:12846543 original size:41 final size:41
Alignment explanation
Indices: 12846455--12846547 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 41
12846445 AATATTTAAA
*
12846455 TTAAATAAAATATTAATATTTTACAATATAAATAATTAAATT
1 TTAAAT-AAATATTAATATTTGACAATATAAATAATTAAATT
* * *
12846497 ATAAATAAATATTAATA-TTGA-AATTATCAATTATTAATATT
1 TTAAATAAATATTAATATTTGACAA-TATAAATAATTAA-ATT
12846538 TTAAATAAAT
1 TTAAATAAAT
12846548 TATCAATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 2 0.05
40 14 0.32
41 23 0.52
42 5 0.11
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (41 bp):
TTAAATAAATATTAATATTTGACAATATAAATAATTAAATT
Found at i:12846549 original size:27 final size:27
Alignment explanation
Indices: 12846517--12846569 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
12846507 ATTAATATTG
12846517 AAATTATCAATTATTAATATTTTAAAT
1 AAATTATCAATTATTAATATTTTAAAT
12846544 AAATTATCAATTATTAATATTTTAAA
1 AAATTATCAATTATTAATATTTTAAA
12846570 AATAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATTATCAATTATTAATATTTTAAAT
Found at i:12846583 original size:80 final size:80
Alignment explanation
Indices: 12846338--12846592 Score: 228
Period size: 80 Copynumber: 3.2 Consensus size: 80
12846328 AATAATATTT
* * * * *
12846338 AAATTAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAACTAAATAATCAATTAT
1 AAATAAAAT-AAATATTAATATTGAAATTATCAATTATTAATATTTTAAATAAATTATCAATTAT
*
12846403 TAAT-TTTCAAAAATA
65 TAATATTTTAAAAATA
* * * *
12846418 AAATAAAATAAA-A-T-A-ATTG--ATCATCATAATATTTAA-A--TTAAATAAAATATTAATAT
1 AAATAAAATAAATATTAATATTGAAATTATCA-ATTA-TTAATATTTTAAATAAATTATCAAT-T
* *
12846474 TTTACA-A-TATAAATAATTA
63 ATTA-ATATTTTAAA-AA-TA
*
12846493 AATTATAAATAAATATTAATATTGAAATTATCAATTATTAATATTTTAAATAAATTATCAATTAT
1 AAATA-AAATAAATATTAATATTGAAATTATCAATTATTAATATTTTAAATAAATTATCAATTAT
12846558 TAATATTTTAAAAATA
65 TAATATTTTAAAAATA
*
12846574 AAATAAAATAAAAATTAAT
1 AAATAAAATAAATATTAAT
12846593 CATAATAATA
Statistics
Matches: 135, Mismatches: 21, Indels: 38
0.70 0.11 0.20
Matches are distributed among these distances:
72 13 0.10
73 13 0.10
74 7 0.05
75 13 0.10
76 8 0.06
77 2 0.01
78 2 0.01
79 4 0.03
80 29 0.21
81 11 0.08
82 13 0.10
83 20 0.15
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (80 bp):
AAATAAAATAAATATTAATATTGAAATTATCAATTATTAATATTTTAAATAAATTATCAATTATT
AATATTTTAAAAATA
Found at i:12846638 original size:15 final size:15
Alignment explanation
Indices: 12846614--12846680 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
12846604 TTAAATTAAA
12846614 TAAA-TATTAATATT
1 TAAATTATTAATATT
12846628 TAAATTATTAAT-TAT
1 TAAATTATTAATAT-T
12846643 TAATATT-TTAATTAAATT
1 TAA-ATTATTAA-T--ATT
*
12846661 CTAGATTATTAATATT
1 -TAAATTATTAATATT
12846677 TAAA
1 TAAA
12846681 AAATCTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 17
0.69 0.03 0.28
Matches are distributed among these distances:
14 5 0.12
15 18 0.43
16 7 0.17
18 5 0.12
19 7 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
TAAATTATTAATATT
Found at i:12846646 original size:22 final size:23
Alignment explanation
Indices: 12846598--12846680 Score: 96
Period size: 22 Copynumber: 3.5 Consensus size: 23
12846588 TTAATCATAA
* *
12846598 TAATATTTAAATTAAATAAATAT
1 TAATATTTAAATTAATTAATTAT
12846621 TAATATTTAAATT-ATTAATTAT
1 TAATATTTAAATTAATTAATTAT
*
12846643 TAATATTTTAATTAAATTCTAGATTAT
1 TAATATTTAAATT-AA-T-TA-ATTAT
12846670 TAATATTTAAA
1 TAATATTTAAA
12846681 AAATCTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
22 19 0.37
23 13 0.25
24 1 0.02
25 1 0.02
26 2 0.04
27 15 0.29
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
TAATATTTAAATTAATTAATTAT
Found at i:12846690 original size:155 final size:155
Alignment explanation
Indices: 12846342--12846628 Score: 418
Period size: 155 Copynumber: 1.9 Consensus size: 155
12846332 ATATTTAAAT
* ** ** *
12846342 TAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAACTAAATAATCAATTATTAAT
1 TAAAT-AAATATTAATATTGAAATTATAAAAAATTAATATTTTAAATAAATAATCAATTATTAAT
* *
12846407 TTTCAAAAATAAAATAAAATAAAATAATTGATCATCATAATATTTAAATTAAATAAAATATTAAT
65 TTTCAAAAATAAAATAAAATAAAATAATTAATCATAATAATATTTAAATTAAATAAAATATTAAT
12846472 ATTTTACAATATAAATAATTAAATTA
130 ATTTTACAATATAAATAATTAAATTA
* ** *
12846498 TAAATAAATATTAATATTGAAATTATCAATTATTAATATTTTAAATAAATTATCAATTATTAATA
1 TAAATAAATATTAATATTGAAATTATAAAAAATTAATATTTTAAATAAATAATCAATTATTAAT-
*
12846563 TTTTAAAAATAAAATAAAAT-AAA-AATTAATCATAATAATATTTAAATTAAAT-AAATATTAAT
65 TTTCAAAAATAAAATAAAATAAAATAATTAATCATAATAATATTTAAATTAAATAAAATATTAAT
12846625 ATTT
130 ATTT
12846629 AAATTATTAA
Statistics
Matches: 123, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
153 14 0.11
154 27 0.22
155 58 0.47
156 24 0.20
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (155 bp):
TAAATAAATATTAATATTGAAATTATAAAAAATTAATATTTTAAATAAATAATCAATTATTAATT
TTCAAAAATAAAATAAAATAAAATAATTAATCATAATAATATTTAAATTAAATAAAATATTAATA
TTTTACAATATAAATAATTAAATTA
Found at i:12852630 original size:26 final size:26
Alignment explanation
Indices: 12852601--12852684 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 26
12852591 AAAATTGATT
*
12852601 TCTAATTAAAGATATTATAGTATAAC
1 TCTAATTAAAGATATTATAATATAAC
* *
12852627 TCTAATT--AGATATTGTAATCT-A-
1 TCTAATTAAAGATATTATAATATAAC
* * * *
12852649 GCTAAGTAAAAATATTATATTATAAC
1 TCTAATTAAAGATATTATAATATAAC
*
12852675 TCTAACTAAA
1 TCTAATTAAA
12852685 TAATTTATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
22 5 0.12
23 1 0.02
24 21 0.49
25 1 0.02
26 15 0.35
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (26 bp):
TCTAATTAAAGATATTATAATATAAC
Found at i:12853842 original size:27 final size:26
Alignment explanation
Indices: 12853803--12853853 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
12853793 AGAGGAACAA
12853803 AAAAAGAAGAAAA-GAAAGGCAAACC
1 AAAAAGAAGAAAAGGAAAGGCAAACC
*
12853828 AAAAAGAGAGAAAAAGGAAGGGCAAA
1 AAAAAGA-AG-AAAAGGAAAGGCAAA
12853854 TGGTGAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 2 0.09
27 4 0.18
28 9 0.41
ACGTcount: A:0.67, C:0.08, G:0.25, T:0.00
Consensus pattern (26 bp):
AAAAAGAAGAAAAGGAAAGGCAAACC
Found at i:12858470 original size:42 final size:42
Alignment explanation
Indices: 12858407--12858573 Score: 244
Period size: 42 Copynumber: 4.0 Consensus size: 42
12858397 TGTTGTTGTG
*
12858407 GACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * *
12858449 GACTCGGCTATGTGCGAGTAGGAGTGCACATAAGCCATTGTT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
12858491 GACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * * *
12858533 GACCCGGCTATATGCGAGTGGGAGTACGCATAAGCCGTTGC
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
12858574 ATATGAGATG
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 112 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:12859860 original size:31 final size:30
Alignment explanation
Indices: 12859795--12859861 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
12859785 TCCACGTAAT
*
12859795 AGGTAGTGTTAAGGTTATACCTCCTTAAAA
1 AGGTAGTGTTAAGGTTATACCTCCTAAAAA
12859825 AGGTAGTGTTAAGGTTATACCTCC-AAGCAAA
1 AGGTAGTGTTAAGGTTATACCTCCTAA--AAA
12859856 AGGTAG
1 AGGTAG
12859862 AGAGGTCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 1 0.03
30 24 0.71
31 9 0.26
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (30 bp):
AGGTAGTGTTAAGGTTATACCTCCTAAAAA
Found at i:12859961 original size:37 final size:37
Alignment explanation
Indices: 12859870--12859963 Score: 145
Period size: 37 Copynumber: 2.5 Consensus size: 37
12859860 AGAGAGGTCA
**
12859870 TGCTTGATCCTTAAAAGAAATTTCGTTGTAGAGGTTG
1 TGCTTGATCCTTAAAAGGCATTTCGTTGTAGAGGTTG
*
12859907 TGCTTGATTCTTAAAAGGCATTT-GATTGTAGAGGTTG
1 TGCTTGATCCTTAAAAGGCATTTCG-TTGTAGAGGTTG
12859944 TGCTTGATCCTTAAAAGGCA
1 TGCTTGATCCTTAAAAGGCA
12859964 ATGGCTTGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 1 0.02
37 51 0.98
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (37 bp):
TGCTTGATCCTTAAAAGGCATTTCGTTGTAGAGGTTG
Found at i:12859973 original size:37 final size:37
Alignment explanation
Indices: 12859870--12859980 Score: 143
Period size: 37 Copynumber: 3.0 Consensus size: 37
12859860 AGAGAGGTCA
* *
12859870 TGCTTGATCCTTAAAA-GAAATTTCGTTGTAGAGGTTG
1 TGCTTGATCCTTAAAAGGCAATTGC-TTGTAGAGGTTG
* * *
12859907 TGCTTGATTCTTAAAAGGCATTTGATTGTAGAGGTTG
1 TGCTTGATCCTTAAAAGGCAATTGCTTGTAGAGGTTG
* *
12859944 TGCTTGATCCTTAAAAGGCAATGGCTTGTAAAGGTTG
1 TGCTTGATCCTTAAAAGGCAATTGCTTGTAGAGGTTG
12859981 ATCCTAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 59 0.94
38 4 0.06
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (37 bp):
TGCTTGATCCTTAAAAGGCAATTGCTTGTAGAGGTTG
Found at i:12860673 original size:140 final size:140
Alignment explanation
Indices: 12860421--12860698 Score: 484
Period size: 140 Copynumber: 2.0 Consensus size: 140
12860411 AGAAGGAGAG
*
12860421 CCATCAACTTTGGCTTCAAACGAAGGGTGGATCGAAGAACCATGGTGATCAAAGAAGCCCATTAT
1 CCATCAACTTTGGCTTCAAACGAAGGGTGGATCAAAGAACCATGGTGATCAAAGAAGCCCATTAT
* * *
12860486 CACCCTTGATTCCATCCCTTTTTACCCCCCACTCGATAAAGTAGCTATCTTCTAGAAAAGAGTTA
66 CACCCCTGATTCCATCCCTTTTTACCCCCCACTCAATAAAGTAGCTATCCTCTAGAAAAGAGTTA
12860551 GTCAACCAGT
131 GTCAACCAGT
* *
12860561 CCATCAACTTTGGCTTCAAACGAAGGGTGGATCAAAGAAGCATGGTGATCAAAGAAGCTCATTAT
1 CCATCAACTTTGGCTTCAAACGAAGGGTGGATCAAAGAACCATGGTGATCAAAGAAGCCCATTAT
**
12860626 CACCCCTGATTCCATCCCTTTTTACCCCCTGCTCAATAAAGTAGCTATCCTCTAGAAAAGAGTTA
66 CACCCCTGATTCCATCCCTTTTTACCCCCCACTCAATAAAGTAGCTATCCTCTAGAAAAGAGTTA
12860691 GTCAACCA
131 GTCAACCA
12860699 ATTGGAAGTT
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 130 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (140 bp):
CCATCAACTTTGGCTTCAAACGAAGGGTGGATCAAAGAACCATGGTGATCAAAGAAGCCCATTAT
CACCCCTGATTCCATCCCTTTTTACCCCCCACTCAATAAAGTAGCTATCCTCTAGAAAAGAGTTA
GTCAACCAGT
Found at i:12863818 original size:20 final size:20
Alignment explanation
Indices: 12863793--12863848 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
12863783 TTGAGTTGTT
12863793 ATCTATCGATAGATGGACAC-
1 ATCTATCGATAGATGG-CACG
*
12863813 ATCTATCGATAGATAGGCTCG
1 ATCTATCGATAGAT-GGCACG
*
12863834 ATCTATCAATAGATG
1 ATCTATCGATAGATG
12863849 TTCTTCAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (20 bp):
ATCTATCGATAGATGGCACG
Found at i:12865274 original size:2 final size:2
Alignment explanation
Indices: 12865259--12865323 Score: 69
Period size: 2 Copynumber: 32.5 Consensus size: 2
12865249 TTTGATGAAT
* *
12865259 TA TA TA TT TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
12865300 TG TA TG TA TA TGA TA TA TA AA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA T
12865324 GCCTATCAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12868126 original size:20 final size:20
Alignment explanation
Indices: 12868101--12868138 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12868091 CTATTTGGAT
12868101 GTCATTTATTGATAGATTTG
1 GTCATTTATTGATAGATTTG
12868121 GTCATTTATTGATAGATT
1 GTCATTTATTGATAGATT
12868139 GGCAATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (20 bp):
GTCATTTATTGATAGATTTG
Found at i:12869577 original size:21 final size:22
Alignment explanation
Indices: 12869553--12869606 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
12869543 ACAAAACCCT
12869553 AAGTGGAAAAATTCAAGGAAA-
1 AAGTGGAAAAATTCAAGGAAAC
12869574 AAGTGTG-AAAATTCAAGGAAAC
1 AAGTG-GAAAAATTCAAGGAAAC
*
12869596 AAGTGAAAAAA
1 AAGTGGAAAAA
12869607 AGGTAAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.57, C:0.06, G:0.22, T:0.15
Consensus pattern (22 bp):
AAGTGGAAAAATTCAAGGAAAC
Found at i:12876546 original size:19 final size:19
Alignment explanation
Indices: 12876522--12876559 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12876512 CCATTTAACT
*
12876522 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
12876541 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
12876560 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:12882212 original size:31 final size:32
Alignment explanation
Indices: 12882177--12882250 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 32
12882167 AAATCAAAAA
* * *
12882177 GACTAAATTGAAG-AACAATTTAAAGTATTGG
1 GACTAAATTGAAGTAAAAATTCAAAGTATGGG
* * *
12882208 GACTAATTTG-GGTAAAAATTCAATGTATGGG
1 GACTAAATTGAAGTAAAAATTCAAAGTATGGG
12882239 GACTAAATTGAA
1 GACTAAATTGAA
12882251 CAAAAAAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.30
Consensus pattern (32 bp):
GACTAAATTGAAGTAAAAATTCAAAGTATGGG
Found at i:12882441 original size:16 final size:15
Alignment explanation
Indices: 12882415--12882444 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12882405 CTGGAACCTT
12882415 TAACCCTTGAAATTC
1 TAACCCTTGAAATTC
12882430 TAACCACTTGAAATT
1 TAACC-CTTGAAATT
12882445 GAGAGATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (15 bp):
TAACCCTTGAAATTC
Found at i:12884323 original size:21 final size:21
Alignment explanation
Indices: 12884295--12884353 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
12884285 AATGAAGTAG
12884295 AAGGTTTAAATGAAGATGAAA
1 AAGGTTTAAATGAAGATGAAA
*
12884316 AGGGTTTAAATGAAGATGAAA
1 AAGGTTTAAATGAAGATGAAA
12884337 AAGGTTTAAATGAAGAT
1 AAGGTTTAAATGAAGAT
12884354 TATTTTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGGTTTAAATGAAGATGAAA
Found at i:12887342 original size:20 final size:21
Alignment explanation
Indices: 12887293--12887345 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
12887283 AATCCTATAG
*
12887293 AAACATAAAA-AGTAATAAAT
1 AAACATAAAATAGCAATAAAT
*
12887313 AAAAACTAAAATA-CAATAAAT
1 AAACA-TAAAATAGCAATAAAT
12887334 AAACATAAAATA
1 AAACATAAAATA
12887346 AAATTAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.72, C:0.08, G:0.02, T:0.19
Consensus pattern (21 bp):
AAACATAAAATAGCAATAAAT
Found at i:12889937 original size:35 final size:36
Alignment explanation
Indices: 12889871--12889983 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 36
12889861 TGTGAGTGCA
* *
12889871 CACACTGATGATATATGCCATGTGCGATGTGGGAGTG
1 CACA-TGATGATATATGCCTTGTGCGGTGTGGGAGTG
12889908 CACATGATGATAT-TGCCTTGTGCGGTGTGGGAGTG
1 CACATGATGATATATGCCTTGTGCGGTGTGGGAGTG
* *
12889943 CACAGGATGAT-TCTAG-CTATGTGCGGTGT-GGAGGTG
1 CACATGATGATATAT-GCCT-TGTGCGGTGTGGGA-GTG
12889979 CACAT
1 CACAT
12889984 AAGCTGGTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
34 1 0.01
35 36 0.53
36 27 0.40
37 4 0.06
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.28
Consensus pattern (36 bp):
CACATGATGATATATGCCTTGTGCGGTGTGGGAGTG
Found at i:12892972 original size:24 final size:24
Alignment explanation
Indices: 12892945--12893013 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
12892935 TAGTAAAGCG
* *
12892945 AGTGAAGTTGCTACTGGTGCACTA
1 AGTGAAGTTGCTACTAGTGCACCA
* *
12892969 AGTGAAGCTGCTACTATTGCACCA
1 AGTGAAGTTGCTACTAGTGCACCA
*
12892993 AGTGAACTTGCTACTAGTGCA
1 AGTGAAGTTGCTACTAGTGCA
12893014 AGTCAACTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (24 bp):
AGTGAAGTTGCTACTAGTGCACCA
Found at i:12901942 original size:29 final size:28
Alignment explanation
Indices: 12901895--12901952 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
12901885 CCGAACCTTG
*
12901895 TCTTTTTCTTTTTTCTCCTTTCTTTCTT
1 TCTTTTTCTTTTTTCTCCTTTCTCTCTT
12901923 TCTTTCTTCCTTTTTT-TCCTTTCTCTCTT
1 TCTTT-TT-CTTTTTTCTCCTTTCTCTCTT
12901952 T
1 T
12901953 GCTTCCAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (28 bp):
TCTTTTTCTTTTTTCTCCTTTCTCTCTT
Found at i:12907069 original size:62 final size:62
Alignment explanation
Indices: 12906972--12907097 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
12906962 TTCTTAATCT
* *
12906972 AGCAAAGATATACATTTCTCGTACTTCCACTGCCTACTCGATGAAAGAGCCGGAAGTGTTCA
1 AGCAAAGATATACATTTCTCATACTTCCACTGCCTACTCGATGAAAGAGCCGAAAGTGTTCA
12907034 AGCAAAGATATACATTTCTCATACTTCCACTGCCTACTCGATGAAAGAGCCGAAAGTGTTCA
1 AGCAAAGATATACATTTCTCATACTTCCACTGCCTACTCGATGAAAGAGCCGAAAGTGTTCA
12907096 AG
1 AG
12907098 TTCCACATGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (62 bp):
AGCAAAGATATACATTTCTCATACTTCCACTGCCTACTCGATGAAAGAGCCGAAAGTGTTCA
Found at i:12912059 original size:96 final size:98
Alignment explanation
Indices: 12911874--12912076 Score: 270
Period size: 96 Copynumber: 2.1 Consensus size: 98
12911864 CCGTTTAACA
* ** * *
12911874 TGTTTTATTTTGTTTTTCTTCCATTTTCTTTTATTTTTTCTGGAGAACGCATTGGGCATTATTTT
1 TGTTTTATTTTGTTTTTCTTCCATTTTCTTTTATTTTTACCAGAGAACCCATTGCGC--TATTTT
*
12911939 CCTTTCATTTTCAAGTTCATGTTTTCTTGTTTTTTC
64 CCGTTCATTTTCAAGTTCATGTTTTCTTG-TTTTTC
*
12911975 TGTTTTATTTT-TTTTAT-TT-CATTTTCTTTTATTTTTACCAGAGAACCCATTTCGC-ATTTTC
1 TGTTTTATTTTGTTTT-TCTTCCATTTTCTTTTATTTTTACCAGAGAACCCATTGCGCTATTTTC
*
12912036 CGTTCATTTTCCAGTTCATGTTTTCTTGTTTTTC
65 CGTTCATTTTCAAGTTCATGTTTTCTTGTTTTTC
12912070 TGTTTTA
1 TGTTTTA
12912077 CTTTCCTTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
95 13 0.14
96 32 0.34
99 30 0.32
100 6 0.06
101 12 0.13
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (98 bp):
TGTTTTATTTTGTTTTTCTTCCATTTTCTTTTATTTTTACCAGAGAACCCATTGCGCTATTTTCC
GTTCATTTTCAAGTTCATGTTTTCTTGTTTTTC
Found at i:12912309 original size:20 final size:22
Alignment explanation
Indices: 12912284--12912335 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 22
12912274 CGCTTTCTGA
12912284 GTCGCCGG-ACCGCCG-C-CTTT
1 GTCGCCGGCA-CGCCGCCTCTTT
12912304 GTCGCCGGCACGCCGCCCTCTTT
1 GTCGCCGGCACGCCG-CCTCTTT
12912327 GTCGCCGGC
1 GTCGCCGGC
12912336 CGTTGTTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.46
21 1 0.04
22 1 0.04
23 13 0.46
ACGTcount: A:0.04, C:0.46, G:0.31, T:0.19
Consensus pattern (22 bp):
GTCGCCGGCACGCCGCCTCTTT
Found at i:12916430 original size:25 final size:22
Alignment explanation
Indices: 12916402--12916451 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 22
12916392 ATAATAATCA
12916402 TATAAAATATTAAATTATATATAAT
1 TATAAAATATT-AATTA-AT-TAAT
*
12916427 TATAAAATGTTAATTAATTAAT
1 TATAAAATATTAATTAATTAAT
12916449 TAT
1 TAT
12916452 TGAAGACTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 2 0.08
24 5 0.21
25 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAAAATATTAATTAATTAAT
Found at i:12925440 original size:30 final size:30
Alignment explanation
Indices: 12925381--12925439 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12925371 TAATTTTAAT
* * *
12925381 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAACTTAATTAATATAAAATAAAAA
12925411 TATAAAAACTTAATTAA-ATAAAATAAAAA
1 TATAAAAACTTAATTAATATAAAATAAAAA
12925440 AAAACTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (30 bp):
TATAAAAACTTAATTAATATAAAATAAAAA
Found at i:12927311 original size:28 final size:29
Alignment explanation
Indices: 12927268--12927329 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
12927258 ATGTCTTTGG
*
12927268 GTAATTTTTCAGTTTTTA-GG-GCAAAAAT
1 GTAATTTTTCA-CTTTTACGGAGCAAAAAT
12927296 GTAATTTTTCACTTTTACGGGAGCAAAAAT
1 GTAATTTTTCACTTTTAC-GGAGCAAAAAT
12927326 GTAA
1 GTAA
12927330 ATTTCAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.17
28 11 0.37
29 2 0.07
30 12 0.40
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (29 bp):
GTAATTTTTCACTTTTACGGAGCAAAAAT
Done.