Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 85 of 172
Found at i:28268185 original size:45 final size:45
Alignment explanation
Indices: 28268106--28268212 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
28268096 CAATATCTGG
* * *
28268106 AAGACGTTATGGCATCACGATTTCAATGAATAAGACTAGAGCTGA
1 AAGATGTTATGGCATCACGATTTCAATCAATAAGACCAGAGCTGA
* *
28268151 AAGATGTTATGGCATCACGA-TTCTAA-CAAGTAAGACCATAGTTGA
1 AAGATGTTATGGCATCACGATTTC-AATCAA-TAAGACCAGAGCTGA
*
28268196 AAGATGCTATGGCATCA
1 AAGATGTTATGGCATCA
28268213 TGAATCAGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
44 5 0.09
45 49 0.91
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (45 bp):
AAGATGTTATGGCATCACGATTTCAATCAATAAGACCAGAGCTGA
Found at i:28268300 original size:46 final size:46
Alignment explanation
Indices: 28268181--28268383 Score: 138
Period size: 45 Copynumber: 4.5 Consensus size: 46
28268171 TTCTAACAAG
* ** * *
28268181 TAAGACCATAGTTGAAAGATGC-TATGGCATCATGAATCAG--ACGAA
1 TAAGACCATGGTTGAAAGACACATATGGCAACA--AATCAGAAATGAA
* *
28268226 TAA-ATCCATGGTTGAAAGACA-TTATGGCAACACGA-C-GTAAAATGAA
1 TAAGA-CCATGGTTGAAAGACACATATGGCAACA-AATCAG--AAATGAA
* * *
28268272 TAAGACCATGGTAGAAAGACACAT-TGGCATCAAATCAGGAATGAA
1 TAAGACCATGGTTGAAAGACACATATGGCAACAAATCAGAAATGAA
* * * *
28268317 TAAGACCATGGTTGAAAGACACCATA--GCATCTAGTCAGGAATGAA
1 TAAGACCATGGTTGAAAGACA-CATATGGCAACAAATCAGAAATGAA
*
28268362 TAAGACCATGGTTGAAAAACAC
1 TAAGACCATGGTTGAAAGACAC
28268384 CATGGCATCC
Statistics
Matches: 130, Mismatches: 16, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 3 0.02
45 89 0.68
46 33 0.25
47 3 0.02
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGACACATATGGCAACAAATCAGAAATGAA
Found at i:28268334 original size:45 final size:45
Alignment explanation
Indices: 28268266--28268392 Score: 193
Period size: 45 Copynumber: 2.8 Consensus size: 45
28268256 CACGACGTAA
*
28268266 AATGAATAAGACCATGGTAGAAAGACA-CATTGGCATCAAATCAGG
1 AATGAATAAGACCATGGTTGAAAGACACCA-TGGCATCAAATCAGG
* * *
28268311 AATGAATAAGACCATGGTTGAAAGACACCATAGCATCTAGTCAGG
1 AATGAATAAGACCATGGTTGAAAGACACCATGGCATCAAATCAGG
*
28268356 AATGAATAAGACCATGGTTGAAAAACACCATGGCATC
1 AATGAATAAGACCATGGTTGAAAGACACCATGGCATC
28268393 CTTCAACCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
45 73 0.97
46 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (45 bp):
AATGAATAAGACCATGGTTGAAAGACACCATGGCATCAAATCAGG
Found at i:28278469 original size:47 final size:47
Alignment explanation
Indices: 28278406--28278510 Score: 174
Period size: 47 Copynumber: 2.2 Consensus size: 47
28278396 CCCTTCGGGA
* * * *
28278406 CTTATCACATTTATACACTTTTACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGCCCATTCGGC
28278453 CTTATCACATATATACACTTTCACATCCATCACATTGCCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGCCCATTCGGC
28278500 CTTATCACATA
1 CTTATCACATA
28278511 ATTAATACTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGCCCATTCGGC
Found at i:28283725 original size:10 final size:10
Alignment explanation
Indices: 28283710--28283734 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28283700 GGCATGTTTG
28283710 AATGTGTGAA
1 AATGTGTGAA
28283720 AATGTGTGAA
1 AATGTGTGAA
28283730 AATGT
1 AATGT
28283735 TTTGTCTTGA
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:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (10 bp):
AATGTGTGAA
Found at i:28285907 original size:27 final size:27
Alignment explanation
Indices: 28285875--28286051 Score: 219
Period size: 27 Copynumber: 6.6 Consensus size: 27
28285865 CCCTAATTGA
**
28285875 TAAAATGACTATTTTGCCCTTGTGAGG
1 TAAAATGACTATTTTGCCCTCATGAGG
* * **
28285902 TGAAATGACTGTTTTGCCCTTTTGAGG
1 TAAAATGACTATTTTGCCCTCATGAGG
*
28285929 TAAAATAACTATTTTGCCCTCATGAGG
1 TAAAATGACTATTTTGCCCTCATGAGG
* * *
28285956 TAAAATGATTATTTTGCCCTTATAAGG
1 TAAAATGACTATTTTGCCCTCATGAGG
* *
28285983 TAAAATGGCTATTTTGCCCTCATAAGG
1 TAAAATGACTATTTTGCCCTCATGAGG
* *
28286010 TAAAATGACTGTTTTGCCCTCGTGAGG
1 TAAAATGACTATTTTGCCCTCATGAGG
*
28286037 TAAAATGGCTATTTT
1 TAAAATGACTATTTT
28286052 TCTTTTATGT
Statistics
Matches: 129, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTCATGAGG
Found at i:28286082 original size:81 final size:81
Alignment explanation
Indices: 28285875--28286082 Score: 184
Period size: 81 Copynumber: 2.6 Consensus size: 81
28285865 CCCTAATTGA
* * ** * ** ** *
28285875 TAAAATGACTATTTTGCCCTTGTGAGGTGAAATGACTGTTTTGCCCTTTTGAGGTAAAATAACTA
1 TAAAATGACTATTTTGCCCTTATAAGGCAAAATGACTATAATGCCCTCATAAGGTAAAATAACTA
28285940 TTTTGCCCTCATGAGG
66 TTTTGCCCTCATGAGG
* * * ** * *
28285956 TAAAATGATTATTTTGCCCTTATAAGGTAAAATGGCTATTTTGCCCTCATAAGGTAAAATGACTG
1 TAAAATGACTATTTTGCCCTTATAAGGCAAAATGACTATAATGCCCTCATAAGGTAAAATAACTA
*
28286021 TTTTGCCCTCGTGAGG
66 TTTTGCCCTCATGAGG
* * ** **
28286037 TAAAATGGCTATTTTTCTTTTATGTGGCAAAATGACTGA-AATGCCC
1 TAAAATGACTATTTTGCCCTTATAAGGCAAAATGACT-ATAATGCCC
28286083 CTACATGGCA
Statistics
Matches: 103, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
81 102 0.99
82 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (81 bp):
TAAAATGACTATTTTGCCCTTATAAGGCAAAATGACTATAATGCCCTCATAAGGTAAAATAACTA
TTTTGCCCTCATGAGG
Found at i:28288233 original size:27 final size:26
Alignment explanation
Indices: 28288193--28288252 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
28288183 CCACATATAT
* *
28288193 ATATCTATTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28288219 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28288246 ATATCTG
1 ATATCTG
28288253 GCAGCCTCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28292577 original size:16 final size:16
Alignment explanation
Indices: 28292556--28292590 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28292546 CATGAGTAAA
28292556 ATGAGTACTTGATGTT
1 ATGAGTACTTGATGTT
28292572 ATGAGTACTTGATGTT
1 ATGAGTACTTGATGTT
28292588 ATG
1 ATG
28292591 TTATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (16 bp):
ATGAGTACTTGATGTT
Found at i:28293296 original size:40 final size:40
Alignment explanation
Indices: 28293241--28293375 Score: 225
Period size: 40 Copynumber: 3.4 Consensus size: 40
28293231 TATGTGCATA
*
28293241 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCTCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
28293281 GCATTCGTGCGGGTTATTATAACCGGGTTAAGGCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
28293321 CCATTCGTGCGGGTTATTATAACCGGGGTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
28293361 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
28293376 GTTACATCCG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:28293399 original size:80 final size:80
Alignment explanation
Indices: 28293242--28293392 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 80
28293232 ATGTGCATAG
* * * *
28293242 CATTCGTGCGGGTTATTATAACCGGGTTAAGTCTCGAAGGCATTCGTGCGGGTTATTATAACCGG
1 CATTCGTGCGGGTTATTATAACCGGGGTAAGTCCCGAAGGCATTCGTGCGGGTTATTACAACCGA
** *
28293307 GTTAAGGCCCGAAGC
66 GCCAAAGCCCGAAGC
* * *
28293322 CATTCGTGCGGGTTATTATAACCGGGGTAAGTCCCGAAGGCATTCGTGCTGGTTGTTACATCCGA
1 CATTCGTGCGGGTTATTATAACCGGGGTAAGTCCCGAAGGCATTCGTGCGGGTTATTACAACCGA
28293387 GCCAAA
66 GCCAAA
28293393 TTCCGAAAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
CATTCGTGCGGGTTATTATAACCGGGGTAAGTCCCGAAGGCATTCGTGCGGGTTATTACAACCGA
GCCAAAGCCCGAAGC
Found at i:28300121 original size:63 final size:63
Alignment explanation
Indices: 28300022--28300877 Score: 1712
Period size: 63 Copynumber: 13.6 Consensus size: 63
28300012 ATAGTTAAAG
28300022 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300085 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300148 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300211 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300274 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300337 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300400 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300463 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300526 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300589 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300652 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300715 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300778 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
28300841 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTT
1 GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTT
28300878 GTTTCTTCTT
Statistics
Matches: 793, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 793 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (63 bp):
GAAGGAAATGGGTGAAAGAAACAAAGTCTTTATTCTTTCACCCATTTCCTTCAGGCGACGCGT
Found at i:28302196 original size:40 final size:40
Alignment explanation
Indices: 28302141--28302235 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
28302131 TATGTGCATA
* *
28302141 GCATTCGTGCGGGTTATTATAACCGTGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAACTCCCGAAG
*
28302181 GCATTCGTGCGGGTTATTATAACTGGGTTAACTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAACTCCCGAAG
*
28302221 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
28302236 GTTACATCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAACTCCCGAAG
Found at i:28307126 original size:27 final size:26
Alignment explanation
Indices: 28307082--28307133 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28307072 GGACTACCGA
*
28307082 TTTACCCCTAGAGGGTAAAATGACTAT
1 TTTACCCCTAGAGCGT-AAATGACTAT
* *
28307109 TTTACCCCTCGTGCGTAAATGACTA
1 TTTACCCCTAGAGCGTAAATGACTA
28307134 ACTTGTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (26 bp):
TTTACCCCTAGAGCGTAAATGACTAT
Found at i:28307861 original size:27 final size:26
Alignment explanation
Indices: 28307823--28307882 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
28307813 CCACATATAT
* *
28307823 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28307849 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28307876 ATATCTG
1 ATATCTG
28307883 GCAGCCTTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28309283 original size:20 final size:21
Alignment explanation
Indices: 28309258--28309297 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28309248 CGTGTGACCC
28309258 ATTTTTCAGTTTT-TTTCAAT
1 ATTTTTCAGTTTTATTTCAAT
**
28309278 ATTTTTTTGTTTTATTTCAA
1 ATTTTTCAGTTTTATTTCAA
28309298 ATTAGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTTTTCAGTTTTATTTCAAT
Found at i:28315571 original size:71 final size:71
Alignment explanation
Indices: 28315455--28315593 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
28315445 ACACATGGTC
*
28315455 GTGTCTCTGCCTGTGTGGAATATACCTAGACTATTTTCCAAGCTTTGGTCAACCTTAATCTCTTA
1 GTGTCTCAGCCTGTGTGGAATATACCTAGACTATTTTCCAAGCTTTGGTCAACCTTAATCTCTTA
28315520 CACCAT
66 CACCAT
28315526 GTGTCTCAGCCTGTGTGGAATATACCTAGACTATTTTCCAAGCTTTGGTCAACCTTAATCTCTTA
1 GTGTCTCAGCCTGTGTGGAATATACCTAGACTATTTTCCAAGCTTTGGTCAACCTTAATCTCTTA
28315591 CAC
66 CAC
28315594 ACTTATACAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (71 bp):
GTGTCTCAGCCTGTGTGGAATATACCTAGACTATTTTCCAAGCTTTGGTCAACCTTAATCTCTTA
CACCAT
Found at i:28317828 original size:30 final size:30
Alignment explanation
Indices: 28317794--28317855 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
28317784 TCGTTAACTC
*
28317794 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTACCCCT
* * * *
28317824 AAACTTTTGCATATTTACACTTTTACCCCT
1 AAACTTTGGCAAAATTACAATTTTACCCCT
28317854 AA
1 AA
28317856 GCTTGGGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.37
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTACCCCT
Found at i:28318826 original size:13 final size:13
Alignment explanation
Indices: 28318808--28318846 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
28318798 GAACATTATT
28318808 AAAAACATGAAAC
1 AAAAACATGAAAC
*
28318821 AAAAACACGAAAC
1 AAAAACATGAAAC
*
28318834 ACAAACAT-AAAC
1 AAAAACATGAAAC
28318846 A
1 A
28318847 TAATCTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.69, C:0.21, G:0.05, T:0.05
Consensus pattern (13 bp):
AAAAACATGAAAC
Found at i:28318899 original size:13 final size:13
Alignment explanation
Indices: 28318881--28318905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28318871 CATGAAAGAA
28318881 ATAAAAGCATGAT
1 ATAAAAGCATGAT
28318894 ATAAAAGCATGA
1 ATAAAAGCATGA
28318906 ATACGAAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
ATAAAAGCATGAT
Found at i:28322751 original size:12 final size:12
Alignment explanation
Indices: 28322736--28322760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28322726 ATACAGATTT
28322736 AGTTTCAAATTC
1 AGTTTCAAATTC
28322748 AGTTTCAAATTC
1 AGTTTCAAATTC
28322760 A
1 A
28322761 AATTCAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AGTTTCAAATTC
Found at i:28338229 original size:44 final size:42
Alignment explanation
Indices: 28338181--28338298 Score: 109
Period size: 44 Copynumber: 2.8 Consensus size: 42
28338171 CAATAGTTAG
*
28338181 CCGAAGCTAGAATGATTCTGCACACTTAGTGCCATCTTAACTAA
1 CCGAAGCTAGAATGATTCTGCACACTTAGTGCCATCAT-A-TAA
* *
28338225 CCGAAGCTA-AGTCGATATC-GCACACTTAGTGCC-TCATATAG
1 CCGAAGCTAGAAT-GAT-TCTGCACACTTAGTGCCATCATATAA
** * *
28338266 CCGAAGCTAGTTTAAATCT-CACACTTAGTGCCA
1 CCGAAGCTAGAATGATTCTGCACACTTAGTGCCA
28338299 ATTACCATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
40 15 0.24
41 12 0.19
42 2 0.03
43 5 0.08
44 26 0.42
45 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
CCGAAGCTAGAATGATTCTGCACACTTAGTGCCATCATATAA
Found at i:28359551 original size:13 final size:13
Alignment explanation
Indices: 28359535--28359574 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
28359525 TTTAAGCTAA
28359535 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
28359548 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
28359561 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28359574 A
1 A
28359575 TTGCCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28360767 original size:13 final size:13
Alignment explanation
Indices: 28360746--28360816 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
28360736 AAATTTTTTC
28360746 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
28360759 AAAGTACTTCTCA
1 AAAGCACTTCTCA
*
28360772 AAAGCAC-TCTTCC
1 AAAGCACTTC-TCA
* *
28360785 ACAGCACTTTTCA
1 AAAGCACTTCTCA
*
28360798 AAAGCACTTTTCA
1 AAAGCACTTCTCA
28360811 AAAGCA
1 AAAGCA
28360817 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
12 2 0.04
13 46 0.94
14 1 0.02
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.25
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:28362746 original size:81 final size:81
Alignment explanation
Indices: 28362608--28362933 Score: 485
Period size: 81 Copynumber: 4.0 Consensus size: 81
28362598 AGGTCGTTAT
* *
28362608 ATAACCGTAATACCCCTGTAGAGTAAAATGACTGTAATGCCCCTATAGAGTAAAATGACCGTAAT
1 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
28362673 GCCCCTATAGAGTAAA
66 GCCCCTATAGAGTAAA
** * *
28362689 ACGACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCTCTGTAGACTAAAATGACCGTAAT
1 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
* *
28362754 GCCCTTGTAGAGTAAA
66 GCCCCTATAGAGTAAA
* * * *
28362770 ATAAGCATAATGCCCCTATAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGATCGTAAT
1 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
*
28362835 GCCCCTATAGGGTAAA
66 GCCCCTATAGAGTAAA
28362851 ATAACCGTAATGCCCCTGTACGA-TAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAA
1 ATAACCGTAATGCCCCTGTA-GAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAA
**
28362915 TATCCCTATATG-GTAAA
65 TGCCCCTATA-GAGTAAA
28362932 AT
1 AT
28362934 GACGATTTTT
Statistics
Matches: 218, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
81 215 0.99
82 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (81 bp):
ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
GCCCCTATAGAGTAAA
Found at i:28362936 original size:27 final size:27
Alignment explanation
Indices: 28362611--28362915 Score: 423
Period size: 27 Copynumber: 11.3 Consensus size: 27
28362601 TCGTTATATA
*
28362611 ACCGTAATACCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* *
28362638 ACTGTAATGCCCCTATAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* *
28362665 ACCGTAATGCCCCTATAGAGTAAAACG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
28362692 ACCGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* * *
28362719 ACTGTAATGCCTCTGTAGACTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* *
28362746 ACCGTAATGCCCTTGTAGAGTAAAATA
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* * *
28362773 AGCATAATGCCCCTATAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
*
28362800 ACTGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* * * *
28362827 ATCGTAATGCCCCTATAGGGTAAAATA
1 ACCGTAATGCCCCTGTAGAGTAAAATG
28362854 ACCGTAATGCCCCTGTACGA-TAAAATG
1 ACCGTAATGCCCCTGTA-GAGTAAAATG
*
28362881 ACTGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
28362908 ACCGTAAT
1 ACCGTAAT
28362916 ATCCCTATAT
Statistics
Matches: 241, Mismatches: 35, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 238 0.99
28 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
ACCGTAATGCCCCTGTAGAGTAAAATG
Found at i:28363337 original size:28 final size:28
Alignment explanation
Indices: 28363303--28363366 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
28363293 TGTACCGTAT
*
28363303 TGTTACTGCATTA-GGCGTAGGCCCACAC
1 TGTTACTG-AATAGGGCGTAGGCCCACAC
* *
28363331 TGTTACTGAATAGGGCTTAGGCCCAGAC
1 TGTTACTGAATAGGGCGTAGGCCCACAC
28363359 TG-TACTGA
1 TGTTACTGA
28363367 TACTGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (28 bp):
TGTTACTGAATAGGGCGTAGGCCCACAC
Found at i:28363372 original size:33 final size:33
Alignment explanation
Indices: 28363329--28363391 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
28363319 GTAGGCCCAC
*
28363329 ACTGTTACTGAATAGGGCTTAGGCCCAGACTGT
1 ACTGATACTGAATAGGGCTTAGGCCCAGACTGT
28363362 ACTGATACTGAATAGGGCTTAGGCCCAGAC
1 ACTGATACTGAATAGGGCTTAGGCCCAGAC
28363392 CGTGTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (33 bp):
ACTGATACTGAATAGGGCTTAGGCCCAGACTGT
Found at i:28373447 original size:49 final size:50
Alignment explanation
Indices: 28373367--28373612 Score: 307
Period size: 49 Copynumber: 4.9 Consensus size: 50
28373357 AGCTATTGTG
*
28373367 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * **
28373417 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * **
28373467 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28373517 AGGTCACGTGTGTAGTACCAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28373567 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
28373613 GCTTTGGCTA
Statistics
Matches: 165, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
49 81 0.49
50 47 0.28
51 37 0.22
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:28373503 original size:28 final size:28
Alignment explanation
Indices: 28373472--28373555 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
28373462 AACTTCGATC
28373472 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
28373500 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
*
28373522 ACGTGTGTAGTACCAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
28373550 ACGTGT
1 ACGTGT
28373556 ACCGGATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 1 0.02
24 3 0.07
25 6 0.15
26 3 0.07
27 2 0.05
28 14 0.34
29 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:28379666 original size:27 final size:27
Alignment explanation
Indices: 28379628--28379934 Score: 409
Period size: 27 Copynumber: 11.4 Consensus size: 27
28379618 AGGTCGTTAT
28379628 ATGACCGTAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
** *
28379655 ATGATTGTAATG-CCCTGTAGAGTTAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
28379681 ATGGCCGTAATGCCCTTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
28379708 ATGACCATAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* * *
28379735 ATGATCGTAATGCCTCTATAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* * *
28379762 ATAACTGTAATGCCCCTATAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
28379789 ATAATCGTAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
28379816 ATGACTGTAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
28379843 ATGATCGTAATGCCCCTGTAGGGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* * *
28379870 ATAATCGTAATGCCCCTGTAGGGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
28379897 ATGACCATAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
28379924 ATGACTGTAAT
1 ATGACCGTAAT
28379935 ACCTATGGTA
Statistics
Matches: 244, Mismatches: 35, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 22 0.09
27 222 0.91
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
ATGACCGTAATGCCCCTGTAGAGTAAA
Found at i:28380144 original size:27 final size:27
Alignment explanation
Indices: 28380114--28380170 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28380104 TGTCACATGC
* *
28380114 ACTGTTACTGGTGGCTAT-GCCACAATT
1 ACTGATACTAGTGGCT-TCGCCACAATT
*
28380141 ACTGATACTAGTGGCTTCGCCACATTT
1 ACTGATACTAGTGGCTTCGCCACAATT
28380168 ACT
1 ACT
28380171 ATTTATGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (27 bp):
ACTGATACTAGTGGCTTCGCCACAATT
Found at i:28385776 original size:43 final size:43
Alignment explanation
Indices: 28385715--28385851 Score: 186
Period size: 43 Copynumber: 3.2 Consensus size: 43
28385705 AAAAAAATGT
*
28385715 CGCTAAAGAACATGACCTTTAGCAGCGCTTTTCCCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * *
28385758 CGCTAAAGATCATGACCTTTAGCGGTGCTTTTCCAAAAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* *
28385801 CGCTAAA-AAGCATTACCTTTAGCGGCGCTTTTCCCACAAATGC
1 CGCTAAAGAA-CATGACCTTTAGCGGCGCTTTTCCCACAAACGC
*
28385844 CGTTAAAG
1 CGCTAAAG
28385852 GTCAAAAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 79 0.99
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
Found at i:28391596 original size:41 final size:41
Alignment explanation
Indices: 28391510--28391638 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 41
28391500 AAATTGGGGA
* * *
28391510 TTTTTTGCAGCATTTTTAC-AAAAACGCCATTGTATCTCAA-
1 TTTTTT-CAGCATTTTTACTAAAAACGCCACTATAGCTCAAC
** * *
28391550 TTTTTTGTGGCGTTTTTACTAAAAACGCCACTATAGCTTAAC
1 TTTTTT-CAGCATTTTTACTAAAAACGCCACTATAGCTCAAC
* * * *
28391592 TTTTTTCAGCATTTTCACTAAAAACGTCACTATTGCTCAAT
1 TTTTTTCAGCATTTTTACTAAAAACGCCACTATAGCTCAAC
28391633 TTTTTT
1 TTTTTT
28391639 TGTCATTTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
40 16 0.22
41 50 0.69
42 6 0.08
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.43
Consensus pattern (41 bp):
TTTTTTCAGCATTTTTACTAAAAACGCCACTATAGCTCAAC
Found at i:28391794 original size:15 final size:14
Alignment explanation
Indices: 28391774--28391838 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
28391764 TAAATATTAA
28391774 AATTTTAAGTTTTT
1 AATTTTAAGTTTTT
28391788 AAGTTTTTAA-TTTTT
1 AA--TTTTAAGTTTTT
*
28391803 AATTTTTTAATTTTTT
1 AA--TTTTAAGTTTTT
*
28391819 AATTTTCAA-TTTTC
1 AATTTT-AAGTTTTT
28391833 AATTTT
1 AATTTT
28391839 CAAAATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
14 16 0.36
15 16 0.36
16 13 0.29
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (14 bp):
AATTTTAAGTTTTT
Found at i:28391817 original size:23 final size:23
Alignment explanation
Indices: 28391776--28391831 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
28391766 AATATTAAAA
*
28391776 TTTTAAGTTTTTAAGTTTTTAAT
1 TTTTAATTTTTTAAGTTTTTAAT
*
28391799 TTTTAATTTTTTAATTTTTTAAT
1 TTTTAATTTTTTAAGTTTTTAAT
*
28391822 TTTCAATTTT
1 TTTTAATTTT
28391832 CAATTTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTAATTTTTTAAGTTTTTAAT
Found at i:28391841 original size:7 final size:7
Alignment explanation
Indices: 28391776--28391838 Score: 72
Period size: 8 Copynumber: 8.4 Consensus size: 7
28391766 AATATTAAAA
28391776 TTTTAAGT
1 TTTTAA-T
28391784 TTTTAAGT
1 TTTTAA-T
28391792 TTTTAAT
1 TTTTAAT
28391799 TTTTAATT
1 TTTTAA-T
28391807 TTTTAATT
1 TTTTAA-T
28391815 TTTTAAT
1 TTTTAAT
*
28391822 TTTCAAT
1 TTTTAAT
*
28391829 TTTCAAT
1 TTTTAAT
28391836 TTT
1 TTT
28391839 CAAAATTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
7 24 0.45
8 29 0.55
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (7 bp):
TTTTAAT
Found at i:28392438 original size:14 final size:14
Alignment explanation
Indices: 28392420--28392500 Score: 76
Period size: 14 Copynumber: 5.8 Consensus size: 14
28392410 TCCTAAAAAT
28392420 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
28392434 CAAACACC-AAACC-
1 TAAAC-CCTAAACCA
**
28392447 TAAAAACTCAAACCA
1 TAAACCCT-AAACCA
*
28392462 TAAACCCTAAATCA
1 TAAACCCTAAACCA
*
28392476 TAAACCCTAAATCA
1 TAAACCCTAAACCA
*
28392490 TAAACCATAAA
1 TAAACCCTAAA
28392501 ACTTACATCC
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 43 0.78
15 8 0.15
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:28392924 original size:40 final size:39
Alignment explanation
Indices: 28392869--28392992 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 39
28392859 TTTTGCGGTG
*
28392869 TTTTTCAAAAAGCGCCGCTAACACTCGATCTTTAGCAGCA
1 TTTTTAAAAAAGCGCCGCTAACACTCGATCTTTAGC-GCA
** *
28392909 TTTTTAAAAAAGCGCCGCTAATGCTCGATCTTTAGCGACG
1 TTTTTAAAAAAGCGCCGCTAACACTCGATCTTTAGCG-CA
* * *
28392949 TTTTTAAAAAAGCGCCACTAATGA-TTGATCTTTAGCGGCA
1 TTTTTAAAAAAGCGCCGCTAA-CACTCGATCTTTAGC-GCA
28392989 TTTT
1 TTTT
28392993 CTTACTAGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 70 0.97
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (39 bp):
TTTTTAAAAAAGCGCCGCTAACACTCGATCTTTAGCGCA
Found at i:28394975 original size:43 final size:43
Alignment explanation
Indices: 28394813--28394978 Score: 158
Period size: 43 Copynumber: 3.9 Consensus size: 43
28394803 TTCGATATAC
* * * *
28394813 GATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGA
1 GATTACGTGTAAGACCATGTCTGGGACGTTGGCATTGATATT-T
* * * * *
28394856 GATTTATGTGTAAGACCATGTCTAGGACATCGACATTG-TATTT
1 GA-TTACGTGTAAGACCATGTCTGGGACGTTGGCATTGATATTT
* * * *
28394899 GATTTCGTGTAAGACCCTGTCTGAGATAG-TGGCATTGATATTT
1 GATTACGTGTAAGACCATGTCTGGGA-CGTTGGCATTGATATTT
*
28394942 GATTACATGTAAGACCATGTCTGGGACGTTGGCATTG
1 GATTACGTGTAAGACCATGTCTGGGACGTTGGCATTG
28394979 TACAAGCTTT
Statistics
Matches: 95, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
42 26 0.27
43 40 0.42
44 29 0.31
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACGTTGGCATTGATATTT
Found at i:28399922 original size:25 final size:25
Alignment explanation
Indices: 28399883--28399940 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
28399873 CGTGTGGTTG
28399883 ACACGGCCCTAGACACGGACGTGTT
1 ACACGGCCCTAGACACGGACGTGTT
* *
28399908 ATACGGCCCTGGACACGGACGTGTT
1 ACACGGCCCTAGACACGGACGTGTT
28399933 ACACGGCC
1 ACACGGCC
28399941 GTGTGTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (25 bp):
ACACGGCCCTAGACACGGACGTGTT
Found at i:28403070 original size:5 final size:5
Alignment explanation
Indices: 28403046--28403122 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
28403036 TTTTTATAAA
* *
28403046 TATAT TAT-T TA-AT TAGAT TATAT TAT-T ATATTAT TATATT GTAAAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT TATA-T -TATAT
28403092 TATAT TA-AT TATAT TATA- -ATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
28403123 AAATAAATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
3 3 0.05
4 11 0.19
5 36 0.61
6 5 0.08
7 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:28403073 original size:8 final size:8
Alignment explanation
Indices: 28403062--28403116 Score: 56
Period size: 8 Copynumber: 6.2 Consensus size: 8
28403052 ATTTAATTAG
28403062 ATTATATT
1 ATTATATT
28403070 ATTATATT
1 ATTATATT
28403078 ATTATATTGT
1 ATTATA-T-T
28403088 AAATTATATT
1 --ATTATATT
28403098 AATTATATT
1 -ATTATATT
*
28403107 ATAATATT
1 ATTATATT
28403115 AT
1 AT
28403117 ATTATAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
8 23 0.55
9 10 0.24
10 2 0.05
11 1 0.02
12 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (8 bp):
ATTATATT
Found at i:28403076 original size:26 final size:29
Alignment explanation
Indices: 28403046--28403108 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
28403036 TTTTTATAAA
*
28403046 TATATTATT-TAAT-TAGATTATATT-AT
1 TATATTATTATAATGTAAATTATATTAAT
*
28403072 TATATTATTATATTGTAAATTATATTAAT
1 TATATTATTATAATGTAAATTATATTAAT
28403101 TATATTAT
1 TATATTAT
28403109 AATATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 9 0.28
27 3 0.09
28 10 0.31
29 10 0.31
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TATATTATTATAATGTAAATTATATTAAT
Found at i:28403267 original size:15 final size:15
Alignment explanation
Indices: 28403231--28403260 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
28403221 AATATAAGAA
28403231 ATTATTATTATATATT
1 ATTA-TATTATATATT
28403247 ATTATATTATATAT
1 ATTATATTATATAT
28403261 ATATATAAAG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATATTATATATT
Found at i:28403367 original size:16 final size:15
Alignment explanation
Indices: 28403321--28403368 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
28403311 GGGACAAAAC
*
28403321 AGAAAGAAAAAGAAA
1 AGAAAGAAAAGGAAA
* *
28403336 GGAAAGAAGAGAGAAA
1 AGAAAGAAAAG-GAAA
28403352 AGAAAGAATAAGGAAA
1 AGAAAGAA-AAGGAAA
28403368 A
1 A
28403369 TAAGGTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 8 0.31
16 16 0.62
17 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AGAAAGAAAAGGAAA
Found at i:28406501 original size:18 final size:18
Alignment explanation
Indices: 28406478--28406521 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
28406468 ATACACACAA
*
28406478 AGTAAGCTAACTTAGCTT
1 AGTAAGCCAACTTAGCTT
28406496 AGTAAGCCAACTTAGCTT
1 AGTAAGCCAACTTAGCTT
28406514 AGTAAGCC
1 AGTAAGCC
28406522 TTAAGCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (18 bp):
AGTAAGCCAACTTAGCTT
Found at i:28409034 original size:10 final size:10
Alignment explanation
Indices: 28409015--28409064 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
28409005 TTAAATTCTA
28409015 AAAGATAAAT
1 AAAGATAAAT
28409025 ACAA-ATAAAT
1 A-AAGATAAAT
*
28409035 AAAGATAATT
1 AAAGATAAAT
28409045 AAAGATAAAT
1 AAAGATAAAT
*
28409055 AAAAATAAAT
1 AAAGATAAAT
28409065 CCTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:28409862 original size:96 final size:97
Alignment explanation
Indices: 28409732--28409915 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 97
28409722 ATTTAATTTA
* * ** * *
28409732 TTTATTTTTACTTAGGAATATATTGAACCTTTTGATGCGAAGAGATATGACAGCCAAGCA-CTCC
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCT-C
28409796 ACCCCAGTTACTCAGCCCAACATACTCCTTATT
65 ACCCCAGTTACTCAGCCCAACATACTCCTTATT
*
28409829 TTTATTTTT-CTTAAGAACATATCAAACCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCA
* *
28409893 CCCCGGTTACTCAGCCTAACATA
66 CCCCAGTTACTCAGCCCAACATA
28409916 TTCTTAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
96 66 0.86
97 11 0.14
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCA
CCCCAGTTACTCAGCCCAACATACTCCTTATT
Found at i:28411038 original size:21 final size:21
Alignment explanation
Indices: 28411012--28411056 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
28411002 ATAAATAATT
*
28411012 AAATAATAAATAATTAAGATA
1 AAATAATAAATAATTAAAATA
28411033 AAATAATAAATAATTAAAATA
1 AAATAATAAATAATTAAAATA
28411054 AAA
1 AAA
28411057 AAAATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAATAAATAATTAAAATA
Found at i:28411077 original size:12 final size:12
Alignment explanation
Indices: 28411060--28411084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28411050 AATAAAAAAA
28411060 ATAAAGAGAAAC
1 ATAAAGAGAAAC
28411072 ATAAAGAGAAAC
1 ATAAAGAGAAAC
28411084 A
1 A
28411085 AAAATTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (12 bp):
ATAAAGAGAAAC
Found at i:28418939 original size:10 final size:10
Alignment explanation
Indices: 28418920--28418962 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
28418910 TTAAATTCTA
28418920 AAAGATAAAT
1 AAAGATAAAT
28418930 ACAA-ATAAAT
1 A-AAGATAAAT
* *
28418940 AAATATAATT
1 AAAGATAAAT
28418950 AAAGATAAAT
1 AAAGATAAAT
28418960 AAA
1 AAA
28418963 AGTAAATCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 2 0.07
10 24 0.86
11 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:28420933 original size:49 final size:49
Alignment explanation
Indices: 28420855--28421004 Score: 187
Period size: 49 Copynumber: 3.1 Consensus size: 49
28420845 CTTCGGGACT
* * * *
28420855 TATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* * * * *
28420902 TGTCACTTATATATACACTTCCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
* *
28420951 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
28421000 TATCA
1 TATCA
28421005 TCATTTCATA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 6 0.07
48 1 0.01
49 82 0.92
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.32
Consensus pattern (49 bp):
TATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCC
Found at i:28428570 original size:54 final size:54
Alignment explanation
Indices: 28428373--28428573 Score: 199
Period size: 55 Copynumber: 3.7 Consensus size: 54
28428363 TTTACTTTTT
* * * * * *** *
28428373 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGACGTCCTTTCCTTATA
* * *
28428426 GAACTTACCAATGCCATGCCTTGGCATGGTCTTACATG-GGACCTTTGCCTTATA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGACGTCCTTT-CCTTATA
* * * *
28428480 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGACTTCCTTTCCTTATA
1 G-AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGACGTCCTTTCCTTATA
* * *
28428535 GAACTTATCAATTCCACGCCTTGGCTTGGTCTTACATGA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA
28428574 TATCCTTATC
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.03
53 40 0.33
54 33 0.27
55 41 0.33
56 5 0.04
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGACGTCCTTTCCTTATA
Found at i:28428580 original size:54 final size:54
Alignment explanation
Indices: 28428373--28428580 Score: 224
Period size: 53 Copynumber: 3.9 Consensus size: 54
28428363 TTTACTTTTT
* * * * * * *
28428373 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTTCCTTATA
* **
28428426 GAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTT-CCTTATA
* * *
28428480 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGACT-TCCTTTCCTTATA
1 G-AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA-TATCCTTTCCTTATA
* * *
28428535 GAACTTATCAATTCCACGCCTTGGCTTGGTCTTACATGATATCCTT
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
28428581 ATCTTACCAA
Statistics
Matches: 131, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
52 4 0.03
53 43 0.33
54 38 0.29
55 41 0.31
56 5 0.04
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTTCCTTATA
Found at i:28428616 original size:47 final size:47
Alignment explanation
Indices: 28428561--28428680 Score: 195
Period size: 47 Copynumber: 2.6 Consensus size: 47
28428551 CGCCTTGGCT
*
28428561 TGGTCTTACATGATATCCTTATCTTACCAAATGACATGTTCCAAACA
1 TGGTCTTACATGGTATCCTTATCTTACCAAATGACATGTTCCAAACA
* * *
28428608 TTGTCTTACATGGTATCCTTTTCTTACCAAATGCCATGTTCCAAACA
1 TGGTCTTACATGGTATCCTTATCTTACCAAATGACATGTTCCAAACA
*
28428655 TGGTCTTACATGGTATCCTTGTCTTA
1 TGGTCTTACATGGTATCCTTATCTTA
28428681 GTGCTAACGC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (47 bp):
TGGTCTTACATGGTATCCTTATCTTACCAAATGACATGTTCCAAACA
Found at i:28433269 original size:24 final size:24
Alignment explanation
Indices: 28433237--28433317 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 24
28433227 GATTAAGCTG
* *
28433237 AAACGGTAAGCTCTGACGAGCTAA
1 AAACAGTAAGCTCTAACGAGCTAA
* * * * *
28433261 AAACAGTAAGCTTTTATGGGCT-G
1 AAACAGTAAGCTCTAACGAGCTAA
* * *
28433284 AAACAGAAAGCTCCAACAAGCTAA
1 AAACAGTAAGCTCTAACGAGCTAA
28433308 AAACAGTAAG
1 AAACAGTAAG
28433318 TTCTTATGAG
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
23 15 0.37
24 26 0.63
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (24 bp):
AAACAGTAAGCTCTAACGAGCTAA
Found at i:28433284 original size:47 final size:47
Alignment explanation
Indices: 28433232--28433331 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 47
28433222 AGCTCGATTA
* * ** *
28433232 AGCTGAAACGGTAAGCTCTGACGAGCTAAAAACAGTAAGCTT-TTATG
1 AGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAG-TTCTTATG
*
28433279 GGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAGTTCTTATG
1 AGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAGTTCTTATG
28433326 AGCTGA
1 AGCTGA
28433332 TATATCAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 2 0.04
47 43 0.96
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (47 bp):
AGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAGTTCTTATG
Found at i:28433329 original size:24 final size:24
Alignment explanation
Indices: 28433254--28433329 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
28433244 AAGCTCTGAC
28433254 GAGCTAAAAACAGTAAGCTT-TTAT
1 GAGCTAAAAACAGTAAG-TTCTTAT
* * * * ** *
28433278 GGGCT-GAAACAGAAAGCTCCAAC
1 GAGCTAAAAACAGTAAGTTCTTAT
*
28433301 AAGCTAAAAACAGTAAGTTCTTAT
1 GAGCTAAAAACAGTAAGTTCTTAT
28433325 GAGCT
1 GAGCT
28433330 GATATATCAG
Statistics
Matches: 34, Mismatches: 16, Indels: 4
0.63 0.30 0.07
Matches are distributed among these distances:
22 1 0.03
23 13 0.38
24 20 0.59
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (24 bp):
GAGCTAAAAACAGTAAGTTCTTAT
Found at i:28442431 original size:141 final size:141
Alignment explanation
Indices: 28442177--28442445 Score: 434
Period size: 141 Copynumber: 1.9 Consensus size: 141
28442167 AATTTGCATC
* * *
28442177 ATATATCAAATGGCCAACTTACCTTATTTTCGAATAGGTAATCAACTAACTCATACCTGATATTC
1 ATATATCAAATAGCCAACTTACCTTATTTTCAAATAGGTAATCAACTAACTCATACCTGATAGTC
*
28442242 TTAGCTTATTTTACACCATCGTTCACAACTTATCATTGCCCGTTGAACCATTC-GTAATTGAATA
66 TTAGCTCATTTTACACCATCGTTCACAACTTATCATTGCCCGTTGAACCATTCAG-AATTGAATA
28442306 GGATACTCAGAT
130 GGATACTCAGAT
*
28442318 ATATATCAAATAGCCAACTTACCTTATTTTCAAATAGGTAATCAACTAACTCATACCTGATCGTC
1 ATATATCAAATAGCCAACTTACCTTATTTTCAAATAGGTAATCAACTAACTCATACCTGATAGTC
* * *
28442383 TTAGCTCGTTTTACACCATCGTTCA-AATTTTATCATTTCCCGTTGAACCATTCAGAATTGAAT
66 TTAGCTCATTTTACACCATCGTTCACAA-CTTATCATTGCCCGTTGAACCATTCAGAATTGAAT
28442446 CATATATCAA
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
140 2 0.02
141 115 0.97
142 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (141 bp):
ATATATCAAATAGCCAACTTACCTTATTTTCAAATAGGTAATCAACTAACTCATACCTGATAGTC
TTAGCTCATTTTACACCATCGTTCACAACTTATCATTGCCCGTTGAACCATTCAGAATTGAATAG
GATACTCAGAT
Found at i:28442566 original size:40 final size:43
Alignment explanation
Indices: 28442457--28442568 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
28442447 ATATATCAAA
* * * **
28442457 CAATGCCAATGTCCTAGACGTGGTCTTACATGCTATCTCATAT
1 CAATGCCAATGTCCTAGACATGGTCTTACACGCAATCAAATAT
* *
28442500 CAATGCCACTGTCCTAGACAGGGTCTTACACG-AATCAAATA-
1 CAATGCCAATGTCCTAGACATGGTCTTACACGCAATCAAATAT
*
28442541 CGATGCCAATGTCC-AGACATGGTCTTAC
1 CAATGCCAATGTCCTAGACATGGTCTTAC
28442569 TCATAACGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 13 0.22
41 12 0.20
42 6 0.10
43 28 0.47
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (43 bp):
CAATGCCAATGTCCTAGACATGGTCTTACACGCAATCAAATAT
Found at i:28442626 original size:45 final size:44
Alignment explanation
Indices: 28442496--28442627 Score: 123
Period size: 45 Copynumber: 3.0 Consensus size: 44
28442486 ATGCTATCTC
* * *
28442496 ATATCAATGCCACTGTCCTAGACAGGGTCTTACAC-GAATC-A-A-
1 ATATCGATGCCAATGTCC-AGACATGGTCTTACACAGAA-CGACAT
* *
28442538 ATA-CGATGCCAATGTCCAGACATGGTCTTACTCATAACGACAT
1 ATATCGATGCCAATGTCCAGACATGGTCTTACACAGAACGACAT
* *
28442581 ATATCGATGTCAATGTCCCAGACGTGGTCTTACACAAGAAC-ACAT
1 ATATCGATGCCAATGT-CCAGACATGGTCTTACAC-AGAACGACAT
28442626 AT
1 AT
28442628 CGAAAATCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
40 15 0.20
41 15 0.20
42 4 0.05
43 3 0.04
44 11 0.15
45 22 0.30
46 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (44 bp):
ATATCGATGCCAATGTCCAGACATGGTCTTACACAGAACGACAT
Found at i:28444406 original size:48 final size:48
Alignment explanation
Indices: 28444335--28444566 Score: 437
Period size: 48 Copynumber: 4.8 Consensus size: 48
28444325 GTTAAATTGT
28444335 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
*
28444383 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
28444431 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
28444479 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
* *
28444527 CGATGCCATGTCCCAGACATGGTCTTATACTAGCACACAT
1 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACAT
28444567 ATCAACCAAA
Statistics
Matches: 180, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 180 1.00
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.25
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGC
Found at i:28455062 original size:34 final size:34
Alignment explanation
Indices: 28455019--28455088 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
28455009 ACTTCATACT
28455019 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
1 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
28455053 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
1 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
28455087 TA
1 TA
28455089 CCCATGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (34 bp):
TATCAAAGAACATAAATCTTAACCAGATTTCCAA
Found at i:28460729 original size:48 final size:48
Alignment explanation
Indices: 28460658--28460890 Score: 252
Period size: 48 Copynumber: 4.9 Consensus size: 48
28460648 TAAATTGCCG
* * * *
28460658 ATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATGTCGAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCA
* * ** ** *
28460706 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATTTTAATACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCA
* * **
28460754 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCA
* * * * *
28460802 ATGCCATGTCCTAGACATGCTCTTACACTGGCTCTCATAAT-GTGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCCA
* *
28460850 ATGCCATGTCCCAGACATGGTCTTACGCTAGCACACATATC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATC
28460891 AACCAAATGT
Statistics
Matches: 150, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
47 2 0.01
48 146 0.97
49 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCA
Found at i:28460819 original size:96 final size:96
Alignment explanation
Indices: 28460655--28460890 Score: 303
Period size: 96 Copynumber: 2.5 Consensus size: 96
28460645 GGTTAAATTG
* * * * * *
28460655 CCGATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATGTCGAGGCCAATGCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCAATGCCATGTCCCAG
* **
28460720 ACATGGTCTTACACTAGCTCTCATTTTAAT-A
66 ACATGCTCTTACACTAGCTCTCATAAT-ATGA
** *
28460751 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCTGATGCCATGTCCTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCAATGCCATGTCCCAG
* * *
28460816 ACATGCTCTTACACTGGCTCTCATAATGTGG
66 ACATGCTCTTACACTAGCTCTCATAATATGA
* *
28460847 CCAATGCCATGTCCCAGACATGGTCTTACGCTAGCACACATATC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATC
28460891 AACCAAATGT
Statistics
Matches: 122, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
95 1 0.01
96 121 0.99
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCAATGCCATGTCCCAG
ACATGCTCTTACACTAGCTCTCATAATATGA
Found at i:28465757 original size:49 final size:49
Alignment explanation
Indices: 28465660--28465759 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 49
28465650 TTTGTGTGTG
* *
28465660 TTATCGAGATAGCTTTGGCTATATATATATTGGCACTTCAGGTGCAAGA
1 TTATCGAGATAGCTTCGGCTATATATATATTGGCACTTCAGGTACAAGA
* * * *
28465709 TTATTGAGATAGCTTCGGCTATATTTTTATTGGCACTT-ATTGTACAAGA
1 TTATCGAGATAGCTTCGGCTATATATATATTGGCACTTCA-GGTACAAGA
28465758 TT
1 TT
28465760 CCAAGGTATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (49 bp):
TTATCGAGATAGCTTCGGCTATATATATATTGGCACTTCAGGTACAAGA
Found at i:28466779 original size:12 final size:12
Alignment explanation
Indices: 28466762--28466787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28466752 GGTTTGGCAT
28466762 GGCCTAGCACAC
1 GGCCTAGCACAC
28466774 GGCCTAGCACAC
1 GGCCTAGCACAC
28466786 GG
1 GG
28466788 GCGTGTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:28478152 original size:71 final size:71
Alignment explanation
Indices: 28478074--28478215 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
28478064 AATCAGAATA
*
28478074 GTGGTTTCGTGACCATAAATCCAAGATAGAAATAATTATTTTATAATTATTTTGAGGTTTATGAT
1 GTGGTTTCGTGACCATAAATCCAAGATAGAAATAATTATTTTATAATTATTTTGAGGTTAATGAT
28478139 ATGATT
66 ATGATT
*
28478145 GTGGTTTCGTGACCATAAATCCGAGATAGAAATAATTATTTTATAATTATTTTGAGGTTAATGAT
1 GTGGTTTCGTGACCATAAATCCAAGATAGAAATAATTATTTTATAATTATTTTGAGGTTAATGAT
28478210 ATGATT
66 ATGATT
28478216 TCATGATTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.42
Consensus pattern (71 bp):
GTGGTTTCGTGACCATAAATCCAAGATAGAAATAATTATTTTATAATTATTTTGAGGTTAATGAT
ATGATT
Found at i:28485168 original size:79 final size:80
Alignment explanation
Indices: 28485008--28485232 Score: 264
Period size: 79 Copynumber: 2.8 Consensus size: 80
28484998 TTGAATGATG
* * * * * *
28485008 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCAT
28485071 TTGTGCGAGATACTAAA
64 TTGTGCGAGATACTAAA
*
28485088 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCA
*
28485149 TTTGTGCGAGTTACTAAA
63 TTTGTGCGAGATACTAAA
** *
28485167 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
28485232 G
66 G
28485233 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
78 2 0.02
79 68 0.54
80 46 0.37
81 9 0.07
82 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:28485196 original size:40 final size:40
Alignment explanation
Indices: 28485008--28485232 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
28484998 TTGAATGATG
* * * *
28485008 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28485048 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28485088 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28485128 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28485167 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28485208 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28485233 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
39 35 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28485224 original size:119 final size:120
Alignment explanation
Indices: 28485008--28485232 Score: 291
Period size: 119 Copynumber: 1.9 Consensus size: 120
28484998 TTGAATGATG
*
28485008 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
28485073 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
66 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
* * * **
28485128 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
28485190 TTGTGCGA-ATTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTG
64 TTGTGCGAGA-TACTA-AATCCGGACTAAGAT-CCGAAGGCATTTG
28485233 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
118 3 0.03
119 69 0.75
120 20 0.22
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28485254 original size:79 final size:78
Alignment explanation
Indices: 28485015--28485265 Score: 244
Period size: 79 Copynumber: 3.2 Consensus size: 78
28485005 ATGTCCGGGC
* * * *
28485015 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGCGAA-TTACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCG
* *
28485078 AGATACTAAATCCGGAC
64 AG-GACTAAATCCGG-T
28485095 TAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGC
1 TAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGC
*
28485156 GAGTTACTAAATCCGGGT
63 GAG-GACTAAATCC-GGT
* * **
28485174 TAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
28485239 GAGCTATATCCGGT
66 GA-CTAAATCCGGT
* *
28485253 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
28485266 TACGTGATTT
Statistics
Matches: 146, Mismatches: 14, Indels: 23
0.80 0.08 0.13
Matches are distributed among these distances:
78 2 0.01
79 81 0.55
80 53 0.36
81 9 0.06
82 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (78 bp):
TAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
GACTAAATCCGGT
Found at i:28500879 original size:48 final size:48
Alignment explanation
Indices: 28500803--28500932 Score: 190
Period size: 48 Copynumber: 2.7 Consensus size: 48
28500793 ACACCCTAAT
* * * *
28500803 TGCCAATATCATGGCCTGAAGCCAAATCAATGTAGCTCGCA-TTCGAAG
1 TGCCGATATCATGGCCTGAAGCCAAATCAATGTAACTCGCACCT-AAAG
*
28500851 TGCCGATATCATGGCCTGAAGCCAAATCAATGTAACTTGCACCTAAAG
1 TGCCGATATCATGGCCTGAAGCCAAATCAATGTAACTCGCACCTAAAG
*
28500899 TGCCGATATCATGGCCCGAAGCCAAATCAATGTA
1 TGCCGATATCATGGCCTGAAGCCAAATCAATGTA
28500933 TTCCGTAATG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
48 74 0.99
49 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (48 bp):
TGCCGATATCATGGCCTGAAGCCAAATCAATGTAACTCGCACCTAAAG
Found at i:28504099 original size:24 final size:24
Alignment explanation
Indices: 28504072--28504159 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
28504062 CCTTGGTCAA
* *
28504072 CTCCTAAATCTTCTCCTTTATCAG
1 CTCCTAAATCCTCTCCCTTATCAG
* *
28504096 CTCCTAAAGCCTCCCCCTTATCAG
1 CTCCTAAATCCTCTCCCTTATCAG
28504120 CTCCTAAATCCTCTCCCTTATCAG
1 CTCCTAAATCCTCTCCCTTATCAG
*
28504144 CTCCTAAATCTTCTCC
1 CTCCTAAATCCTCTCC
28504160 TGACAGCCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.20, C:0.41, G:0.05, T:0.34
Consensus pattern (24 bp):
CTCCTAAATCCTCTCCCTTATCAG
Found at i:28510685 original size:26 final size:26
Alignment explanation
Indices: 28510656--28510708 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
28510646 TCAAACTTGC
28510656 ATTTAGGTCAATTTA-CTCCTAAGGGT
1 ATTTAGGT-AATTTATCTCCTAAGGGT
* * *
28510682 ATTTCGGTACTTTATCTCCTATGGGT
1 ATTTAGGTAATTTATCTCCTAAGGGT
28510708 A
1 A
28510709 AAATTGTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAAGGGT
Found at i:28511991 original size:24 final size:23
Alignment explanation
Indices: 28511963--28512063 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 23
28511953 CCAAATCCTG
28511963 CTCCTTGATCAGCTCCTAAATCTT
1 CTCCTT-ATCAGCTCCTAAATCTT
* * *
28511987 CTCCTTTATCAACTCCTAAAGCCT
1 CTCC-TTATCAGCTCCTAAATCTT
*
28512011 CTCCCTTATTAGCTCCTAAATCCTT
1 CT-CCTTATCAGCTCCTAAAT-CTT
28512036 -TCCCTTATCAGCTCCTAAATCTT
1 CT-CCTTATCAGCTCCTAAATCTT
*
28512059 TTCCT
1 CTCCT
28512064 AATAGCGTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
23 6 0.09
24 53 0.82
25 6 0.09
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.39
Consensus pattern (23 bp):
CTCCTTATCAGCTCCTAAATCTT
Found at i:28523850 original size:52 final size:51
Alignment explanation
Indices: 28523772--28523894 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
28523762 GAGGAAGTGC
*
28523772 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
28523824 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
*
28523875 AAAAGGGCTT-TGCCCGAGTT
1 AAAAGGGCTTATGCCCCAGTT
28523895 ATTAAAGAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
50 9 0.13
51 24 0.35
52 36 0.52
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:28523869 original size:25 final size:26
Alignment explanation
Indices: 28523772--28523894 Score: 178
Period size: 26 Copynumber: 4.8 Consensus size: 26
28523762 GAGGAAGTGC
**
28523772 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28523798 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28523824 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28523850 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28523875 AAAAGGGCTT-TGCCCGAGTT
1 AAAAGGGCTTATGCCCCAGTT
28523895 ATTAAAGAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 32 0.36
26 56 0.64
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28531997 original size:46 final size:44
Alignment explanation
Indices: 28531940--28532115 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 44
28531930 TATTTGGGCA
* *
28531940 TCCGAAATCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*** * *
28531986 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAAG
*
28532033 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*
28532079 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28532116 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 66 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:28532095 original size:93 final size:93
Alignment explanation
Indices: 28531936--28532107 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
28531926 AGGATATTTG
* *
28531936 GGCATCCGAAATCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
28532001 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
** * *
28532029 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGA
28532093 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
28532108 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:28535041 original size:20 final size:20
Alignment explanation
Indices: 28535016--28535062 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
28535006 GATGTGATAT
*
28535016 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
28535036 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
28535056 ACATGAT
1 ACATGAT
28535063 GAATTCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:28535183 original size:51 final size:51
Alignment explanation
Indices: 28535112--28535208 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
28535102 GAGGAAGTGC
*
28535112 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATACCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTT-TACCCCAGTTTATTG
*
28535164 AAAAGGGCTT-TGCCCCAGTTTACCAAAAAGGGCTTTTCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTTACCCCAGTT
28535209 ATTAAAGAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 9 0.21
51 24 0.56
52 10 0.23
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTTACCCCAGTTTATTG
Found at i:28535185 original size:25 final size:26
Alignment explanation
Indices: 28535112--28535208 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
28535102 GAGGAAGTGC
28535112 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
28535138 AAAAGGGCTTATACCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28535164 AAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28535189 AAAAGGGCTT-TTCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28535209 ATTAAAGAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 30 0.48
26 33 0.52
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28542165 original size:26 final size:26
Alignment explanation
Indices: 28542097--28542167 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
28542087 CCTGTATAGT
*
28542097 TATGCTCACACAAGCTATGAAATGAC
1 TATGCTCACACAAGCTGTGAAATGAC
* **
28542123 TATGCTCACACGAGCTGTGAAATGGG
1 TATGCTCACACAAGCTGTGAAATGAC
* *
28542149 TCTGCTCACACTAGCTGTG
1 TATGCTCACACAAGCTGTG
28542168 GGTTGGAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (26 bp):
TATGCTCACACAAGCTGTGAAATGAC
Found at i:28548285 original size:173 final size:172
Alignment explanation
Indices: 28547988--28548344 Score: 635
Period size: 173 Copynumber: 2.1 Consensus size: 172
28547978 AGGTAATGTT
* *
28547988 TAATGAAA-GTATGTTTATGTTCATGAAATTGATGATTTCAACTGATTTGTTTATGTATATGACT
1 TAATGAAATATATGTTTATGTTCATGAAATTGATGATTTCAACTGATTTGTTCATGTATATGACT
* *
28548052 TATCTTATGTTATTTCAAGTGACTTATGAGTTGATGTTCTAACATGTGTTGTGGATGATGCTTAT
66 TATCTTATGTTATTTCAAGTGACTTATGAGTTGATGCTCTAACATGTCTTGTGGATGATGCTTAT
28548117 GCTTGTGCCAAACTTATGTTTGGATTATATAATGCTTAATCA
131 GCTTGTGCCAAACTTATGTTTGGATTATATAATGCTTAATCA
*
28548159 TATTGAAATATATGTTTATGTTCATGAAATTGATGATTTCAACTGATGTTGTTCATGTATATGAC
1 TAATGAAATATATGTTTATGTTCATGAAATTGATGATTTCAACTGAT-TTGTTCATGTATATGAC
* *
28548224 TTATCTTATGTTATTTTAAGTGATTTATGAGTTGATGCTCTAACATGTCTTGTGGATGATGCTTA
65 TTATCTTATGTTATTTCAAGTGACTTATGAGTTGATGCTCTAACATGTCTTGTGGATGATGCTTA
28548289 TGCTTGTGCCAAACTTATGTTTGGATTATATAATGCTTAATCA
130 TGCTTGTGCCAAACTTATGTTTGGATTATATAATGCTTAATCA
28548332 TAATGAAATATAT
1 TAATGAAATATAT
28548345 TGAAATGGTA
Statistics
Matches: 176, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
171 7 0.04
172 37 0.21
173 132 0.75
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (172 bp):
TAATGAAATATATGTTTATGTTCATGAAATTGATGATTTCAACTGATTTGTTCATGTATATGACT
TATCTTATGTTATTTCAAGTGACTTATGAGTTGATGCTCTAACATGTCTTGTGGATGATGCTTAT
GCTTGTGCCAAACTTATGTTTGGATTATATAATGCTTAATCA
Found at i:28555518 original size:16 final size:16
Alignment explanation
Indices: 28555492--28555534 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
28555482 GCATATCCCG
*
28555492 AAAAGCCGAAATGCCA
1 AAAAGCTGAAATGCCA
* *
28555508 AAAAGTTGAAATGTCA
1 AAAAGCTGAAATGCCA
28555524 AAAAGCTGAAA
1 AAAAGCTGAAA
28555535 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (16 bp):
AAAAGCTGAAATGCCA
Found at i:28555677 original size:18 final size:19
Alignment explanation
Indices: 28555641--28555677 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28555631 TGAATTGGCC
*
28555641 AAATGGGCCGGAGTGGGCT
1 AAATGGGCCCGAGTGGGCT
28555660 AAATGGGCCCGA-TGGGCT
1 AAATGGGCCCGAGTGGGCT
28555678 GTTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.19, G:0.43, T:0.16
Consensus pattern (19 bp):
AAATGGGCCCGAGTGGGCT
Found at i:28559696 original size:24 final size:24
Alignment explanation
Indices: 28559609--28559738 Score: 192
Period size: 24 Copynumber: 5.4 Consensus size: 24
28559599 TTGGAGGCCT
*
28559609 AGCCTCTTTTAATAAATGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
*
28559633 ATCCCTTTTTTAATAACTGGGGCATA
1 AGCCC--TTTTAATAACTGGGGCATA
28559659 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
28559682 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
28559706 AGCCTTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
28559730 AGCCCTTTT
1 AGCCCTTTT
28559739 GCACTTCCTC
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
23 24 0.25
24 52 0.54
25 16 0.16
26 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:28559810 original size:9 final size:9
Alignment explanation
Indices: 28559796--28559852 Score: 60
Period size: 9 Copynumber: 5.9 Consensus size: 9
28559786 ATCTCTTGTG
28559796 CATATCATA
1 CATATCATA
*
28559805 CATATCATGTG
1 CATATCA--TA
28559816 CATATCATA
1 CATATCATA
*
28559825 CATATCATGTG
1 CATATCA--TA
28559836 CATATCATA
1 CATATCATA
28559845 CATATCAT
1 CATATCAT
28559853 GTTTATCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 24 0.60
11 16 0.40
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:28559815 original size:20 final size:20
Alignment explanation
Indices: 28559792--28559854 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
28559782 GAACATCTCT
28559792 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
28559812 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
28559832 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
28559852 TGT
1 TGT
28559855 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:28559821 original size:11 final size:11
Alignment explanation
Indices: 28559792--28559843 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
28559782 GAACATCTCT
28559792 TGTGCATATCA
1 TGTGCATATCA
*
28559803 --TACATATCA
1 TGTGCATATCA
28559812 TGTGCATATCA
1 TGTGCATATCA
*
28559823 --TACATATCA
1 TGTGCATATCA
28559832 TGTGCATATCA
1 TGTGCATATCA
28559843 T
1 T
28559844 ACATATCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 16 0.48
11 17 0.52
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:28559920 original size:25 final size:25
Alignment explanation
Indices: 28559892--28559940 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28559882 TATATAAACC
28559892 CTAGGGGCAAAACGGTCATTTTTAA
1 CTAGGGGCAAAACGGTCATTTTTAA
28559917 CTAGGGGCAAAACGGTCATTTTTA
1 CTAGGGGCAAAACGGTCATTTTTA
28559941 TATTATAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (25 bp):
CTAGGGGCAAAACGGTCATTTTTAA
Found at i:28567914 original size:13 final size:13
Alignment explanation
Indices: 28567896--28567920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28567886 TACGTTGGCA
28567896 TCGATATGTGATT
1 TCGATATGTGATT
28567909 TCGATATGTGAT
1 TCGATATGTGAT
28567921 GTGCGATTAA
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:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (13 bp):
TCGATATGTGATT
Found at i:28567942 original size:45 final size:44
Alignment explanation
Indices: 28567891--28567975 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
28567881 TTTAATACGT
* * * *
28567891 TGGCATCGATATGTGATTTCGATATGTGATGTGCGATTAAGACCA
1 TGGCATCGATATGTGACTTCAATATATG-TGTGCGAGTAAGACCA
28567936 TGGCATCGATATGTGACTTCAATATATGTGTGCGAGTAAG
1 TGGCATCGATATGTGACTTCAATATATGTGTGCGAGTAAG
28567976 TCCACGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 11 0.31
45 25 0.69
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (44 bp):
TGGCATCGATATGTGACTTCAATATATGTGTGCGAGTAAGACCA
Found at i:28567990 original size:101 final size:101
Alignment explanation
Indices: 28567811--28568030 Score: 302
Period size: 101 Copynumber: 2.2 Consensus size: 101
28567801 GTGAATTACA
* * *
28567811 ATATGTGATGTGCGAGTAAGACCATAGCATTGATGTGCGATTCTTATATATGTGCGCGAGTAAGA
1 ATATGTGATGTGCGAGTAAGACCATAGCATCGATATGCGATTCTAATATATGTGCGCGAGTAAGA
28567876 CCACGTTTAATACGTTGGCATCGATATGTGATTTCG
66 CCACGTTTAATACGTTGGCATCGATATGTGATTTCG
* * * *
28567912 ATATGTGATGTGCGATTAAGACCATGGCATCGATATGTGACTTC-AATATATGTGTGCGAGTAAG
1 ATATGTGATGTGCGAGTAAGACCATAGCATCGATATGCGA-TTCTAATATATGTGCGCGAGTAAG
* *
28567976 TCCACGTTTTATACGTTGGCATCGATATGTGA-TTCTG
65 ACCACGTTTAATACGTTGGCATCGATATGTGATTTC-G
* *
28568013 ATATATG-TGTGTGAGTAA
1 ATATGTGATGTGCGAGTAA
28568031 AACCCTATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
100 12 0.11
101 90 0.86
102 3 0.03
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (101 bp):
ATATGTGATGTGCGAGTAAGACCATAGCATCGATATGCGATTCTAATATATGTGCGCGAGTAAGA
CCACGTTTAATACGTTGGCATCGATATGTGATTTCG
Found at i:28571251 original size:16 final size:16
Alignment explanation
Indices: 28571232--28571266 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28571222 GCAAAAGCTG
*
28571232 AAATGCCGAAAAGCCA
1 AAATGCCAAAAAGCCA
*
28571248 AAATGCTAAAAAGCCA
1 AAATGCCAAAAAGCCA
28571264 AAA
1 AAA
28571267 GTGTGGCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATGCCAAAAAGCCA
Found at i:28571531 original size:28 final size:29
Alignment explanation
Indices: 28571477--28571537 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
28571467 GAAAGCATGT
*
28571477 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGAGATTTGGGCCTAATGGGCC
*
28571506 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGAGATTTGGGCCTAATGGGCC
28571534 ATAT
1 ATAT
28571538 ACATGTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (29 bp):
ATATGAATGAGATTTGGGCCTAATGGGCC
Found at i:28576616 original size:43 final size:43
Alignment explanation
Indices: 28576555--28576636 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
28576545 ACATATCAAT
*
28576555 TCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACGAAGCCTGCTAGGCACAAAGGCCCGAATACACA
28576598 TCACCGGCACGAAGCCTGCTAGGCACAAAGGCCCGAATA
1 TCACCGGCACGAAGCCTGCTAGGCACAAAGGCCCGAATA
28576637 TAATACCAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.34, G:0.26, T:0.10
Consensus pattern (43 bp):
TCACCGGCACGAAGCCTGCTAGGCACAAAGGCCCGAATACACA
Found at i:28576696 original size:38 final size:38
Alignment explanation
Indices: 28576629--28576712 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
28576619 GGCACAAAGG
* * * *
28576629 CCCGAATATAATACCAGCACTAGGGCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
28576667 CCCGGATATAATACCAGTACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
28576705 CCCGAATA
1 CCCGAATA
28576713 CACATCAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:28579975 original size:12 final size:12
Alignment explanation
Indices: 28579958--28579985 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28579948 CATACACGCC
28579958 CGTGTGCTAGGT
1 CGTGTGCTAGGT
28579970 CGTGTGCTAGGT
1 CGTGTGCTAGGT
28579982 CGTG
1 CGTG
28579986 ACAAACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.18, G:0.43, T:0.32
Consensus pattern (12 bp):
CGTGTGCTAGGT
Found at i:28588645 original size:19 final size:19
Alignment explanation
Indices: 28588621--28588662 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28588611 TGAAAATGTG
*
28588621 TATGTTATGTCTACAAATT
1 TATGTTATGCCTACAAATT
**
28588640 TATGTTATGCCTATGAATT
1 TATGTTATGCCTACAAATT
28588659 TATG
1 TATG
28588663 ATAACACATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (19 bp):
TATGTTATGCCTACAAATT
Found at i:28596497 original size:85 final size:85
Alignment explanation
Indices: 28596351--28596529 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
28596341 GGCCGGCCAT
28596351 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
28596416 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
28596436 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
28596501 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
28596521 GAGCATGGG
1 GAGCATGGG
28596530 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:28612493 original size:39 final size:40
Alignment explanation
Indices: 28612279--28612501 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
28612269 TTGAATGCTG
* * * * * *
28612279 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
28612319 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
28612359 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* **
28612399 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
28612439 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
28612478 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28612502 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 34 0.21
40 117 0.74
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:28612521 original size:79 final size:80
Alignment explanation
Indices: 28612354--28612536 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
28612344 GTGCGAGATA
* * *
28612354 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
28612419 CATTCGTGCAAGTTG
66 CATTCGAACAAGGAG
* * * *
28612434 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
28612498 CATTTGAACGAGGAG
66 CATTCGAACAAGGAG
* *
28612513 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
28612537 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACAAGGAG
Found at i:28614115 original size:74 final size:74
Alignment explanation
Indices: 28613994--28614140 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 74
28613984 TAGACCATCT
*
28613994 AGAAACACGGGAAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTGCGACCAGATCTGAGGC
1 AGAAACACGGGAAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTGCAACCAGATCTGAGGC
28614059 TCGTGCTCC
66 TCGTGCTCC
28614068 AGAAACACGGGAAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTGCAACCAGATCTGAGGC
1 AGAAACACGGGAAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTGCAACCAGATCTGAGGC
28614133 TCGTGCTC
66 TCGTGCTC
28614141 TTGCTAGGGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.19
Consensus pattern (74 bp):
AGAAACACGGGAAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTGCAACCAGATCTGAGGC
TCGTGCTCC
Found at i:28629925 original size:130 final size:130
Alignment explanation
Indices: 28629691--28629926 Score: 436
Period size: 130 Copynumber: 1.8 Consensus size: 130
28629681 TTCTAACACC
*
28629691 GTCTCACACAACTTTAAATATCTCATTATCGGAAATTCCTTTGCTTACACGGTTTCTTTTATAAG
1 GTCTCACACAACTTTAAATATCTCATTATCGGAAATTCCTTTGCTTACACGGTTCCTTTTATAAG
* *
28629756 AAACTAGACTCATTAAGCTTTAATTTCATGTCTCCTTCAGCAGGATTACAGTGTCATTCTGCGCT
66 AAACTAGACTCATTAAGATTTAATTTCATGTCTCATTCAGCAGGATTACAGTGTCATTCTGCGCT
*
28629821 GTCTCACACAACTTTAAGTATCTCATTATCGGAAATTCCTTTGCTTACACGGTTCCTTTTATAAG
1 GTCTCACACAACTTTAAATATCTCATTATCGGAAATTCCTTTGCTTACACGGTTCCTTTTATAAG
28629886 AAACTAGACTCATTAAGATTTAATTTCATGTCTCATTCAGC
66 AAACTAGACTCATTAAGATTTAATTTCATGTCTCATTCAGC
28629927 CTCTAATTCA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 102 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (130 bp):
GTCTCACACAACTTTAAATATCTCATTATCGGAAATTCCTTTGCTTACACGGTTCCTTTTATAAG
AAACTAGACTCATTAAGATTTAATTTCATGTCTCATTCAGCAGGATTACAGTGTCATTCTGCGCT
Found at i:28632944 original size:40 final size:40
Alignment explanation
Indices: 28632850--28633030 Score: 188
Period size: 40 Copynumber: 4.5 Consensus size: 40
28632840 TACTCGAATG
* *
28632850 ATATCCAGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACT
* * *
28632891 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGACT
* *
28632931 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * * **
28632971 ATATCCGGGTTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
**
28633010 ATATCC-GGCTAAACCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
28633031 ATGCTTGATT
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
38 12 0.10
39 16 0.14
40 61 0.52
41 27 0.23
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:28636387 original size:33 final size:33
Alignment explanation
Indices: 28636350--28636414 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
28636340 ACATGTTCCA
* *
28636350 GAAGTGTTTTTTCTATCTAACTTGGATCCTCCG
1 GAAGTGCTTTTTCTATCTAACTTGCATCCTCCG
28636383 GAAGTGCTTTTTCTATCTAACTTGCATCCTCC
1 GAAGTGCTTTTTCTATCTAACTTGCATCCTCC
28636415 AAAATCCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (33 bp):
GAAGTGCTTTTTCTATCTAACTTGCATCCTCCG
Found at i:28639821 original size:43 final size:42
Alignment explanation
Indices: 28639735--28639853 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 42
28639725 CATAGGATTT
* * ** *
28639735 TCGATATGTGTTCTCATGTAAGACCATGTCTAGGATGTTGGCA
1 TCGATATGTGAT-TCATGTAAGACCATGTCTGGGACATCGGCA
28639778 TCGATATGTGATTACATGTAAGACCATGTCTGGGACATCGGCA
1 TCGATATGTGATT-CATGTAAGACCATGTCTGGGACATCGGCA
* * *
28639821 TCG-TATTTGATTCGTGTAAGACCCTGTCTGGGA
1 TCGATATGTGATTCATGTAAGACCATGTCTGGGA
28639854 TAGTTATGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 19 0.28
42 9 0.13
43 39 0.58
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (42 bp):
TCGATATGTGATTCATGTAAGACCATGTCTGGGACATCGGCA
Found at i:28643371 original size:39 final size:40
Alignment explanation
Indices: 28643274--28643371 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
28643264 CGGATGATAA
* * *
28643274 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTACTATAT
28643314 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTA-CTATAT
*
28643354 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28643372 TACTTGGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 17 0.32
40 36 0.68
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTACTATAT
Found at i:28650429 original size:21 final size:22
Alignment explanation
Indices: 28650389--28650432 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28650379 ATGCAACCCA
* *
28650389 TCCCATAACCATCCAGCACACC
1 TCCCATAACCAACCAACACACC
28650411 TCCCAT-ACCAACCAACACACC
1 TCCCATAACCAACCAACACACC
28650432 T
1 T
28650433 GTGGGGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.50, G:0.02, T:0.14
Consensus pattern (22 bp):
TCCCATAACCAACCAACACACC
Found at i:28650640 original size:20 final size:20
Alignment explanation
Indices: 28650615--28650657 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28650605 ACGTGTATGT
28650615 AGTATGTCATACTCATAACC
1 AGTATGTCATACTCATAACC
28650635 AGTATGTCATACTCATAACC
1 AGTATGTCATACTCATAACC
28650655 AGT
1 AGT
28650658 CATATAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTATGTCATACTCATAACC
Found at i:28654258 original size:22 final size:22
Alignment explanation
Indices: 28654233--28654303 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
28654223 GTTCTAGGGT
28654233 CACACGAGCATGTCCCTTGGAC
1 CACACGAGCATGTCCCTTGGAC
* * ** *
28654255 CACACGGGCATGTTCCAAGG-T
1 CACACGAGCATGTCCCTTGGAC
*
28654276 CACACGAGCGTGTCCCTTGGAC
1 CACACGAGCATGTCCCTTGGAC
28654298 CACACG
1 CACACG
28654304 GGTGTGTGAG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 15 0.41
22 22 0.59
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (22 bp):
CACACGAGCATGTCCCTTGGAC
Found at i:28658126 original size:54 final size:54
Alignment explanation
Indices: 28658043--28658171 Score: 179
Period size: 54 Copynumber: 2.4 Consensus size: 54
28658033 CCCCAGATTT
* *
28658043 TAAAATTACCGAAATACCCCTGGTTTGTAAAATTACAAAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTGGTGTGTAAAATTACAAAAATACCCTTATAGTG
* ***
28658097 TAAAATTATCGAAATACCCCT-GTAGTGTAAAATTATTGAAATACCCTTATAGTG
1 TAAAATTACCGAAATACCCCTGGT-GTGTAAAATTACAAAAATACCCTTATAGTG
*
28658151 TAAAATTACCAAAATACCCCT
1 TAAAATTACCGAAATACCCCT
28658172 ATAGGGAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
53 2 0.03
54 64 0.97
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCCTGGTGTGTAAAATTACAAAAATACCCTTATAGTG
Found at i:28658175 original size:27 final size:27
Alignment explanation
Indices: 28658043--28658171 Score: 152
Period size: 27 Copynumber: 4.8 Consensus size: 27
28658033 CCCCAGATTT
*
28658043 TAAAATTACCGAAATACCCCTGGT-TTG
1 TAAAATTACCGAAATACCCCT-GTAGTG
** *
28658070 TAAAATTACAAAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTGTAGTG
*
28658097 TAAAATTATCGAAATACCCCTGTAGTG
1 TAAAATTACCGAAATACCCCTGTAGTG
** * *
28658124 TAAAATTATTGAAATACCCTTATAGTG
1 TAAAATTACCGAAATACCCCTGTAGTG
*
28658151 TAAAATTACCAAAATACCCCT
1 TAAAATTACCGAAATACCCCT
28658172 ATAGGGAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 2 0.02
27 84 0.98
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTGTAGTG
Found at i:28658183 original size:54 final size:54
Alignment explanation
Indices: 28658081--28658183 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
28658071 AAAATTACAA
* * * * * *
28658081 AAATACCCTTGTAGTGTAAAATTATCGAAATACCCCTGTAGTGTAAAATTATTG
1 AAATACCCTTATAGTGTAAAATTACCAAAATACCCCTATAGGGAAAAATTATTG
28658135 AAATACCCTTATAGTGTAAAATTACCAAAATACCCCTATAGGGAAAAAT
1 AAATACCCTTATAGTGTAAAATTACCAAAATACCCCTATAGGGAAAAAT
28658184 GACTATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.29
Consensus pattern (54 bp):
AAATACCCTTATAGTGTAAAATTACCAAAATACCCCTATAGGGAAAAATTATTG
Found at i:28658631 original size:27 final size:28
Alignment explanation
Indices: 28658601--28658661 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
28658591 GTGCCAATTG
*
28658601 TATTTACATG-TGGCTCTGTGTTGATCA
1 TATTTACATGATGACTCTGTGTTGATCA
*
28658628 TATTTA-TTGATGACTCTGTGTTGATCA
1 TATTTACATGATGACTCTGTGTTGATCA
28658655 TATTTAC
1 TATTTAC
28658662 CCATGGCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (28 bp):
TATTTACATGATGACTCTGTGTTGATCA
Found at i:28658674 original size:27 final size:27
Alignment explanation
Indices: 28658611--28658674 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
28658601 TATTTACATG
***
28658611 TGGCTCTGTGTTGATCATATTTATTGA
1 TGGCTCTGTGTTGATCATATTTACCCA
*
28658638 TGACTCTGTGTTGATCATATTTACCCA
1 TGGCTCTGTGTTGATCATATTTACCCA
*
28658665 TGGCTGTGTG
1 TGGCTCTGTG
28658675 CCGATTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (27 bp):
TGGCTCTGTGTTGATCATATTTACCCA
Found at i:28665670 original size:15 final size:15
Alignment explanation
Indices: 28665650--28665701 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28665640 AATACAAAAC
28665650 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28665665 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
28665684 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
28665699 ATT
1 ATT
28665702 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Done.