Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 87 of 153
Found at i:27472540 original size:76 final size:80
Alignment explanation
Indices: 27472400--27472556 Score: 198
Period size: 78 Copynumber: 2.0 Consensus size: 80
27472390 AAACTCGAAC
* * *
27472400 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTAGGCTTGCGGG
1 ATAACACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTAAGCCTGCGGG
27472465 -ATTTAA-CCCGGAT
66 TATTTAAGCCCGGAT
* * * *
27472478 ATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGATATAATTCCAGCA-TATAGCCTGCGG
1 ATAACACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTA-AGCCTGCGG
*
27472540 GTCTTTAAGCCCGGAT
65 GTATTTAAGCCCGGAT
27472556 A
1 A
27472557 CACATCAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
75 2 0.03
76 26 0.38
77 8 0.12
78 32 0.47
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (80 bp):
ATAACACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTAAGCCTGCGGG
TATTTAAGCCCGGAT
Found at i:27480213 original size:200 final size:200
Alignment explanation
Indices: 27479870--27480272 Score: 797
Period size: 200 Copynumber: 2.0 Consensus size: 200
27479860 TTAGATCAAG
27479870 AAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAGATTGTGGACTAAATTGCAAAATCTTTG
1 AAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAGATTGTGGACTAAATTGCAAAATCTTTG
27479935 TATTTTGGTACCAAGGTAAGTTCATGTGTAAATAATGTATCATAATGGTTATTTTTAAGTTATTG
66 TATTTTGGTACCAAGGTAAGTTCATGTGTAAATAATGTATCATAATGGTTATTTTTAAGTTATTG
27480000 ATGTTAATTATATGTTATGCTAAATTTTATTATGAAATGTATGCTTTGTGGTTAATTTCAAATAA
131 ATGTTAATTATATGTTATGCTAAATTTTATTATGAAATGTATGCTTTGTGGTTAATTTCAAATAA
27480065 TATGT
196 TATGT
27480070 AAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAGATTGTGGACTAAATTGCAAAATCTTTG
1 AAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAGATTGTGGACTAAATTGCAAAATCTTTG
27480135 TATTTTGGTACCAAGGTAAGTTCATGTGTAAATAATGTATCATAATGGTTATTTTTAAGTTATTG
66 TATTTTGGTACCAAGGTAAGTTCATGTGTAAATAATGTATCATAATGGTTATTTTTAAGTTATTG
*
27480200 ATGTTAATTATATGTTATGCTGAATTTTATTATGAAATGTATGCTTTGTGGTTAATTTCAAATAA
131 ATGTTAATTATATGTTATGCTAAATTTTATTATGAAATGTATGCTTTGTGGTTAATTTCAAATAA
27480265 TATGT
196 TATGT
27480270 AAA
1 AAA
27480273 TTATGTGAAC
Statistics
Matches: 202, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 202 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (200 bp):
AAAGACGTGGAATCGACCTCAATCGAGGAAAAGAAAAGATTGTGGACTAAATTGCAAAATCTTTG
TATTTTGGTACCAAGGTAAGTTCATGTGTAAATAATGTATCATAATGGTTATTTTTAAGTTATTG
ATGTTAATTATATGTTATGCTAAATTTTATTATGAAATGTATGCTTTGTGGTTAATTTCAAATAA
TATGT
Found at i:27480475 original size:46 final size:46
Alignment explanation
Indices: 27480425--27480600 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
27480415 TGATTGAGCA
27480425 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27480471 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
27480516 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
27480564 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27480601 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27480581 original size:93 final size:93
Alignment explanation
Indices: 27480422--27480593 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
27480412 GGATGATTGA
*
27480422 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
27480487 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
27480515 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
27480579 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
27480594 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27484308 original size:44 final size:42
Alignment explanation
Indices: 27484229--27484340 Score: 109
Period size: 44 Copynumber: 2.6 Consensus size: 42
27484219 ATGACATAGG
* * * * *
27484229 ATTTCGTGTAAGACCATATTTGGGACGTTCGCATCGATTTCTG
1 ATTTCGTGTAAGACCATATCTAGGACGATCGCATCG-TATCTA
* *
27484272 TTTTACGTGTAAGACCATGTCTAGGAC-ATCGACATCGTATCTA
1 ATTT-CGTGTAAGACCATATCTAGGACGATCG-CATCGTATCTA
* *
27484315 ATTTCGTGTAAGACCCTATCTGGGAC
1 ATTTCGTGTAAGACCATATCTAGGAC
27484341 AGTGGCATCG
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 19 0.34
43 13 0.23
44 24 0.43
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
ATTTCGTGTAAGACCATATCTAGGACGATCGCATCGTATCTA
Found at i:27484341 original size:42 final size:42
Alignment explanation
Indices: 27484229--27484352 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
27484219 ATGACATAGG
* * * *
27484229 ATTTCGTGTAAGACCATATTTGGGACGTTCGCATCGATTTCTG
1 ATTTCGTGTAAGACCATATCTGGGAC-ATCGCATCGATATCTA
* * *
27484272 TTTTACGTGTAAGACCATGTCTAGGACATCGACATCG-TATCTA
1 ATTT-CGTGTAAGACCATATCTGGGACATCG-CATCGATATCTA
* *
27484315 ATTTCGTGTAAGACCCTATCTGGGACAGTGGCATCGAT
1 ATTTCGTGTAAGACCATATCTGGGACA-TCGCATCGAT
27484353 GTTTGATTAC
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
42 25 0.38
43 16 0.25
44 24 0.37
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
ATTTCGTGTAAGACCATATCTGGGACATCGCATCGATATCTA
Found at i:27485656 original size:22 final size:22
Alignment explanation
Indices: 27485622--27485694 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
27485612 GACTCACCAT
* * *
27485622 AGCTCGTATGAGCTTCCTGTTC
1 AGCTCGAAAGAGCTTCCCGTTC
*
27485644 AGCTCGAAAGAGCTTCCCGTTT
1 AGCTCGAAAGAGCTTCCCGTTC
27485666 AGCTC-AATAGAGCTTCCCGGTTTC
1 AGCTCGAA-AGAGCTTCCC-G-TTC
27485690 AGCTC
1 AGCTC
27485695 AATCGAGCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 2 0.05
22 33 0.77
23 1 0.02
24 7 0.16
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (22 bp):
AGCTCGAAAGAGCTTCCCGTTC
Found at i:27485702 original size:24 final size:22
Alignment explanation
Indices: 27485631--27485703 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
27485621 TAGCTCGTAT
* *
27485631 GAGCTTCCTGTTCAGCTCGAA-A
1 GAGCTTCCCGTTTAGCTC-AATA
27485653 GAGCTTCCCGTTTAGCTCAATA
1 GAGCTTCCCGTTTAGCTCAATA
*
27485675 GAGCTTCCCGGTTTCAGCTCAATC
1 GAGCTTCCC-GTTT-AGCTCAATA
27485699 GAGCT
1 GAGCT
27485704 CACTGTTATC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
21 2 0.04
22 26 0.58
23 4 0.09
24 13 0.29
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (22 bp):
GAGCTTCCCGTTTAGCTCAATA
Found at i:27488080 original size:79 final size:78
Alignment explanation
Indices: 27487978--27488200 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
27487968 GCTCCTCGTT
* *
27487978 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
27488043 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
27488058 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
27488122 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
27488136 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
27488199 GA
63 GA
27488201 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:27488095 original size:39 final size:40
Alignment explanation
Indices: 27487978--27488200 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
27487968 GCTCCTCGTT
* *
27487978 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
27488018 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
27488058 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
27488097 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
27488136 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
27488177 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27488201 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:27504779 original size:126 final size:126
Alignment explanation
Indices: 27504544--27504803 Score: 355
Period size: 126 Copynumber: 2.1 Consensus size: 126
27504534 CTTTTGGGCT
* *
27504544 GACACTTTCCGAAGTGTTGGGATAGACTTGTCGACATACACTTTGGCCAACTCTTTGTATTAAGG
1 GACACTTTCCGAAGTGTTAGGATAGACTTGTCGACATACACTTTGGCCAACTATTTGTATTAAGG
* *
27504609 TTGGGATAGGTATGCCTAAGGCAACACTTAAATAAGAGTTGGTTTTGTCCAGTACTATGCC
66 TTGGGATAGGCATGCCTAAGGCAACACTTAAATAAGAGTCGGTTTTGTCCAGTACTATGCC
* * *
27504670 GACATTTTCCTAAGTGTTAGGATAGACTTG-CTGACATATGA-TTTGGCCAACTATTTGTA-TAT
1 GACACTTTCCGAAGTGTTAGGATAGACTTGTC-GACATA-CACTTTGGCCAACTATTTGTATTA-
* * ** * *
27504732 GGGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGTTTTGTCCAACACTATACT
63 AGGTTGGGATAGGCATGCCTAAGGCAACACTTAAATAAGAGTCGGTTTTGTCCAGTACTATGCC
27504796 GACACTTT
1 GACACTTT
27504804 TGGGCTGACA
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
125 3 0.03
126 113 0.97
127 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (126 bp):
GACACTTTCCGAAGTGTTAGGATAGACTTGTCGACATACACTTTGGCCAACTATTTGTATTAAGG
TTGGGATAGGCATGCCTAAGGCAACACTTAAATAAGAGTCGGTTTTGTCCAGTACTATGCC
Found at i:27507559 original size:15 final size:15
Alignment explanation
Indices: 27507539--27507569 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27507529 TGTAGCTCTG
27507539 ATACCATTAAATGTA
1 ATACCATTAAATGTA
27507554 ATACCATTAAATGTA
1 ATACCATTAAATGTA
27507569 A
1 A
27507570 CACCTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
ATACCATTAAATGTA
Found at i:27510310 original size:40 final size:38
Alignment explanation
Indices: 27510256--27510378 Score: 104
Period size: 40 Copynumber: 3.1 Consensus size: 38
27510246 CGTTTGAATT
* *
27510256 AAAAATGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-TTTT-C
* * * * *
27510296 AAAAACGCCGCTAAAGATCGAGCATTAGTGGCAAATTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGC--GTTTTC
* * *
27510336 GAAAACACCGCCAAAAAT-AAGCATTAGCGGCGTTTTCC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTT-C
27510374 AAAAA
1 AAAAA
27510379 GCACCACTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
37 4 0.06
38 4 0.06
39 11 0.17
40 41 0.64
41 4 0.06
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTC
Found at i:27518481 original size:43 final size:43
Alignment explanation
Indices: 27518416--27518560 Score: 127
Period size: 44 Copynumber: 3.3 Consensus size: 43
27518406 AAGTTATGTT
* * *
27518416 TTTAGCGGTGTTTCTGT-GAGAAGCGCCGCTAAAGGTTTGATC
1 TTTAGCGGCGTTTGTATAGAGAAGCGCCGCTAAAGGTTTGATC
* * *
27518458 TATAGCGGCGTTT-T-TGACGAGAAGCACCGCTAAA-GTTCATGGTC
1 TTTAGCGGCGTTTGTAT-A-GAGAAGCGCCGCTAAAGGTT--TGATC
* * * *
27518502 TTTAGCGGCGTTTGTATAAAAAAGCGCCGCAAAAGGTCTTGTTC
1 TTTAGCGGCGTTTGTATAGAGAAGCGCCGCTAAAGGT-TTGATC
27518546 TTTAGCGGCGTTTGT
1 TTTAGCGGCGTTTGT
27518561 TTCTAAAAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 14 0.17
43 15 0.18
44 47 0.56
45 4 0.05
46 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTATAGAGAAGCGCCGCTAAAGGTTTGATC
Found at i:27518684 original size:22 final size:22
Alignment explanation
Indices: 27518652--27518695 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27518642 TAGCGGTGCT
*
27518652 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
27518674 AAAAAGTGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
27518696 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:27531033 original size:40 final size:40
Alignment explanation
Indices: 27530983--27531195 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
27530973 AAGAAAATGT
* * *
27530983 CCCTAAATGCACATGCGTGCCCCTGATTGTACTTCGGTAC
1 CCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * *
27531023 CCCTGAATGCACATATG-GGCCCTTTTTGTACTTCGGTAC
1 CCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * * *
27531062 CTCTGAATGTACATATGTGCCCCTGTTTGTACTTTGATAC
1 CCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* *
27531102 CCCTGAATGCACATACGTGCCCCTTTTTGTACTTGGGTAC
1 CCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * *
27531142 CCCTGAATGCACATACATGCCCCTATTTGTACTTCAGTTC
1 CCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* *
27531182 CCTTGAAGGCACAT
1 CCCTGAATGCACAT
27531196 TTGTGCTCTA
Statistics
Matches: 147, Mismatches: 25, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
39 34 0.23
40 113 0.77
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.32
Consensus pattern (40 bp):
CCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTAC
Found at i:27531092 original size:20 final size:20
Alignment explanation
Indices: 27531069--27531133 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
27531059 TACCTCTGAA
27531069 TGTACATATGTGCCCCTGTT
1 TGTACATATGTGCCCCTGTT
* * **
27531089 TGTAC-TTTGATACCCCTGAA
1 TGTACATATG-TGCCCCTGTT
* * *
27531109 TGCACATACGTGCCCCTTTT
1 TGTACATATGTGCCCCTGTT
27531129 TGTAC
1 TGTAC
27531134 TTGGGTACCC
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.84
21 2 0.06
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTACATATGTGCCCCTGTT
Found at i:27531215 original size:119 final size:119
Alignment explanation
Indices: 27530983--27531221 Score: 268
Period size: 119 Copynumber: 2.0 Consensus size: 119
27530973 AAGAAAATGT
* * *
27530983 CCCTAAATGCACATGCGTGCCCCTGATTGTACTTCGGTACCCCTGAATGCACATATGGGCCCTTT
1 CCCTAAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCCTGAATGCACATATGGCCCCTAT
* * *** * *
27531048 TTGTACTTCGGTACCTCTGAATGTACATATGTGCCCCTGTTTGTACTTTGATAC
66 TTGTACTTCGGTACCTCTGAAGGCACATATGTGCCCCTAAATGCACTTTAATAC
* ** *
27531102 CCCTGAATGCACATACGTGCCCCTTTTTGTACTTGGGTACCCCTGAATGCACATACAT-GCCCCT
1 CCCTAAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCCTGAATGCACAT--ATGGCCCCT
* * * *
27531166 ATTTGTACTTCAGTTCC-CTTGAAGGCACATTTGTG-CTCTAAATGCACTTTAATAC
64 ATTTGTACTTCGGTACCTC-TGAAGGCACATATGTGCCCCTAAATGCACTTTAATAC
27531221 C
1 C
27531222 TCGGTATTGC
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
119 65 0.66
120 32 0.32
121 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (119 bp):
CCCTAAATGCACATACGTGCCCCTGATTGTACTTCGGTACCCCTGAATGCACATATGGCCCCTAT
TTGTACTTCGGTACCTCTGAAGGCACATATGTGCCCCTAAATGCACTTTAATAC
Found at i:27533729 original size:56 final size:56
Alignment explanation
Indices: 27533659--27533776 Score: 139
Period size: 56 Copynumber: 2.1 Consensus size: 56
27533649 TCTATGCCTG
* * * * *
27533659 TGTGGGTATACTGACTTGGGACACAC-GATCAAACCACACGCCCGTGTGCTAGGCCA
1 TGTGAGTATACTGACTTAGGACACACAG-CCAAACCACACACCCGTATGCTAGGCCA
* * * *
27533715 TGTGAGTATACTGACTTAGGTCACACAGCCAAACTACACATCCGTATGCTAGGCCG
1 TGTGAGTATACTGACTTAGGACACACAGCCAAACCACACACCCGTATGCTAGGCCA
27533771 TGTGAG
1 TGTGAG
27533777 CTATTTGAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 51 0.98
57 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.22
Consensus pattern (56 bp):
TGTGAGTATACTGACTTAGGACACACAGCCAAACCACACACCCGTATGCTAGGCCA
Found at i:27534813 original size:25 final size:25
Alignment explanation
Indices: 27534763--27534856 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
27534753 ATTCATATAT
*
27534763 GCTCATACGAGCTGTA-AACGGGAA
1 GCTCATACGAGCTGAATAACGGGAA
* *
27534787 GCTCCTCCGAGCTGAATAACGGGAA
1 GCTCATACGAGCTGAATAACGGGAA
* * *
27534812 GCTCATAAGAGCTGAATATCGAGAA
1 GCTCATACGAGCTGAATAACGGGAA
* *
27534837 GCTCATGCGAGCTGTATAAC
1 GCTCATACGAGCTGAATAAC
27534857 AGACTGCTCG
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
24 13 0.23
25 44 0.77
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGGAA
Found at i:27534916 original size:25 final size:24
Alignment explanation
Indices: 27534809--27534926 Score: 94
Period size: 25 Copynumber: 4.8 Consensus size: 24
27534799 TGAATAACGG
* * *
27534809 GAAGCTCATAAGAGCTGAATATCGA
1 GAAGCTCATAAGAGTTGTATAAC-A
** *
27534834 GAAGCTCATGCGAGCTGTATAACA
1 GAAGCTCATAAGAGTTGTATAACA
* *
27534858 GACTGCTCGTAAGAGTTGTATAACA
1 GA-AGCTCATAAGAGTTGTATAACA
*
27534883 GGAAACTCATAAGAGTTGTA-AATCGA
1 -GAAGCTCATAAGAGTTGTATAA-C-A
*
27534909 GAAGCTCATAAGACTTGT
1 GAAGCTCATAAGAGTTGT
27534927 GGTGTGTCCG
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
24 5 0.07
25 67 0.89
26 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (24 bp):
GAAGCTCATAAGAGTTGTATAACA
Found at i:27536830 original size:5 final size:5
Alignment explanation
Indices: 27536815--27536848 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
27536805 AAGATTTGGC
27536815 TATAA -ATAA TATAA TATAA TATAA TATAA T-TAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
27536849 TATTGTACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:27536960 original size:31 final size:30
Alignment explanation
Indices: 27536925--27536984 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 30
27536915 CAGTTAGATG
27536925 CTACAACCCTTTAAGAAAACACATAAAATTC
1 CTACAACCCTTTAAGAAAACACA-AAAATTC
27536956 CTACAACCCTTTAAGAAAACACAAAAATT
1 CTACAACCCTTTAAGAAAACACAAAAATT
27536985 TTATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.22
Consensus pattern (30 bp):
CTACAACCCTTTAAGAAAACACAAAAATTC
Found at i:27537667 original size:170 final size:170
Alignment explanation
Indices: 27537385--27537724 Score: 680
Period size: 170 Copynumber: 2.0 Consensus size: 170
27537375 GGTTGTAAAA
27537385 AAGCCTATTTATACGACAAATTAATAGGTTAAATAATAAGAAAATCTAGACTAATCAGAGTTTGA
1 AAGCCTATTTATACGACAAATTAATAGGTTAAATAATAAGAAAATCTAGACTAATCAGAGTTTGA
27537450 TTGAAACAAATAAACAGAGTTTAACTAGAAGGTTATTTCTCAAATTTGAATGAAATAGGAGTCAT
66 TTGAAACAAATAAACAGAGTTTAACTAGAAGGTTATTTCTCAAATTTGAATGAAATAGGAGTCAT
27537515 ACTTAACAAATCTCCACCTTGACTCATATTTCCACAACGC
131 ACTTAACAAATCTCCACCTTGACTCATATTTCCACAACGC
27537555 AAGCCTATTTATACGACAAATTAATAGGTTAAATAATAAGAAAATCTAGACTAATCAGAGTTTGA
1 AAGCCTATTTATACGACAAATTAATAGGTTAAATAATAAGAAAATCTAGACTAATCAGAGTTTGA
27537620 TTGAAACAAATAAACAGAGTTTAACTAGAAGGTTATTTCTCAAATTTGAATGAAATAGGAGTCAT
66 TTGAAACAAATAAACAGAGTTTAACTAGAAGGTTATTTCTCAAATTTGAATGAAATAGGAGTCAT
27537685 ACTTAACAAATCTCCACCTTGACTCATATTTCCACAACGC
131 ACTTAACAAATCTCCACCTTGACTCATATTTCCACAACGC
27537725 CATCTTTGCT
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (170 bp):
AAGCCTATTTATACGACAAATTAATAGGTTAAATAATAAGAAAATCTAGACTAATCAGAGTTTGA
TTGAAACAAATAAACAGAGTTTAACTAGAAGGTTATTTCTCAAATTTGAATGAAATAGGAGTCAT
ACTTAACAAATCTCCACCTTGACTCATATTTCCACAACGC
Found at i:27547030 original size:19 final size:20
Alignment explanation
Indices: 27546986--27547130 Score: 68
Period size: 21 Copynumber: 6.8 Consensus size: 20
27546976 ACAAAACTAG
27546986 AAAATAATTCAAAATAATTTT
1 AAAA-AATTCAAAATAATTTT
27547007 AAAAAATTCAAAAT-A-TTT
1 AAAAAATTCAAAATAATTTT
27547025 ATAAAAATTCCAAAAATTCATAATTTT
1 A-AAAAATT-C--AAA---ATAATTTT
* *
27547052 AAAAAAAT--AAA-AATTCT
1 AAAAAATTCAAAATAATTTT
* *
27547069 AAGAAAATTTAAAA-AATATAT
1 AA-AAAATTCAAAATAAT-TTT
* *
27547090 AGGAAAAAGTTAAAAATATTTTT
1 A--AAAAA-TTCAAAATAATTTT
27547113 AAAAAAATTCAAAATAAT
1 -AAAAAATTCAAAATAAT
27547131 AATTTTGAGG
Statistics
Matches: 97, Mismatches: 9, Indels: 36
0.68 0.06 0.25
Matches are distributed among these distances:
17 7 0.07
18 10 0.10
19 8 0.08
20 17 0.18
21 18 0.19
22 12 0.12
23 9 0.09
24 3 0.03
25 2 0.02
26 7 0.07
27 4 0.04
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:27549178 original size:15 final size:14
Alignment explanation
Indices: 27549149--27549192 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
27549139 CTTGAGCCTT
27549149 ATTT-ATTTA-TTC
1 ATTTCATTTATTTC
27549161 ATTTCATTTTATTTC
1 ATTTCA-TTTATTTC
27549176 ATTTCATTTATTT-
1 ATTTCATTTATTTC
27549189 ATTT
1 ATTT
27549193 ACAAGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.14
13 5 0.17
14 11 0.38
15 9 0.31
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTCATTTATTTC
Found at i:27549772 original size:11 final size:10
Alignment explanation
Indices: 27549724--27549772 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
27549714 TAACATGTTG
*
27549724 AATTTTAATT
1 AATTTTTATT
*
27549734 AATTTTATAATA
1 AATTTT-T-ATT
27549746 AATTTTTATT
1 AATTTTTATT
27549756 AATTTTTATT
1 AATTTTTATT
*
27549766 TATTTTT
1 AATTTTT
27549773 GACAGATTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTTTATT
Found at i:27553042 original size:237 final size:237
Alignment explanation
Indices: 27552627--27553088 Score: 735
Period size: 237 Copynumber: 1.9 Consensus size: 237
27552617 CGGGAGTAGC
* *
27552627 CATTTTTGAATGTTGTCGTATCCTGCGCGATGTTCCAAGGTTAAAACCCTCGTAATCGTCCTTTG
1 CATTTTTGAATGTTGTCATATCCTGCGCGATGCTCCAAGGTTAAAACCCTCGTAATCGTCCTTTG
* * * *
27552692 GTGGGAACAGTATAGGTACGATCTCGCCTATTACGTTGATCATCTTATGACTAAAATTTTTGTCA
66 GTAGGAACAGTATAGGTACGACCTCGCCTATTACGTTGATCATCTTACGACTAAAATTTTTATCA
*
27552757 GACGAGCCGGGTGGTGGACTTGAATTTCCAACATCATCAGTACTACTGTGTAGAGGCCTTGATGT
131 GACGAGCCGGGTGGTGGACTTGAATTTCCAACATCATCAGTACTACTGTGTAGAGGCCTCGATGT
27552822 CTCATTTATCGGTGGTGGACAGGACCGAGTACCAGGAGTGGA
196 CTCATTTATCGGTGGTGGACAGGACCGAGTACCAGGAGTGGA
* * * * *
27552864 CATTTTTGAATGTTGTCATATCTTGCGTGATGCTCTAGGGTTGAAACCCTCGTAATCGTCCTTTG
1 CATTTTTGAATGTTGTCATATCCTGCGCGATGCTCCAAGGTTAAAACCCTCGTAATCGTCCTTTG
* *
27552929 GTAGGAACAGTATAGGTATGACCTCGCCTATTACGTTGATCGTCTTACGACTAAAATTTTTATCA
66 GTAGGAACAGTATAGGTACGACCTCGCCTATTACGTTGATCATCTTACGACTAAAATTTTTATCA
* * * * * *
27552994 GATGAGTCGGGTGGTGGGCTTGAATTTCCAACATCGTCAGTACTACTGTGTGGAGGCGTCGATGT
131 GACGAGCCGGGTGGTGGACTTGAATTTCCAACATCATCAGTACTACTGTGTAGAGGCCTCGATGT
*
27553059 CTCATTTATCGGTGGTTGACAGGACCGAGT
196 CTCATTTATCGGTGGTGGACAGGACCGAGT
27553089 GGTGGACGAC
Statistics
Matches: 204, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
237 204 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (237 bp):
CATTTTTGAATGTTGTCATATCCTGCGCGATGCTCCAAGGTTAAAACCCTCGTAATCGTCCTTTG
GTAGGAACAGTATAGGTACGACCTCGCCTATTACGTTGATCATCTTACGACTAAAATTTTTATCA
GACGAGCCGGGTGGTGGACTTGAATTTCCAACATCATCAGTACTACTGTGTAGAGGCCTCGATGT
CTCATTTATCGGTGGTGGACAGGACCGAGTACCAGGAGTGGA
Found at i:27553656 original size:21 final size:22
Alignment explanation
Indices: 27553630--27553672 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
27553620 TCGATTTTGG
27553630 TCTTCTTC-TTTTTTTCTTTTT
1 TCTTCTTCATTTTTTTCTTTTT
27553651 TCTTCTTCTATTTTTTTCTTTT
1 TCTTCTTC-ATTTTTTTCTTTT
27553673 GACCGGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TCTTCTTCATTTTTTTCTTTTT
Found at i:27564452 original size:13 final size:13
Alignment explanation
Indices: 27564436--27564460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27564426 GTTTTCAAAG
27564436 TATTTTTTGTTAT
1 TATTTTTTGTTAT
27564449 TATTTTTTGTTA
1 TATTTTTTGTTA
27564461 ATTCTTGTTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TATTTTTTGTTAT
Found at i:27580432 original size:7 final size:7
Alignment explanation
Indices: 27580420--27580479 Score: 120
Period size: 7 Copynumber: 8.6 Consensus size: 7
27580410 TAGTCGATTG
27580420 GTATTTA
1 GTATTTA
27580427 GTATTTA
1 GTATTTA
27580434 GTATTTA
1 GTATTTA
27580441 GTATTTA
1 GTATTTA
27580448 GTATTTA
1 GTATTTA
27580455 GTATTTA
1 GTATTTA
27580462 GTATTTA
1 GTATTTA
27580469 GTATTTA
1 GTATTTA
27580476 GTAT
1 GTAT
27580480 ATAACTAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:27581803 original size:96 final size:96
Alignment explanation
Indices: 27581628--27582073 Score: 345
Period size: 108 Copynumber: 4.2 Consensus size: 96
27581618 TTGAGGTATT
* * * *
27581628 ACTTAACAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTATAATTTAATTGACAA
1 ACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTATAATTAAATTGACAA
27581693 ACCCTAACAAAAACCCTAACCCTAACCCTTA
66 ACCCTAACAAAAACCCTAACCCTAACCCTTA
27581724 ACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTATAATTAAATTTATAA
1 ACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAA-T-T-A-T-AA--T-T-A
*
27581789 TTTAATTGACAAACCCTAACAAAAACCCTAACCCTAATCCTTA
57 ---AATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTTA
*
27581832 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTA
1 ACTTAAAAACCCTAAA--C-TAA-TT---TA--CTAAA--AATTTA-T--AAATTTATAAA-TTA
* * ***
27581897 TGATTTATAATT-AAATTTATAATTTAATTGACAAACCCTAACCCTAACCCTAACCCTTA
51 T-AATTA-AATTGACA---A-ACCCT-A---ACAAA----AACCCTAACCCTAACCCTTA
* * *
27581956 ACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTATAATTTAATTGACAA
1 ACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTATAATTAAATTGACAA
27582021 ACCCTAACAAAACTCTAACCCTAACCCTAACCCTTA
66 ACCCTAAC-AAA----AACCCTAACCCTAACCCTTA
27582057 ACTTAAAAACCCTAAAC
1 ACTTAAAAACCCTAAAC
27582074 CCTTAACATA
Statistics
Matches: 287, Mismatches: 23, Indels: 75
0.75 0.06 0.19
Matches are distributed among these distances:
96 44 0.15
97 1 0.00
98 1 0.00
99 1 0.00
100 3 0.01
101 45 0.16
103 2 0.01
104 3 0.01
105 1 0.00
107 4 0.01
108 60 0.21
109 4 0.01
110 11 0.04
111 3 0.01
112 5 0.02
113 11 0.04
115 7 0.02
116 3 0.01
117 8 0.03
119 8 0.03
120 9 0.03
121 4 0.01
122 14 0.05
124 35 0.12
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (96 bp):
ACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTATAATTAAATTGACAA
ACCCTAACAAAAACCCTAACCCTAACCCTTA
Found at i:27581855 original size:22 final size:22
Alignment explanation
Indices: 27581818--27581870 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
27581808 CAAAAACCCT
*
27581818 AACCCT-AATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
27581839 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
27581861 AACCCTAAAC
1 AACCCTAAAC
27581871 TAATTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:27581855 original size:130 final size:124
Alignment explanation
Indices: 27581710--27581972 Score: 429
Period size: 130 Copynumber: 2.1 Consensus size: 124
27581700 CAAAAACCCT
27581710 AACCCT-AACCCTTAACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTA
1 AACCCTAAACCCTTAACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTA
*
27581774 TAATTAAATTTATAATTTAATTGACAAACCCTAACAAAAACCCTAACCCTAATCCTTAACTTAAA
66 TAATTAAATTTATAATTTAATTGACAAACCCT------AACCCTAACCCTAACCCTTAACTTAAA
* * *
27581839 AACCCTAAACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATGATTTA
1 AACCCTAAACCCTTAACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTA
27581904 TAATTAAATTTATAATTTAATTGACAAACCCTAACCCTAACCCTAACCCTTAACTTAAA
66 TAATTAAATTTATAATTTAATTGACAAACCCTAACCCTAACCCTAACCCTTAACTTAAA
27581963 AACCCTAAAC
1 AACCCTAAAC
27581973 TAATTTATTA
Statistics
Matches: 129, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
124 36 0.28
129 6 0.05
130 87 0.67
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (124 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTA
TAATTAAATTTATAATTTAATTGACAAACCCTAACCCTAACCCTAACCCTTAACTTAAA
Found at i:27581881 original size:22 final size:22
Alignment explanation
Indices: 27581829--27581884 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
27581819 ACCCTAATCC
**
27581829 TTAACTTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAAACAA
27581851 TTAACTTAAAAACCCTAAACTAA
1 TTAACTTAAAAACCCTAAAC-AA
*
27581874 TTTA-TTAAAAA
1 TTAACTTAAAAA
27581885 TTTATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAACTTAAAAACCCTAAACAA
Found at i:27581965 original size:102 final size:101
Alignment explanation
Indices: 27581839--27582073 Score: 348
Period size: 102 Copynumber: 2.3 Consensus size: 101
27581829 TTAACTTAAA
*
27581839 AACCCTAAACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATGATTTA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTA
* * * *
27581904 TAATTAAATTTATAATTTA-ATTGAC-AAACCCTAACCCT
65 TAATTAAATTGACAA---ACACTAACAAAACCCTAACCCT
27581942 AACCCTAACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTAT
1 AACCCTAACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTAT
* * *
27582007 AATTTAATTGACAAACCCTAACAAAACTCTAACCCT
66 AATTAAATTGACAAACACTAACAAAACCCTAACCCT
27582043 AACCCTAACCCTTAACTTAAAAACCCTAAAC
1 AACCCTAACCCTTAACTTAAAAACCCTAAAC
27582074 CCTTAACATA
Statistics
Matches: 122, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
99 1 0.01
100 3 0.02
101 43 0.35
102 69 0.57
103 6 0.05
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (101 bp):
AACCCTAACCCTTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTAT
AATTAAATTGACAAACACTAACAAAACCCTAACCCT
Found at i:27582098 original size:232 final size:232
Alignment explanation
Indices: 27581658--27582095 Score: 614
Period size: 225 Copynumber: 1.9 Consensus size: 232
27581648 TTTATTAAAA
27581658 ATTTATAAATTTATAATTTATAATTTAATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTT
1 ATTTATAAATTTATAATTTATAATTTAATTGACAAACCCT-----AAACCCTAACCCTAACCCTT
*
27581723 AACTTAAAAACCCTAAACTAATTTACTAAAAATTTATAAATTTATAAATTATAATTAAATTTATA
61 AACTTAAAAACCCTAAACTAATTTA-T---AATTTAAAAATTTATAAATTATAATTAAATTTATA
*
27581788 ATTTAATTGACAAACCCTAACAAAAACCCTAACCCTAATCCTTAACTTAAAAACCCTAAACCCTT
122 ATTTAATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTTAACTTAAAAACCCTAAACCCTT
*
27581853 AACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATG
187 AACTAAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATG
27581899 ATTTAT-AA-TTA-AATTTATAATTTAATTGACAAACCCT-AACCCTAACCCTAACCCTTAACTT
1 ATTTATAAATTTATAATTTATAATTTAATTGACAAACCCTAAACCCTAACCCTAACCCTTAACTT
27581960 AAAAACCCTAAACTAA-TT-T-A-TTAAAAATTTATAAATT-T-A-T-AATTTATAATTTAATTG
66 AAAAACCCTAAACTAATTTATAATTTAAAAATTTATAAATTATAATTAAATTTATAATTTAATTG
27582017 ACAAACCCTAACAAAACTCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAC-
131 ACAAACCCTAAC-AAA----AACCCTAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACT
*
27582081 ATAAAAACTCTAAAC
191 A-AAAAACCCTAAAC
27582096 CCTTAACTTA
Statistics
Matches: 187, Mismatches: 4, Indels: 28
0.85 0.02 0.13
Matches are distributed among these distances:
220 29 0.16
221 4 0.02
222 1 0.01
223 1 0.01
224 16 0.09
225 56 0.30
229 1 0.01
231 2 0.01
232 40 0.21
238 26 0.14
239 3 0.02
240 2 0.01
241 6 0.03
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (232 bp):
ATTTATAAATTTATAATTTATAATTTAATTGACAAACCCTAAACCCTAACCCTAACCCTTAACTT
AAAAACCCTAAACTAATTTATAATTTAAAAATTTATAAATTATAATTAAATTTATAATTTAATTG
ACAAACCCTAACAAAAACCCTAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTAAAAA
ACCCTAAACTAATTTATTAAAAATTTATAAATTTATG
Found at i:27582160 original size:22 final size:21
Alignment explanation
Indices: 27582043--27582157 Score: 151
Period size: 22 Copynumber: 5.4 Consensus size: 21
27582033 CTCTAACCCT
27582043 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
27582064 AACCCTAAACCCTTAACATAAA
1 AACCCT-AACCCTTAACTTAAA
*
27582086 AACTCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
27582108 AACCCTAACCCTTATCTT-AA
1 AACCCTAACCCTTAACTTAAA
* *
27582128 AACATCTAACTCTTAACTTAAA
1 AAC-CCTAACCCTTAACTTAAA
27582150 AACCCTAA
1 AACCCTAA
27582158 ACTAATTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
20 5 0.06
21 33 0.40
22 44 0.54
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:27582193 original size:26 final size:26
Alignment explanation
Indices: 27582160--27582211 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
27582150 AACCCTAAAC
27582160 TAATTTATTAAA-A-ATTTATAAATTTA
1 TAATTTA-TAAATATATTTAT-AATTTA
27582186 TAATTTATAAATATATTTATAATTTA
1 TAATTTATAAATATATTTATAATTTA
27582212 ATTGACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 4 0.17
26 14 0.58
27 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTTATAAATATATTTATAATTTA
Found at i:27582269 original size:21 final size:21
Alignment explanation
Indices: 27582243--27582292 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
27582233 CCCTACCCCT
27582243 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
27582264 AACCCTAACTCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
27582285 AACCCTAA
1 AACCCTAA
27582293 ACTAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:27582273 original size:135 final size:135
Alignment explanation
Indices: 27582108--27582582 Score: 673
Period size: 135 Copynumber: 3.4 Consensus size: 135
27582098 TTAACTTAAA
* *
27582108 AACCCTAACCCTTATCTT-AAAACATCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAA
1 AACCCTAACCCTTAACTTAAAAAC-CCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAA
27582172 AATTTATAAATTTATAATTTATAAATATATTTATAATTTAATTGACAAACCCTAATAAAAACCCT
65 AATTTATAAATTTATAATTTATAAATATATTTATAATTTAATTGACAAACCCTAATAAAAACCCT
*
27582237 ACCCCT
130 AACCCT
27582243 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAAA
27582308 ATTTATAAATTTATAATTTATAAATATATTTATAATTTAATTGACAAACCCTAATAAAAACCCTA
66 ATTTATAAATTTATAATTTATAAATATATTTATAATTTAATTGACAAACCCTAATAAAAACCCTA
27582373 ACCCT
131 ACCCT
* *
27582378 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAACATTTAACTTAAAAC
1 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAA-A-CTAA-TT--TA-
*
27582443 CCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTATAATTACATTTATAATTTAATTGAC
60 -TTAAA--AATTTA-T--AAATTTAT-AATTTATAA---AT-A-T--ATTTATAATTTAATTGAC
* *
27582508 AGACCCTAACAAAAACCCTAACCCT
111 AAACCCTAATAAAAACCCTAACCCT
*
27582533 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAA
27582583 CCCTTAAATT
Statistics
Matches: 310, Mismatches: 9, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
135 176 0.57
136 6 0.02
137 3 0.01
138 2 0.01
140 1 0.00
142 4 0.01
144 6 0.02
145 1 0.00
147 8 0.03
148 9 0.03
151 2 0.01
152 1 0.00
153 1 0.00
155 90 0.29
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (135 bp):
AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAAA
ATTTATAAATTTATAATTTATAAATATATTTATAATTTAATTGACAAACCCTAATAAAAACCCTA
ACCCT
Found at i:27582328 original size:26 final size:26
Alignment explanation
Indices: 27582295--27582346 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
27582285 AACCCTAAAC
27582295 TAATTTATTAAA-A-ATTTATAAATTTA
1 TAATTTA-TAAATATATTTAT-AATTTA
27582321 TAATTTATAAATATATTTATAATTTA
1 TAATTTATAAATATATTTATAATTTA
27582347 ATTGACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 4 0.17
26 14 0.58
27 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTTATAAATATATTTATAATTTA
Found at i:27582404 original size:21 final size:21
Alignment explanation
Indices: 27582378--27582447 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
27582368 CCCTAACCCT
*
27582378 AACCCTAACCCTTAACTTAAA
1 AACCCTAACACTTAACTTAAA
*
27582399 AACCCTAACTCTTAACTTAAA
1 AACCCTAACACTTAACTTAAA
*
27582420 AACCCTAACATTTAACTT-AA
1 AACCCTAACACTTAACTTAAA
27582440 AACCCTAA
1 AACCCTAA
27582448 ACTAATTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 10 0.22
21 36 0.78
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCTAACACTTAACTTAAA
Found at i:27582477 original size:155 final size:156
Alignment explanation
Indices: 27582243--27582604 Score: 629
Period size: 155 Copynumber: 2.3 Consensus size: 156
27582233 CCCTACCCCT
27582243 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAAA
* *
27582308 ATTTATAAATTTATAATTTATAAATATATTTATAATTTAATTGACAAACCCTAATAAAAACCCTA
66 ATTTATAAATTTATAATTTATAAATACATTTATAATTTAATTGACAAACCCTAACAAAAACCCTA
27582373 ACCCTAACCCTAACCCTTAACTTAAA
131 ACCCTAACCCTAACCCTTAACTTAAA
*
27582399 AACCCTAACTCTTAACTTAAAAACCCTAACAT-TTAACTT-AAAACCCTAAACTAATTTATTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAC-TCTTAACTTAAAAACCCTAAACTAATTTATTAAA
* *
27582462 AATTTATAAATTTATAATTTATAATTACATTTATAATTTAATTGACAGACCCTAACAAAAACCCT
65 AATTTATAAATTTATAATTTATAAATACATTTATAATTTAATTGACAAACCCTAACAAAAACCCT
27582527 AACCCTAACCCTAACCCTTAACTTAAA
130 AACCCTAACCCTAACCCTTAACTTAAA
* * *
27582554 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAAATTAAAAACCTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAA
27582605 ACCATACCAT
Statistics
Matches: 194, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
155 147 0.76
156 46 0.24
157 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (156 bp):
AACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTAAAAACCCTAAACTAATTTATTAAAA
ATTTATAAATTTATAATTTATAAATACATTTATAATTTAATTGACAAACCCTAACAAAAACCCTA
ACCCTAACCCTAACCCTTAACTTAAA
Found at i:27582559 original size:21 final size:21
Alignment explanation
Indices: 27582533--27582599 Score: 125
Period size: 21 Copynumber: 3.2 Consensus size: 21
27582523 CCCTAACCCT
27582533 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
27582554 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
27582575 AACCCTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAA
27582596 AACC
1 AACC
27582600 TTAAAACCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:27585933 original size:125 final size:124
Alignment explanation
Indices: 27585705--27586140 Score: 570
Period size: 125 Copynumber: 3.5 Consensus size: 124
27585695 CAAACATGCT
* * * * ** * * *
27585705 ACTGTTGCAAAAGTGCGCCCACGAGGGCGCGGTTTCATAAATTCTTCTGATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTAAGAAATTCTTCTGATAAAGCATCCTACTT
* * * * *
27585770 GAAGCATTTTTTATACTATTCATTCAGAAATGTCAACTCAAAATTATATTTTTAGGACCT
66 GAAGCGTTTTTTATACTATTCACTCAGAAACGTCAACTCGAAATTAT-TTTTTAGGACCA
* * *
27585830 ATTGTAGCAAAAGCGTGTCCACGTGGGCGCAATTTAAGAAATTCTTCTAATAAAGCATCCTACTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTAAGAAATTCTTCTGATAAAGCATCCTACTT
*
27585895 GAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
66 GAAGCGTTTTTTATACTATTCACTCAGAAACGTCAACTCGAAATTATTTTTT-AGGACCA
* * * *
27585955 ACTGGAGCAAAAGCACGTCCACGTGGGTGCAATTTTAGAAATTCTTCTGATAAAGCATCC-ATCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTAAGAAATTCTTCTGATAAAGCATCCTA-CT
** *
27586019 TGAAGCG-TTTTTATACTATTTTCTCAGAAGCGTCAACTCGAAATTATTTTTTTAGGACCA
65 TGAAGCGTTTTTTATACTATTCACTCAGAAACGTCAACTCGAAATTA-TTTTTTAGGACCA
* * *
27586079 ACTGTAGCAAAAGCGCGTCCACGTGGGCACGATTTCAGAAATTCTTCTGATAAAGCATCCTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTAAGAAATTCTTCTGATAAAGCATCCTA
27586141 AACCCTAAAC
Statistics
Matches: 273, Mismatches: 34, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
124 103 0.38
125 170 0.62
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTAAGAAATTCTTCTGATAAAGCATCCTACTT
GAAGCGTTTTTTATACTATTCACTCAGAAACGTCAACTCGAAATTATTTTTTAGGACCA
Found at i:27586228 original size:21 final size:22
Alignment explanation
Indices: 27586189--27586230 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27586179 CTTTAAAACC
* *
27586189 CTAAAAACCTTAAACCCTAACT
1 CTAAAAACCTCAAAACCTAACT
27586211 CTAAAAA-CTCAAAACCTAAC
1 CTAAAAACCTCAAAACCTAAC
27586231 AATGGAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (22 bp):
CTAAAAACCTCAAAACCTAACT
Found at i:27587846 original size:12 final size:12
Alignment explanation
Indices: 27587829--27587883 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
27587819 TCAAAGGTAG
27587829 TTTTTTATTTAT
1 TTTTTTATTTAT
**
27587841 TTTTTTGGCTTAT
1 TTTTTT-ATTTAT
*
27587854 TTATTTATTTAT
1 TTTTTTATTTAT
*
27587866 TTATTTATTTAT
1 TTTTTTATTTAT
27587878 TTTTTT
1 TTTTTT
27587884 GTTTGTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
12 27 0.75
13 9 0.25
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:27587857 original size:4 final size:4
Alignment explanation
Indices: 27587850--27587879 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
27587840 TTTTTTTGGC
27587850 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
27587880 TTTTGTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:27588867 original size:21 final size:21
Alignment explanation
Indices: 27588837--27588877 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27588827 TCTTCTTAGT
27588837 TATTTATTTTAATTTGCTTTC
1 TATTTATTTTAATTTGCTTTC
* * *
27588858 TATTTTTTTTATTTTTCTTT
1 TATTTATTTTAATTTGCTTT
27588878 GCATATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (21 bp):
TATTTATTTTAATTTGCTTTC
Found at i:27588922 original size:24 final size:25
Alignment explanation
Indices: 27588880--27588938 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
27588870 TTTTCTTTGC
* ** *
27588880 ATATTATTTACTTTTAATTG-CTTT
1 ATATTATTTACCTCAAATTGTCTAT
27588904 ATATTATTTACCTCAAATTGTTCTAT
1 ATATTATTTACCTCAAATTG-TCTAT
27588930 ATATTATTT
1 ATATTATTT
27588939 CGTTTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 17 0.59
26 12 0.41
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (25 bp):
ATATTATTTACCTCAAATTGTCTAT
Found at i:27592515 original size:24 final size:24
Alignment explanation
Indices: 27592407--27592538 Score: 180
Period size: 25 Copynumber: 5.5 Consensus size: 24
27592397 ATACGGAACA
* *
27592407 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
**
27592430 AA-A-CAGAGAGCACTGACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
27592452 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
27592477 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
*
27592502 AATATCAGAAAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
27592526 AATATCAGAGAGC
1 AATATCAGAGAGC
27592539 GCACTAAAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
22 17 0.17
23 4 0.04
24 36 0.37
25 41 0.42
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:27592521 original size:49 final size:49
Alignment explanation
Indices: 27592406--27592538 Score: 175
Period size: 49 Copynumber: 2.8 Consensus size: 49
27592396 TATACGGAAC
* * * **
27592406 AAATA-CAGAGAGCACAAATGTGCTAA-A-CAGAGAGCACTGACGTGCT
1 AAATATCAGAAAGCACCAACGTGCTAATATCAGAGAGCACCAACGTGCT
*
27592452 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 AAATATCAGAAAGCACCAACGTGCTAAT-ATCAGAGAGCACCAACGTGCT
27592502 -AATATCAGAAAGCACCAACGTGCTAATATCAGAGAGC
1 AAATATCAGAAAGCACCAACGTGCTAATATCAGAGAGC
27592539 GCACTAAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
46 5 0.06
47 19 0.24
48 10 0.13
49 27 0.35
50 17 0.22
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (49 bp):
AAATATCAGAAAGCACCAACGTGCTAATATCAGAGAGCACCAACGTGCT
Found at i:27593375 original size:12 final size:13
Alignment explanation
Indices: 27593358--27593389 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27593348 GATTTCCATC
27593358 AATTCAAT-CACT
1 AATTCAATCCACT
27593370 AATTC-ATCCACT
1 AATTCAATCCACT
27593382 AATTCAAT
1 AATTCAAT
27593390 ATAAGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTCAATCCACT
Found at i:27593578 original size:11 final size:11
Alignment explanation
Indices: 27593562--27593587 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27593552 TCTTTCTTTC
27593562 TTTCTCCCCTG
1 TTTCTCCCCTG
27593573 TTTCTCCCCTG
1 TTTCTCCCCTG
27593584 TTTC
1 TTTC
27593588 GTTTCAATTT
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:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:27593657 original size:5 final size:5
Alignment explanation
Indices: 27593647--27593681 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
27593637 TATATATATA
*
27593647 ATAAT ATAAT ATAAT ATTAT AATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAA
27593682 CAACTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:27593667 original size:21 final size:22
Alignment explanation
Indices: 27593638--27593681 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
27593628 CTTTTGCTTT
27593638 ATATATATAATAATATAATATA
1 ATATATATAATAATATAATATA
27593660 ATAT-TATAATAATATAATATA
1 ATATATATAATAATATAATATA
27593681 A
1 A
27593682 CAACTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATAATAATATAATATA
Found at i:27599228 original size:24 final size:24
Alignment explanation
Indices: 27599120--27599251 Score: 180
Period size: 25 Copynumber: 5.5 Consensus size: 24
27599110 ATACGGAACA
* *
27599120 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
**
27599143 AA-A-CAGAGAGCACTGACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
27599165 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
27599190 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
*
27599215 AATATCAGAAAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
27599239 AATATCAGAGAGC
1 AATATCAGAGAGC
27599252 GCGCTAAAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
22 17 0.17
23 4 0.04
24 36 0.37
25 41 0.42
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:27599234 original size:49 final size:49
Alignment explanation
Indices: 27599119--27599251 Score: 175
Period size: 49 Copynumber: 2.8 Consensus size: 49
27599109 TATACGGAAC
* * * **
27599119 AAATA-CAGAGAGCACAAATGTGCTAA-A-CAGAGAGCACTGACGTGCT
1 AAATATCAGAAAGCACCAACGTGCTAATATCAGAGAGCACCAACGTGCT
*
27599165 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 AAATATCAGAAAGCACCAACGTGCTAAT-ATCAGAGAGCACCAACGTGCT
27599215 -AATATCAGAAAGCACCAACGTGCTAATATCAGAGAGC
1 AAATATCAGAAAGCACCAACGTGCTAATATCAGAGAGC
27599252 GCGCTAAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
46 5 0.06
47 19 0.24
48 10 0.13
49 27 0.35
50 17 0.22
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (49 bp):
AAATATCAGAAAGCACCAACGTGCTAATATCAGAGAGCACCAACGTGCT
Found at i:27600090 original size:12 final size:13
Alignment explanation
Indices: 27600073--27600104 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27600063 GATTTCCATC
27600073 AATTCAAT-CACT
1 AATTCAATCCACT
27600085 AATTC-ATCCACT
1 AATTCAATCCACT
27600097 AATTCAAT
1 AATTCAAT
27600105 ATAAGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTCAATCCACT
Found at i:27600293 original size:11 final size:11
Alignment explanation
Indices: 27600277--27600302 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27600267 TCTTTCTTTC
27600277 TTTCTCCCCTG
1 TTTCTCCCCTG
27600288 TTTCTCCCCTG
1 TTTCTCCCCTG
27600299 TTTC
1 TTTC
27600303 GTTTCAATTT
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:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:27600372 original size:5 final size:5
Alignment explanation
Indices: 27600362--27600396 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
27600352 TATATATATA
*
27600362 ATAAT ATAAT ATAAT ATTAT AATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAA
27600397 CAACTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:27600382 original size:21 final size:22
Alignment explanation
Indices: 27600353--27600396 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
27600343 CTTTTGCTTT
27600353 ATATATATAATAATATAATATA
1 ATATATATAATAATATAATATA
27600375 ATAT-TATAATAATATAATATA
1 ATATATATAATAATATAATATA
27600396 A
1 A
27600397 CAACTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATAATAATATAATATA
Found at i:27600745 original size:65 final size:68
Alignment explanation
Indices: 27600673--27600808 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 68
27600663 CTGATTTACC
27600673 GGAACAAAGTCCCGGAAATGCA-TTTT-TTTAATCTATTTAAATA-AATTTTACCATATAATCAA
1 GGAACAAAGTCCCGGAAATGCATTTTTATTTAATCTATTTAAATATAATTTTACCATATAATCAA
27600735 TAA
66 TAA
**
27600738 GGAACAAAGTCCCGGAAATGCATTTTTTTTATTTAATCTATTTAAATATTTTTTTACCATATAAT
1 GGAACAAAGTCCCGGAAATGCA---TTTTTATTTAATCTATTTAAATATAATTTTACCATATAAT
27600803 CAATAA
63 CAATAA
27600809 AATTTTATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
65 22 0.35
69 4 0.06
70 17 0.27
71 20 0.32
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (68 bp):
GGAACAAAGTCCCGGAAATGCATTTTTATTTAATCTATTTAAATATAATTTTACCATATAATCAA
TAA
Found at i:27610643 original size:948 final size:948
Alignment explanation
Indices: 27608331--27611242 Score: 4824
Period size: 948 Copynumber: 3.0 Consensus size: 948
27608321 AATTTAAGAT
*
27608331 TGCCTAAAAATGAATGGTGCAATGGAAGCAGCCAATAAAAATATCAAGAAAATTGTGTGGAAAAT
1 TGCCTAAAAATGAATGGTGCAATGGAAGCGGCCAATAAAAATATC------A----G-GGAAAAT
* * *
27608396 GACTGAGACTTACAAGAACTGGCATGAGAAATAAACAGATAAGACTTACAAGGACTTACAATGAC
55 GACTGAGACTTACAAGGACTGGCATGAGAAATAAACAGACAAGACTTACAAGGACTTACAAGGAC
* * *
27608461 TGGAACGAGATGAAAATCAGATGGCTGATGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAAT
120 TGGCACGAGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAAC
27608526 AGACAAGAGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATAT
185 AGACAAGAGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATAT
*
27608591 CGAAGAGGGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCTATATGTGAAGAATCGTG
250 CGAAGAGGGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTG
27608656 AGTATCCTAACCAGGCAACTGAGAATGATAAAAGGGCTCTGAGAA-ACTAGCCATTGATTATGTC
315 AGTATCCTAA-CAGGCAACTGAGAATGATAAAAGGGCTCTGAGAAGACTAGCCATTGATTATGTC
* * * * *
27608720 TTAGATTGGGACATCTTATATAAAAATGGAAAGGAACATGTACTATTAAGATGTGTGGACGCTGT
379 TTAGATGGGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACGCTGT
27608785 GAAGGCTAAGAAAATCTTAGAGGAAGTCCATGAGGGTATTTGCGGAACGCATGCCAGTGGGTTCA
444 GAAGGCTAAGAAAATCTTAGAGGAAGTCCATGAGGGTATTTGCGGAACGCATGCCAGTGGGTTCA
* * *
27608850 CAATGGTTAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAATGAGATTGTATCAAT
509 CAATGGCTAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAAT
*
27608915 TATGCCAAGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGTATGCACCTCCTTTGCCTCT
574 TATGCCAAGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTTGCCTCT
* *
27608980 TCATGTTATGACTTCTCCATGGCCTTTCTCTATGTGGGGTAT-GATGTCATTGGGCCAATATTGT
639 TCATGTTATGACTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCAATATCGT
*
27609044 CGAAGGCTTCTAATGGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAA
704 CGAAGGCTTCTAATAGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAA
27609109 GCTGCTTCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATG
769 GCTGCTTCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATG
* *
27609174 TCGATATGGAATGCCCGAAAGAATCATATCTGACAATAGGTTGAATTTGAACAAGAGCTTAATAG
834 TCGATATGGAATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAG
* * *
27609239 TAGATGTCTGCAGTCAATTTAAGATCAGGCACCATGATTCGTCACCGTAC
899 TGGATGTCTGCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTAC
*
27609289 TGCCTAAAAATGAATGGTGCAATGGAAGCGGACAATAAAAATATCAAGAAAATTGTGGGAAAAAT
1 TGCCTAAAAATGAATGGTGCAATGGAAGCGGCCAATAAAAATATC------A----GGG-AAAAT
* *
27609354 GACTGAGACTTACAAGGACTGGCATGAGAAATAAATAAACAAGACTTACAAGGACTTACAAGGAC
55 GACTGAGACTTACAAGGACTGGCATGAGAAATAAACAGACAAGACTTACAAGGACTTACAAGGAC
* *
27609419 TGGCACGATATGAAAATCAGATGGCTGACGCATTGGCTACTCTAGCCTCCATGATTAAAATGAAC
120 TGGCACGAGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAAC
*
27609484 AGACAAGAGGACATGAAGCCTATCCAGATGAGCATCTATGGAACCCCAGCTCACTGTTACAATAT
185 AGACAAGAGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATAT
* ** * *
27609549 CGAAGAGAGAGAAAATAATGATAGCCCTTGGTATAAAGATATATTGTGATATGTGAAAAATCGTG
250 CGAAGAGGGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTG
*
27609614 AGTATCCTAACTAGGCAACTGAGAAGGATAAAAGGGCTCTGAGAAGACTAGCCATTGATTATGTC
315 AGTATCCTAAC-AGGCAACTGAGAATGATAAAAGGGCTCTGAGAAGACTAGCCATTGATTATGTC
* *
27609679 TTAGATGGTGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGATGCTGT
379 TTAGATGGGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACGCTGT
* * *
27609744 GAAGGCTAAGAAAATATCAGAGGAAGTCCATGAGGGTATTTGCGGAACGCATGCCAATGGGTTCA
444 GAAGGCTAAGAAAATCTTAGAGGAAGTCCATGAGGGTATTTGCGGAACGCATGCCAGTGGGTTCA
*
27609809 CAATGGCTAGACAGATTATGAGGTTCGGGTACTGCTGGTCCACCATAGAAGGAGATTGCATCAAT
509 CAATGGCTAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAAT
* **
27609874 TATGCCAAGAAGTGCCATAAATGCCTAATTTATGGTGATAAAGTGCATGCACCTCCTTCACCTCT
574 TATGCCAAGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTTGCCTCT
* *
27609939 TCATGTTATGACTTCTCCATAGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCAATAACGT
639 TCATGTTATGACTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCAATATCGT
27610004 CGAAGGCTTCTAATAGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAA
704 CGAAGGCTTCTAATAGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAA
* *
27610069 GCTACTTCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAATGAGATCATATG
769 GCTGCTTCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATG
*
27610134 TCGATATGGAATGCTCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAG
834 TCGATATGGAATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAG
*
27610199 CGGATGTCTGCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTAC
899 TGGATGTCTGCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTAC
* *
27610249 TGCCTAAAAATGAATGGTGCAATAGAAGCGGCCAATAAAAATATC-GGGAAAATGACTAAGACTT
1 TGCCTAAAAATGAATGGTGCAATGGAAGCGGCCAATAAAAATATCAGGGAAAATGACTGAGACTT
* * *
27610313 ATAAGGACTGGCATCAGAAATAAACAGACAATACTTACAAGGACTTACAAGGACTGGCACGAGAT
66 ACAAGGACTGGCATGAGAAATAAACAGACAAGACTTACAAGGACTTACAAGGACTGGCACGAGAT
* *
27610378 GAAAATCAGATGGCTGACGCGTTGGTTACTCTAGCCTCCATGATTAAAATGAACAGACAATAGGA
131 GAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAGAGGA
*
27610443 CATGAAGCCTATCCAGATGAGCATCTATGAAATCCCAGCTCACTGTTACAATATCGAAGAGGGAG
196 CATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAGGGAG
*
27610508 AAAAGGATGATAGCCCTTGGTATAAAGATATATTACGATATGTGAAGAATCGTGAGTATCCTGAA
261 AAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCCT-AA
* ** * * *
27610573 CAGGTAGGTGAGAATGATAAGAGAGCTCTGAGAAGACTAGCCATTGACTATGTCTTAGATGGGGA
325 CAGGCAACTGAGAATGATAAAAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATGGGGA
*
27610638 GATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACGCTATGAAGGCTAAGA
390 GATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACGCTGTGAAGGCTAAGA
* * *
27610703 AAATCTTAGAGGAGGTCCATGAGAGTATTTGCGGAATGCATGCCAGTGGGTTCACAATGGCTAGA
455 AAATCTTAGAGGAAGTCCATGAGGGTATTTGCGGAACGCATGCCAGTGGGTTCACAATGGCTAGA
*
27610768 CAGATTATGAGATTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCAAGAA
520 CAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCAAGAA
*
27610833 GTACCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTTGCCTCTTCATGTTATGA
585 GTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTTGCCTCTTCATGTTATGA
27610898 CTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCAATATCG-CTGAAGGCTTC
650 CTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCAATATCGTC-GAAGGCTTC
27610962 TAATAGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCTTCGT
714 TAATAGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCTTCGT
* *
27611027 ATGCTAATATCACAAAGTTAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATATGGA
779 ATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATATGGA
* * * *
27611092 ATGCCCGAAAGAATCATATCTGACAATGCGTTGAATTTGAACAACAGTTCAATAGTGGAGGTCTG
844 ATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGTGGATGTCTG
27611157 CAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTAC
909 CAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTAC
* * *
27611197 TGTCTAAAAATGAATGGTGAAATGGAAGCGGCTAATAAAAATATCA
1 TGCCTAAAAATGAATGGTGCAATGGAAGCGGCCAATAAAAATATCA
27611243 AGAAAATTGT
Statistics
Matches: 1837, Mismatches: 110, Indels: 23
0.93 0.06 0.01
Matches are distributed among these distances:
947 1 0.00
948 883 0.48
949 6 0.00
957 3 0.00
958 345 0.19
959 302 0.16
960 297 0.16
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (948 bp):
TGCCTAAAAATGAATGGTGCAATGGAAGCGGCCAATAAAAATATCAGGGAAAATGACTGAGACTT
ACAAGGACTGGCATGAGAAATAAACAGACAAGACTTACAAGGACTTACAAGGACTGGCACGAGAT
GAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAGAGGA
CATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAGGGAG
AAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCCTAAC
AGGCAACTGAGAATGATAAAAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATGGGGAG
ATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACGCTGTGAAGGCTAAGAA
AATCTTAGAGGAAGTCCATGAGGGTATTTGCGGAACGCATGCCAGTGGGTTCACAATGGCTAGAC
AGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCAAGAAG
TGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTTGCCTCTTCATGTTATGAC
TTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCAATATCGTCGAAGGCTTCTA
ATAGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCTTCGTAT
GCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATATGGAAT
GCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGTGGATGTCTGCA
GTCAATTTAAGATCAGACACCATAATTCGTCACCGTAC
Found at i:27613405 original size:132 final size:132
Alignment explanation
Indices: 27613154--27613569 Score: 566
Period size: 132 Copynumber: 3.2 Consensus size: 132
27613144 TGGATTGAAG
* * ** *
27613154 AAGATGGTGAATCTTATCTTCCCGAGGTAGTAGATAAGCAGATTTAAGCCACCAGTCCTGTCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
* * *
27613219 CTGAGCAGCAGTGGAGTAGGTTGAAGATTATGGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
66 CTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCTTAAGCAGTAGTGGAGCAGAT
*
27613284 CC
131 CA
* * *
27613286 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCAATCCTATCTTC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
* *
27613351 CTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCCTGTCTCCTTAAGTAGTAGTGGAGCAGAT
66 CTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCTTAAGCAGTAGTGGAGCAGAT
27613416 CA
131 CA
* * *
27613418 AAGATGGTGAATCTTATCTTCCTAAGGTAGTAGGGAAGCAGATTTAAACCACCAGTCCTATCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
** * * * * *
27613483 CAAAGTAGCAGTGGAGTAGGTTCAAGATTGTAGATCATGTAT-CTCTGAGCAGTAGTGGAGCAGA
66 CTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCT-TAAGCAGTAGTGGAGCAGA
*
27613547 TCG
130 TCA
* *
27613550 AAGACAGCGAATCTTA-CTTC
1 AAGACGGTGAATCTTATCTTC
27613570 TTCAACGTTA
Statistics
Matches: 250, Mismatches: 33, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
131 6 0.02
132 244 0.98
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
CTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCTTAAGCAGTAGTGGAGCAGAT
CA
Found at i:27613612 original size:50 final size:50
Alignment explanation
Indices: 27613553--27613717 Score: 213
Period size: 50 Copynumber: 3.3 Consensus size: 50
27613543 CAGATCGAAG
* * * *
27613553 ACAGCGAATCTTACTTCTTCAACGTTACAGTAAAACAGATTGAAGCTACA
1 ACAGCGAATCTTACTTCTCCGACGTTGCAGTAAAACAGATTAAAGCTACA
* * * * * *
27613603 ACAGTGAATCTTACTTCCCCGACGTTGCAGTGAAGCGGGTTAAAGCTACA
1 ACAGCGAATCTTACTTCTCCGACGTTGCAGTAAAACAGATTAAAGCTACA
* * *
27613653 ACAGCGAATCTTAGTTCTCCGACGTTGCAATAAAATAGATTAAAGCTACA
1 ACAGCGAATCTTACTTCTCCGACGTTGCAGTAAAACAGATTAAAGCTACA
27613703 ACAGCGAATCTTACT
1 ACAGCGAATCTTACT
27613718 ACCCTAGCAT
Statistics
Matches: 95, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (50 bp):
ACAGCGAATCTTACTTCTCCGACGTTGCAGTAAAACAGATTAAAGCTACA
Found at i:27615209 original size:25 final size:25
Alignment explanation
Indices: 27615155--27615220 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
27615145 TTTTGAACTT
* *
27615155 ATATTATTTCTTTTAAATTGTTCTA
1 ATATTATTTATTTTAAATTGTTCCA
*
27615180 TTATTATTTATTTTAAATT-TTCCA
1 ATATTATTTATTTTAAATTGTTCCA
**
27615204 CATATTATGCATTTTAA
1 -ATATTATTTATTTTAA
27615221 GCTATATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (25 bp):
ATATTATTTATTTTAAATTGTTCCA
Found at i:27615472 original size:23 final size:23
Alignment explanation
Indices: 27615440--27615487 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
27615430 TGGTTATTTA
* *
27615440 TTTTAATTTGCTTTGTATGTTAT
1 TTTTAATTTGCTTTGCATATTAT
*
27615463 TTTTATTTTGCTTTGCATATTAT
1 TTTTAATTTGCTTTGCATATTAT
27615486 TT
1 TT
27615488 ACTTTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.67
Consensus pattern (23 bp):
TTTTAATTTGCTTTGCATATTAT
Found at i:27621864 original size:24 final size:24
Alignment explanation
Indices: 27621837--27621885 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
27621827 TAAACAACTT
27621837 TTGAATTAATGGTTTATCATATTA
1 TTGAATTAATGGTTTATCATATTA
27621861 TTGAATTAATGGTTTATCATATTA
1 TTGAATTAATGGTTTATCATATTA
27621885 T
1 T
27621886 AACATGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (24 bp):
TTGAATTAATGGTTTATCATATTA
Found at i:27622835 original size:26 final size:27
Alignment explanation
Indices: 27622787--27622837 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
27622777 TAAACCAAAC
*
27622787 TTTTAATAAGCACTTTTCCACAACACT
1 TTTTAATAAGCACTTTTCAACAACACT
27622814 TTTTAA-AAGCACTTCTT-AACAACA
1 TTTTAATAAGCACTT-TTCAACAACA
27622838 ATGCTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (27 bp):
TTTTAATAAGCACTTTTCAACAACACT
Found at i:27645267 original size:24 final size:23
Alignment explanation
Indices: 27645240--27645326 Score: 79
Period size: 24 Copynumber: 3.8 Consensus size: 23
27645230 GAGGGTGGTG
* *
27645240 AAGGTGGTGAGGTTGTTGGTAATA
1 AAGGTGGTGAGGGTGTTGG-AGTA
* *
27645264 AAGGTGGTGAGGGTG-AGG-GTG
1 AAGGTGGTGAGGGTGTTGGAGTA
* * *
27645285 AGGGTGGTGAGGTTGCTGGCAGTA
1 AAGGTGGTGAGGGTGTTGG-AGTA
27645309 AAGGTGGTGAGGGTGTTG
1 AAGGTGGTGAGGGTGTTG
27645327 AGGATCAGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 2 0.04
24 31 0.63
ACGTcount: A:0.20, C:0.02, G:0.52, T:0.26
Consensus pattern (23 bp):
AAGGTGGTGAGGGTGTTGGAGTA
Found at i:27645311 original size:45 final size:43
Alignment explanation
Indices: 27645225--27645323 Score: 137
Period size: 45 Copynumber: 2.3 Consensus size: 43
27645215 GGTAATGAAA
* *
27645225 GTGGTGAGGGT-GGTGAAGGTGGTGAGGTTGTTGGTAATAAAG
1 GTGGTGAGGGTGGGTGAAGGTGGTGAGGTTGCTGGCAATAAAG
* *
27645267 GTGGTGAGGGTGAGGGTGAGGGTGGTGAGGTTGCTGGCAGTAAAG
1 GTGGTGAGGGT--GGGTGAAGGTGGTGAGGTTGCTGGCAATAAAG
27645312 GTGGTGAGGGTG
1 GTGGTGAGGGTG
27645324 TTGAGGATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 11 0.22
43 1 0.02
45 38 0.76
ACGTcount: A:0.18, C:0.02, G:0.55, T:0.25
Consensus pattern (43 bp):
GTGGTGAGGGTGGGTGAAGGTGGTGAGGTTGCTGGCAATAAAG
Found at i:27646948 original size:21 final size:21
Alignment explanation
Indices: 27646908--27646958 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
27646898 ATTTATAACA
* *
27646908 TATTCAATTCTCATCTCTTGC
1 TATTCAAATCTCATCACTTGC
27646929 TATTTCAAATCTCAT-ACTTGC
1 TA-TTCAAATCTCATCACTTGC
27646950 TATTCAAAT
1 TATTCAAAT
27646959 AGCTTTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (21 bp):
TATTCAAATCTCATCACTTGC
Found at i:27648123 original size:9 final size:9
Alignment explanation
Indices: 27648109--27648140 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
27648099 TAGTTTCATC
27648109 TTTCTTTCT
1 TTTCTTTCT
27648118 TTTCTTTCT
1 TTTCTTTCT
*
27648127 TTCCTTTCT
1 TTTCTTTCT
27648136 TTTCT
1 TTTCT
27648141 CCCTATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:27648125 original size:13 final size:13
Alignment explanation
Indices: 27648107--27648137 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27648097 CCTAGTTTCA
*
27648107 TCTTTCTTTCTTT
1 TCTTTCTTTCCTT
27648120 TCTTTCTTTCCTT
1 TCTTTCTTTCCTT
27648133 TCTTT
1 TCTTT
27648138 TCTCCCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTCTTTCCTT
Found at i:27648195 original size:14 final size:14
Alignment explanation
Indices: 27648176--27648221 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
27648166 TTCTATTCTT
27648176 TATTTATTTTATTA
1 TATTTATTTTATTA
*
27648190 TATTTACTTTATTA
1 TATTTATTTTATTA
* *
27648204 T-TATATTATA-TA
1 TATTTATTTTATTA
27648216 TATTTA
1 TATTTA
27648222 CTTAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:27648231 original size:26 final size:25
Alignment explanation
Indices: 27648179--27648232 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
27648169 TATTCTTTAT
* * *
27648179 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
27648204 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
27648230 TTA
1 TTA
27648233 AGTAATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:27648244 original size:26 final size:26
Alignment explanation
Indices: 27648189--27648246 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
27648179 TTATTTTATT
* * * *
27648189 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
27648215 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
27648241 ATATTT
1 ATATTT
27648247 TATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:27650240 original size:159 final size:158
Alignment explanation
Indices: 27649909--27650367 Score: 561
Period size: 159 Copynumber: 2.9 Consensus size: 158
27649899 AACAAAGGAT
* * * *
27649909 CATGCATTCAACCTAACACAACAGGAGCACAGGTATATCGTAAACACTTTTTCATTGTCAATTCC
1 CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCGTAAACACTTTTT-AATGTCAATTCC
* *
27649974 AAAATATTAAAATCTAATTT-GGGTTCTAATTTTTTTGGTCTTAGTCTGGTACTAGTACGAGAAC
65 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACTAGTACGAGAAC
* * *
27650038 TAGAAACCCAAAAAATAACAACATAACAC
130 TAGAAACCAAAAAAAGAACAACAGAACAC
* * * **
27650067 CATGCATTAAGCCTAATACAACTGGATCACAGGTATATCGTATACACTATTTTAATGTCAATTTA
1 CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCGTAAACACT-TTTTAATGTCAATTCC
* * * *
27650132 AAAATATTTTAATCTAATTTGGGGTTTTGATTTTTTTGGTGTTAGTCTGGTA-TGAGTA-TACGA
65 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACT-AGTACGA-GA
**
27650195 ACTAGAAGTCAAAAAAAGAACAACAGAACAC
128 ACTAGAAACCAAAAAAAGAACAACAGAACAC
* *
27650226 CATGCATTCAGCCTAACACAACTGGATCGCAGGTATATCGTAAACATTTTTTTAATGTCAATTCC
1 CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCGTAAACA-CTTTTTAATGTCAATTCC
* * * * *
27650291 AAATTATTTAAATCTAATTTGGGGTTCTGA--CTTTTGTTCTCT-GTCTGGTACAAGTATGAGAA
65 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCT-TAGTCTGGTACTAGTACGAGAA
* *
27650353 CTACAAGCCAAAAAA
129 CTAGAAACCAAAAAA
27650368 GGATGGCATA
Statistics
Matches: 256, Mismatches: 37, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
157 35 0.14
158 73 0.29
159 147 0.57
160 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (158 bp):
CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCGTAAACACTTTTTAATGTCAATTCCA
AAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACTAGTACGAGAACT
AGAAACCAAAAAAAGAACAACAGAACAC
Found at i:27650583 original size:82 final size:82
Alignment explanation
Indices: 27650444--27650647 Score: 329
Period size: 82 Copynumber: 2.5 Consensus size: 82
27650434 TAAAGATGGT
* * **
27650444 TAACATGTTTTGTTTGTTTTTT-AAATGATTTGTTGAAATGGTTGGTTAACATTTTACTACTATA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTATTGAAATGGTTGGTTAACAACTTACTACTATA
27650508 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
27650525 TAACATATTTTGTTTGTTTTTTGAAATGATTTATTGAAATGGTTGGTTAACAACTTACTACTATA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTATTGAAATGGTTGGTTAACAACTTACTACTATA
* *
27650590 TGATCATTTTGTTAGTA
66 GGATCATTTTGTTAGCA
*
27650607 TAACATATTTTGTTTGGTTTTTTGAAATGATTTTTTGAAAT
1 TAACATATTTTGTTT-GTTTTTTGAAATGATTTATTGAAAT
27650648 ATGTATACTA
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
81 21 0.18
82 69 0.61
83 24 0.21
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.50
Consensus pattern (82 bp):
TAACATATTTTGTTTGTTTTTTGAAATGATTTATTGAAATGGTTGGTTAACAACTTACTACTATA
GGATCATTTTGTTAGCA
Found at i:27651925 original size:21 final size:21
Alignment explanation
Indices: 27651901--27651945 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
27651891 CAAATACAGT
27651901 TCCAATGTCATACTTATCAAC
1 TCCAATGTCATACTTATCAAC
27651922 TCCAATGTCATACTTATCAAC
1 TCCAATGTCATACTTATCAAC
27651943 TCC
1 TCC
27651946 GTAATCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (21 bp):
TCCAATGTCATACTTATCAAC
Found at i:27652174 original size:112 final size:115
Alignment explanation
Indices: 27652018--27652228 Score: 347
Period size: 112 Copynumber: 1.9 Consensus size: 115
27652008 TACTTTAATA
*
27652018 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATT-AAAAAAT-AAAAAAAATC-CCCAAT
1 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
27652080 TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
66 TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
*
27652130 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTTAAAAAATCAAAAAAAATCACACAAT
1 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
* * * *
27652195 TTTTTATGAACCTTAAAACAAATCGGCTAAATAT
66 TTCTTATGAACCCTAAAAAAAATCAGCTAAATAT
27652229 ACAGTGCCTA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 39 0.43
113 7 0.08
114 10 0.11
115 35 0.38
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (115 bp):
TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
Found at i:27652732 original size:16 final size:16
Alignment explanation
Indices: 27652702--27652731 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27652692 TTAGTTAGGG
27652702 ATTTTAATTTATTTTA
1 ATTTTAATTTATTTTA
27652718 ATTTTAA-TTATTTT
1 ATTTTAATTTATTTT
27652732 TTAAGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTAATTTATTTTA
Found at i:27656915 original size:30 final size:30
Alignment explanation
Indices: 27656876--27656932 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
27656866 TTTTATAAAT
27656876 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
27656906 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
27656933 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:27657128 original size:13 final size:13
Alignment explanation
Indices: 27657109--27657156 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
27657099 TAAACCAAAT
27657109 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
27657122 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
27657135 TTTTCTATAGCAC
1 TTTTCAAAAGCAC
27657148 TTTTCAAAA
1 TTTTCAAAA
27657157 ACAATGAAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:27660515 original size:14 final size:14
Alignment explanation
Indices: 27660496--27660540 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
27660486 ATTCATCAAC
27660496 ATCTCATCTCACAT
1 ATCTCATCTCACAT
27660510 ATCTCA-CATCACAT
1 ATCTCATC-TCACAT
* *
27660524 ATCACATATCACAT
1 ATCTCATCTCACAT
27660538 ATC
1 ATC
27660541 GATGGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 26 0.96
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (14 bp):
ATCTCATCTCACAT
Found at i:27660528 original size:21 final size:21
Alignment explanation
Indices: 27660494--27660533 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27660484 CCATTCATCA
* *
27660494 ACATCTCATCTCACATATCTC
1 ACATCACATATCACATATCTC
27660515 ACATCACATATCACATATC
1 ACATCACATATCACATATC
27660534 ACATATCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (21 bp):
ACATCACATATCACATATCTC
Found at i:27660529 original size:7 final size:7
Alignment explanation
Indices: 27660504--27660540 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
27660494 ACATCTCATC
27660504 TCACATA
1 TCACATA
* *
27660511 TCTCACA
1 TCACATA
27660518 TCACATA
1 TCACATA
27660525 TCACATA
1 TCACATA
27660532 TCACATA
1 TCACATA
27660539 TC
1 TC
27660541 GATGGTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (7 bp):
TCACATA
Found at i:27665339 original size:41 final size:42
Alignment explanation
Indices: 27665286--27665421 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 42
27665276 TGCTTCCACA
*
27665286 TTGCTTCCTTTTTAGTCTAAACCTT-GAGGTTGCTTTCCCAAG
1 TTGCCTCCTTTTTAGTCTAAA-CTTGGAGGTTGCTTTCCCAAG
* * * *
27665328 TTGCCTCTTTTTTTGTCTGAACTTGGATGTTGCTTTCCCAAG
1 TTGCCTCCTTTTTAGTCTAAACTTGGAGGTTGCTTTCCCAAG
* * * * * * * *
27665370 TTGCTTCCTTTTTTGTTTAGACATGGATGTTGCTTTTCCATG
1 TTGCCTCCTTTTTAGTCTAAACTTGGAGGTTGCTTTCCCAAG
*
27665412 TTGCTTCCTT
1 TTGCCTCCTT
27665422 GATATTTTTC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 3 0.04
42 77 0.96
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (42 bp):
TTGCCTCCTTTTTAGTCTAAACTTGGAGGTTGCTTTCCCAAG
Found at i:27665360 original size:42 final size:42
Alignment explanation
Indices: 27665314--27665421 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
27665304 AAACCTTGAG
* *
27665314 GTTGCTTTCCCAAGTTGCCTCTTTTTTTGTCTGA-ACTTGGAT
1 GTTGCTTTCCCAAGTTGCCTCCTTTTTTGT-TGAGACATGGAT
* *
27665356 GTTGCTTTCCCAAGTTGCTTCCTTTTTTGTTTAGACATGGAT
1 GTTGCTTTCCCAAGTTGCCTCCTTTTTTGTTGAGACATGGAT
* * *
27665398 GTTGCTTTTCCATGTTGCTTCCTT
1 GTTGCTTTCCCAAGTTGCCTCCTT
27665422 GATATTTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 2 0.03
42 57 0.97
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (42 bp):
GTTGCTTTCCCAAGTTGCCTCCTTTTTTGTTGAGACATGGAT
Found at i:27668477 original size:9 final size:9
Alignment explanation
Indices: 27668463--27668502 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
27668453 TTTTGTTAAA
27668463 AATTAACCG
1 AATTAACCG
27668472 AATTAACCG
1 AATTAACCG
*
27668481 AATTACCCG
1 AATTAACCG
*
27668490 AATTACCCG
1 AATTAACCG
27668499 AATT
1 AATT
27668503 GAATCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:27668749 original size:38 final size:39
Alignment explanation
Indices: 27668705--27668797 Score: 161
Period size: 38 Copynumber: 2.4 Consensus size: 39
27668695 ACTTAAGAGT
* *
27668705 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTTGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
27668743 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
27668782 TAGACTTTAGTTTTAG
1 TAGACTTTAGTTTTAG
27668798 GGCCAGTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
38 27 0.52
39 25 0.48
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.52
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:27671254 original size:71 final size:71
Alignment explanation
Indices: 27671164--27671328 Score: 321
Period size: 71 Copynumber: 2.3 Consensus size: 71
27671154 AAAATCATAT
*
27671164 ATAAACAACTATTGATAAAACTAATTTAATAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
1 ATAAATAACTATTGATAAAACTAATTTAATAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
27671229 CAAAAC
66 CAAAAC
27671235 ATAAATAACTATTGATAAAACTAATTTAATAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
1 ATAAATAACTATTGATAAAACTAATTTAATAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
27671300 CAAAAC
66 CAAAAC
27671306 ATAAATAACTATTGATAAAACTA
1 ATAAATAACTATTGATAAAACTA
27671329 GTTAGCATTG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (71 bp):
ATAAATAACTATTGATAAAACTAATTTAATAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
CAAAAC
Found at i:27671782 original size:18 final size:18
Alignment explanation
Indices: 27671759--27671824 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
27671749 TTCATCAATT
*
27671759 TGAACATCATTTGAGATG
1 TGAACATCATTTGAAATG
27671777 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
27671795 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
*
27671813 TGAACATTATTT
1 TGAACATCATTT
27671825 CTCATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:27673868 original size:14 final size:14
Alignment explanation
Indices: 27673833--27673876 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
27673823 GAACACCAGC
* *
27673833 ACCAGCAAAAAAGA
1 ACCAGCAGAGAAGA
27673847 ACCAGCAGAGAAGA
1 ACCAGCAGAGAAGA
27673861 ACCAGCAGAGAAGA
1 ACCAGCAGAGAAGA
27673875 AC
1 AC
27673877 AAACGTGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.55, C:0.23, G:0.23, T:0.00
Consensus pattern (14 bp):
ACCAGCAGAGAAGA
Found at i:27674125 original size:17 final size:18
Alignment explanation
Indices: 27674092--27674126 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27674082 GCTTAGTTTT
27674092 ATTGAGTTGGATAATTGG
1 ATTGAGTTGGATAATTGG
27674110 ATTGAGTTGG-TAATTGG
1 ATTGAGTTGGATAATTGG
27674127 GTTGGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (18 bp):
ATTGAGTTGGATAATTGG
Found at i:27674130 original size:12 final size:13
Alignment explanation
Indices: 27674110--27674142 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27674100 GGATAATTGG
27674110 ATTGAGTT-GGTA
1 ATTGAGTTGGGTA
*
27674122 ATTGGGTTGGGTA
1 ATTGAGTTGGGTA
27674135 ATTGAGTT
1 ATTGAGTT
27674143 TGGTTGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (13 bp):
ATTGAGTTGGGTA
Found at i:27674131 original size:30 final size:31
Alignment explanation
Indices: 27674092--27674155 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
27674082 GCTTAGTTTT
27674092 ATTGAGTTGGATAATTG-GATTGAGTTGG-TA
1 ATTGAGTTGGATAATTGAGATTG-GTTGGATA
* * *
27674122 ATTGGGTTGGGTAATTGAGTTTGGTTGGATA
1 ATTGAGTTGGATAATTGAGATTGGTTGGATA
27674153 ATT
1 ATT
27674156 TTATTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.42
Consensus pattern (31 bp):
ATTGAGTTGGATAATTGAGATTGGTTGGATA
Found at i:27674205 original size:17 final size:16
Alignment explanation
Indices: 27674185--27674237 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
27674175 GTTAACCGAA
27674185 TAATTGGGTTAGGTTGG
1 TAATTGGGTT-GGTTGG
27674202 TAATTGGGTT-G--GG
1 TAATTGGGTTGGTTGG
27674215 TAATTGGGTTTGGTTGG
1 TAATTGGG-TTGGTTGG
27674232 ATAATT
1 -TAATT
27674238 TTATTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 2 0.06
17 12 0.39
18 5 0.16
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (16 bp):
TAATTGGGTTGGTTGG
Found at i:27674213 original size:12 final size:13
Alignment explanation
Indices: 27674196--27674224 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27674186 AATTGGGTTA
27674196 GGTT-GGTAATTG
1 GGTTGGGTAATTG
27674208 GGTTGGGTAATTG
1 GGTTGGGTAATTG
27674221 GGTT
1 GGTT
27674225 TGGTTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (13 bp):
GGTTGGGTAATTG
Found at i:27674239 original size:82 final size:82
Alignment explanation
Indices: 27674102--27674266 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 82
27674092 ATTGAGTTGG
27674102 ATAATTGGATTGAGTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTAA
1 ATAATTGGATTGAGTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTAA
27674167 TCTTTTCGGTTAACCGA
66 TCTTTTCGGTTAACCGA
* *
27674184 ATAATTGGGTT-AGGTTGGTAATTGGGTTGGGTAATTGGGTTTGGTTGGATAATTTTATTTATTA
1 ATAATTGGATTGA-GTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTA
*
27674248 ATTTTTTCGGTTAACCGA
65 ATCTTTTCGGTTAACCGA
27674266 A
1 A
27674267 AAAATTTAGT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.01
82 78 0.99
ACGTcount: A:0.24, C:0.04, G:0.27, T:0.45
Consensus pattern (82 bp):
ATAATTGGATTGAGTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTAA
TCTTTTCGGTTAACCGA
Found at i:27691509 original size:6 final size:6
Alignment explanation
Indices: 27691498--27691531 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
27691488 ATAAATAAAT
27691498 AAATAG AAATAG AAATAG AAATAG AAATAG AAAT
1 AAATAG AAATAG AAATAG AAATAG AAATAG AAAT
27691532 GCAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (6 bp):
AAATAG
Found at i:27692453 original size:44 final size:45
Alignment explanation
Indices: 27692342--27692783 Score: 296
Period size: 45 Copynumber: 9.7 Consensus size: 45
27692332 TTACATTCGT
* * * * * *
27692342 TCCACTGCAATTTCAAGGAAATAAGACTTGCTATCTTCAGTCTGT
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* * * * * *
27692387 TCCACTGCAATTTC-AGAAAGATAAGACTCGTAAT-TTCAACCTGC
1 TCCACTGCAACTTCAAG-GAGATAAGATTTGTTATCTTCAATCTGC
* *
27692431 TCCACTGCAACTTCAAGGAGATAAGGTTTG-TATATTCAATCTGC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* * *
27692475 CCCACTGCAACTTCAAGGGGATAAGGTTTGTTA-CTTCAACCTGCTTTGC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAA--T-C--TGC
* * * * *
27692524 TGCGAC-GTAACTTC-A-GAGGTAAGATTTGTTATCTTCAGTCTAC
1 T-CCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* * ** *
27692567 TCCATTGCAACTTCAAGGAGATAAGACTCGTTATGGTAGATTTAAT-TCGAC
1 TCCACTGCAACTTCAAGGAGATAAGA----TT-TGTTATCTTCAATCT-G-C
* * * *
27692618 -CTACTGCAACTTC--GGAGGTATAAGAATAG-TAGCTTCAATCTGC
1 TCCACTGCAACTTCAAGGA-G-ATAAGATTTGTTATCTTCAATCTGC
* * * * *
27692661 TCCACTGCAACTTCAGGGAGATAGGATTGGTTATCTTCAACCTAC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* *
27692706 TCCACTGCAACTTCAAGAAGATAAGATTTGTTATCTTCAGTCTGC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* *
27692751 TCCACTGCAACTTTAAGGAGATAAGACTTGTTA
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTA
27692784 CGAAGTGATC
Statistics
Matches: 310, Mismatches: 59, Indels: 56
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.01
43 13 0.04
44 102 0.33
45 121 0.39
46 6 0.02
47 14 0.05
48 9 0.03
49 14 0.05
50 28 0.09
51 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
Found at i:27693043 original size:44 final size:42
Alignment explanation
Indices: 27692943--27693531 Score: 345
Period size: 44 Copynumber: 13.7 Consensus size: 42
27692933 GTCTGATGCG
* * * **
27692943 ATCTGCTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT---TGGTTTTCA
* * * *
27692987 ATCCGCTTCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * * *
27693031 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGG-ATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* * * *
27693072 ATTTGCTCTACTGTAACTTCAGAGAGATAAGATCTCTGGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTTTTCA
* * * *
27693116 ATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * * * *
27693160 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
*
27693201 ATCTGCTCTACTGCAACTTCAGAGG-GATAAGATTTGTGGTTTT-A
1 ATCTGCTCCACTGCAACTTCAG-GGAGATAAGA--T-TGGTTTTCA
* * * * * * * *
27693245 ATCCGCTCCATTGTAGCTTTAGGGAGATAGGGTTGGCTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * ** *
27693289 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-GAATGCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* *
27693330 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTTTTCA
* * * * * *
27693374 ATCCGCTCCATTGTAACTTTAGGGAGATAGGATTGGCTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * * * * * *
27693418 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAG-ATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* **
27693459 ATCTGCTCTACTGCAACTTCAGAAAGAT-AGCATCTGTAGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG-AT-TG--GTTTTCA
*
27693503 ATCCGCTCCACTGCAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
27693532 GGACTGGTGT
Statistics
Matches: 406, Mismatches: 108, Indels: 61
0.71 0.19 0.11
Matches are distributed among these distances:
40 2 0.00
41 124 0.31
42 15 0.04
43 13 0.03
44 248 0.61
45 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
Found at i:27693130 original size:85 final size:84
Alignment explanation
Indices: 27692995--27693449 Score: 271
Period size: 85 Copynumber: 5.3 Consensus size: 84
27692985 TAATCCGCTT
*
27692995 CACTGCAACTTCAG-GAAGATAGGA-T-TGGTTTCTTCAATCTGCTCCACTGCAACTTTAGGGAG
1 CACTGCAACTTCAGAG-AGATAAGATTCTGG-TT-TT-AATCTGCTCCACTGCAACTTTAGGGAG
*
27693057 ATAAGATTGGATGCGATTTGCTC
62 ATAAGATTGGATGCGATCTGCTC
* * *
27693080 TACTGTAACTTCAGAGAGATAAGATCTCTGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATA
1 CACTGCAACTTCAGAGAGATAAGAT-TCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATA
* * * *
27693145 GGATTGGCTTCTTCTATCTGCTC
65 AGATTGG---ATGCGATCTGCTC
* * * * * * *
27693168 CACTGCAACTTCAGGGAGATAAGA--CTAGATGTGATCTGCTCTACTGCAACTTCAGAGG-GATA
1 CACTGCAACTTCAGAGAGATAAGATTCTGGTTTTAATCTGCTCCACTGCAACTTTAG-GGAGATA
* *** *
27693230 AGATTTGTGGTTTTAATCCGCTC
65 AGA--T-TGGATGCGATCTGCTC
* * * * * ** ** *
27693253 CATTGTAGCTTTAGGGAGAT-AGGGT-TGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGA
1 CACTGCAACTTCAGAGAGATAAGATTCTGG-TT-TT-AATCTGCTCCACTGCAACTTTAGGGAGA
* * *
27693316 TAAGACTGAATGCAATCTGCTC
63 TAAGATTGGATGCGATCTGCTC
* * * * *
27693338 TACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTAATCCGCTCCATTGTAACTTTAGGGAGATA
1 CACTGCAACTTCAGAGAGATAAGA-TTCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATA
* * *
27693403 GGATTGGCTTCTTCTG-TCTGCTC
65 AGATTGG---ATGC-GATCTGCTC
* *
27693426 CACTGCAACTTTAGGGAGATAAGA
1 CACTGCAACTTCAGAGAGATAAGA
27693450 CTAGATGCGA
Statistics
Matches: 282, Mismatches: 64, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
84 2 0.01
85 164 0.58
86 10 0.04
87 10 0.04
88 96 0.34
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (84 bp):
CACTGCAACTTCAGAGAGATAAGATTCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATAA
GATTGGATGCGATCTGCTC
Found at i:27693553 original size:129 final size:129
Alignment explanation
Indices: 27692937--27693534 Score: 867
Period size: 129 Copynumber: 4.6 Consensus size: 129
27692927 AATAAAGTCT
* ** ** *
27692937 GATGCGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * * * * * *
27693002 ACTTCAGGAAGATAGGATTGGTTTCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTG
66 ACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * *
27693066 GATGCGATTTGCTCTACTGTAACTTCAGAGAGATAAGATCTCTGGTTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
27693131 ACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
66 ACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * * * *
27693195 GATGTGATCTGCTCTACTGCAACTTCAGAGGGATAAGATTTGTGGTTTTAATCCGCTCCATTGTA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * *
27693260 GCTTTAGGGAGATAGGGTTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-
66 ACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * * *
27693323 GAATGCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTAATCCGCTCCATTGT
1 G-ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGC
* *
27693388 AACTTTAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTA
65 AACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* *
27693453 GATGCGATCTGCTCTACTGCAACTTCAGAAAGAT-AGCATCTGTAGTTTTAATCCGCTCCACTGC
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAG-ATCTGTGGTTTTAATCCGCTCCACTGC
*
27693517 AACTTCAGGGAGATAGGA
65 AACTTTAGGGAGATAGGA
27693535 CTGGTGTTTT
Statistics
Matches: 427, Mismatches: 39, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
128 3 0.01
129 423 0.99
130 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
ACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
Found at i:27694004 original size:24 final size:23
Alignment explanation
Indices: 27693972--27694028 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
27693962 CAGATTGCCC
27693972 CCACTGTAATCTTCAAGGTCCAAT
1 CCACTGTAAT-TTCAAGGTCCAAT
* * *
27693996 CCACTGTAA-TTCTATGTTCAAT
1 CCACTGTAATTTCAAGGTCCAAT
27694018 CCACTGTAATT
1 CCACTGTAATT
27694029 CTTGGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 1 0.03
24 9 0.31
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (23 bp):
CCACTGTAATTTCAAGGTCCAAT
Found at i:27694980 original size:11 final size:10
Alignment explanation
Indices: 27694964--27695024 Score: 70
Period size: 11 Copynumber: 5.8 Consensus size: 10
27694954 GGCCTCTCTT
27694964 TTTTCTTTTTC
1 TTTT-TTTTTC
*
27694975 TTTTCTTCTTC
1 TTTT-TTTTTC
27694986 TTTTTTTTTC
1 TTTTTTTTTC
27694996 TTTTTTTTCTC
1 TTTTTTTT-TC
27695007 TTTTTTTTT-
1 TTTTTTTTTC
27695016 TATTTTTTT
1 T-TTTTTTT
27695025 AAATATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
9 1 0.02
10 21 0.46
11 24 0.52
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:27695015 original size:21 final size:20
Alignment explanation
Indices: 27694958--27695024 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 20
27694948 CACATTGGCC
27694958 TCTCTTTTTTCTTTTTCTTTTCT
1 TCTCTTTTTT-TTTTT-TTTT-T
27694981 TCTTCTTTTTTTTTCTTTTTTT
1 TC-TCTTTTTTTTT-TTTTTTT
27695003 TCTCTTTTTTTTTTATTTTTT
1 TCTCTTTTTTTTTT-TTTTTT
27695024 T
1 T
27695025 AAATATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.02
21 18 0.44
22 3 0.07
23 9 0.22
24 10 0.24
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (20 bp):
TCTCTTTTTTTTTTTTTTTT
Found at i:27698917 original size:107 final size:106
Alignment explanation
Indices: 27698740--27698934 Score: 300
Period size: 107 Copynumber: 1.8 Consensus size: 106
27698730 GATTTAAGAG
* * * * * *
27698740 GATATTTGGCTATTTGGTCAAACGAGAAGTCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAAT
27698805 TTCCAAACGCAAAATATTGTCTTATTTTGAAATTTTAAAAA
66 TTCCAAACGCAAAATATTGTCTTATTTTGAAATTTTAAAAA
* *
27698846 GATATTTGACTATTTGGTCGAATGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAA
1 GATATTTGACTATTTGGTCAAACG-AAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAA
*
27698911 TTTCCAAATGCAAAATATTGTCTT
65 TTTCCAAACGCAAAATATTGTCTT
27698935 TATTATTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 21 0.27
107 58 0.73
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (106 bp):
GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAAT
TTCCAAACGCAAAATATTGTCTTATTTTGAAATTTTAAAAA
Found at i:27699166 original size:73 final size:73
Alignment explanation
Indices: 27699079--27699214 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 73
27699069 TCAGGTTTAG
* *
27699079 AAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAAAT
1 AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAAAT
27699144 TTGAGGAA
66 TTGAGGAA
*
27699152 AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTTCCGAGATCGTTTAAAA
1 AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
27699215 CTTGAATTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (73 bp):
AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAAAT
TTGAGGAA
Found at i:27699659 original size:47 final size:47
Alignment explanation
Indices: 27699567--27699659 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
27699557 GAAAATGAAT
*
27699567 AAAATTATAGAAATATAAAAAGATATATATGAATATATATGTATATA
1 AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
* *
27699614 AAAATTATA-AAATATAAAAA-ATATATATATAAGTATGTATATATAT
1 AAAATTATAGAAATATAAAAAGATATATAT-GAA-TATATATATATAT
27699660 TCGTGAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 8 0.20
46 13 0.32
47 20 0.49
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (47 bp):
AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
Found at i:27700701 original size:20 final size:20
Alignment explanation
Indices: 27700676--27700717 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
27700666 AAATCCCAAA
27700676 TTGCTACTTTTGATTTTGTC
1 TTGCTACTTTTGATTTTGTC
27700696 TTGCTACTTTTGATTTTGTC
1 TTGCTACTTTTGATTTTGTC
27700716 TT
1 TT
27700718 TCTTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (20 bp):
TTGCTACTTTTGATTTTGTC
Found at i:27703331 original size:3 final size:3
Alignment explanation
Indices: 27703323--27703357 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27703313 GCAAATTTGT
27703323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27703358 TCATGTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27703810 original size:48 final size:47
Alignment explanation
Indices: 27703749--27703859 Score: 138
Period size: 45 Copynumber: 2.4 Consensus size: 47
27703739 TATTATAAAA
27703749 TCAAATAATTATTTCAAACACAAAT-ATTATTTTTATATGTAAAATATT
1 TCAAATAATTATTTCAAA-A-AAATCATTATTTTTATATGTAAAATATT
* * * * *
27703797 TTAAATAACTATTTC--AAATATCATTATTTTTATATGTGAAGTATT
1 TCAAATAATTATTTCAAAAAAATCATTATTTTTATATGTAAAATATT
27703842 TCAAATAATTATTTCAAA
1 TCAAATAATTATTTCAAA
27703860 TACACATACA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
44 3 0.06
45 35 0.66
46 1 0.02
47 1 0.02
48 13 0.25
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (47 bp):
TCAAATAATTATTTCAAAAAAATCATTATTTTTATATGTAAAATATT
Found at i:27703833 original size:45 final size:45
Alignment explanation
Indices: 27703774--27703861 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
27703764 AAACACAAAT
*
27703774 ATTATTTTTATATGTAAAATATTTTAAATAACTATTTCAAATATC
1 ATTATTTTTATATGTAAAATATTTCAAATAACTATTTCAAATATC
* * *
27703819 ATTATTTTTATATGTGAAGTATTTCAAATAATTATTTCAAATA
1 ATTATTTTTATATGTAAAATATTTCAAATAACTATTTCAAATA
27703862 CACATACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (45 bp):
ATTATTTTTATATGTAAAATATTTCAAATAACTATTTCAAATATC
Found at i:27704026 original size:109 final size:105
Alignment explanation
Indices: 27703875--27704103 Score: 227
Period size: 107 Copynumber: 2.1 Consensus size: 105
27703865 ATACAAAATA
* *
27703875 TATAATACTAAAATTTACCACACCAATGGTACGGAATGAAAAATAA-ATATTTCACATATAAGAA
1 TATAATACTAGAATTTACCACACCAATGGTAC-GAATGAAAAATAAGACATTTCA-A-AT-A-AA
*
27703939 TTATA-TTAACTAAA-AATAATGATATTTGAAATAATTGA-TTGATTT
61 TTACATTTAA--AAATAATAATGATATTTGAAATAATT-ATTTGATTT
* * * **
27703984 TATAATACTAGAATTTACCATACCCATATTGTA-G-ATGAAAAAATAATGACATTTGAAATATTT
1 TATAATACTAGAATTTACCACA-CCA-ATGGTACGAATG-AAAAATAA-GACATTTCAAATAAAT
27704047 TACATTTAAAAATAATAATGATATTTGAAATAATTATTTGATTT
62 TACATTTAAAAATAATAATGATATTTGAAATAATTATTTGATTT
*
27704091 TATAATATTAGAA
1 TATAATACTAGAA
27704104 ATCCCTATAC
Statistics
Matches: 103, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
106 4 0.04
107 45 0.44
108 8 0.08
109 31 0.30
110 4 0.04
111 11 0.11
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (105 bp):
TATAATACTAGAATTTACCACACCAATGGTACGAATGAAAAATAAGACATTTCAAATAAATTACA
TTTAAAAATAATAATGATATTTGAAATAATTATTTGATTT
Found at i:27718461 original size:26 final size:26
Alignment explanation
Indices: 27718406--27718461 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
27718396 ATTACATTGG
* *
27718406 TAATCACTCAACTATAAATAATTTTT
1 TAATCACTCAACTATAAATAATTATA
* *
27718432 TAATTACTCAATTATGAAA-AATTATA
1 TAATCACTCAACTAT-AAATAATTATA
27718458 TAAT
1 TAAT
27718462 AGTTGCTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATCACTCAACTATAAATAATTATA
Found at i:27723911 original size:22 final size:21
Alignment explanation
Indices: 27723871--27723917 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
27723861 ATCACGTATA
* *
27723871 AATCATGTTTAAATTTATTCT
1 AATCATGTCTAAATATATTCT
*
27723892 AATCATGATCTAAATATATTTT
1 AATCATG-TCTAAATATATTCT
27723914 AATC
1 AATC
27723918 TAGAGATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (21 bp):
AATCATGTCTAAATATATTCT
Done.