Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 95 of 120
Found at i:28070349 original size:26 final size:26
Alignment explanation
Indices: 28070319--28070371 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28070309 AAGATAATTG
28070319 AAGCAACTAAGTAAGGAAAGAAACTA
1 AAGCAACTAAGTAAGGAAAGAAACTA
28070345 AAGCAACTAAGTAAGGAAAGAAACTA
1 AAGCAACTAAGTAAGGAAAGAAACTA
28070371 A
1 A
28070372 CCCGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.11, G:0.19, T:0.11
Consensus pattern (26 bp):
AAGCAACTAAGTAAGGAAAGAAACTA
Found at i:28070525 original size:5 final size:5
Alignment explanation
Indices: 28070515--28070545 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
28070505 AAACAAATAT
28070515 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
28070546 ATTCTATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:28085224 original size:22 final size:22
Alignment explanation
Indices: 28085199--28085262 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
28085189 TTAGACCATA
*
28085199 GTGATTTTATTTATAAATCATG
1 GTGATTTTCTTTATAAATCATG
28085221 GTGATTTTCTTTATAAATCATG
1 GTGATTTTCTTTATAAATCATG
*
28085243 GTGTTTTTCTTTATAAATCA
1 GTGATTTTCTTTATAAATCA
28085263 CGGAATCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (22 bp):
GTGATTTTCTTTATAAATCATG
Found at i:28087300 original size:6 final size:6
Alignment explanation
Indices: 28087286--28087323 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
28087276 AAAAATTAGA
*
28087286 TTAGGG TTAGTG TTAGGG TTAGGG TTAGGG TTTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG T
28087324 GTTTTTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:28088023 original size:19 final size:17
Alignment explanation
Indices: 28087990--28088022 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28087980 ATATATTTTA
28087990 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
28088007 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
28088023 TATATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:28093169 original size:27 final size:27
Alignment explanation
Indices: 28093139--28093226 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 27
28093129 CTGTCTCATT
*
28093139 GGACTTTCCTATGTTTAACGTCCCGTC
1 GGACTATCCTATGTTTAACGTCCCGTC
* *
28093166 GGACTATCCTGTGTTTAACGTCCTGTC
1 GGACTATCCTATGTTTAACGTCCCGTC
* * * *
28093193 GGACTATCCCATGTTTAACATCCCATT
1 GGACTATCCTATGTTTAACGTCCCGTC
28093220 GGACTAT
1 GGACTAT
28093227 ATACAATGCC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (27 bp):
GGACTATCCTATGTTTAACGTCCCGTC
Found at i:28093305 original size:57 final size:57
Alignment explanation
Indices: 28093232--28093376 Score: 193
Period size: 57 Copynumber: 2.5 Consensus size: 57
28093222 ACTATATACA
* * **
28093232 ATGCCACAGTGTCTTTCAACTATGGTCTTACTCATTATA-TCGTCAAATCATCTTTTG
1 ATGCCATAGCGTCTTTCAACTATGGTCTTACTCACAATACT-GTCAAATCATCTTTTG
* * *
28093289 ATGCCATAGCGTCTTTCAGCTATGGTATTACTCACAATACTGTCATATCATCTTTTG
1 ATGCCATAGCGTCTTTCAACTATGGTCTTACTCACAATACTGTCAAATCATCTTTTG
* *
28093346 ATTCCATAGCATCTTTCAACTATGGTCTTAC
1 ATGCCATAGCGTCTTTCAACTATGGTCTTAC
28093377 ACAATATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
57 75 0.99
58 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.39
Consensus pattern (57 bp):
ATGCCATAGCGTCTTTCAACTATGGTCTTACTCACAATACTGTCAAATCATCTTTTG
Found at i:28095033 original size:30 final size:31
Alignment explanation
Indices: 28094998--28095057 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
28094988 AAACTTTTTA
*
28094998 TTTTCCACC-AAAATTTTTATTCCC-TCCCAC
1 TTTTCC-CCTAAAACTTTTATTCCCTTCCCAC
28095028 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
28095058 TCCCATTCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 2 0.07
30 20 0.74
31 5 0.19
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTATTCCCTTCCCAC
Found at i:28095823 original size:5 final size:5
Alignment explanation
Indices: 28095813--28095838 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28095803 CTCGAAAATT
28095813 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
28095839 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:28101943 original size:22 final size:22
Alignment explanation
Indices: 28101903--28101944 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28101893 AATTTAACCA
**
28101903 TTTTTTATTTTTATTTTAATAT
1 TTTTTTATTTTTAACTTAATAT
*
28101925 TTTTTTGTTTTTAACTTAAT
1 TTTTTTATTTTTAACTTAAT
28101945 TGTTACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTATTTTTAACTTAATAT
Found at i:28104488 original size:21 final size:22
Alignment explanation
Indices: 28104463--28104505 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28104453 GGAGAGAGGA
28104463 AAAAAAT-AAAATAATAAAAAG
1 AAAAAATAAAAATAATAAAAAG
*
28104484 -AAAAATAAAAATAATCAAAAG
1 AAAAAATAAAAATAATAAAAAG
28104505 A
1 A
28104506 TTATCCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAAAATAAAAATAATAAAAAG
Found at i:28122172 original size:20 final size:22
Alignment explanation
Indices: 28122131--28122173 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
28122121 ACATAAGCAC
28122131 TTTAGTTAAGTATTAATTAAAT
1 TTTAGTTAAGTATTAATTAAAT
*
28122153 TTTAG-TAAGT-TTAGTTAAAT
1 TTTAGTTAAGTATTAATTAAAT
28122173 T
1 T
28122174 CAATAAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTAGTTAAGTATTAATTAAAT
Found at i:28124272 original size:14 final size:14
Alignment explanation
Indices: 28124249--28124281 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28124239 CTTGTTATTG
28124249 TTTC-TTGTTTGTT
1 TTTCTTTGTTTGTT
28124262 TTTCTTTGTTTGTT
1 TTTCTTTGTTTGTT
28124276 TTTCTT
1 TTTCTT
28124282 ATATTCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (14 bp):
TTTCTTTGTTTGTT
Found at i:28124518 original size:31 final size:29
Alignment explanation
Indices: 28124451--28124518 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
28124441 GGTGCACATA
* *
28124451 AGTTTTTATGTGTGTTTATTTTTGTTTTT
1 AGTTTTTATGTGTGTTTATTTTTGTATGT
*
28124480 ATGTTTTATTTGTGTGTTTATTCTTT-TATGT
1 A-GTTTT-TATGTGTGTTTATT-TTTGTATGT
28124511 AGTTTTTA
1 AGTTTTTA
28124519 AAAAAAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.06
30 10 0.31
31 17 0.53
32 3 0.09
ACGTcount: A:0.13, C:0.01, G:0.16, T:0.69
Consensus pattern (29 bp):
AGTTTTTATGTGTGTTTATTTTTGTATGT
Found at i:28128075 original size:37 final size:37
Alignment explanation
Indices: 28128017--28128225 Score: 246
Period size: 37 Copynumber: 5.7 Consensus size: 37
28128007 ATACTCCCTG
* *
28128017 ATTTGGCTTGTTATCAGGTGGATTAGCTCTTATGAGC
1 ATTTGGCGTGTTATCGGGTGGATTAGCTCTTATGAGC
* *
28128054 ATTTAGCGTGTTATCGGGTGGATTACCTCTTATGAGC
1 ATTTGGCGTGTTATCGGGTGGATTAGCTCTTATGAGC
* * *
28128091 ATTTGGTGTGTTACCAGGTGGATTAGCTCTTATGAGC
1 ATTTGGCGTGTTATCGGGTGGATTAGCTCTTATGAGC
* *
28128128 ATTTGGTGTGTTA-CTGGGTGGACTAGCTCTTATGAGC
1 ATTTGGCGTGTTATC-GGGTGGATTAGCTCTTATGAGC
* *
28128165 ATTTGGCGTGTTATCAGGG-GAAGTAGCTCTTATGAGC
1 ATTTGGCGTGTTATC-GGGTGGATTAGCTCTTATGAGC
* *
28128202 GA-TTGGTGTGTT-TCGGTTGGATTA
1 -ATTTGGCGTGTTATCGGGTGGATTA
28128226 CTTGTGTACT
Statistics
Matches: 149, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.01
36 7 0.05
37 135 0.91
38 5 0.03
ACGTcount: A:0.18, C:0.13, G:0.31, T:0.38
Consensus pattern (37 bp):
ATTTGGCGTGTTATCGGGTGGATTAGCTCTTATGAGC
Found at i:28128139 original size:74 final size:74
Alignment explanation
Indices: 28128017--28128226 Score: 277
Period size: 74 Copynumber: 2.9 Consensus size: 74
28128007 ATACTCCCTG
* *
28128017 ATTTGGCT-TGTTATCAGGTGGATTAGCTCTTATGAGCATTTAGCGTGTTATCGGGTGGATTACC
1 ATTTGG-TGTGTTATCAGGTGGATTAGCTCTTATGAGCATTTGGTGTGTTATCGGGTGGATTACC
28128081 TCTTATGAGC
65 TCTTATGAGC
* * *
28128091 ATTTGGTGTGTTACCAGGTGGATTAGCTCTTATGAGCATTTGGTGTGTTA-CTGGGTGGACTAGC
1 ATTTGGTGTGTTATCAGGTGGATTAGCTCTTATGAGCATTTGGTGTGTTATC-GGGTGGATTACC
28128155 TCTTATGAGC
65 TCTTATGAGC
* * *
28128165 ATTTGGCGTGTTATCAGG-GGAAGTAGCTCTTATGAGCGA-TTGGTGTGTT-TCGGTTGGATTAC
1 ATTTGGTGTGTTATCAGGTGG-ATTAGCTCTTATGAGC-ATTTGGTGTGTTATCGGGTGGATTAC
28128227 TTGTGTACTC
Statistics
Matches: 120, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
73 12 0.10
74 107 0.89
75 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.30, T:0.38
Consensus pattern (74 bp):
ATTTGGTGTGTTATCAGGTGGATTAGCTCTTATGAGCATTTGGTGTGTTATCGGGTGGATTACCT
CTTATGAGC
Found at i:28130702 original size:22 final size:22
Alignment explanation
Indices: 28130647--28130703 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
28130637 ACTGGTCGCT
** * *
28130647 ATGTCGCAACACGGAATTCTCT
1 ATGTCGCAACATAGAAATCTCA
*
28130669 ATGTCACAACATAGAAATCTCA
1 ATGTCGCAACATAGAAATCTCA
28130691 ATGTCGCAACATA
1 ATGTCGCAACATA
28130704 AGGACCAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (22 bp):
ATGTCGCAACATAGAAATCTCA
Found at i:28142009 original size:102 final size:103
Alignment explanation
Indices: 28141833--28142044 Score: 381
Period size: 102 Copynumber: 2.1 Consensus size: 103
28141823 TTAAATTAAC
*
28141833 TTTACAATCTAGTCCCTTTTCACATTCTAAGCTTAAAATCTATCAATTTCAAGTCTAATTCTTCA
1 TTTACAATCTAGTCCCTTTTCACATTCTAAGCTTAAAATCCATCAATTTCAAGTCTAATTCTTCA
*
28141898 ACAAATAAACAATGGTAATTTT-CTAAACTTTAACAGT
66 ACAAATAAACAATGGTAATTTTCCAAAACTTTAACAGT
* *
28141935 TTTACAATCTAGTCCTTTTTCACATTCTAAGCTTAAAATCCATCAATTTCAAGTCTAGTTCTTCA
1 TTTACAATCTAGTCCCTTTTCACATTCTAAGCTTAAAATCCATCAATTTCAAGTCTAATTCTTCA
28142000 ACAAATAAACAATGGTAATTTTCCAAAACTTTAACAGT
66 ACAAATAAACAATGGTAATTTTCCAAAACTTTAACAGT
28142038 TTTACAA
1 TTTACAA
28142045 GTTTGTACAT
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 84 0.80
103 21 0.20
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (103 bp):
TTTACAATCTAGTCCCTTTTCACATTCTAAGCTTAAAATCCATCAATTTCAAGTCTAATTCTTCA
ACAAATAAACAATGGTAATTTTCCAAAACTTTAACAGT
Found at i:28148267 original size:22 final size:22
Alignment explanation
Indices: 28148242--28148387 Score: 211
Period size: 22 Copynumber: 6.6 Consensus size: 22
28148232 TGGGTATAGT
*
28148242 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
28148264 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
28148286 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
28148308 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
28148330 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
28148352 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
28148374 ACGTACTAAGCTCT
1 ACGTACTAAGCTCT
28148388 GCAAAACAAT
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 112 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:28151353 original size:23 final size:23
Alignment explanation
Indices: 28151318--28151387 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
28151308 AATGTTATTG
*
28151318 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
28151341 TTTAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
28151364 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28151387 A
1 A
28151388 CTCGTGTGGC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28156982 original size:64 final size:64
Alignment explanation
Indices: 28156901--28157030 Score: 224
Period size: 64 Copynumber: 2.0 Consensus size: 64
28156891 GGTTATATTT
28156901 TACCACAAATAATACATAAGCTACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGG
1 TACCACAAATAATACATAAGCTACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGG
* * * *
28156965 TACCATAAATAGTACATAAGCTACTTTAACCTTGGTTCCTTTAAGTGCGGAAAAAATAAAGAGG
1 TACCACAAATAATACATAAGCTACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGG
28157029 TA
1 TA
28157031 AAAAGAATCA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (64 bp):
TACCACAAATAATACATAAGCTACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGG
Found at i:28157060 original size:64 final size:63
Alignment explanation
Indices: 28156907--28157060 Score: 186
Period size: 64 Copynumber: 2.4 Consensus size: 63
28156897 ATTTTACCAC
* *
28156907 AAATAATACATAAGCTACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGGTACCAT
1 AAATAATACATAAGC-ACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGGTACAAA
* * *
28156971 AAATAGTACATAAGCTACTTTAACCTTGGTTCCTTTAAGTGCGGAAAAAATAAAGAGGTA-AAA
1 AAATAATACATAAGC-ACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGGTACAAA
* *
28157034 AGAATCAAATTCATAAG-ACTTGAACCT
1 A-AAT--AATACATAAGCACTTTAACCT
28157061 AAGTTCTCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.03
64 69 0.87
66 8 0.10
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (63 bp):
AAATAATACATAAGCACTTTAACCTTGGTTCATTTAAGTGCAGAAAAAATAAAGAGGTACAAA
Found at i:28165466 original size:2 final size:2
Alignment explanation
Indices: 28165459--28165495 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28165449 TAAAGCTTAT
28165459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28165496 TAACTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28169327 original size:4 final size:4
Alignment explanation
Indices: 28169318--28169428 Score: 204
Period size: 4 Copynumber: 27.8 Consensus size: 4
28169308 AGCACATAAA
*
28169318 TATC TATC TATC TATC CATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
28169366 TATC TATT TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
28169414 TATC TATC TATC TAT
1 TATC TATC TATC TAT
28169429 ATAAGGACTT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 103 1.00
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:28171674 original size:41 final size:41
Alignment explanation
Indices: 28171605--28171692 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
28171595 AATTATACTC
*
28171605 TGAATTGCACATATGAGCCCCTGTTTGTACTTCGGTAACCT
1 TGAATTGCACATATGAGCCCCTGGTTGTACTTCGGTAACCT
* * *
28171646 TGAATTGCACATATGTGCCCTTGGTTGTACTTCGGTACCCT
1 TGAATTGCACATATGAGCCCCTGGTTGTACTTCGGTAACCT
28171687 TGAATT
1 TGAATT
28171693 ACAGATAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (41 bp):
TGAATTGCACATATGAGCCCCTGGTTGTACTTCGGTAACCT
Found at i:28173290 original size:42 final size:43
Alignment explanation
Indices: 28173214--28173310 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 43
28173204 GCCAATCGTA
* **
28173214 CGACAGACCGTGTAACTTTCGAAATAGTTGCACACGACCATG-
1 CGACAGACCGTGTAACATTCGAAATACCTGCACACGACCATGT
*
28173256 CGACAGACCGTGTAACATTCGAAATACCCT-CACACGACTATGT
1 CGACAGACCGTGTAACATTCGAAATA-CCTGCACACGACCATGT
*
28173299 C-ACAGGCCGTGT
1 CGACAGACCGTGT
28173311 GCTACACCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 46 0.96
43 2 0.04
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (43 bp):
CGACAGACCGTGTAACATTCGAAATACCTGCACACGACCATGT
Found at i:28176978 original size:16 final size:15
Alignment explanation
Indices: 28176931--28176994 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
28176921 TTCAGAGATC
* *
28176931 AAGAAAGAGAAGAAA
1 AAGAAAGAAAAAAAA
28176946 AAG-AAGTAAAAAGAAA
1 AAGAAAG-AAAAA-AAA
28176962 AAGGAACAGAAAAAAAA
1 AA-GAA-AGAAAAAAAA
*
28176979 AAGAAAGGAAAAAAA
1 AAGAAAGAAAAAAAA
28176994 A
1 A
28176995 CGTAAAGGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
14 3 0.07
15 16 0.39
16 8 0.20
17 6 0.15
18 6 0.15
19 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAAAAAA
Found at i:28177001 original size:16 final size:15
Alignment explanation
Indices: 28176972--28177016 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28176962 AAGGAACAGA
28176972 AAAAAAAAAGAAAGG
1 AAAAAAAAAGAAAGG
*
28176987 AAAAAAAACGTAAAGG
1 AAAAAAAAAG-AAAGG
*
28177003 AGAAAAGAAAGAAA
1 A-AAAAAAAAGAAA
28177017 AATGTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 9 0.36
16 9 0.36
17 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAGAAAGG
Found at i:28177976 original size:85 final size:84
Alignment explanation
Indices: 28177845--28178196 Score: 370
Period size: 85 Copynumber: 4.1 Consensus size: 84
28177835 TAATTTACAA
* * * * * *
28177845 TTACTGCCACTTGTAG--GTGTACAACATATTTGGAAATTAAAGAAACTGCCACTTGGTTCGTGA
1 TTACTGCCACTTGTTGTAGTGCACAACATATTTGTAGATTAAACAAACTGCCACTTGGTTCATGA
*
28177908 TTGAACCACATATTTGCAG
66 TCGAACCACATATTTGCAG
* * * * *
28177927 TTACTACCATTTGTTATAGTTGCAAAACATATTTGTAGATTAAACAAACTGCCATTTGGTTCATG
1 TTACTGCCACTTGTTGTAG-TGCACAACATATTTGTAGATTAAACAAACTGCCACTTGGTTCATG
28177992 ATCGAACCACATATTTGCAG
65 ATCGAACCACATATTTGCAG
* * * * *
28178012 TCACTGTCACTTGTTGTGGGTACACAACATATTT-TCAGATTAAACAAATTGCCACTTGGTTCAT
1 TTACTGCCACTTGTTGT-AGTGCACAACATATTTGT-AGATTAAACAAACTGCCACTTGGTTCAT
* *
28178076 GATCGAACTACATATTTGCAC
64 GATCGAACCACATATTTGCAG
* * * * *
28178097 TTACTGCCACTTGTTGTGAGTGTACAACAAATTTGCT-GATTAAATAAACTGCCACTCGGTTCGT
1 TTACTGCCACTTGTTGT-AGTGCACAACATATTTG-TAGATTAAACAAACTGCCACTTGGTTCAT
*
28178161 GATCGAACCACATTGTTTGCAG
64 GATCGAACCACA-TATTTGCAG
28178183 ATTAAACTGCCACT
1 -TT--ACTGCCACT
28178197 CTTCCTCTTT
Statistics
Matches: 222, Mismatches: 37, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
82 12 0.05
84 2 0.01
85 188 0.85
86 8 0.04
87 3 0.01
89 9 0.04
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (84 bp):
TTACTGCCACTTGTTGTAGTGCACAACATATTTGTAGATTAAACAAACTGCCACTTGGTTCATGA
TCGAACCACATATTTGCAG
Found at i:28178148 original size:170 final size:171
Alignment explanation
Indices: 28177865--28178182 Score: 417
Period size: 170 Copynumber: 1.9 Consensus size: 171
28177855 TTGTAGGTGT
* * * * *
28177865 ACAACATATTTGGAAATTAAAGAAACTGCCACTTGGTTCGTGATTGAACCACATATTTGCAGTTA
1 ACAACATATTTGCAAATTAAACAAACTGCCACTTGGTTCATGATCGAACCACATATTTGCACTTA
* * * *
28177930 CTACCATTTGTTATAGTTGCAAAACATATTTGTAGATTAAACAAACTGCCATTTGGTTCATGATC
66 CTACCACTTGTTATAGTTGCAAAACAAATTTGTAGATTAAACAAACTGCCACTCGGTTCATGATC
28177995 GAACCACA-TATTTGCAGTCACTGTCACTTGTTGTGGGTAC
131 GAACCACATTATTTGCAGTCACTGTCACTTGTTGTGGGTAC
* * * *
28178035 ACAACATATTTTCAGATTAAACAAATTGCCACTTGGTTCATGATCGAACTACATATTTGCACTTA
1 ACAACATATTTGCAAATTAAACAAACTGCCACTTGGTTCATGATCGAACCACATATTTGCACTTA
* * * * * *
28178100 CTGCCACTTGTTGTGAG-TGTACAACAAATTTGCT-GATTAAATAAACTGCCACTCGGTTCGTGA
66 CTACCACTTGTTAT-AGTTGCAAAACAAATTTG-TAGATTAAACAAACTGCCACTCGGTTCATGA
*
28178163 TCGAACCACATTGTTTGCAG
129 TCGAACCACATTATTTGCAG
28178183 ATTAAACTGC
Statistics
Matches: 125, Mismatches: 20, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
170 114 0.91
171 11 0.09
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (171 bp):
ACAACATATTTGCAAATTAAACAAACTGCCACTTGGTTCATGATCGAACCACATATTTGCACTTA
CTACCACTTGTTATAGTTGCAAAACAAATTTGTAGATTAAACAAACTGCCACTCGGTTCATGATC
GAACCACATTATTTGCAGTCACTGTCACTTGTTGTGGGTAC
Found at i:28180183 original size:119 final size:119
Alignment explanation
Indices: 28179845--28180185 Score: 339
Period size: 119 Copynumber: 2.9 Consensus size: 119
28179835 CCTTTTGAGC
** * * * *
28179845 AATTGGCTAAGGTGAGAGGTCTCA-TCCCTCTTATGCATTTGAAGGCCAAGGCGAGAGGTCTTGT
1 AATTGGCTAAGGTGAGAGGTCTCATTCCC-CTTACACCTTTGAAGGCTAATGCGAGAGGTCTTGC
* * *
28179909 CT-TGTTGGTAGAATTAGCCAAATGCCAAGGCATGAGGTGTTACCCCTCTTATGG
65 CTCTCTTGGTAGAATCAGCCAAATGCCAAGGCATGAGGTCTTACCCCTCTTATGG
* * * * ** **
28179963 AATTGGCTAAGGTAAGAGGTCTCGTCCCCCTCACACCCCTGAAGGCTAATGAAAGAGGTCTCAT-
1 AATTGGCTAAGGTGAGAGGTCTCATTCCCCTTACACCTTTGAAGGCTAATGCGAGAGGTCT--TG
* * * * * * *
28180027 CC-CTCTTGGTAGAACCAACCAAATTCCAAGGAATGAGGTCTTATCCTTTTTATGG
64 CCTCTCTTGGTAGAATCAGCCAAATGCCAAGGCATGAGGTCTTACCCCTCTTATGG
* *
28180082 AATTGGTTAAGGTGAGAGGTCTCATTCCCCTTACACCTTTGAAAGCTAATGCGAGAGGTCTTGCC
1 AATTGGCTAAGGTGAGAGGTCTCATTCCCCTTACACCTTTGAAGGCTAATGCGAGAGGTCTTGCC
* * * * * *
28180147 TCTCTTAGTGGAATCAGCCGAAGGCCAATGCGTGAGGTC
66 TCTCTTGGTAGAATCAGCCAAATGCCAAGGCATGAGGTC
28180186 CCATAACTAT
Statistics
Matches: 173, Mismatches: 44, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
117 1 0.01
118 46 0.27
119 125 0.72
120 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (119 bp):
AATTGGCTAAGGTGAGAGGTCTCATTCCCCTTACACCTTTGAAGGCTAATGCGAGAGGTCTTGCC
TCTCTTGGTAGAATCAGCCAAATGCCAAGGCATGAGGTCTTACCCCTCTTATGG
Found at i:28184021 original size:20 final size:20
Alignment explanation
Indices: 28183993--28184037 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
28183983 AAGGATCCAA
*
28183993 CCAACATACCAGTTTGGAAT
1 CCAATATACCAGTTTGGAAT
28184013 CCAATATACCAGTTTGGAAT
1 CCAATATACCAGTTTGGAAT
28184033 CCAAT
1 CCAAT
28184038 GCCTCGTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (20 bp):
CCAATATACCAGTTTGGAAT
Found at i:28184292 original size:15 final size:16
Alignment explanation
Indices: 28184272--28184304 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
28184262 CATCCCAATC
28184272 CATAATTAC-TTTAAT
1 CATAATTACATTTAAT
28184287 CATAATTACATTTAAT
1 CATAATTACATTTAAT
28184303 CA
1 CA
28184305 ATATATAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
CATAATTACATTTAAT
Found at i:28192788 original size:41 final size:41
Alignment explanation
Indices: 28192625--28192811 Score: 200
Period size: 41 Copynumber: 4.6 Consensus size: 41
28192615 ATTCGGGCTC
* * *
28192625 TATGCCTAGCAGGCTTTATGCTC-GTGAATTATAACAAGCTT
1 TATGCCTAGCAGGCTTTATGC-CGGTGTATCATATCAAGCTT
* * *
28192666 TATGCCTAGCAGGCTTCATGCCGGTGTACCATATCAGGCTT
1 TATGCCTAGCAGGCTTTATGCCGGTGTATCATATCAAGCTT
** *
28192707 TATGCCTAGCAGGCTTCGTGCCGGTGTATCATATCTAGCTT
1 TATGCCTAGCAGGCTTTATGCCGGTGTATCATATCAAGCTT
* * **
28192748 TGTGCCTAGAAGGCTTTATGCCGGTGTATTTTAAT-AAGCTT
1 TATGCCTAGCAGGCTTTATGCCGGTGTATCAT-ATCAAGCTT
*
28192789 TATACCTCA-CAGGCTTTATGCCG
1 TATGCCT-AGCAGGCTTTATGCCG
28192812 ACGTGGTATC
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 119 0.97
42 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (41 bp):
TATGCCTAGCAGGCTTTATGCCGGTGTATCATATCAAGCTT
Found at i:28195715 original size:2 final size:2
Alignment explanation
Indices: 28195704--28195739 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28195694 TGTACCTTGT
28195704 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28195740 TAGTTTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28196387 original size:20 final size:19
Alignment explanation
Indices: 28196358--28196395 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28196348 AATAATTAAA
28196358 ATAAATAAATACTATATAT
1 ATAAATAAATACTATATAT
*
28196377 ATAATATAAATAGTATATA
1 ATAA-ATAAATACTATATA
28196396 ATTTAGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (19 bp):
ATAAATAAATACTATATAT
Found at i:28212196 original size:14 final size:15
Alignment explanation
Indices: 28212176--28212216 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
28212166 TTTGTTTGCC
28212176 AGTAAAATGTTTTC-
1 AGTAAAATGTTTTCT
* *
28212190 CGTAAAATGATTTCT
1 AGTAAAATGTTTTCT
28212205 AG-AAAATGTTTT
1 AGTAAAATGTTTT
28212217 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (15 bp):
AGTAAAATGTTTTCT
Found at i:28212229 original size:34 final size:35
Alignment explanation
Indices: 28212185--28212251 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28212175 CAGTAAAATG
*
28212185 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
28212219 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
28212252 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:28214861 original size:6 final size:6
Alignment explanation
Indices: 28214850--28214900 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
28214840 ATCAAGGATG
** *
28214850 GGGGAA GGGGAA AAGGAA GAGGAA GGGGAA GGGGAA GGGGAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
28214898 GGG
1 GGG
28214901 AAGATTTGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:28220780 original size:22 final size:22
Alignment explanation
Indices: 28220731--28220780 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28220721 AAGTTGGGTT
* *
28220731 CCACGTTGTGACGAGCCATTTC
1 CCACATTGTAACGAGCCATTTC
**
28220753 AAACATTGTAACGAGCCATTTC
1 CCACATTGTAACGAGCCATTTC
28220775 CCACAT
1 CCACAT
28220781 CGTGACATCG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (22 bp):
CCACATTGTAACGAGCCATTTC
Found at i:28228909 original size:9 final size:9
Alignment explanation
Indices: 28228895--28228950 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
28228885 AGTATTTTCA
28228895 AATTTATAT
1 AATTTATAT
28228904 AATTTAATAT
1 AATTT-ATAT
*
28228914 TATTTATAT
1 AATTTATAT
* *
28228923 AAATAAT-T
1 AATTTATAT
*
28228931 AATTTATCT
1 AATTTATAT
28228940 AATTTATAT
1 AATTTATAT
28228949 AA
1 AA
28228951 ACAATCTCGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 6 0.16
9 24 0.63
10 8 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
AATTTATAT
Found at i:28229660 original size:11 final size:13
Alignment explanation
Indices: 28229636--28229667 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28229626 TAGTTTATTA
28229636 ATATTTTAATATG
1 ATATTTTAATATG
28229649 AT-TTTTAA-ATG
1 ATATTTTAATATG
28229660 ATATTTTA
1 ATATTTTA
28229668 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:28231939 original size:29 final size:31
Alignment explanation
Indices: 28231897--28231958 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
28231887 TAGTAAAAGT
* *
28231897 AAAATTACATTTTAGCCCCTT-AAAATTATA
1 AAAATTACAATTTAACCCCTTAAAAATTATA
* *
28231927 AAAATT-CAATTTAATCCTTTAAAAATTATA
1 AAAATTACAATTTAACCCCTTAAAAATTATA
28231957 AA
1 AA
28231959 GATATAGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAATTACAATTTAACCCCTTAAAAATTATA
Found at i:28234245 original size:14 final size:14
Alignment explanation
Indices: 28234226--28234265 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28234216 AATATTATAG
28234226 TTTTATTTAATTAT
1 TTTTATTTAATTAT
28234240 TTTTATATT-ATTAT
1 TTTTAT-TTAATTAT
*
28234254 TTTTATTAAATT
1 TTTTATTTAATT
28234266 TTCACAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTATTTAATTAT
Found at i:28236339 original size:12 final size:12
Alignment explanation
Indices: 28236324--28236352 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28236314 ATGGCAACAC
28236324 CAATGTTGTCAT
1 CAATGTTGTCAT
28236336 CAATGTTGTCAT
1 CAATGTTGTCAT
28236348 CAATG
1 CAATG
28236353 CTAGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (12 bp):
CAATGTTGTCAT
Found at i:28238191 original size:20 final size:21
Alignment explanation
Indices: 28238161--28238202 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
28238151 CGTGGTAAGT
28238161 TGTTGCATGTAACCATCTACA
1 TGTTGCATGTAACCATCTACA
*
28238182 TGTT-CATGTAACCATTTACA
1 TGTTGCATGTAACCATCTACA
28238202 T
1 T
28238203 ACGCATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTTGCATGTAACCATCTACA
Found at i:28238209 original size:20 final size:20
Alignment explanation
Indices: 28238165--28238211 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28238155 GTAAGTTGTT
**
28238165 GCATGTAACCATCTACATGT
1 GCATGTAACCATCTACATAC
* *
28238185 TCATGTAACCATTTACATAC
1 GCATGTAACCATCTACATAC
28238205 GCATGTA
1 GCATGTA
28238212 TGTGACAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (20 bp):
GCATGTAACCATCTACATAC
Found at i:28238652 original size:10 final size:10
Alignment explanation
Indices: 28238637--28238664 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28238627 AGTAATTTTA
28238637 AAATTAAAAT
1 AAATTAAAAT
28238647 AAATTAAAAT
1 AAATTAAAAT
28238657 AAATTAAA
1 AAATTAAA
28238665 GACTAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:28240620 original size:3 final size:3
Alignment explanation
Indices: 28240612--28240672 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
28240602 AGAATAACAT
* * * *
28240612 TAA TAA TAA TGA TGA TAA TGA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
28240660 CAA TAA TAA TAA T
1 TAA TAA TAA TAA T
28240673 CTAAGGTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28240777 original size:23 final size:22
Alignment explanation
Indices: 28240750--28240810 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
28240740 ATATATTTAG
28240750 AAAAATAAATAAAAATAATAAT
1 AAAAATAAATAAAAATAATAAT
* *
28240772 ACAAAACT-AATTAATATAATAAT
1 A-AAAA-TAAATAAAAATAATAAT
28240795 AAGTAAATAAATAAAA
1 AA--AAATAAATAAAA
28240811 GGAAAAGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
22 2 0.07
23 19 0.63
24 9 0.30
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAAATAAATAAAAATAATAAT
Found at i:28242417 original size:44 final size:44
Alignment explanation
Indices: 28242360--28242704 Score: 241
Period size: 44 Copynumber: 7.7 Consensus size: 44
28242350 TCACCATTTT
* *
28242360 AATCCGCTTCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
* * * * ** *
28242404 AATCTACTCCACTGTAACTTCAGAGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
* * * ** *
28242448 AACCTGCTCCACTGTAACTTTAGGGAGATAAGG-TTGGTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGAT-AGGATT-AATAGCTTC
* * * * *
28242493 AGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTTGTTATAGTAGATTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA----TTA-A-TAGCTTC
* * * * * *
28242543 AATCCGAC-CTACTGCAACTTCAGAGG-TATAGGATTTATCA-TTTT
1 AATCTG-CTCCACTGCAACTTCAG-GGAGATAGGATTAAT-AGCTTC
*
28242587 AATCTGCTCCACTACAACTTCAGGGAGATAGGATTAATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
* * * * *
28242631 AATCTGCTCCACTACAACCTCAGGGAGATAAGATTAGTATCTT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
* *
28242674 AAACTTGCTCCACTGCAACTTCAGGAAGATA
1 AATC-TGCTCCACTGCAACTTCAGGGAGATA
28242705 AGGTTTGTTA
Statistics
Matches: 236, Mismatches: 49, Indels: 32
0.74 0.15 0.10
Matches are distributed among these distances:
43 7 0.03
44 160 0.68
45 36 0.15
46 2 0.01
49 2 0.01
50 26 0.11
51 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
Found at i:28242599 original size:183 final size:182
Alignment explanation
Indices: 28242357--28242715 Score: 411
Period size: 183 Copynumber: 2.0 Consensus size: 182
28242347 GATTCACCAT
* **
28242357 TTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTACTCCACTGTAAC
1 TTTAATCCGCCTCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTACTCCACTACAAC
** * ** * * * *
28242422 TTCAGAGAGATAAGATTGGTATCTTCAACCTGCTCCACTGTAACTTTAGGGAGATAAGGTTGGTT
66 TTCAGAGAGATAAGATTAATAGCTTCAACCTGCTCCACTACAACCTCAGGGAGATAAGATTAG-T
* * * *
28242487 ATCTT-CAGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTTGTTATAGTAGA
130 ATCTTAAACT-TGCTCCACTGCAACTTCAGGAAGATAAGACTTGTTATAGTAGA
* * * * *
28242540 TTTAATCCGACCT-ACTGCAACTTCAGAGG-TATAGGATTTATCA-TTTTAATCTGCTCCACTAC
1 TTTAATCCG-CCTCACTGCAACTTCAG-GGAGATAGGATTAAT-AGCTTCAATCTACTCCACTAC
* * *
28242602 AACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCACTACAACCTCAGGGAGATAAGATTA
63 AACTTCAGAGAGATAAGATTAATAGCTTCAACCTGCTCCACTACAACCTCAGGGAGATAAGATTA
**
28242667 GTATCTTAAACTTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTAT
128 GTATCTTAAACTTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTTAT
28242716 CTTCATTCTT
Statistics
Matches: 146, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
182 39 0.27
183 102 0.70
184 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (182 bp):
TTTAATCCGCCTCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTACTCCACTACAAC
TTCAGAGAGATAAGATTAATAGCTTCAACCTGCTCCACTACAACCTCAGGGAGATAAGATTAGTA
TCTTAAACTTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTTATAGTAGA
Found at i:28242661 original size:227 final size:227
Alignment explanation
Indices: 28242266--28242720 Score: 703
Period size: 227 Copynumber: 2.0 Consensus size: 227
28242256 TTGTGGTTTT
* *
28242266 AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTTTTATGGTAGATTTAATCCGACCTACTGC
1 AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTACTGC
* * * *
28242331 AATTTTAGAGGTATAGGATTCACCATTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTA
66 AACTTCAGAGGTATAGGATTCACCATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTA
** * * *
28242396 ATAGCTTCAATCTACTCCACTGTAACTTCAGAGAGATAAGATTGGTATCTTCAACCTGCTCCACT
131 ATAGCTTCAATCTACTCCACTACAACCTCAGAGAGATAAGATTAGTATCTTAAACCTGCTCCACT
* * *
28242461 GTAACTTTAGGGAGATAAGGTTGGTTATCTTC
196 GCAACTTCAGGAAGATAAGGTTGGTTATCTTC
* *
28242493 AGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTACTGC
1 AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTACTGC
* * *
28242558 AACTTCAGAGGTATAGGATTTATCATTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATTA
66 AACTTCAGAGGTATAGGATTCACCATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTA
* * *
28242623 ATAGCTTCAATCTGCTCCACTACAACCTCAGGGAGATAAGATTAGTATCTTAAACTTGCTCCACT
131 ATAGCTTCAATCTACTCCACTACAACCTCAGAGAGATAAGATTAGTATCTTAAACCTGCTCCACT
*
28242688 GCAACTTCAGGAAGATAAGGTTTGTTATCTTC
196 GCAACTTCAGGAAGATAAGGTTGGTTATCTTC
28242720 A
1 A
28242721 TTCTTAATTT
Statistics
Matches: 205, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
227 205 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (227 bp):
AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTACTGC
AACTTCAGAGGTATAGGATTCACCATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTA
ATAGCTTCAATCTACTCCACTACAACCTCAGAGAGATAAGATTAGTATCTTAAACCTGCTCCACT
GCAACTTCAGGAAGATAAGGTTGGTTATCTTC
Found at i:28242909 original size:51 final size:51
Alignment explanation
Indices: 28242838--28242951 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
28242828 ATCCGCTTCA
* *
28242838 CTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAATAAGATTCACTAC
1 CTTCAGCTTTAATCTATTCCACTGCAAAGCCAGGGAAATAAGATTCACTAC
* * * * **
28242889 CTTTAGCTTTAATTTGTTCCACTGCAAAGCCAGGGCAATAAGATTCACTGT
1 CTTCAGCTTTAATCTATTCCACTGCAAAGCCAGGGAAATAAGATTCACTAC
28242940 CTTCAGCTTTAA
1 CTTCAGCTTTAA
28242952 CGCTAGAGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
CTTCAGCTTTAATCTATTCCACTGCAAAGCCAGGGAAATAAGATTCACTAC
Found at i:28243019 original size:51 final size:51
Alignment explanation
Indices: 28242964--28243100 Score: 148
Period size: 51 Copynumber: 2.7 Consensus size: 51
28242954 CTAGAGAGAT
* *
28242964 AAGATTTGCTGCCTTTAGATTTAATCTGCTCCGCTGCAACGCCAGGGAAAC
1 AAGATTTGCTGCCTTTAGATTTAATCTGCTCCACTGCAACGCCAAGGAAAC
* ** * * * * *
28243015 AAGATTCGCTAACTTTAGCTTTAATCTGTTCCACTGTAACGCCAAGGAGAT
1 AAGATTTGCTGCCTTTAGATTTAATCTGCTCCACTGCAACGCCAAGGAAAC
* * * *
28243066 AGGATTTGCTGCCTTCAGTTTTAATCCGCTCCACT
1 AAGATTTGCTGCCTTTAGATTTAATCTGCTCCACT
28243101 TCAATTTTAA
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (51 bp):
AAGATTTGCTGCCTTTAGATTTAATCTGCTCCACTGCAACGCCAAGGAAAC
Found at i:28243071 original size:261 final size:260
Alignment explanation
Indices: 28242736--28243467 Score: 1032
Period size: 261 Copynumber: 2.8 Consensus size: 260
28242726 AATTTGCTCA
* * * *
28242736 CTGCAATGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTATAACGCCAATG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAGG
* * * * *
28242801 AGATAGGATTTGCTACCTTTAGCATTAATCCGCTTCACTTCAGCTTTAATCTATTCCATTGCAAT
66 AGATAGGATTTGCTGCCTTTAGCTTTAATCCGCTCCACTTCAACTTTAATCTATTCCACTGCAAT
* * *
28242866 GCCAGGGAAATAAGATTCACTACCTTTAGCTTTAATTTGTTCCACTGCAAAGCCAGGGCAATAAG
131 GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGG-AATAAG
* *
28242931 ATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTTGCTGCCTTTAGATTTAATCTGCTCC
195 ATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTCGCTGCCTTCAGATTTAATCTGCTCC
28242996 G
260 G
* *
28242997 CTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCACTGTAACGCCAAGG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAGG
* * *
28243062 AGATAGGATTTGCTGCCTTCAGTTTTAATCCGCTCCACTTCAATTTTAATCTATTCCACTGCAAT
66 AGATAGGATTTGCTGCCTTTAGCTTTAATCCGCTCCACTTCAACTTTAATCTATTCCACTGCAAT
* * * *
28243127 GCCAGGGAAACAATATTTGCTACCTTTAGCTTTAATCTGTTTCATTGCAAAGCCAGGGAAGTAAG
131 GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGGAA-TAAG
** * * * *
28243192 ATTCGTTGTCTTCATCTTTAACGCTAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTTC
195 ATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTCGCTGCCTTCAGATTTAATCTGCTCC
28243257 G
260 G
* * * * * * *
28243258 CTGCAACGCCGGGGAAACAAGATTTGCCACCTTTAGCTTTAATTTATCCCACTGTAATGCTAAGG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAGG
* *** * *
28243323 AGATGGGATTCATTGCCTTTAGCTTTAATCCGCCCCACTTCAACTTTAATCTATTCCACTGCAAA
66 AGATAGGATTTGCTGCCTTTAGCTTTAATCCGCTCCACTTCAACTTTAATCTATTCCACTGCAAT
* *
28243388 GCCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAG
131 GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGG-AATAAG
*
28243453 ATTCACTGCCTTCAG
195 ATTCACTGTCTTCAG
28243468 TCCGCTCCAC
Statistics
Matches: 412, Mismatches: 57, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
260 2 0.00
261 408 0.99
262 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (260 bp):
CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAGG
AGATAGGATTTGCTGCCTTTAGCTTTAATCCGCTCCACTTCAACTTTAATCTATTCCACTGCAAT
GCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGGAATAAGA
TTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTCGCTGCCTTCAGATTTAATCTGCTCCG
Found at i:28243205 original size:123 final size:123
Alignment explanation
Indices: 28242983--28243468 Score: 355
Period size: 123 Copynumber: 3.8 Consensus size: 123
28242973 TGCCTTTAGA
* *
28242983 TTTAATCTGCTCCGCTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCA
1 TTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCA
* * * *
28243048 CTGTAACGCCAAGGAGATAGGATTTGCTGCCTTCAGTTTTAATCCGCTCCACTTCAAT
66 CTGCAAAGCCAAGGAGATAAGATTCGCTGCCTTCAGTTTTAATCCGCTCCACTTCAAT
* * * * * *
28243106 TTTAATCTATTCCACTGCAATGCCAGGGAAACAATATTTGCTACCTTTAGCTTTAATCTGTTTCA
1 TTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCA
* * * * * *
28243171 TTGCAAAGCCAGGGA-AGTAAGATTCGTTGTCTTCATCTTTAACGCTAGGGAGATAAGATTCGCT
66 CTGCAAAGCCAAGGAGA-TAAGATTCGCTGCCTTCA--GTT-----T-------T-A-ATCCGCT
* **
28243235 GC-CTTCAGC
114 CCACTTCAAT
* * * * * * * * * *
28243244 TTTAATCTGCTTCGCTGCAACGCCGGGGAAACAAGATTTGCCACCTTTAGCTTTAATTTATCCCA
1 TTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCA
* * * ** ** * * * *
28243309 CTGTAATGCTAAGGAGATGGGATTCATTGCCTTTAGCTTTAATCCGCCCCACTTCAAC
66 CTGCAAAGCCAAGGAGATAAGATTCGCTGCCTTCAGTTTTAATCCGCTCCACTTCAAT
* * * *
28243367 TTTAATCTATTCCACTGCAAAGCCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCA
1 TTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCA
* * * *
28243432 CTGCAACGCCAGGGAAATAAGATTCACTGCCTTCAGT
66 CTGCAAAGCCAAGGAGATAAGATTCGCTGCCTTCAGT
28243469 CCGCTCCACT
Statistics
Matches: 273, Mismatches: 71, Indels: 38
0.71 0.19 0.10
Matches are distributed among these distances:
122 7 0.03
123 169 0.62
124 1 0.00
125 2 0.01
130 1 0.00
131 1 0.00
136 1 0.00
137 1 0.00
138 82 0.30
139 8 0.03
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (123 bp):
TTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATCTGTTCCA
CTGCAAAGCCAAGGAGATAAGATTCGCTGCCTTCAGTTTTAATCCGCTCCACTTCAAT
Found at i:28249580 original size:22 final size:22
Alignment explanation
Indices: 28249541--28249598 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
28249531 ATATATTTAG
28249541 AAAAATAAATAATAATAATAAT
1 AAAAATAAATAATAATAATAAT
*
28249563 AAAAACTAACTAAT-ATAATAAT
1 AAAAA-TAAATAATAATAATAAT
28249585 AAGTAAATAAATAA
1 AA--AAATAAATAA
28249599 AAGGAAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 15 0.48
23 13 0.42
24 3 0.10
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATAAATAATAATAATAAT
Found at i:28251898 original size:49 final size:48
Alignment explanation
Indices: 28251826--28251976 Score: 162
Period size: 49 Copynumber: 3.1 Consensus size: 48
28251816 GGGTGGTACA
* *
28251826 AGTTGCTATCCAGATTGGCGTATGAGTTGGATGTCTGGTAGGGCATGTT
1 AGTTGCTAACCAGATTGGTGTATG-GTTGGATGTCTGGTAGGGCATGTT
* *
28251875 AGTTGCTAACCAGATTGGTGTATGTGCTTGG-TTTCTAGTAGGGCATGTT
1 AGTTGCTAACCAGATTGGTGTATG-G-TTGGATGTCTGGTAGGGCATGTT
* * * *
28251924 AGTTGCTAATCAGCTTGGTGCTATGGGT-GATGCCATCGGTAGGGCATGTT
1 AGTTGCTAACCAGATTGGTG-TATGGTTGGATGTC-T-GGTAGGGCATGTT
28251974 AGT
1 AGT
28251977 AGATAACTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
47 1 0.01
48 3 0.03
49 59 0.69
50 23 0.27
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (48 bp):
AGTTGCTAACCAGATTGGTGTATGGTTGGATGTCTGGTAGGGCATGTT
Found at i:28255736 original size:2 final size:2
Alignment explanation
Indices: 28255729--28255755 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28255719 GTGAAAGTTC
28255729 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28255756 ATTGTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28272702 original size:68 final size:69
Alignment explanation
Indices: 28272551--28272684 Score: 193
Period size: 68 Copynumber: 2.0 Consensus size: 69
28272541 TTTTAATAGT
* * *
28272551 TTAATATTAAA-TTAAGTTTAATACTTATCTTAATAATATTTTATTAATTTATTATTAAATTGAT
1 TTAATATTAAATTTAAGTTTAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGAT
28272615 TATC
66 TATC
* *
28272619 TTAATATTAAATTTAA-TTTAATATTTATCTTGATAAATATTATATTAA-TTAATATTAAAGTGA
1 TTAATATTAAATTTAAGTTTAATACTTATCTTAAT-AATATTATATTAATTTAATATTAAAGTGA
28272682 TTA
65 TTA
28272685 AGTTTAATCA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 43 0.73
69 16 0.27
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (69 bp):
TTAATATTAAATTTAAGTTTAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:28274898 original size:34 final size:34
Alignment explanation
Indices: 28274855--28274925 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
28274845 AGGCTTGAAA
28274855 AACATACCATGCAAGTGAATTGAAGCTTCACTGT
1 AACATACCATGCAAGTGAATTGAAGCTTCACTGT
*
28274889 AACATACCATGCAAGTGAATTGAAGCTTTACTGT
1 AACATACCATGCAAGTGAATTGAAGCTTCACTGT
28274923 AAC
1 AAC
28274926 TTAGCTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (34 bp):
AACATACCATGCAAGTGAATTGAAGCTTCACTGT
Found at i:28276994 original size:21 final size:20
Alignment explanation
Indices: 28276935--28276995 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
28276925 TAGTTATATA
*
28276935 CCTTAATTAACTTATAAATAAT
1 CCTTAATTAA--TATAATTAAT
28276957 CC-TAATT-ATATTAATTAAT
1 CCTTAATTAATA-TAATTAAT
28276976 CCTTAATTAATATACATTAA
1 CCTTAATTAATATA-ATTAA
28276996 ACATATTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 9 0.26
20 8 0.24
21 13 0.38
22 2 0.06
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (20 bp):
CCTTAATTAATATAATTAAT
Found at i:28280885 original size:14 final size:14
Alignment explanation
Indices: 28280866--28280908 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28280856 ATTTAATTGG
28280866 TAAATTAATTTATT
1 TAAATTAATTTATT
*
28280880 TAAATTAATTT-TA
1 TAAATTAATTTATT
*
28280893 TAAATATTATTTATT
1 TAAAT-TAATTTATT
28280908 T
1 T
28280909 TTTGAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 16 0.67
15 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAAATTAATTTATT
Found at i:28286208 original size:33 final size:33
Alignment explanation
Indices: 28286157--28286266 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
28286147 ATCTCGATAG
* **
28286157 ACTACCTCTATTTTATGTTTACTGCCCTAG-CGA
1 ACTATCTCTATTCCATGTTTACTG-CCTAGACGA
* * *
28286190 ACTATCTTTATTCCATGTTTATTGCCTTGACGA
1 ACTATCTCTATTCCATGTTTACTGCCTAGACGA
* * *
28286223 ACTATCTCTATTCCGTGTTTACTGTCCCA-ACGG
1 ACTATCTCTATTCCATGTTTACTG-CCTAGACGA
28286256 ACTATCTCTAT
1 ACTATCTCTAT
28286267 GGATGTCATG
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 4 0.06
33 57 0.90
34 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (33 bp):
ACTATCTCTATTCCATGTTTACTGCCTAGACGA
Found at i:28286376 original size:63 final size:63
Alignment explanation
Indices: 28286273--28286429 Score: 226
Period size: 63 Copynumber: 2.5 Consensus size: 63
28286263 CTATGGATGT
* * *
28286273 CATGGAGTCTTTCATCCATGGTTTTACACCGATTCACCATCCTGGCACATTATCTTTTAATGC
1 CATGGAGTCTTTCATCCATGGTCTTACACTGATTCACCATCCTGGCACACTATCTTTTAATGC
* * ** *
28286336 C-TCGGAGTCTTTCATCCATGGTCTTACACTGATTCGCCATCTTGGTGCACTATCTTTTGATGC
1 CAT-GGAGTCTTTCATCCATGGTCTTACACTGATTCACCATCCTGGCACACTATCTTTTAATGC
28286399 CATGGAGTCTTTCATCCATGGTCTTACACTG
1 CATGGAGTCTTTCATCCATGGTCTTACACTG
28286430 TATACCTTAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
62 1 0.01
63 82 0.98
64 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (63 bp):
CATGGAGTCTTTCATCCATGGTCTTACACTGATTCACCATCCTGGCACACTATCTTTTAATGC
Found at i:28289013 original size:3 final size:3
Alignment explanation
Indices: 28289007--28289032 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28288997 TTCTTCTTCT
28289007 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
28289033 TTCGATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:28289308 original size:161 final size:161
Alignment explanation
Indices: 28289043--28289367 Score: 623
Period size: 161 Copynumber: 2.0 Consensus size: 161
28289033 TTCGATTGTA
28289043 AAAGGTTGATATTTTGTCACCTCATGAGGTGATGTAGATCAAACCCAGAATGCCGAAACACTGAA
1 AAAGGTTGATATTTTGTCACCTCATGAGGTGATGTAGATCAAACCCAGAATGCCGAAACACTGAA
*
28289108 ACTAATAAATTTACATATAGGCCAAAAGCCATTGCTTGAGAGTTTCTTTTTTCCTCTTTCTCTGT
66 ACTAATAAATTTACATATAGGCCAAAAGCCATTGCTTGAGAGTTTCTCTTTTCCTCTTTCTCTGT
* *
28289173 CTGTTGCGCTGTTTTTGTGTTATTGGTGGTT
131 CTGTTGCCCTGTTTTTGGGTTATTGGTGGTT
28289204 AAAGGTTGATATTTTGTCACCTCATGAGGTGATGTAGATCAAACCCAGAATGCCGAAACACTGAA
1 AAAGGTTGATATTTTGTCACCTCATGAGGTGATGTAGATCAAACCCAGAATGCCGAAACACTGAA
28289269 ACTAATAAATTTACATATAGGCCAAAAGCCATTGCTTGAGAGTTTCTCTTTTCCTCTTTCTCTGT
66 ACTAATAAATTTACATATAGGCCAAAAGCCATTGCTTGAGAGTTTCTCTTTTCCTCTTTCTCTGT
28289334 CTGTTGCCCTGTTTTTGGGTTATTGGTGGTT
131 CTGTTGCCCTGTTTTTGGGTTATTGGTGGTT
28289365 AAA
1 AAA
28289368 TTTCAATAAA
Statistics
Matches: 161, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (161 bp):
AAAGGTTGATATTTTGTCACCTCATGAGGTGATGTAGATCAAACCCAGAATGCCGAAACACTGAA
ACTAATAAATTTACATATAGGCCAAAAGCCATTGCTTGAGAGTTTCTCTTTTCCTCTTTCTCTGT
CTGTTGCCCTGTTTTTGGGTTATTGGTGGTT
Found at i:28291584 original size:2 final size:2
Alignment explanation
Indices: 28291577--28291610 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28291567 ACTTGATCAT
28291577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28291611 CATCCAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28294367 original size:29 final size:30
Alignment explanation
Indices: 28294312--28294369 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
28294302 TTGAATTTAT
* * * *
28294312 TTGATTCTTTTTAATAGTATAGGGGCTAAA
1 TTGATTCTATTTAATAATAAAGAGGCTAAA
28294342 TTGA-TCTATTTAATAATAAAGAGGCTAA
1 TTGATTCTATTTAATAATAAAGAGGCTAA
28294370 TTTAAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (30 bp):
TTGATTCTATTTAATAATAAAGAGGCTAAA
Found at i:28295104 original size:43 final size:43
Alignment explanation
Indices: 28295005--28295228 Score: 274
Period size: 43 Copynumber: 5.3 Consensus size: 43
28294995 TTTTAGAAAT
* * * *
28295005 AAACGCCGCTATAGATTAGGAGCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
28295047 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
*
28295090 AAACGCCGCTATAGATC-AGAACCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAG-ACCTTTAGCGGCGCTTTTCCCAC
* * * *
28295132 AAACGCCGCTATAGCTCAAGATCTTTAGCGACGCTTATCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * ** * * *
28295175 AAAAGCCGCTATAGGTCGTGACTTTTAGCGGCACTTTTCCTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
28295218 AAACGCCGCTA
1 AAACGCCGCTA
28295229 AAAACATATA
Statistics
Matches: 157, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
42 71 0.45
43 86 0.55
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:28295151 original size:85 final size:85
Alignment explanation
Indices: 28295005--28295228 Score: 315
Period size: 85 Copynumber: 2.6 Consensus size: 85
28294995 TTTTAGAAAT
* *
28295005 AAACGCCGCTATAGATTAGGAGCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGACC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGACC
* *
28295070 TTTAGCGGCGCTTTTCCCAC
66 TTTAGCGACGCTTATCCCAC
* * *
28295090 AAACGCCGCTATAGATCAGAACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGCTCAAGATC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGACC
28295155 TTTAGCGACGCTTATCCCAC
66 TTTAGCGACGCTTATCCCAC
* * * * *
28295175 AAAAGCCGCTATAGGTC-GTGACTTTTAGCGGCACTTTTCCTACAAACGCCGCTA
1 AAACGCCGCTATAGATCAG-GACCTTTAGCGGCGCTTTTAC-ACAAACGCCGCTA
28295229 AAAACATATA
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
84 1 0.01
85 110 0.89
86 13 0.10
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGACC
TTTAGCGACGCTTATCCCAC
Found at i:28295456 original size:9 final size:9
Alignment explanation
Indices: 28295442--28295467 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28295432 AATAAATATC
28295442 ATGCTTATA
1 ATGCTTATA
28295451 ATGCTTATA
1 ATGCTTATA
28295460 ATGCTTAT
1 ATGCTTAT
28295468 TGAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (9 bp):
ATGCTTATA
Found at i:28298033 original size:284 final size:286
Alignment explanation
Indices: 28297479--28298120 Score: 936
Period size: 284 Copynumber: 2.2 Consensus size: 286
28297469 TAAAGATATA
* * *
28297479 ATAAAAGGTCTCAGACATCCAAGGAAGG-ATAAAAGCAGCACATA-CTCTCAAGCCCGGAGAAAA
1 ATAAAAGGTCTCAGACATCCAAGGAAGGAAT-GAAGCAGCACA-AGCTCTCAAGCCCGGCGAAAG
**
28297542 GCGAAAGCTCTCAGGTGGCCACTGCGAATGTTTTGAGAAACAAGCCCTACAACTTATCATCATAA
64 GCGAAAGCTCTCAGACGGCCACTGCGAATGTTTTGAGAAACAAGCCCTACAACTTATCATCATAA
** *
28297607 ACCCATACACATGAAATATATTATCATTTGACTCAATTTTATGAATATCGTTTATCAATGGAACT
129 ACCCATACACAACAAATATATTATCATTTGACTCAATTTTAAGAATATCGTTTATCAATGGAACT
* * *
28297672 GAAAAAAAAAAGGGAAAAATATACAACCAGATTTCTGAGAAAATAATTTGATTTTCAAGCGCAAA
194 GAAAAAAAAAAGGGAAAAATATACAACCAGATTTCTGAGAAAATAACTGGATTTTCAAGCACAAA
28297737 TAATGAAAAACAAC-T-ATATACAAGTC
259 TAATGAAAAACAACATCATATACAAGTC
*
28297763 ATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCTGGCGAAAGGC
1 ATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGAAAGGC
* * * ***
28297828 GAAAGCTCTTAGACGGCCACTGCTAATGTTTTGAGAAACAAGCCTTTGGA-TTATCATCATAAAC
66 GAAAGCTCTCAGACGGCCACTGCGAATGTTTTGAGAAACAAGCCCTACAACTTATCATCATAAAC
* * * *
28297892 CCATACACAACAAATATATTTTCCTTTGACTGAATTTTAAGAATATCGTTTATCAATTGAACTGA
131 CCATACACAACAAATATATTATCATTTGACTCAATTTTAAGAATATCGTTTATCAATGGAACTG-
* * * * *
28297957 AAAAAAAAAAGGGAAAAAATGTACAACCAGATTTCTGAGGAAGTGACTGGGTTTTCAAGCACAAA
195 AAAAAAAAAAGGG-AAAAATATACAACCAGATTTCTGAGAAAATAACTGGATTTTCAAGCACAAA
*
28298022 TAATG-AAAACAACAATCATATAGAAGTC
259 TAATGAAAAACAAC-ATCATATACAAGTC
*
28298050 ATAAAAGGTCTCAGACATCCAAGGAAGGAAGGAAGCAGCACAAGCTCTCAAGCCCGGCGAAAGGC
1 ATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGAAAGGC
28298115 GAAAGC
66 GAAAGC
28298121 CCAAAAATAA
Statistics
Matches: 321, Mismatches: 30, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
283 72 0.22
284 119 0.37
285 50 0.16
286 1 0.00
287 79 0.25
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (286 bp):
ATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGAAAGGC
GAAAGCTCTCAGACGGCCACTGCGAATGTTTTGAGAAACAAGCCCTACAACTTATCATCATAAAC
CCATACACAACAAATATATTATCATTTGACTCAATTTTAAGAATATCGTTTATCAATGGAACTGA
AAAAAAAAAGGGAAAAATATACAACCAGATTTCTGAGAAAATAACTGGATTTTCAAGCACAAATA
ATGAAAAACAACATCATATACAAGTC
Found at i:28298433 original size:21 final size:22
Alignment explanation
Indices: 28298409--28298458 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
28298399 AACCCTGAAT
* *
28298409 CTCTAAACCCTAAATCACTAA-
1 CTCTAAACCCCAAACCACTAAC
*
28298430 CTCTTAACCCCAAACCACTAAC
1 CTCTAAACCCCAAACCACTAAC
28298452 CTCTAAA
1 CTCTAAA
28298459 TCTTATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (22 bp):
CTCTAAACCCCAAACCACTAAC
Found at i:28298608 original size:95 final size:94
Alignment explanation
Indices: 28298442--28298614 Score: 249
Period size: 95 Copynumber: 1.8 Consensus size: 94
28298432 CTTAACCCCA
* **
28298442 AACCACTAACCTCTAAATCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATTATAA
1 AACCACTAACCCCTAAATCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAA
28298507 ACCCTAACCCTAACCCGACCCCAAATCCCT
66 ACCCTAA-CCTAACCCGACCCCAAATCCCT
* * * *
28298537 AACCCCTAACCCCTAAA-CATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTA
1 AACCACTAACCCCTAAATC-TTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATA
*
28298601 AATCCTAACCTAAC
65 AACCCTAACCTAAC
28298615 ACTAAATCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
94 7 0.10
95 62 0.90
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (94 bp):
AACCACTAACCCCTAAATCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAA
ACCCTAACCTAACCCGACCCCAAATCCCT
Found at i:28298643 original size:29 final size:28
Alignment explanation
Indices: 28298609--28298671 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
28298599 TAAATCCTAA
*
28298609 CCTAACACTAAATCTATAAACCTTAAATC
1 CCTAACACTAAATCTATAAACCTT-AACC
* * * *
28298638 CCTAACTCTTAATCTCTAACCCTTAACC
1 CCTAACACTAAATCTATAAACCTTAACC
28298666 CCTAAC
1 CCTAAC
28298672 CCATAAACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (28 bp):
CCTAACACTAAATCTATAAACCTTAACC
Found at i:28298656 original size:14 final size:14
Alignment explanation
Indices: 28298629--28298673 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
28298619 AATCTATAAA
28298629 CCTTAAATCCCTAAC
1 CCTT-AATCCCTAAC
* *
28298644 TCTTAATCTCTAAC
1 CCTTAATCCCTAAC
*
28298658 CCTTAACCCCTAAC
1 CCTTAATCCCTAAC
28298672 CC
1 CC
28298674 ATAAACCTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTTAATCCCTAAC
Found at i:28299196 original size:40 final size:41
Alignment explanation
Indices: 28299087--28299283 Score: 297
Period size: 41 Copynumber: 4.8 Consensus size: 41
28299077 AAATGTTTTT
* *
28299087 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
28299128 GCGGCGCTTTCTAAAAAACGCCGCTAAAGATATGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
**
28299169 GCGGTTC-TTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
28299209 GCGGCGCTTTCTCAAAAACGCCGCTAAATATCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
28299250 GCGGCGCTTTTTTTAAAAACGCCGCTAAAGATCT
1 GCGGCGC-TTTCTCAAAAACGCCGCTAAAGATCT
28299284 AAAAGGTACA
Statistics
Matches: 141, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
40 36 0.26
41 82 0.58
42 23 0.16
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:28299235 original size:81 final size:83
Alignment explanation
Indices: 28299087--28299283 Score: 303
Period size: 81 Copynumber: 2.4 Consensus size: 83
28299077 AAATGTTTTT
*
28299087 GCGGCGCTTTT-TTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCG
1 GCGGCGCTTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCG
28299151 CTAAAGATATGAGCATTA
66 CTAAAGATATGAGCATTA
*
28299169 GC-G-G-TTCTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCC
1 GCGGCGCTT-TTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTCTAAAAAACGCC
* *
28299231 GCTAAATATCTGAGCATTA
65 GCTAAAGATATGAGCATTA
* *
28299250 GCGGCGCTTTTTTTAAAAACGCCGCTAAAGATCT
1 GCGGCGCTTTTCTCAAAAACGCCGCTAAAGATCT
28299284 AAAAGGTACA
Statistics
Matches: 104, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
79 2 0.02
80 3 0.03
81 70 0.67
82 3 0.03
83 24 0.23
84 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (83 bp):
GCGGCGCTTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCG
CTAAAGATATGAGCATTA
Found at i:28299448 original size:40 final size:39
Alignment explanation
Indices: 28299338--28299451 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 39
28299328 TTTTTCCAAA
* *
28299338 AAACGCCGCTAATGCT-AATTTTTAGCGGCGCTTTACTGG
1 AAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACT-G
*
28299377 AAACGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACAT-
1 AAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTTAC-TG
*
28299416 AAAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTT
1 AAA-CGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
28299452 TTGTCCAAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
39 19 0.28
40 47 0.70
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (39 bp):
AAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACTG
Found at i:28299542 original size:19 final size:20
Alignment explanation
Indices: 28299504--28299547 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
28299494 GTGTAGTGCC
28299504 TAGATATGATATATGCAATCT
1 TAGATATGA-ATATGCAATCT
*
28299525 TAGATATG-ATATGTAATCT
1 TAGATATGAATATGCAATCT
28299544 TAGA
1 TAGA
28299548 AGATGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (20 bp):
TAGATATGAATATGCAATCT
Found at i:28300204 original size:20 final size:20
Alignment explanation
Indices: 28300181--28300238 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
28300171 TATATGTACG
*
28300181 TATATATATATTATACTTTC
1 TATATATATATTATAATTTC
* *
28300201 TATACATATTTTATAATTTC
1 TATATATATATTATAATTTC
28300221 TATATATATATATATAAT
1 TATATATATAT-TATAAT
28300239 CATTATCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATATATTATAATTTC
Found at i:28300211 original size:52 final size:52
Alignment explanation
Indices: 28300154--28300317 Score: 158
Period size: 52 Copynumber: 3.1 Consensus size: 52
28300144 TATGATTTAT
*
28300154 ATATTTATTACCTTATATATATGTACGTATATATATATTATACTTTCTATAC
1 ATATTTATTACTTTATATATATGTACGTATATATATATTATACTTTCTATAC
* * * * *
28300206 ATATTT-TATAATTTCTATATATATA--TATATA-ATCATTAT-CTTTATGATCTAT
1 ATATTTAT-TACTTTATATATATGTACGTATATATAT-ATTATACTTTCT-A--TAC
* *
28300258 ATATTTATTAACTTATATATATATGTACGTATATATGTATTATACTTTCTATCC
1 ATATTTATT-ACTT-TATATATATGTACGTATATATATATTATACTTTCTATAC
28300312 ATATTT
1 ATATTT
28300318 TATAATTTCT
Statistics
Matches: 87, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
49 7 0.08
50 12 0.14
51 1 0.01
52 28 0.32
53 4 0.05
54 17 0.20
56 12 0.14
57 6 0.07
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.52
Consensus pattern (52 bp):
ATATTTATTACTTTATATATATGTACGTATATATATATTATACTTTCTATAC
Found at i:28300233 original size:104 final size:106
Alignment explanation
Indices: 28300123--28300337 Score: 344
Period size: 106 Copynumber: 2.0 Consensus size: 106
28300113 TTTTTTAGTT
* * * *
28300123 TATATATGTAATTATTATTTTTATGATTTATATATTTATT-ACCT-TATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACCTATATATATATGTACGTATAT
28300186 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
*
28300227 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACCTATATATATATGTACGTATAT
* * *
28300292 ATGTATTATACTTTCTATCCATATTTTATAATTTCTATATG
66 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
28300333 TATAT
1 TATAT
28300338 TTTTCTTTAT
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
104 36 0.36
105 3 0.03
106 62 0.61
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.53
Consensus pattern (106 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACCTATATATATATGTACGTATAT
ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
Found at i:28300331 original size:56 final size:55
Alignment explanation
Indices: 28300167--28300337 Score: 187
Period size: 56 Copynumber: 3.2 Consensus size: 55
28300157 TTTATTACCT
*
28300167 TATATATATGTACGTATATATATATTATACTTTCTATACATATTTTATAATTTCTA
1 TATATATATGTACGTATATAT-TATTATACTTTCTATCCATATTTTATAATTTCTA
* * * *
28300223 TATATATA--TA--TATA-ATCATTAT-CTTTATGATCTATATATTTATTAA-CT-TA
1 TATATATATGTACGTATATATTATTATACTTTCT-ATCCATAT-TTTA-TAATTTCTA
28300273 TATATATATGTACGTATATATGTATTATACTTTCTATCCATATTTTATAATTTCTA
1 TATATATATGTACGTATATAT-TATTATACTTTCTATCCATATTTTATAATTTCTA
*
28300329 TATGTATAT
1 TATATATAT
28300338 TTTTCTTTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
49 5 0.05
50 21 0.23
51 7 0.08
52 9 0.10
54 9 0.10
55 7 0.08
56 30 0.32
57 5 0.05
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (55 bp):
TATATATATGTACGTATATATTATTATACTTTCTATCCATATTTTATAATTTCTA
Found at i:28300688 original size:24 final size:24
Alignment explanation
Indices: 28300633--28300688 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
28300623 ATGTACTTTC
* * *
28300633 TTTTCTTTATTTTTTTATATGTTT
1 TTTTATTTATGTTTTCATATGTTT
* * *
28300657 GTTGATTTATGTTTTCATATTTTT
1 TTTTATTTATGTTTTCATATGTTT
28300681 TTTTATTT
1 TTTTATTT
28300689 TGCTCATTTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.04, G:0.07, T:0.75
Consensus pattern (24 bp):
TTTTATTTATGTTTTCATATGTTT
Found at i:28300737 original size:201 final size:202
Alignment explanation
Indices: 28300352--28300754 Score: 799
Period size: 202 Copynumber: 2.0 Consensus size: 202
28300342 CTTTATTCTC
28300352 ATGAATGTATTATATATATAAATATATTTTTTATATAAATTTTTTTTTCATAATTTCAATGTATA
1 ATGAATGTATTATATATATAAATATATTTTTTATATAAATTTTTTTTTCATAATTTCAATGTATA
28300417 TATTATGTACTTTCTTTTCTTTATTTTTTTATATGTTTGTTGATTTATGTTTTCATATTTTTTTT
66 TATTATGTACTTTCTTTTCTTTATTTTTTTATATGTTTGTTGATTTATGTTTTCATATTTTTTTT
28300482 TTATTTTGCTCATTTATTTGATACTTTGCATGTCATTGTTTTTTTAAATTTTGTTTATTTATTTG
131 TTATTTTGCTCATTTATTTGATACTTTGCATGTCATTGTTTTTTTAAATTTTGTTTATTTATTTG
28300547 TCTATCT
196 TCTATCT
28300554 ATGAATGTATTATATATATAAATATATTTTTTATATAAATTTTTTTTTCATAATTTCAATGTATA
1 ATGAATGTATTATATATATAAATATATTTTTTATATAAATTTTTTTTTCATAATTTCAATGTATA
28300619 TATTATGTACTTTCTTTTCTTTATTTTTTTATATGTTTGTTGATTTATGTTTTCATA-TTTTTTT
66 TATTATGTACTTTCTTTTCTTTATTTTTTTATATGTTTGTTGATTTATGTTTTCATATTTTTTTT
28300683 TTATTTTGCTCATTTATTTGATACTTTGCATGTCATTGTTTTTTTAAATTTTGTTTATTTATTTG
131 TTATTTTGCTCATTTATTTGATACTTTGCATGTCATTGTTTTTTTAAATTTTGTTTATTTATTTG
28300748 TCTATCT
196 TCTATCT
28300755 TATTTCTATA
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 79 0.39
202 122 0.61
ACGTcount: A:0.24, C:0.06, G:0.07, T:0.62
Consensus pattern (202 bp):
ATGAATGTATTATATATATAAATATATTTTTTATATAAATTTTTTTTTCATAATTTCAATGTATA
TATTATGTACTTTCTTTTCTTTATTTTTTTATATGTTTGTTGATTTATGTTTTCATATTTTTTTT
TTATTTTGCTCATTTATTTGATACTTTGCATGTCATTGTTTTTTTAAATTTTGTTTATTTATTTG
TCTATCT
Found at i:28304736 original size:57 final size:56
Alignment explanation
Indices: 28304672--28304799 Score: 184
Period size: 57 Copynumber: 2.3 Consensus size: 56
28304662 GAAATTCACT
* * *
28304672 TGAAATTGATATAAACTTATTGATTAATGATAGAATATGACACTTAAATGAATTATG
1 TGAAATTGGTATAAACTTATGGATTAACGATAGAATATGACA-TTAAATGAATTATG
* * * *
28304729 TGAAATTGGTTTAAACTTATGGATTGACGATAGAATATGACATTGAATGAGTTATG
1 TGAAATTGGTATAAACTTATGGATTAACGATAGAATATGACATTAAATGAATTATG
28304785 TGAAATTGGTATAAA
1 TGAAATTGGTATAAA
28304800 TTGGTAATGT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
56 26 0.41
57 37 0.59
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (56 bp):
TGAAATTGGTATAAACTTATGGATTAACGATAGAATATGACATTAAATGAATTATG
Found at i:28319961 original size:50 final size:48
Alignment explanation
Indices: 28319907--28320175 Score: 248
Period size: 50 Copynumber: 5.6 Consensus size: 48
28319897 AGTGTGACAA
*
28319907 TGTAAGACCATGTCTAGGACATGGCATCAGCACAGACCGAGGAGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCAC-GA-CGAGGAGTGCTAG
** * *
28319957 TGTAAGATGATGTCTGGGACATGGCATCAGCACGGACAGAGGAGAG-TCAA
1 TGTAAGACCATGTCTGGGACATGGCATCAGCAC-GAC-GAGGAGTGCT-AG
* * * *
28320007 TGTAAGACCATGTCTGGGACATGGCATCGGCTCGA-GATGAGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCACGACGAGGAGTGCTAG
* * *
28320054 TGTAAGACCATGTCTGGGACATGGCATC-GACACCGA-TATGTGA-TCCCA-
1 TGTAAGACCATGTCTGGGACATGGCATCAG-CA-CGACGA-G-GAGTGCTAG
* * * *
28320102 TGTAAGACCATGTCTGGGACATGGTATCGGCTCGA-GATGAGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCACGACGAGGAGTGCTAG
28320149 CT-TAAGACCATGTCTGGGACATGGCAT
1 -TGTAAGACCATGTCTGGGACATGGCAT
28320176 TGACACCGAT
Statistics
Matches: 183, Mismatches: 25, Indels: 25
0.79 0.11 0.11
Matches are distributed among these distances:
45 2 0.01
46 4 0.02
47 64 0.35
48 33 0.18
49 9 0.05
50 71 0.39
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCACGACGAGGAGTGCTAG
Found at i:28320072 original size:47 final size:47
Alignment explanation
Indices: 28319907--28320175 Score: 272
Period size: 47 Copynumber: 5.6 Consensus size: 47
28319897 AGTGTGACAA
* * * *
28319907 TGTAAGACCATGTCTAGGACATGGCATCAGCACAGACCGAGGAGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAC-GA--GATGAGTGCCAG
** * * * * *
28319957 TGTAAGATGATGTCTGGGACATGGCATCAGCACGGACAGAGGAGAGTCAA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAC-G--AGATGAGTGCCAG
*
28320007 TGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGTGCCAG
* * * *
28320054 TGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCCA-
1 TGTAAGACCATGTCTGGGACATGGCATCGGCA-CGAGATGAG-TGCCAG
* * *
28320102 TGTAAGACCATGTCTGGGACATGGTATCGGCTCGAGATGAGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGTGCCAG
28320149 CT-TAAGACCATGTCTGGGACATGGCAT
1 -TGTAAGACCATGTCTGGGACATGGCAT
28320176 TGACACCGAT
Statistics
Matches: 184, Mismatches: 29, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
46 3 0.02
47 70 0.38
48 37 0.20
49 5 0.03
50 68 0.37
52 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGTGCCAG
Found at i:28320125 original size:48 final size:46
Alignment explanation
Indices: 28319906--28320223 Score: 223
Period size: 48 Copynumber: 6.6 Consensus size: 46
28319896 GAGTGTGACA
* * *
28319906 ATGTAAGACCATGTCTAGGACATGGCATCAGCACAGACCGAG--GAGTGCT
1 ATGTAAGACCATGTCTGGGACATGGCATC-G-AC---CCGAGATGAGTCCC
** * *
28319955 AGTGTAAGATGATGTCTGGGACATGGCATCAGCACGGACAGAGGA-GAGT-CA
1 A-TGTAAGACCATGTCTGGGACATGGCATC-G-AC---CCGA-GATGAGTCCC
* * *
28320006 ATGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCC
1 ATGTAAGACCATGTCTGGGACATGGCATCGACCCGAGATGAGTCCC
* *
28320052 AGTGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
1 A-TGTAAGACCATGTCTGGGACATGGCATCGAC-CCGAGATGAG-TCCC
* * * * *
28320101 ATGTAAGACCATGTCTGGGACATGGTATCGGCTCGAGATGAGTGCT
1 ATGTAAGACCATGTCTGGGACATGGCATCGACCCGAGATGAGTCCC
* * *
28320147 A-GCTTAAGACCATGTCTGGGACATGGCATTGACACCGATATGTGATCCC
1 ATG--TAAGACCATGTCTGGGACATGGCATCGAC-CCGAGATGAG-TCCC
* * *
28320196 ATGTAAGACCATATTTGGGATATGGCAT
1 ATGTAAGACCATGTCTGGGACATGGCAT
28320224 TGGCGTCCTA
Statistics
Matches: 221, Mismatches: 35, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
44 2 0.01
45 7 0.03
46 5 0.02
47 63 0.29
48 66 0.30
49 9 0.04
50 62 0.28
51 3 0.01
52 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
ATGTAAGACCATGTCTGGGACATGGCATCGACCCGAGATGAGTCCC
Found at i:28320135 original size:95 final size:95
Alignment explanation
Indices: 28319906--28320223 Score: 390
Period size: 95 Copynumber: 3.3 Consensus size: 95
28319896 GAGTGTGACA
* * * * **
28319906 ATGTAAGACCATGTCTAGGACATGGCATCAGCACAGACCGAGGAGTGCTAGTGTAAGATGATGTC
1 ATGTAAGACCATGTCTGGGACATGGCATCGGCTC-GA--GATGAGTGCTAGTGTAAGACCATGTC
* * * * *
28319971 TGGGACATGGCATC-AGCACGGACAGAGGAGAGT-CA
63 TGGGACATGGCATCGA-CACCG--ATATGTGA-TCCC
*
28320006 ATGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCCAGTGTAAGACCATGTCTGG
1 ATGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTGG
28320071 GACATGGCATCGACACCGATATGTGATCCC
66 GACATGGCATCGACACCGATATGTGATCCC
*
28320101 ATGTAAGACCATGTCTGGGACATGGTATCGGCTCGAGATGAGTGCTAGCT-TAAGACCATGTCTG
1 ATGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAG-TGTAAGACCATGTCTG
*
28320165 GGACATGGCATTGACACCGATATGTGATCCC
65 GGACATGGCATCGACACCGATATGTGATCCC
* * *
28320196 ATGTAAGACCATATTTGGGATATGGCAT
1 ATGTAAGACCATGTCTGGGACATGGCAT
28320224 TGGCGTCCTA
Statistics
Matches: 196, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
94 1 0.01
95 120 0.61
96 1 0.01
97 40 0.20
98 1 0.01
99 2 0.01
100 31 0.16
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (95 bp):
ATGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTGG
GACATGGCATCGACACCGATATGTGATCCC
Found at i:28320225 original size:48 final size:48
Alignment explanation
Indices: 28320006--28320223 Score: 230
Period size: 48 Copynumber: 4.6 Consensus size: 48
28319996 AGGAGAGTCA
* * * * *
28320006 ATGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGATGAG-TGCC
1 ATGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
28320052 AGTGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
1 A-TGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
* * * * * * *
28320101 ATGTAAGACCATGTCTGGGACATGGTATCGGC-TCGAGATGAG-TGCT
1 ATGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
*
28320147 A-GCTTAAGACCATGTCTGGGACATGGCATTGACACCGATATGTGATCCC
1 ATG--TAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
* * *
28320196 ATGTAAGACCATATTTGGGATATGGCAT
1 ATGTAAGACCATGTCTGGGACATGGCAT
28320224 TGGCGTCCTA
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 4 0.03
47 63 0.45
48 65 0.46
49 7 0.05
50 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (48 bp):
ATGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCCC
Found at i:28326685 original size:22 final size:23
Alignment explanation
Indices: 28326657--28326700 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28326647 AGCACATACA
*
28326657 CATATTTTCCATATATA-ATATG
1 CATATTTTCAATATATATATATG
*
28326679 CATATTTTTAATATATATATAT
1 CATATTTTCAATATATATATAT
28326701 ATATCCAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
CATATTTTCAATATATATATATG
Found at i:28332236 original size:50 final size:48
Alignment explanation
Indices: 28332127--28332256 Score: 136
Period size: 48 Copynumber: 2.7 Consensus size: 48
28332117 TAAAAGGTGG
* *
28332127 GACCAAGGTGAAAGCC-TACAAAGGGCGCTTTAAGTCAAAAAAAAGAGA
1 GACCAAGGTGAAA-CCTTACAAAGGGCGCCTTAAGTAAAAAAAAAGAGA
* * *
28332175 GACCAGGGTGAAACCTTACAAAGGGAGCCTTGAGTAAAAAAAAATGGAGA
1 GACCAAGGTGAAACCTTACAAAGGGCGCCTTAAGTAAAAAAAAA--GAGA
* * * **
28332225 GGCTAAGGTGAAAACTCGCAAAGGGCGCCTTA
1 GACCAAGGTGAAACCTTACAAAGGGCGCCTTA
28332257 GACCAAAGGG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
47 2 0.03
48 36 0.55
50 28 0.42
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.14
Consensus pattern (48 bp):
GACCAAGGTGAAACCTTACAAAGGGCGCCTTAAGTAAAAAAAAAGAGA
Found at i:28333624 original size:89 final size:88
Alignment explanation
Indices: 28333473--28334040 Score: 548
Period size: 89 Copynumber: 6.4 Consensus size: 88
28333463 TGAATACAAA
* * *
28333473 AGATCTTATCTTCATGTACTGGCGTGAAGTACATCAAAGATAACAGATCTTGTCTTCCCATACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATCTTCACATACTG
* *
28333538 GTGGCGAAGTAGATCCAAGAAAGC
66 G-CGCGAAGTAGATCAAAGAAAGC
* * *
28333562 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGACAACAGATCTTGTCTTCCCATACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATCTTCACATACTG
* *
28333627 GTGGCGAAGTAGATCAAAGAGAGC
66 G-CGCGAAGTAGATCAAAGAAAGC
* * ** * **
28333651 AAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAACAGATCTTATCTTCATGTACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATCTTCACATACTG
*
28333716 GCGTGAAGTAGATCAAAGATAA-C
66 GCGCGAAGTAGATCAAAGA-AAGC
* * * * * **
28333739 AGATCTTGTCTTC-TCATACTGGTGGCGAAGTAGATCCAAGA-AAGCAGATCTTATCTTCATGTA
1 AGATCTTATCTTCAT-GTACTGG-CGTGAAGTAGATCAAAGATAA-CAGATCTTATCTTCACATA
* * *
28333802 CTGGCGTGAAGTAGATTAAAGATAGC
63 CTGGCGCGAAGTAGATCAAAGAAAGC
* *** * * * * * * ** *
28333828 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGCAAATCTTATCTTCATGTATT
1 AGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAACAGATCTTATCTTCACATACT
* ** *
28333893 GGCGTGAAGTAGATTGAAGAAAAC
65 GGCGCGAAGTAGATCAAAGAAAGC
* * *
28333917 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCATACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATCTTCACATACTG
* * *
28333982 GTGGCGAAGTAGATCGAAGAAAAC
66 G-CGCGAAGTAGATCAAAGAAAGC
* * * *
28334006 AGGTCTTGTCTTCATGTATTGGCGTGAAATAGATC
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATC
28334041 GAATATCGCA
Statistics
Matches: 414, Mismatches: 57, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
87 1 0.00
88 68 0.16
89 344 0.83
90 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (88 bp):
AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATCTTCACATACTG
GCGCGAAGTAGATCAAAGAAAGC
Found at i:28333833 original size:222 final size:222
Alignment explanation
Indices: 28333473--28334040 Score: 1019
Period size: 222 Copynumber: 2.6 Consensus size: 222
28333463 TGAATACAAA
*
28333473 AGATCTTATCTTCATGTACTGGCGTGAAGTACATCAAAGATAACAGATCTTGTCTTCCCATACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
28333538 GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAC
66 GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAC
28333603 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAGAGCAAATCTTATCTTCATGT
131 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAGAGCAAATCTTATCTTCATGT
28333668 ATTGGCGTGAAGTAGATTGAAGAAAAC
196 ATTGGCGTGAAGTAGATTGAAGAAAAC
*
28333695 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCTCATACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
* *
28333760 GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATTAAAGAT
66 GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAC
* *
28333825 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGCAAATCTTATCTTCATGT
131 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAGAGCAAATCTTATCTTCATGT
28333890 ATTGGCGTGAAGTAGATTGAAGAAAAC
196 ATTGGCGTGAAGTAGATTGAAGAAAAC
*
28333917 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCATACTG
1 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
* * * * * *
28333982 GTGGCGAAGTAGATCGAAGAAAACAGGTCTTGTCTTCATGTATTGGCGTGAAATAGATC
66 GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATC
28334041 GAATATCGCA
Statistics
Matches: 331, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 331 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (222 bp):
AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAC
AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAGAGCAAATCTTATCTTCATGT
ATTGGCGTGAAGTAGATTGAAGAAAAC
Found at i:28334020 original size:133 final size:132
Alignment explanation
Indices: 28333473--28334040 Score: 553
Period size: 133 Copynumber: 4.3 Consensus size: 132
28333463 TGAATACAAA
* * * * ***
28333473 AGATCTTATCTTCATGTACTGGCGTGAAGTACATCAAAGATAACAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCATGTACTG
* * * * ** * *
28333538 GTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAC
66 G-CGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCACATACTGGCGCGAAGTAGATCAAAGAA
28333603 AAC
130 AAC
*** * * * * * *
28333606 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAGAGCAAATCTTATCTTCATGTATT
1 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCATGTACT
** ** * *
28333671 GGCGTGAAGTAGATTGAAGAAAACAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
65 GGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCACATACTGGCGCGAAGTAGATCAAAGAA
28333736 AAC
130 AAC
* * * * *
28333739 AGATCTTGTCTTC-TCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTAC
1 AGATCTTGTCTTCAT-GTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCATGTAC
* * * * * * *
28333803 TGGCGTGAAGTAGATTAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
64 TGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCACATACTGG-CGCGAAGTAGATCAAAG
* *
28333868 AGAGC
128 AAAAC
* * * **
28333873 AAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAACAGATCTTATCTTCATGTACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCATGTACTG
** * * * *
28333938 GCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
66 GCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCACATACTGG-CGCGAAGTAGATCAAAGAA
28334003 AAC
130 AAC
* * *
28334006 AGGTCTTGTCTTCATGTATTGGCGTGAAATAGATC
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
28334041 GAATATCGCA
Statistics
Matches: 374, Mismatches: 57, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
133 307 0.82
134 66 0.18
135 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (132 bp):
AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCATGTACTG
GCGTGAAGTAGATCAAAGAAAACAGATCTTATCTTCACATACTGGCGCGAAGTAGATCAAAGAAA
AC
Found at i:28346768 original size:29 final size:31
Alignment explanation
Indices: 28346715--28346782 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
28346705 TACATGATTT
*
28346715 TTTAATTTAATGTACAATTCTATATAT-AAAC
1 TTTAATTTAATGTA-AATTATATATATAAAAC
* * *
28346746 TTTAATTTAGTGT-AATTATATATGTAAAAG
1 TTTAATTTAATGTAAATTATATATATAAAAC
28346776 TTTAATT
1 TTTAATT
28346783 GTGGTACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 10 0.31
30 10 0.31
31 12 0.38
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTAATTTAATGTAAATTATATATATAAAAC
Found at i:28346958 original size:29 final size:30
Alignment explanation
Indices: 28346916--28346974 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
28346906 GAATTTGATC
* **
28346916 AAATCAAACTTTCATGTATACAATTGTACA
1 AAATCAAACGTTCACATATACAATTGTACA
28346946 AAATCAAA-GTTCACATATACAATTGTACA
1 AAATCAAACGTTCACATATACAATTGTACA
28346975 TTAAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAACGTTCACATATACAATTGTACA
Found at i:28348685 original size:25 final size:24
Alignment explanation
Indices: 28348657--28348703 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
28348647 TTAGGAAACA
*
28348657 ATTTGGAAAATTTTAAGATATTTAC
1 ATTTAGAAAATTTTAA-ATATTTAC
**
28348682 ATTTAGATCATTTTAAATATTT
1 ATTTAGAAAATTTTAAATATTT
28348704 TTTATGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTAGAAAATTTTAAATATTTAC
Found at i:28348838 original size:24 final size:26
Alignment explanation
Indices: 28348806--28348856 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28348796 ACATAGTTAT
*
28348806 AAATAATAT-ATTATTTTTTAAATTA
1 AAATAATATAATTATTTTATAAATTA
*
28348831 AAAT-ATATAATTATTTTATAAGTTA
1 AAATAATATAATTATTTTATAAATTA
28348856 A
1 A
28348857 CTTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
AAATAATATAATTATTTTATAAATTA
Found at i:28349313 original size:18 final size:17
Alignment explanation
Indices: 28349290--28349324 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28349280 TATTTTTATC
28349290 GATACCATCTTTGATATT
1 GATACCATCTTTG-TATT
*
28349308 GATACCATTTTTGTATT
1 GATACCATCTTTGTATT
28349325 CTAACTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (17 bp):
GATACCATCTTTGTATT
Found at i:28351027 original size:21 final size:21
Alignment explanation
Indices: 28351003--28351043 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28350993 TTATTTAGAA
*
28351003 GATTATAATGTAAAACAAAAT
1 GATTAAAATGTAAAACAAAAT
* *
28351024 GATTAAAATTTAAAAGAAAA
1 GATTAAAATGTAAAACAAAA
28351044 ATAAAGAAAA
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:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (21 bp):
GATTAAAATGTAAAACAAAAT
Found at i:28352635 original size:27 final size:27
Alignment explanation
Indices: 28352583--28352636 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
28352573 AGTATAGTCC
* *
28352583 GCCGGGATAGTAAATACAGGGTAGTTT
1 GCCGGGATAGTAAACACAGGGAAGTTT
28352610 GCCGGGATAGTAAACAC-GAGGAAGTTT
1 GCCGGGATAGTAAACACAG-GGAAGTTT
28352637 ATTAGGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.22
Consensus pattern (27 bp):
GCCGGGATAGTAAACACAGGGAAGTTT
Found at i:28358199 original size:41 final size:40
Alignment explanation
Indices: 28358167--28358243 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
28358157 GCGTTTGGAC
* *
28358167 AAAAAATGCCGCTAAAAATCGAGCATTAGTGGCGCTTAGA
1 AAAAAACGCCACTAAAAATCGAGCATTAGTGGCGCTTAGA
* * *
28358207 ATAAAACGCCACTAAAGATCTAGCATTAGTGGCGCTT
1 AAAAAACGCCACTAAAAATCGAGCATTAGTGGCGCTT
28358244 GTTTGGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (40 bp):
AAAAAACGCCACTAAAAATCGAGCATTAGTGGCGCTTAGA
Found at i:28359700 original size:7 final size:7
Alignment explanation
Indices: 28359688--28359743 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
28359678 GTTAATTGAC
28359688 GGGTTTA
1 GGGTTTA
28359695 GGGTTTA
1 GGGTTTA
*
28359702 AGGTTTA
1 GGGTTTA
* *
28359709 CGGTTTG
1 GGGTTTA
28359716 GGGTTTA
1 GGGTTTA
*
28359723 AGGTTTA
1 GGGTTTA
**
28359730 TAGTTTA
1 GGGTTTA
28359737 GGGTTTA
1 GGGTTTA
28359744 AGATTTACGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.45
Consensus pattern (7 bp):
GGGTTTA
Found at i:28359708 original size:14 final size:14
Alignment explanation
Indices: 28359689--28359764 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
28359679 TTAATTGACG
*
28359689 GGTTTAGGGTTTAA
1 GGTTTACGGTTTAA
**
28359703 GGTTTACGGTTTGG
1 GGTTTACGGTTTAA
*
28359717 GGTTTAAGGTTTATA
1 GGTTTACGGTTTA-A
*
28359732 -GTTTAGGGTTTAA
1 GGTTTACGGTTTAA
*
28359745 GATTTACGG-TTAA
1 GGTTTACGGTTTAA
*
28359758 GGCTTAC
1 GGTTTAC
28359765 AGTATAGTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 10 0.20
14 39 0.80
ACGTcount: A:0.21, C:0.05, G:0.32, T:0.42
Consensus pattern (14 bp):
GGTTTACGGTTTAA
Found at i:28359714 original size:21 final size:21
Alignment explanation
Indices: 28359689--28359755 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
28359679 TTAATTGACG
28359689 GGTTTAGGGTTTAAGGTTTAC
1 GGTTTAGGGTTTAAGGTTTAC
* *
28359710 GGTTTGGGGTTTAAGGTTTAT
1 GGTTTAGGGTTTAAGGTTTAC
* *
28359731 AGTTTAGGGTTTAAGATTTAC
1 GGTTTAGGGTTTAAGGTTTAC
28359752 GGTT
1 GGTT
28359756 AAGGCTTACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.19, C:0.03, G:0.33, T:0.45
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGGTTTAC
Found at i:28359897 original size:15 final size:15
Alignment explanation
Indices: 28359879--28359908 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28359869 GCTATTTTAA
*
28359879 AATATAAATGTAAAT
1 AATATAAATATAAAT
28359894 AATATAAATATAAAT
1 AATATAAATATAAAT
28359909 TATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:28360155 original size:21 final size:20
Alignment explanation
Indices: 28360115--28360152 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28360105 AATATATTGA
*
28360115 TGTATTTATCTTTTAAAATG
1 TGTAATTATCTTTTAAAATG
*
28360135 TGTAATTATTTTTTAAAA
1 TGTAATTATCTTTTAAAA
28360153 ATGCATTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TGTAATTATCTTTTAAAATG
Found at i:28360712 original size:19 final size:20
Alignment explanation
Indices: 28360671--28360714 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
28360661 AATTGTCATC
*
28360671 TCCCCTAAATCCCTAAAATT
1 TCCCCTAAATCCCTAAAAGT
*
28360691 TCCCCT-AATCCCTAATAGT
1 TCCCCTAAATCCCTAAAAGT
28360710 TCCCC
1 TCCCC
28360715 AAACCCGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.27, C:0.41, G:0.02, T:0.30
Consensus pattern (20 bp):
TCCCCTAAATCCCTAAAAGT
Found at i:28361269 original size:22 final size:22
Alignment explanation
Indices: 28361225--28361269 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28361215 CCTTCTGTAA
* *
28361225 TGGAAAAAAAAAATGGTTGAGT
1 TGGAAAAAAAAAATGATTAAGT
28361247 TGGAAAAAGAAAAAT-ATTAAGT
1 TGGAAAAA-AAAAATGATTAAGT
28361269 T
1 T
28361270 ATCATTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (22 bp):
TGGAAAAAAAAAATGATTAAGT
Found at i:28368207 original size:43 final size:43
Alignment explanation
Indices: 28368160--28368301 Score: 171
Period size: 43 Copynumber: 3.3 Consensus size: 43
28368150 CGTTTTTGAA
*
28368160 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGCTTGTGGG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGATTGTGGG
* * * * *
28368203 AAAAGCGCCGCTAAA-AGTCAAGATCTATAGCGGCAATTGTGGG
1 AAAAGCGCCGCTAAAGA-ACATGACCTTTAGCGGCGATTGTGGG
* * *
28368246 ATAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGT-GG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGATTGTGGG
28368288 AATAAGCGCCGCTA
1 AA-AAGCGCCGCTA
28368302 GCGGCGCTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 4 0.05
43 76 0.94
44 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGATTGTGGG
Found at i:28368217 original size:86 final size:85
Alignment explanation
Indices: 28368117--28368301 Score: 219
Period size: 86 Copynumber: 2.2 Consensus size: 85
28368107 CGTTTTACGA
** * ** *
28368117 AAAAGCGCCGCTAAAAGTCGCCATCAATTA-TGGCGTTTTTGAAAAAAGCGCCGCTAAAGAACAT
1 AAAAGCGCCGCTAAAAGTCAACATCAA-TAGCGGCAATTGTGAAAAAAGCGCCGCTAAAGAACAT
*
28368181 GACCTTTAGCGGCGCTTGTGGG
65 GACATTTAGCGGCGCTTGT-GG
* * ** *
28368203 AAAAGCGCCGCTAAAAGTCAAGATCTATAGCGGCAATTGTGGGATAAGCGCCGCTAAAGAACATG
1 AAAAGCGCCGCTAAAAGTCAACATCAATAGCGGCAATTGTGAAAAAAGCGCCGCTAAAGAACATG
*
28368268 ACATTTAGCGGCGTTTGTGG
66 ACATTTAGCGGCGCTTGTGG
28368288 AATAAGCGCCGCTA
1 AA-AAGCGCCGCTA
28368302 GCGGCGCTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 6 0.07
86 78 0.93
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (85 bp):
AAAAGCGCCGCTAAAAGTCAACATCAATAGCGGCAATTGTGAAAAAAGCGCCGCTAAAGAACATG
ACATTTAGCGGCGCTTGTGG
Found at i:28368319 original size:27 final size:27
Alignment explanation
Indices: 28368273--28368328 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
28368263 ACATGACATT
* *
28368273 TAGCGGCGTTTGTGGAATAAGCGCCGC
1 TAGCGGCGCTTATGGAATAAGCGCCGC
* *
28368300 TAGCGGCGCTTATGGGATAAGCGTCGC
1 TAGCGGCGCTTATGGAATAAGCGCCGC
28368327 TA
1 TA
28368329 AAGAACATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.23
Consensus pattern (27 bp):
TAGCGGCGCTTATGGAATAAGCGCCGC
Found at i:28368363 original size:43 final size:43
Alignment explanation
Indices: 28368300--28368482 Score: 249
Period size: 43 Copynumber: 4.3 Consensus size: 43
28368290 TAAGCGCCGC
* * * *
28368300 TAGCGGCGCTTATGGGATAAGCGTCGCTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* * *
28368343 TAGCGGCATTTGTGGAATAAGCGCCGCTAAAGAGCATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* *
28368386 TAGCGGCGTTTGTGGGATAACCGCCGCTAAAGAACATGAGCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
* * **
28368429 TTGCGGCGTTTGTGGGATAAGCACCGCTAAAGGTCATGACCTT
1 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
28368472 TAGCGGCGTTT
1 TAGCGGCGTTT
28368483 ATTTCTATAA
Statistics
Matches: 121, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGAACATGACCTT
Found at i:28368388 original size:113 final size:113
Alignment explanation
Indices: 28368187--28368414 Score: 323
Period size: 113 Copynumber: 2.0 Consensus size: 113
28368177 ACATGACCTT
* * * *
28368187 TAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAAGTCAAGATCTATAGCGGCAATTGTGGGATAAGC
1 TAGCGGCGCTTATGGGAAAAGCGCCGCTAAAAGACAAGAGCTATAGCGGCAATTGTGGAATAAGC
*
28368252 GCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATAAGCGCCGC
66 GCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATAACCGCCGC
* * * * *
28368300 TAGCGGCGCTTATGGGATAAGCGTCGCT-AAAGAACATGAGCTTTAGCGGCATTTGTGGAATAAG
1 TAGCGGCGCTTATGGGAAAAGCGCCGCTAAAAG-ACAAGAGCTATAGCGGCAATTGTGGAATAAG
* * *
28368364 CGCCGCTAAAGAGCATGACCTTTAGCGGCGTTTGTGGGATAACCGCCGC
65 CGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATAACCGCCGC
28368413 TA
1 TA
28368415 AAGAACATGA
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
112 4 0.04
113 97 0.96
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (113 bp):
TAGCGGCGCTTATGGGAAAAGCGCCGCTAAAAGACAAGAGCTATAGCGGCAATTGTGGAATAAGC
GCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATAACCGCCGC
Found at i:28368449 original size:86 final size:86
Alignment explanation
Indices: 28368300--28368484 Score: 282
Period size: 86 Copynumber: 2.2 Consensus size: 86
28368290 TAAGCGCCGC
* * *
28368300 TAGCGGCGCTTATGGGATAAGCGTCGCTAAAGAACATGAGCTTTAGCGGCATTTGTGGAATAAGC
1 TAGCGGCGTTTATGGGATAACCGCCGCTAAAGAACATGAGCTTTAGCGGCATTTGTGGAATAAGC
*
28368365 GCCGCTAAAGAG-CATGACCTT
66 ACCGCTAAAG-GTCATGACCTT
* * * *
28368386 TAGCGGCGTTTGTGGGATAACCGCCGCTAAAGAACATGAGCTTTTGCGGCGTTTGTGGGATAAGC
1 TAGCGGCGTTTATGGGATAACCGCCGCTAAAGAACATGAGCTTTAGCGGCATTTGTGGAATAAGC
28368451 ACCGCTAAAGGTCATGACCTT
66 ACCGCTAAAGGTCATGACCTT
28368472 TAGCGGCGTTTAT
1 TAGCGGCGTTTAT
28368485 TTCTATAAAC
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 1 0.01
86 88 0.99
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (86 bp):
TAGCGGCGTTTATGGGATAACCGCCGCTAAAGAACATGAGCTTTAGCGGCATTTGTGGAATAAGC
ACCGCTAAAGGTCATGACCTT
Done.