Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, whole genome shotgun sequence
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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:2910284 original size:12 final size:13
Alignment explanation
Indices: 2910259--2910287 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2910249 TCGGGTCAAC
2910259 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2910272 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
2910284 GGTC
1 GGTC
2910288 GGGTAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2910302 original size:18 final size:17
Alignment explanation
Indices: 2910245--2910315 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 17
2910235 CAACGGTCAA
*
2910245 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
*
2910262 CAACGGGTCGGGTCAACGGT
1 ---CGGGTCGGGTAAACGGT
2910282 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
2910300 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
2910316 GTAAACGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
20 17 0.35
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:2910360 original size:11 final size:10
Alignment explanation
Indices: 2910330--2910381 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
2910320 ACGGGTCGTG
2910330 ACCGGTC-AA
1 ACCGGTCAAA
2910339 ACCGGTCAAA
1 ACCGGTCAAA
2910349 ACCGGTTCAAA
1 ACCGG-TCAAA
*
2910360 ACCGGT-TAA
1 ACCGGTCAAA
2910369 ACCGGTCAAA
1 ACCGGTCAAA
2910379 ACC
1 ACC
2910382 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:2911198 original size:40 final size:40
Alignment explanation
Indices: 2911154--2911244 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
2911144 TGTGCATTTC
2911154 TGTGTTGCGAAAGTGAAATTCGCAA-AGCAAATTTTAATTA
1 TGTGTTGCGAAAGTGAAATTCGCAACA-CAAATTTTAATTA
** * * *
2911194 TGTGTTGTTAAATTGAAATTCGCAACACGAATTTTAGTTA
1 TGTGTTGCGAAAGTGAAATTCGCAACACAAATTTTAATTA
*
2911234 TGTGTTACGAA
1 TGTGTTGCGAA
2911245 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (40 bp):
TGTGTTGCGAAAGTGAAATTCGCAACACAAATTTTAATTA
Found at i:2913470 original size:23 final size:23
Alignment explanation
Indices: 2913444--2913544 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
2913434 CACCACAACT
*
2913444 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
2913467 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
* * *
2913490 CGTAGAATTGCACCGTAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
* * *
2913513 CGTAGAATTACACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
2913536 TATAATAAT
1 CAT-ATAAT
2913545 GTCCATAAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
23 63 0.94
24 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:2913724 original size:103 final size:103
Alignment explanation
Indices: 2913551--2913768 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2913541 TAATGTCCAT
* *
2913551 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2913616 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
2913654 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
2913719 GACTTCACACATGTTCTAAAGAATACATATATATCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATATCCCG
2913757 AAGGACCACATA
1 AAGGACCACATA
2913769 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:2919475 original size:23 final size:23
Alignment explanation
Indices: 2919449--2919531 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
2919439 TGCCACATAT
*
2919449 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGTAGTACCGCGTAG
2919472 AATTGCACCGTAGTACCGCGTAG
1 AATTGCACCGTAGTACCGCGTAG
* *
2919495 AATTGCACTGTAGTGCCGCGTAG
1 AATTGCACCGTAGTACCGCGTAG
2919518 AATTGCACCGTAGT
1 AATTGCACCGTAGT
2919532 GCCATATAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (23 bp):
AATTGCACCGTAGTACCGCGTAG
Found at i:2919532 original size:23 final size:23
Alignment explanation
Indices: 2919426--2919534 Score: 137
Period size: 23 Copynumber: 4.7 Consensus size: 23
2919416 CAGCTCATAT
* * * * *
2919426 AATTGCACTGAAGTGCCACATAT
1 AATTGCACCGTAGTGCCGCGTAG
* *
2919449 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGTAGTGCCGCGTAG
*
2919472 AATTGCACCGTAGTACCGCGTAG
1 AATTGCACCGTAGTGCCGCGTAG
*
2919495 AATTGCACTGTAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCGCGTAG
2919518 AATTGCACCGTAGTGCC
1 AATTGCACCGTAGTGCC
2919535 ATATAATATT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCGCGTAG
Found at i:2919723 original size:103 final size:103
Alignment explanation
Indices: 2919555--2919768 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
2919545 GTCCATAAGG
* *
2919555 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
2919620 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
* *
2919658 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTTTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
* *
2919723 TCACACATGTTTCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
2919761 ACCACATA
1 ACCACATA
2919769 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
Found at i:2921466 original size:31 final size:31
Alignment explanation
Indices: 2921431--2921511 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
2921421 GGATGTTACA
* * *
2921431 CCGAAGAACCTAGGCAATCAGTCCATATATC
1 CCGAAGAACATAGGCAAACAGTCCATACATC
* *
2921462 CCGAAGAACATAGGTAAACAGTCCATACGTC
1 CCGAAGAACATAGGCAAACAGTCCATACATC
* *
2921493 CCGAAGAATATAGGTAAAC
1 CCGAAGAACATAGGCAAAC
2921512 CCTCGACCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (31 bp):
CCGAAGAACATAGGCAAACAGTCCATACATC
Found at i:2923823 original size:11 final size:10
Alignment explanation
Indices: 2923775--2923842 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 10
2923765 CAAAGAAACT
2923775 AAAAATATAA
1 AAAAATATAA
*
2923785 TGAAAATATATA
1 -AAAAATATA-A
* *
2923797 AATAGTATAA
1 AAAAATATAA
2923807 ATAAAATAATAA
1 A-AAAAT-ATAA
2923819 AAAAATATATA
1 AAAAATATA-A
2923830 AAAAATATAA
1 AAAAATATAA
2923840 AAA
1 AAA
2923843 TGTATGTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
10 9 0.19
11 32 0.68
12 6 0.13
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
AAAAATATAA
Found at i:2924143 original size:2 final size:2
Alignment explanation
Indices: 2924136--2924166 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2924126 ATATAATTAA
*
2924136 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2924167 AATAATAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2925659 original size:106 final size:106
Alignment explanation
Indices: 2925474--2926507 Score: 1533
Period size: 106 Copynumber: 9.9 Consensus size: 106
2925464 GCATTTTTCT
* * *
2925474 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
2925538 ACCAGCCGTCCCTTCGTTC-TGAAATTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2925580 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGATAC-GAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-CTGAAATTGGGAAATTGTTTGTTGACA
*
2925644 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2925686 GAGTCCAACATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
2925751 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2925792 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
2925857 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2925898 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
** * *
2925963 CCAGTTGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2926004 GAGTCCAATATCCTTCGCTATAAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
2926069 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
2926110 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTTACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
2926175 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2926216 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----G-AA----G---TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
2926269 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2926310 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTAAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
2926375 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2926416 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
2926480 CCAGCCGTCCCTTCGTTGTGAAGTTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
2926508 ATCCAAGTAT
Statistics
Matches: 850, Mismatches: 62, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
94 84 0.10
97 1 0.00
99 2 0.00
101 2 0.00
103 1 0.00
105 38 0.04
106 720 0.85
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2926285 original size:200 final size:200
Alignment explanation
Indices: 2925830--2926450 Score: 954
Period size: 200 Copynumber: 3.0 Consensus size: 200
2925820 AAATTGGCTC
*
2925830 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* **
2925895 CTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGA
** * *
2925960 CAACCAGTTGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTAT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC--T
2926025 AAAGTTGAAATTGGCT
194 ---G-TG-AA---G-T
2926041 CTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 -TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* * * * *
2926106 TCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTT
65 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTG
* *
2926171 ACAACCAGCGGTCCATTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTG
130 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTG
2926236 TGAAGT
195 TGAAGT
* *
2926242 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
2926307 CTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTAAAATTGGGAAATTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGA
2926372 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
2926437 GAAGT
196 GAAGT
2926442 TGAAATTGG
1 TGAAATTGG
2926451 CTCCGAAATT
Statistics
Matches: 382, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
200 197 0.52
201 1 0.00
202 1 0.00
205 2 0.01
206 2 0.01
207 1 0.00
210 1 0.00
212 177 0.46
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (200 bp):
TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGA
CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
GAAGT
Found at i:2926314 original size:94 final size:94
Alignment explanation
Indices: 2926150--2926450 Score: 422
Period size: 94 Copynumber: 3.1 Consensus size: 94
2926140 ATTGGCTCTA
* * * * *
2926150 AAATTGAGAAGTTGTTTGTTTACAACCAGCGGTCCATTCGTCGTGAAGTTGAACTTACGTTGTCT
1 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
2926215 GGAGTCCAATATCCTTCGCTGTGAAGTTG
66 GGAGTCCAATATCCTTCGCTGTGAAGTTG
*
2926244 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
1 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
2926309 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 GGAGTCCAATATCCTTCGCTGTGAA---G---TT-G
*
2926345 ATCTAAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 -----AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
2926410 TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
61 TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
2926444 AAATTGG
1 AAATTGG
2926451 CTCCGAAATT
Statistics
Matches: 185, Mismatches: 10, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
94 90 0.49
97 1 0.01
99 1 0.01
100 4 0.02
101 1 0.01
103 1 0.01
106 87 0.47
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (94 bp):
AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
GGAGTCCAATATCCTTCGCTGTGAAGTTG
Found at i:2927404 original size:22 final size:21
Alignment explanation
Indices: 2927378--2927429 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
2927368 TGTTTGGTCA
2927378 AAGGTTTGGCATGTGATGCTC
1 AAGGTTTGGCATGTGATGCTC
*
2927399 ATAGGTTTGGCATTTGATGCTC
1 A-AGGTTTGGCATGTGATGCTC
2927421 AACGGTTTG
1 AA-GGTTTG
2927430 ATGGGGTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.19, C:0.13, G:0.31, T:0.37
Consensus pattern (21 bp):
AAGGTTTGGCATGTGATGCTC
Found at i:2928092 original size:22 final size:22
Alignment explanation
Indices: 2928033--2928095 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
2928023 TTTTGTCCCT
2928033 TTTTC-TTTTTGATTTTTG-TTC
1 TTTTCTTTTTTG-TTTTTGCTTC
2928054 TTTT-TTATATTCT-TTTTTGCTTC
1 TTTTCTT-T-TT-TGTTTTTGCTTC
2928077 TTTTCTTTTTTGTTTTTGC
1 TTTTCTTTTTTGTTTTTGC
2928096 CCTTTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
21 6 0.17
22 16 0.46
23 10 0.29
24 3 0.09
ACGTcount: A:0.05, C:0.11, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTTTGTTTTTGCTTC
Found at i:2932676 original size:19 final size:18
Alignment explanation
Indices: 2932596--2932676 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 18
2932586 AATAAGATTT
**
2932596 TAAAAGAAAATAATAATAA
1 TAAAAGAAACCAATAA-AA
** *
2932615 TAAAAGAAAGTAACAAAA
1 TAAAAGAAACCAATAAAA
**
2932633 CTAAAGAGTAAACCAAGGAAA
1 -TAAA-AG-AAACCAATAAAA
2932654 TAAAAGAAACCAATAATAA
1 TAAAAGAAACCAATAA-AA
2932673 TAAA
1 TAAA
2932677 CATAAAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
18 10 0.20
19 26 0.52
20 6 0.12
21 8 0.16
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (18 bp):
TAAAAGAAACCAATAAAA
Found at i:2932874 original size:21 final size:22
Alignment explanation
Indices: 2932825--2932901 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
2932815 ATATAATGAA
*
2932825 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATAT-AAAT
2932850 AATAAAAAATATATATATAAA-
1 AATAAAAAATATATATATAAAT
* *
2932871 AATATAAAAATGTATGTATAATAT
1 AATA-AAAAATATATATATAA-AT
2932895 AATAAAA
1 AATAAAA
2932902 TACTAAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.09
22 17 0.37
23 10 0.22
24 9 0.20
25 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAAAAATATATATATAAAT
Found at i:2932890 original size:22 final size:21
Alignment explanation
Indices: 2932811--2932901 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 21
2932801 CAAAGAAACT
*
2932811 AAAA-ATATA-ATGAAAATAA
1 AAAATATATATATAAAAATAA
*
2932830 ATAAATAGTATAAATAAAATAATAA
1 A-AAATA-TATATAT-AAA-AATAA
2932855 AAAATATATATATAAAAATATA
1 AAAATATATATATAAAAATA-A
* *
2932877 AAAATGTATGTATAATATAATAA
1 AAAATATATATATAA-A-AATAA
2932900 AA
1 AA
2932902 TACTAAATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 5 0.08
22 21 0.36
23 12 0.20
24 11 0.19
25 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATATATATATAAAAATAA
Found at i:2937530 original size:31 final size:31
Alignment explanation
Indices: 2937492--2937585 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
2937482 CCCGAATGAC
* * *
2937492 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
2937523 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2937554 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2937585 C
1 C
2937586 CCTCGACCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2938978 original size:35 final size:35
Alignment explanation
Indices: 2938905--2938979 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
2938895 CGTCACTAAC
**
2938905 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
2938940 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
2938975 AGTAA
1 AGTAA
2938980 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:2939084 original size:24 final size:24
Alignment explanation
Indices: 2939057--2939137 Score: 112
Period size: 23 Copynumber: 3.5 Consensus size: 24
2939047 CATAATTCAA
*
2939057 GTCAGGTATCATATCAGAATCCAG
1 GTCAGGTATCAGATCAGAATCCAG
* *
2939081 GTCATGTATCAGATCAGAATCCAT
1 GTCAGGTATCAGATCAGAATCCAG
*
2939105 GTCA-ATATCAGATCAGAATCCAG
1 GTCAGGTATCAGATCAGAATCCAG
2939128 GTCAGG-ATCA
1 GTCAGGTATCA
2939138 TAATAGAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 25 0.50
24 25 0.50
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
GTCAGGTATCAGATCAGAATCCAG
Found at i:2939162 original size:47 final size:48
Alignment explanation
Indices: 2939040--2939164 Score: 116
Period size: 47 Copynumber: 2.6 Consensus size: 48
2939030 TATATCAAAA
* * * * *
2939040 ATCAAAACATAATTCAAGTCAGG-TATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATTCAAGTC-GGAAATCAGATCAGAATCCAGGTCATGG
* * *
2939088 ATCAGATCAGAATCCATGTC--AATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATTCAAGTCGGAA-ATCAGATCAGAATCCAGGTCATGG
2939134 ATCATAAT-AGAATTCAAGTCGGAAATCAGAT
1 ATCA-AATCAGAATTCAAGTCGGAAATCAGAT
2939165 AAAATATTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
46 15 0.25
47 29 0.48
48 17 0.28
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (48 bp):
ATCAAATCAGAATTCAAGTCGGAAATCAGATCAGAATCCAGGTCATGG
Found at i:2940312 original size:18 final size:18
Alignment explanation
Indices: 2940291--2940326 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2940281 CTTCCATCCG
*
2940291 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2940309 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2940327 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2941634 original size:7 final size:7
Alignment explanation
Indices: 2941622--2941660 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
2941612 GGTCAACGTG
2941622 GGTCAAC
1 GGTCAAC
2941629 GGTCAAC
1 GGTCAAC
2941636 GGGTCAAC
1 -GGTCAAC
2941644 GGTCAAC
1 GGTCAAC
2941651 GGGTCAAC
1 -GGTCAAC
2941659 GG
1 GG
2941661 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:2941641 original size:15 final size:15
Alignment explanation
Indices: 2941621--2941660 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2941611 TGGTCAACGT
2941621 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
2941636 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
2941651 GGGTCAACGG
1 GGGTCAACGG
2941661 GTCGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:2941642 original size:8 final size:8
Alignment explanation
Indices: 2941602--2941676 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
2941592 TCAAAGTTTT
2941602 GGTCAACAG
1 GGTCAAC-G
2941611 TGGTCAACGTG
1 -GGTCAAC--G
2941622 GGTCAAC-
1 GGTCAACG
2941629 GGTCAACG
1 GGTCAACG
2941637 GGTCAAC-
1 GGTCAACG
2941644 GGTCAACG
1 GGTCAACG
2941652 GGTCAACG
1 GGTCAACG
2941660 GGT---CG
1 GGTCAACG
2941665 GGTCAACG
1 GGTCAACG
2941673 GGTC
1 GGTC
2941677 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:2941668 original size:13 final size:13
Alignment explanation
Indices: 2941650--2941725 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
2941640 CAACGGTCAA
2941650 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2941663 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
2941681 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
2941694 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
2941707 CGGGTAAACGGGT
1 CGGGTCAACGGGT
2941720 CGGGTC
1 CGGGTC
2941726 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2941681 original size:18 final size:18
Alignment explanation
Indices: 2941644--2941698 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
2941634 ACGGGTCAAC
2941644 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
2941665 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
2941683 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
2941699 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2941688 original size:31 final size:31
Alignment explanation
Indices: 2941650--2941711 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2941640 CAACGGTCAA
*
2941650 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
2941681 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
2941712 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:2943837 original size:35 final size:35
Alignment explanation
Indices: 2943764--2943838 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
2943754 CGTCACTAAC
**
2943764 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
2943799 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
2943834 AGTAA
1 AGTAA
2943839 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:2943943 original size:24 final size:24
Alignment explanation
Indices: 2943916--2943996 Score: 112
Period size: 23 Copynumber: 3.5 Consensus size: 24
2943906 CATAATTCAA
*
2943916 GTCAGGTATCATATCAGAATCCAG
1 GTCAGGTATCAGATCAGAATCCAG
* *
2943940 GTCATGTATCAGATCAGAATCCAT
1 GTCAGGTATCAGATCAGAATCCAG
*
2943964 GTCA-ATATCAGATCAGAATCCAG
1 GTCAGGTATCAGATCAGAATCCAG
2943987 GTCAGG-ATCA
1 GTCAGGTATCA
2943997 TAATAGAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 25 0.50
24 25 0.50
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
GTCAGGTATCAGATCAGAATCCAG
Found at i:2944021 original size:47 final size:48
Alignment explanation
Indices: 2943899--2944023 Score: 116
Period size: 47 Copynumber: 2.6 Consensus size: 48
2943889 TATATCAAAA
* * * * *
2943899 ATCAAAACATAATTCAAGTCAGG-TATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATTCAAGTC-GGAAATCAGATCAGAATCCAGGTCATGG
* * *
2943947 ATCAGATCAGAATCCATGTC--AATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATTCAAGTCGGAA-ATCAGATCAGAATCCAGGTCATGG
2943993 ATCATAAT-AGAATTCAAGTCGGAAATCAGAT
1 ATCA-AATCAGAATTCAAGTCGGAAATCAGAT
2944024 AAAATATTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
46 15 0.25
47 29 0.48
48 17 0.28
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (48 bp):
ATCAAATCAGAATTCAAGTCGGAAATCAGATCAGAATCCAGGTCATGG
Found at i:2945171 original size:18 final size:18
Alignment explanation
Indices: 2945150--2945185 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2945140 CTTCCATCCG
*
2945150 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2945168 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2945186 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2946493 original size:7 final size:7
Alignment explanation
Indices: 2946481--2946519 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
2946471 GGTCAACGTG
2946481 GGTCAAC
1 GGTCAAC
2946488 GGTCAAC
1 GGTCAAC
2946495 GGGTCAAC
1 -GGTCAAC
2946503 GGTCAAC
1 GGTCAAC
2946510 GGGTCAAC
1 -GGTCAAC
2946518 GG
1 GG
2946520 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:2946500 original size:15 final size:15
Alignment explanation
Indices: 2946480--2946519 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2946470 TGGTCAACGT
2946480 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
2946495 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
2946510 GGGTCAACGG
1 GGGTCAACGG
2946520 GTCGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:2946501 original size:8 final size:8
Alignment explanation
Indices: 2946461--2946535 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
2946451 TCAAAGTTTT
2946461 GGTCAACAG
1 GGTCAAC-G
2946470 TGGTCAACGTG
1 -GGTCAAC--G
2946481 GGTCAAC-
1 GGTCAACG
2946488 GGTCAACG
1 GGTCAACG
2946496 GGTCAAC-
1 GGTCAACG
2946503 GGTCAACG
1 GGTCAACG
2946511 GGTCAACG
1 GGTCAACG
2946519 GGT---CG
1 GGTCAACG
2946524 GGTCAACG
1 GGTCAACG
2946532 GGTC
1 GGTC
2946536 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:2946527 original size:13 final size:13
Alignment explanation
Indices: 2946509--2946584 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
2946499 CAACGGTCAA
2946509 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2946522 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
2946540 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
2946553 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
2946566 CGGGTAAACGGGT
1 CGGGTCAACGGGT
2946579 CGGGTC
1 CGGGTC
2946585 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2946540 original size:18 final size:18
Alignment explanation
Indices: 2946503--2946557 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
2946493 ACGGGTCAAC
2946503 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
2946524 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
2946542 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
2946558 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2946547 original size:31 final size:31
Alignment explanation
Indices: 2946509--2946570 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2946499 CAACGGTCAA
*
2946509 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
2946540 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
2946571 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:2961909 original size:293 final size:294
Alignment explanation
Indices: 2961379--2961973 Score: 1147
Period size: 293 Copynumber: 2.0 Consensus size: 294
2961369 AACTTTGGAT
2961379 CTTGAAAGTATTCTATTAATGTTGAGGGTAAACTATATCATATATCATTGAATTTTATATAATAT
1 CTTGAAAGTATTCTATTAATGTTGAGGGTAAACTATATCATATATCATTGAATTTTATATAATAT
2961444 ATAGTTTATATTATTAAACTTTTAATTGTTTCTGTCACACCCCAAAATGTTAGGGTAAAAATATT
66 ATAGTTTATATTATTAAACTTTTAATTGTTTCTGTCACACCCCAAAA--TTAGGGTAAAAATATT
2961509 AAAAATTCATTAACTAAATATTAGGATTTATTTGGTATTTTAATAATAATTTTAGGTTAAATTAT
129 AAAAATTCATTAACTAAATATTAGGATTTATTTGGTATTTTAATAATAATTTTAGGTTAAATTAT
2961574 AAATCAATGATGTTTCAGGGACTAACCCCATTATTCCCCCTACTTACCTAAACTAAAAATATCTT
194 AAATCAATGATGTTTCAGGGACTAACCCCATTATTCCCCCTACTTACCTAAACTAAAAATATCTT
*
2961639 ATGAAGCTAAAATAAAATAACAGAAAGCTATGAAAC
259 ATGAAGCTAAAATAAAAAAACAGAAAGCTATGAAAC
2961675 CTTGAAAGTATTCTATTAATGTTGAGGGTAAACTATATCATATATCATTGAATTTTATATAATAT
1 CTTGAAAGTATTCTATTAATGTTGAGGGTAAACTATATCATATATCATTGAATTTTATATAATAT
*
2961740 ATAGTTTATATTATTAAACTTTTAATTGTTTCTGTCACACCCCAGAA-TAGGGTAAAAATATTAA
66 ATAGTTTATATTATTAAACTTTTAATTGTTTCTGTCACACCCCAAAATTAGGGTAAAAATATTAA
2961804 AAATTCATTAACTAAATATTAGGATTTATTTGGTATTTTAATAATAATTTTAGGTTAAATTATAA
131 AAATTCATTAACTAAATATTAGGATTTATTTGGTATTTTAATAATAATTTTAGGTTAAATTATAA
2961869 ATCAATGATGTTTCAGGGACTAACCCCATTATTCCCCCTACTTACCTAAACTAAAAATATCTTAT
196 ATCAATGATGTTTCAGGGACTAACCCCATTATTCCCCCTACTTACCTAAACTAAAAATATCTTAT
2961934 GAAGCTAAAATAAAAAAACAGAAAGCTATGAAAC
261 GAAGCTAAAATAAAAAAACAGAAAGCTATGAAAC
2961968 CTTGAA
1 CTTGAA
2961974 CCAATATCCT
Statistics
Matches: 297, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
293 186 0.63
296 111 0.37
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (294 bp):
CTTGAAAGTATTCTATTAATGTTGAGGGTAAACTATATCATATATCATTGAATTTTATATAATAT
ATAGTTTATATTATTAAACTTTTAATTGTTTCTGTCACACCCCAAAATTAGGGTAAAAATATTAA
AAATTCATTAACTAAATATTAGGATTTATTTGGTATTTTAATAATAATTTTAGGTTAAATTATAA
ATCAATGATGTTTCAGGGACTAACCCCATTATTCCCCCTACTTACCTAAACTAAAAATATCTTAT
GAAGCTAAAATAAAAAAACAGAAAGCTATGAAAC
Found at i:2965775 original size:12 final size:12
Alignment explanation
Indices: 2965758--2965782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2965748 AAACTTATAT
2965758 TATTAATGTAAA
1 TATTAATGTAAA
2965770 TATTAATGTAAA
1 TATTAATGTAAA
2965782 T
1 T
2965783 TTTGAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TATTAATGTAAA
Found at i:2968270 original size:2 final size:2
Alignment explanation
Indices: 2968263--2968292 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2968253 AAATAAGAAC
2968263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2968293 TCTAAACAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2977172 original size:15 final size:15
Alignment explanation
Indices: 2977152--2977182 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2977142 TTGTTGAAAA
2977152 TGTGCAAAGGTAAAT
1 TGTGCAAAGGTAAAT
*
2977167 TGTGCAAGGGTAAAT
1 TGTGCAAAGGTAAAT
2977182 T
1 T
2977183 ACTCAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (15 bp):
TGTGCAAAGGTAAAT
Found at i:2982491 original size:31 final size:31
Alignment explanation
Indices: 2982434--2982503 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
2982424 GAACTCAACC
* * *
2982434 CGACCCGACCCGAATATCACACTTAAAAAAA
1 CGACCTGACCCGAATATCAAAATTAAAAAAA
**
2982465 CGACCTGACCCGAATAT-ATAAATTAAAAACT
1 CGACCTGACCCGAATATCA-AAATTAAAAAAA
2982496 CGACCTGA
1 CGACCTGA
2982504 AATAATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.17
Consensus pattern (31 bp):
CGACCTGACCCGAATATCAAAATTAAAAAAA
Found at i:2993722 original size:25 final size:25
Alignment explanation
Indices: 2993688--2993736 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2993678 GGGCATCGAG
2993688 CTTAACGAGTAACGAGTTTAATGAC
1 CTTAACGAGTAACGAGTTTAATGAC
*
2993713 CTTAATGAGTAACGAGTTTAATGA
1 CTTAACGAGTAACGAGTTTAATGA
2993737 GCAATGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (25 bp):
CTTAACGAGTAACGAGTTTAATGAC
Found at i:3007696 original size:20 final size:21
Alignment explanation
Indices: 3007671--3007722 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3007661 TTTTCCCAAT
*
3007671 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3007691 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3007712 TCGCAATGCGA
1 TCGCAATGCGA
3007723 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3007755 original size:61 final size:61
Alignment explanation
Indices: 3007708--3007839 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
3007698 GCGAATTGGG
* * * * *
3007708 AAAATCGCAATGCGATACTGACTATCCCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCCCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
3007769 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCCCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3007830 ATAATCGCAA
1 AAAATCGCAA
3007840 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCCCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3007798 original size:20 final size:20
Alignment explanation
Indices: 3007712--3007825 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
3007702 ATTGGGAAAA
* *
3007712 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* * * *
3007732 TCCCAATGCGATACTTACTA
1 TCGCAACGCGATACTGACTT
* * **
3007752 TCGCAATGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
*
3007773 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
3007793 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
3007813 TCGCAACGCGATA
1 TCGCAACGCGATA
3007826 ATACATAATC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:3008041 original size:22 final size:22
Alignment explanation
Indices: 3008013--3008056 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3008003 CACTCTCTCA
3008013 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3008035 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3008057 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3009697 original size:18 final size:18
Alignment explanation
Indices: 3009676--3009720 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3009666 TCCACTTCGG
*
3009676 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
3009694 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
*
3009712 AAGCCATCA
1 GAGCCATCA
3009721 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.42, G:0.13, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3010256 original size:19 final size:20
Alignment explanation
Indices: 3010202--3010268 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3010192 TAGTTTACTT
* *
3010202 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3010222 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3010242 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3010261 TCGCAACG
1 TCGCAACG
3010269 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3010276 original size:14 final size:14
Alignment explanation
Indices: 3010257--3010314 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3010247 ATGCGAAATG
3010257 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3010271 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
3010287 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3010303 AAAATCGCAACG
1 AAAATCGCAACG
3010315 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3010299 original size:32 final size:33
Alignment explanation
Indices: 3010241--3010331 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3010231 GGAAATGGCT
3010241 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3010274 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3010306 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3010332 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3010367 original size:14 final size:14
Alignment explanation
Indices: 3010348--3010405 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3010338 TTGTGTTTCG
3010348 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3010362 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3010378 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3010394 CGTTGCGATTTT
1 CGTTGCGATTTT
3010406 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3010386 original size:32 final size:33
Alignment explanation
Indices: 3010343--3010421 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
3010333 GCGATTTGTG
*
3010343 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3010375 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3010408 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3010422 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3010440 original size:20 final size:19
Alignment explanation
Indices: 3010406--3010461 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3010396 TTGCGATTTT
*
3010406 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3010425 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
3010445 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3010462 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3012330 original size:14 final size:14
Alignment explanation
Indices: 3012311--3012346 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3012301 ATTGTTTAAT
3012311 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3012325 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3012339 TGATTTGT
1 TGATTTGT
3012347 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3012492 original size:14 final size:14
Alignment explanation
Indices: 3012473--3012526 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
3012463 GAAACTGACT
3012473 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3012487 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
3012506 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3012520 ATCGCAA
1 ATCGCAA
3012527 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:3012823 original size:20 final size:20
Alignment explanation
Indices: 3012807--3012844 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3012797 ATTGCGATTT
3012807 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCTCGTTGCGAAAG
3012827 TCAGAATCTCGTTGCGAA
1 TCAGAATCTCGTTGCGAA
3012845 TTAGGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TCAGAATCTCGTTGCGAAAG
Found at i:3013655 original size:24 final size:24
Alignment explanation
Indices: 3013628--3013681 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3013618 GTATTCGAAA
*
3013628 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
3013652 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
3013676 TTTGAT
1 TTTGAT
3013682 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:3013873 original size:12 final size:12
Alignment explanation
Indices: 3013856--3013880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3013846 ATATAATCCT
3013856 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3013868 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3013880 G
1 G
3013881 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3016195 original size:19 final size:19
Alignment explanation
Indices: 3016173--3016264 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
3016163 GGAAATTACT
3016173 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3016192 ATCGTAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3016206 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3016225 ATCGCAA--CG---TTAAT
1 ATCGCAATGCGAAATGAAA
*
3016239 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3016258 ATCGCAA
1 ATCGCAA
3016265 CGAGGGAATC
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 18 0.34
15 1 0.02
16 4 0.08
17 4 0.08
18 1 0.02
19 25 0.47
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3016215 original size:33 final size:33
Alignment explanation
Indices: 3016173--3016284 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
3016163 GGAAATTACT
*
3016173 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
3016206 ATCGCAATGCGAAATGAAAATCGCAACGTTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3016238 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3016272 ATCGCAATGCGAA
1 ATCGCAATGCGAA
3016285 TTTAATTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.01
33 67 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3016316 original size:33 final size:33
Alignment explanation
Indices: 3016279--3016369 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
3016269 GGAATCGCAA
* * *
3016279 TGCGAATTTAATTTCGCGTTGCTATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3016312 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
3016345 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCGTTGCGAT
3016370 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3016333 original size:19 final size:19
Alignment explanation
Indices: 3016309--3016369 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
3016299 GCTATTCTCT
3016309 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3016328 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3016342 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3016361 CATTGCGAT
1 CGTTGCGAT
3016370 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3016347 original size:14 final size:14
Alignment explanation
Indices: 3016295--3016351 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3016285 TTTAATTTCG
*
3016295 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
*
3016309 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3016328 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3016342 CGTTGCGATT
1 CGTTGCGATT
3016352 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3016495 original size:14 final size:14
Alignment explanation
Indices: 3016476--3016512 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3016466 CATCAATTAA
3016476 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3016490 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3016504 ACAAATCAA
1 ACAAATCAA
3016513 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3023840 original size:21 final size:21
Alignment explanation
Indices: 3023814--3023854 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3023804 TCCTCCTTTG
*
3023814 AAGGGGAACCGATTCCCCCCA
1 AAGGGGAACCGATACCCCCCA
*
3023835 AAGGGGAATCGATACCCCCC
1 AAGGGGAACCGATACCCCCC
3023855 TGGGGTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.24, T:0.10
Consensus pattern (21 bp):
AAGGGGAACCGATACCCCCCA
Found at i:3027557 original size:42 final size:42
Alignment explanation
Indices: 3027510--3027671 Score: 207
Period size: 42 Copynumber: 3.9 Consensus size: 42
3027500 GTGGGAGTGA
* *
3027510 CCTCTTCAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGG
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGGG
* * * * *
3027552 CCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGGG
* * *
3027594 CCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGG
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGGG
* * *
3027636 CCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
3027672 CAGGCGAGTC
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 99 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
CCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGGGG
Found at i:3027631 original size:84 final size:84
Alignment explanation
Indices: 3027505--3027674 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
3027495 GAATGGTGGG
*
3027505 AGTGACCTCTTCAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAG
1 AGTGACCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAG
3027570 TGGACTCTTGAGGGATGAC
66 TGGACTCTTGAGGGATGAC
*
3027589 AGTGGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAG
1 AGTGACCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAG
3027654 TGGACTCTTGAGGGATGAC
66 TGGACTCTTGAGGGATGAC
3027673 AG
1 AG
3027675 GCGAGTCGGG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.21
Consensus pattern (84 bp):
AGTGACCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAG
TGGACTCTTGAGGGATGAC
Found at i:3028070 original size:91 final size:90
Alignment explanation
Indices: 3027893--3028077 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
3027883 ATTTCAAACT
*
3027893 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
3027958 AGAATTGGAAGCAACCGAATAAATTTAC
63 AGAATTGGAAGCAACCGAATAAATTTAC
3027986 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* * *
3028050 GTATTGGCAGCAATCGAATAAATTTAC
64 GAATTGGAAGCAACCGAATAAATTTAC
3028077 T
1 T
3028078 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGAAGCAACCGAATAAATTTAC
Found at i:3029795 original size:20 final size:20
Alignment explanation
Indices: 3029766--3029828 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
3029756 TTTTGGTTGA
3029766 AATGAAAATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
* *
3029786 AATGAGAATCGCAACGCGGA-
1 AATGAAAATCGCAACG-AGAT
**
3029806 AATGACTATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
3029826 AAT
1 AAT
3029829 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAT
Found at i:3029846 original size:33 final size:33
Alignment explanation
Indices: 3029789--3029885 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
3029779 ACGAGATAAT
3029789 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* *
3029823 GATAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
3029856 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
3029886 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:3029913 original size:19 final size:19
Alignment explanation
Indices: 3029886--3029951 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
3029876 AAAATCGCAA
**
3029886 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
3029904 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
3029923 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
3029943 TGCGATTTT
1 TGCGATTTT
3029952 CATTCTTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.40
19 12 0.30
20 12 0.30
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3029943 original size:20 final size:19
Alignment explanation
Indices: 3029897--3029948 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3029887 GCGATTTTGG
**
3029897 TTTCGCG-TGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
3029915 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
3029934 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
3029949 TTTCATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 11 0.37
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:3030473 original size:20 final size:20
Alignment explanation
Indices: 3030448--3030500 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3030438 GCGCTATGTA
3030448 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
3030468 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3030488 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3030501 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3030537 original size:20 final size:20
Alignment explanation
Indices: 3030509--3030562 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3030499 GATTTTGTAT
3030509 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
3030529 TATCACATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3030549 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3030563 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3030581 original size:61 final size:61
Alignment explanation
Indices: 3030449--3030583 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
3030439 CGCTATGTAA
* * * * * * ** *
3030449 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
3030510 ATCGCATTGCGATAGTAAGTATCACATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
3030572 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3030584 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:3030673 original size:21 final size:21
Alignment explanation
Indices: 3030633--3030673 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3030623 ACTGTAGACC
**
3030633 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3030654 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3030674 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:3031105 original size:3 final size:3
Alignment explanation
Indices: 3031097--3031121 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3031087 AATTTTCTAT
3031097 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3031122 AAAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3039372 original size:13 final size:13
Alignment explanation
Indices: 3039356--3039381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3039346 TAATCTAAAT
3039356 ATTTAAAAAATTA
1 ATTTAAAAAATTA
3039369 ATTTAAAAAATTA
1 ATTTAAAAAATTA
3039382 TCATTTATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTAAAAAATTA
Found at i:3042614 original size:26 final size:26
Alignment explanation
Indices: 3042585--3042640 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
3042575 TGTGCCAGAT
* * *
3042585 GGGCGACGGCTCAGGGCAGCATGTAG
1 GGGCGACGGCCCAGAGCAACATGTAG
*
3042611 GGGCGACGGCCCAGAGCAACGTGTAG
1 GGGCGACGGCCCAGAGCAACATGTAG
3042637 GGGC
1 GGGC
3042641 ATCAGTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.46, T:0.09
Consensus pattern (26 bp):
GGGCGACGGCCCAGAGCAACATGTAG
Found at i:3044371 original size:22 final size:22
Alignment explanation
Indices: 3044346--3044389 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3044336 AAAATTATAG
*
3044346 AAAATTATAATAA-AATATTTTT
1 AAAAATAT-ATAATAATATTTTT
3044368 AAAAATATATAATAATATTTTT
1 AAAAATATATAATAATATTTTT
3044390 TAACTTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAATATATAATAATATTTTT
Found at i:3044390 original size:24 final size:23
Alignment explanation
Indices: 3044346--3044392 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3044336 AAAATTATAG
3044346 AAAATTATAATAAAATATTTTTA
1 AAAATTATAATAAAATATTTTTA
*
3044369 AAAATATATAATAATAT-TTTTTA
1 AAAAT-TATAATAAAATATTTTTA
3044392 A
1 A
3044393 CTTTTGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATTATAATAAAATATTTTTA
Found at i:3049050 original size:10 final size:10
Alignment explanation
Indices: 3049025--3049058 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3049015 TTTTAAAATC
*
3049025 TTAAAAAATA
1 TTAAATAATA
3049035 TTAAATAATA
1 TTAAATAATA
*
3049045 TTAAATAATT
1 TTAAATAATA
3049055 TTAA
1 TTAA
3049059 CATTAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAATAATA
Found at i:3049105 original size:19 final size:19
Alignment explanation
Indices: 3049060--3049116 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
3049050 TAATTTTAAC
*
3049060 ATTAAAACTATTTTAAAAT
1 ATTAAAATTATTTTAAAAT
3049079 ATTTAAAATTATATTT-AAAT
1 A-TTAAAATTAT-TTTAAAAT
*
3049099 ATTAAAATCA-TTTAAAAT
1 ATTAAAATTATTTTAAAAT
3049117 TTATTTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 9 0.27
20 14 0.42
21 3 0.09
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAAATTATTTTAAAAT
Found at i:3049115 original size:10 final size:9
Alignment explanation
Indices: 3049061--3049116 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 9
3049051 AATTTTAACA
3049061 TTAAAACTATT
1 TTAAAA-TA-T
3049072 TTAAAATAT
1 TTAAAATAT
3049081 TTAAAATTAT
1 TTAAAA-TAT
*
3049091 ATTTAAATA-
1 -TTAAAATAT
3049100 TTAAAATCAT
1 TTAAAAT-AT
3049110 TTAAAAT
1 TTAAAAT
3049117 TTATTTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.15
9 8 0.21
10 14 0.36
11 11 0.28
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAAAATAT
Found at i:3052885 original size:2 final size:2
Alignment explanation
Indices: 3052878--3052908 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3052868 CGTAAAATAC
*
3052878 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3052909 ATGTTACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3054542 original size:84 final size:83
Alignment explanation
Indices: 3054443--3054692 Score: 313
Period size: 84 Copynumber: 3.0 Consensus size: 83
3054433 CCAGGGGTCT
* * *
3054443 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
* *
3054508 CAAACTCAAAGGTCTTTTG
65 CGAACTCGAAGGTCTTTTG
* *
3054527 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATACCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
3054592 CGAACTCGAAGGTC-TTTG
65 CGAACTCGAAGGTCTTTTG
* * * * * * * *
3054610 GTGACATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAG
*
3054675 TCGAACTCGAGGGTCTTT
64 TCGAACTCGAAGGTCTTT
3054693 GGCATTTCAA
Statistics
Matches: 144, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
83 43 0.30
84 99 0.69
85 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (83 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTTG
Found at i:3054693 original size:84 final size:84
Alignment explanation
Indices: 3054363--3054694 Score: 300
Period size: 84 Copynumber: 4.0 Consensus size: 84
3054353 ACAATTTTAT
* * * * * * * * * *
3054363 TGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGACCTTGAAGCTGAGCGTAAT
* *
3054428 CGAAC-CCAGGGGTCTTT-G
66 CGAACTCGA-AGGTCTTTGG
* * * *
3054446 -G-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTT-AGAGCTGAGCGTAG
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGACCTTGA-AGCTGAGCGTAA
* * *
3054507 TCAAACTCAAAGGTCTTTTGT
65 TCGAACTCGAAGGTC-TTTGG
* * * *
3054528 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT-ACCTTGGAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGACCTTGAAGCTGAGCGTAAT
3054592 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * * * * *
3054611 TGACATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGACCTTGAAGCTGAGCGTAAT
*
3054676 CGAACTCGAGGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
3054695 CATTTCAAGA
Statistics
Matches: 205, Mismatches: 35, Indels: 17
0.80 0.14 0.07
Matches are distributed among these distances:
79 1 0.00
80 21 0.10
81 39 0.19
82 1 0.00
83 43 0.21
84 100 0.49
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (84 bp):
TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGACCTTGAAGCTGAGCGTAAT
CGAACTCGAAGGTCTTTGG
Found at i:3054807 original size:21 final size:21
Alignment explanation
Indices: 3054747--3054815 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
3054737 CAAGGGAAAC
*
3054747 TGTCTCAAGGGAGACGAATTT
1 TGTCTCAAGGGAGACGAAATT
* *
3054768 TGTTTC-A---AGA-GAAA-C
1 TGTCTCAAGGGAGACGAAATT
3054783 TGTCTCAAGGGAGACGAAATT
1 TGTCTCAAGGGAGACGAAATT
3054804 TGTCTCAAGGGA
1 TGTCTCAAGGGA
3054816 AACAATCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
15 5 0.14
16 4 0.11
17 3 0.08
19 3 0.08
20 5 0.14
21 17 0.46
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (21 bp):
TGTCTCAAGGGAGACGAAATT
Found at i:3054826 original size:36 final size:36
Alignment explanation
Indices: 3054697--3054818 Score: 174
Period size: 36 Copynumber: 3.4 Consensus size: 36
3054687 GTCTTTGGCA
* *
3054697 TTTCAAGAGAAACTGTCTCAAGAGAGAC-ACCAATTTG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACGA--AATTTG
*
3054734 TTTCAAGGGAAACTGTCTCAAGGGAGACGAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTG
*
3054770 TTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTG
*
3054806 TCTCAAGGGAAAC
1 TTTCAAGGGAAAC
3054819 AATCTCAAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 50 0.65
37 26 0.34
38 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTG
Found at i:3055383 original size:105 final size:105
Alignment explanation
Indices: 3055199--3056301 Score: 1839
Period size: 105 Copynumber: 10.5 Consensus size: 105
3055189 TATTGTTCCA
* * * * *
3055199 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTATGGAACTG-GAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAA-TGTTTGTTGACAA
3055263 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3055305 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
3055370 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3055410 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGCTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
3055475 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3055515 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
3055580 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3055620 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
3055685 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3055726 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
3055791 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
3055831 AGTCCAATATCCTTCGTTCTGAAGTTGAAATTGACTCTGAAATCGATAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
3055896 AGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3055936 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
3056001 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3056041 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
*
3056106 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3056147 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
* *
3056212 CAGCGGTCTCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
3056253 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
3056302 GTTGAAATTT
Statistics
Matches: 942, Mismatches: 52, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
105 597 0.63
106 344 0.37
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3055778 original size:316 final size:315
Alignment explanation
Indices: 3055199--3056301 Score: 1848
Period size: 316 Copynumber: 3.5 Consensus size: 315
3055189 TATTGTTCCA
* * * *
3055199 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTATGGAACTG-GAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAA-TGTTTGTTGACAA
3055263 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
3055328 GTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
129 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
3055393 GAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGA
194 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
3055458 AATGTTTGCTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
259 AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3055515 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
* *
3055580 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGGAGTCCAATGTCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
3055645 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
3055710 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
195 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
*
3055775 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
260 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
3055831 AGTCCAATATCCTTCGTTCTGAAGTTGAAATTGACTCTGAAATCGATAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
* *
3055896 AGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
3055961 TGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
3056026 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG
196 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-
* *
3056091 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
260 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3056147 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
* *
3056212 CAGCGGTCTCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
3056277 TTGAAATTGGCTCTGAAATTGAGAA
130 TTGAAATTGGCTCTGAAATTGAGAA
3056302 GTTGAAATTT
Statistics
Matches: 738, Mismatches: 45, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
315 203 0.28
316 435 0.59
317 100 0.14
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (315 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3055983 original size:421 final size:420
Alignment explanation
Indices: 3055199--3056301 Score: 1936
Period size: 421 Copynumber: 2.6 Consensus size: 420
3055189 TATTGTTCCA
* * * * *
3055199 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTATGGAACTGGAAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAGTTGTTTGTTGACAAC
3055264 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
3055329 TTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
3055394 AACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA
195 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA
3055459 ATGTTTGCTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
260 ATGTTTGCTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
3055524 TCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCC
325 TCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCC
3055589 TTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
390 TTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
* *
3055620 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTTTGTTGACAAC
3055685 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
3055750 TTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* * *
3055815 AACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTCTGAAGTTGAAATTGACTCTGAAATCGATAA
195 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA
* * *
3055880 ATGTTTGTTGACAACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
260 ATGTTTGCTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
*
3055945 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCC
325 TCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCC
*
3056010 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
390 TTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
3056041 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTGTTTGTTGACAAC
* *
3056106 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGGAGTCCAATGTCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
3056171 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCTCTTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
3056236 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
194 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGA
3056301 A
259 A
3056302 GTTGAAATTT
Statistics
Matches: 647, Mismatches: 32, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
421 548 0.85
422 99 0.15
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (420 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA
TGTTTGCTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
CCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGCCTGG
Found at i:3060256 original size:2 final size:2
Alignment explanation
Indices: 3060249--3060279 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3060239 CGTAAAATAC
*
3060249 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3060280 ATGTTACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3065925 original size:36 final size:37
Alignment explanation
Indices: 3065873--3065956 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
3065863 TTTGAATTGA
*
3065873 ATAATATGA-TTTAATTTAGTTTAAATT-TTT-ACTTT
1 ATAATTTGATTTTAATTTA-TTTAAATTATTTCACTTT
* * *
3065908 ATAGTTTGATTTTAATTTATTTTAATTATTTCATTTT
1 ATAATTTGATTTTAATTTATTTAAATTATTTCACTTT
3065945 ATAATTTGATTT
1 ATAATTTGATTT
3065957 GGTTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 14 0.34
36 12 0.29
37 15 0.37
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (37 bp):
ATAATTTGATTTTAATTTATTTAAATTATTTCACTTT
Found at i:3068761 original size:150 final size:149
Alignment explanation
Indices: 3068188--3068761 Score: 496
Period size: 150 Copynumber: 3.8 Consensus size: 149
3068178 GGCTCAAGCT
* * * * * *
3068188 TTTCATATTCCAATGAACCATTTGAATTAGAACTCTTATGATCATCAGTGAGATGTTTGAAGGAA
1 TTTCATATTCCAATGAAGCAATGGAACTAGAACTCTTATGATCATCAATGGGATGTTTGAAGGAA
** * ** * * * * *
3068253 GATTTGCTT-CCTGTTCGCGGAATCTTTCCCACCAATTCAGATTTCACCTTGCTCAAATCATAAT
66 GATTTGCTTGCCACTGC-CAAAATCTTTCCCACCGATTCGGATTTCACCTTACTCGAATCATGAT
* * * *
3068317 AGTGTTCACAAGCCACAGTTT
130 AATGTACACATG-CACAGTTG
* * * * *
3068338 TTTCAGATTGCAATG-AGCCGATGGAATTAAAACTCTTATGATCATCAATGGGATGTTTGAAGGA
1 TTTCATATTCCAATGAAG-CAATGGAACTAGAACTCTTATGATCATCAATGGGATGTTTGAAGGA
* * ** * * *
3068402 AGATTTG-TTTCGCACTGTCAAAGCCTTCCCCACTGATTCGGATTTCGCCTTACTCGAATCATAG
65 AGATTTGCTTGC-CACTGCCAAAATCTTTCCCACCGATTCGGATTTCACCTTACTCGAATCAT-G
3068466 A-AATGTACACCATGCACAGTTG
128 ATAATGTACA-CATGCACAGTTG
* *
3068488 TTTCATATT-CAGGTGAAGCAATGGAACTAGAACTCTTAGGATCATCAATGGGATGTTTGAAGGA
1 TTTCATATTCCA-ATGAAGCAATGGAACTAGAACTCTTATGATCATCAATGGGATGTTTGAAGGA
* ** * * * * ** * ** ** *
3068552 AGCTTCACGTGTCATTGTCAAAATCTTTCCTGCTGATTTTGAGGTC-CACTTACTTGAATCATGA
65 AGATTTGCTTGCCACTGCCAAAATCTTTCCCACCGATTCGGATTTCAC-CTTACTCGAATCATGA
*
3068616 TAATGTACAGCATGTACAGTTG
129 TAATGTACA-CATGCACAGTTG
* * * *
3068638 TTTCATATTCCGATGAAGCAATGGAACTAGAACTCTTACGATCATCAACGGGATGATTGAAGGAA
1 TTTCATATTCCAATGAAGCAATGGAACTAGAACTCTTATGATCATCAATGGGATGTTTGAAGGAA
* * *
3068703 GATTTG-TTCGCCACTGCCAAAATCTTTCCCACCCATTCGGATTTCATCTTGCTCGAATC
66 GATTTGCTT-GCCACTGCCAAAATCTTTCCCACCGATTCGGATTTCACCTTACTCGAATC
3068762 GTAATAGAGG
Statistics
Matches: 334, Mismatches: 77, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
149 9 0.03
150 315 0.94
151 10 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (149 bp):
TTTCATATTCCAATGAAGCAATGGAACTAGAACTCTTATGATCATCAATGGGATGTTTGAAGGAA
GATTTGCTTGCCACTGCCAAAATCTTTCCCACCGATTCGGATTTCACCTTACTCGAATCATGATA
ATGTACACATGCACAGTTG
Found at i:3075734 original size:152 final size:152
Alignment explanation
Indices: 3075458--3075763 Score: 513
Period size: 152 Copynumber: 2.0 Consensus size: 152
3075448 CATCAGATAG
* * * * *
3075458 TTACTTTTTGTAGTTTTTATCTTCTCAATCAGACGCACAATCGAGTAGAGTTCGATTCAGTTATC
1 TTACTTTTTGCAGTTTCTAGCTTCTCAATCAGACGCACAATCGAGTAGAGTTCGATGCAGTAATC
* *
3075523 TTCTCTGCAGTTCTCATCTTTTGACTAGCTACAGACAACGACCTAAATCTCGATTATCGTGCTGA
66 TTCTCTGCAGTTCTCATCTTTTGACTAACTACAGACAACGACCCAAATCTCGATTATCGTGCTGA
3075588 ATCTCGGCCCAATGATCTCAGA
131 ATCTCGGCCCAATGATCTCAGA
* *
3075610 TTACTTTTTGCAGTTTCTAGCTTTTCAATCAGACGCACAATCGAGTTGAGTTCGATGCAGTAATC
1 TTACTTTTTGCAGTTTCTAGCTTCTCAATCAGACGCACAATCGAGTAGAGTTCGATGCAGTAATC
*
3075675 TTCTCTGCAGTTCTCATCTTTTGACTAACTACAGACAACGACCCAAATCTTGATTATCGTGCTGA
66 TTCTCTGCAGTTCTCATCTTTTGACTAACTACAGACAACGACCCAAATCTCGATTATCGTGCTGA
*
3075740 ATCTCGGCCCAATGATCTTAGA
131 ATCTCGGCCCAATGATCTCAGA
3075762 TT
1 TT
3075764 TCTAGAGCCA
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
152 143 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (152 bp):
TTACTTTTTGCAGTTTCTAGCTTCTCAATCAGACGCACAATCGAGTAGAGTTCGATGCAGTAATC
TTCTCTGCAGTTCTCATCTTTTGACTAACTACAGACAACGACCCAAATCTCGATTATCGTGCTGA
ATCTCGGCCCAATGATCTCAGA
Found at i:3079983 original size:18 final size:18
Alignment explanation
Indices: 3079960--3079995 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3079950 AAGCAAAAGG
*
3079960 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3079978 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3079996 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3080234 original size:20 final size:20
Alignment explanation
Indices: 3080211--3080255 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3080201 AAATCGTAAC
*
3080211 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
*
3080231 GCGAATTTGATTTTCGCATT
1 GCGAATTTGACTTTCGCATT
3080251 GCGAA
1 GCGAA
3080256 AGTGTACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:3080450 original size:64 final size:65
Alignment explanation
Indices: 3080314--3080463 Score: 250
Period size: 64 Copynumber: 2.3 Consensus size: 65
3080304 AATTTAAAAC
3080314 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATAATTATTTACACATCAATTA
** *
3080379 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTT-CTTCATCAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATAATTATTTAC-ACATCAATT
3080442 A
65 A
3080443 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
3080464 ACATCAATTT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
63 1 0.01
64 46 0.57
65 34 0.42
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATAATTATTTACACATCAATTA
Found at i:3081795 original size:21 final size:21
Alignment explanation
Indices: 3081765--3081856 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
3081755 GTGAATCGGG
*
3081765 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
3081786 CTCTTTAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
3081807 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
**
3081828 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
3081849 CTCTTGAA
1 CTCTTGAA
3081857 TAATAGGAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.03
21 57 0.97
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:3081824 original size:42 final size:42
Alignment explanation
Indices: 3081765--3081886 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
3081755 GTGAATCGGG
*
3081765 CTCTTGAACGGTGGGAGGGACCTCTTTAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* * *
3081807 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
*** * **
3081849 CTCTTGAATAATAGGAGATACCTCTTGAACGATGACAG
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAG
3081887 ATGAATCAGG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:3084036 original size:20 final size:20
Alignment explanation
Indices: 3084013--3084079 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
3084003 TCTGAAACTT
*
3084013 AAAAGCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
3084033 AAAATCGAAACGCAAAAATG
1 AAAATCGCAACGCGAAAATG
*
3084053 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
3084072 AAAATCGC
1 AAAATCGC
3084080 GTTGCGATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 8 0.20
20 33 0.80
ACGTcount: A:0.52, C:0.21, G:0.18, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:3084472 original size:22 final size:22
Alignment explanation
Indices: 3084445--3084495 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3084435 GATGGAGATA
3084445 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
3084467 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
3084489 GACGGAT
1 GACGGAT
3084496 GTCGCCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.45, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:3084678 original size:20 final size:20
Alignment explanation
Indices: 3084650--3084698 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3084640 TAAACGCGCT
* *
3084650 TTGCAAATTTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
3084670 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
3084690 TTGAGAATT
1 TTGCGAATT
3084699 ACAAATTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:3084712 original size:20 final size:20
Alignment explanation
Indices: 3084689--3084758 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
3084679 TGACTTATGT
* *
3084689 GTTGAGAATTACAAATTCGC
1 GTTGCGAATTACAGATTCGC
* *
3084709 GTTGTGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
*
3084729 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
*
3084749 ATTGCGAATT
1 GTTGCGAATT
3084759 TGGAAACTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCGC
Found at i:3089909 original size:2 final size:2
Alignment explanation
Indices: 3089904--3089943 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3089894 TTGCTCACAC
3089904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3089944 GAAATAAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3096067 original size:331 final size:331
Alignment explanation
Indices: 3095465--3096128 Score: 1274
Period size: 331 Copynumber: 2.0 Consensus size: 331
3095455 ACCATGGCCA
*
3095465 AACCTAAACCTTCAGAAGCCACCGACTATGTATGCATATGTGTGCGTGCAGCTTATAATATAAAG
1 AACCTAAACCTTCAGAAGCCACCGACTACGTATGCATATGTGTGCGTGCAGCTTATAATATAAAG
3095530 TAAAGAGATTCTTAATTATAGATTGGTATTAATTATAATTAACTGATAGGGATGCAATCATTTTG
66 TAAAGAGATTCTTAATTATAGATTGGTATTAATTATAATTAACTGATAGGGATGCAATCATTTTG
*
3095595 ATTCTCTAACACTAACACATCATGTGTGCATTATCATCAGCTTTCGTAATTTTTTGGACTACAAT
131 ATTCTCTAACACTAACACATCATGTGTGCATTATCATCAGCTTTCGTAATTTTCTGGACTACAAT
3095660 CTAACCCCTAATCGAATTTGTATTTTAATACAATGTGCCTTCGACTTGTATATTTATTAAGGGTT
196 CTAACCCCTAATCGAATTTGTATTTTAATACAATGTGCCTTCGACTTGTATATTTATTAAGGGTT
3095725 TGAATCCTGACGTTTATGAATAGAGTAAATTAAGTTGAGAGGGTCGTATATGCCTTTGCAGTATC
261 TGAATCCTGACGTTTATGAATAGAGTAAATTAAGTTGAGAGGGTCGTATATGCCTTTGCAGTATC
3095790 CTATTT
326 CTATTT
* *
3095796 AACCTAAACCTTCAGAAGCCACCGACTACGTATGTATATGTGTGCGTGCAGCTTATACTATAAAG
1 AACCTAAACCTTCAGAAGCCACCGACTACGTATGCATATGTGTGCGTGCAGCTTATAATATAAAG
3095861 TAAAGAGATTCTTAATTATAGATTGGTATTAATTATAATTAACTGATAGGGATGCAATCATTTTG
66 TAAAGAGATTCTTAATTATAGATTGGTATTAATTATAATTAACTGATAGGGATGCAATCATTTTG
3095926 ATTCTCTAACACTAACACATCATGTGTGCATTATCATCAGCTTTCGTAATTTTCTGGACTACAAT
131 ATTCTCTAACACTAACACATCATGTGTGCATTATCATCAGCTTTCGTAATTTTCTGGACTACAAT
* *
3095991 CTAATCCCTAATCGAATTTGTGTTTTAATACAATGTGCCTTCGACTTGTATATTTATTAAGGGTT
196 CTAACCCCTAATCGAATTTGTATTTTAATACAATGTGCCTTCGACTTGTATATTTATTAAGGGTT
3096056 TGAATCCTGACGTTTATGAATAGAGTAAATTAAGTTGAGAGGGTCGTATATGCCTTTGCAGTATC
261 TGAATCCTGACGTTTATGAATAGAGTAAATTAAGTTGAGAGGGTCGTATATGCCTTTGCAGTATC
3096121 CTATTT
326 CTATTT
3096127 AA
1 AA
3096129 ATTAATTGAT
Statistics
Matches: 327, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
331 327 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (331 bp):
AACCTAAACCTTCAGAAGCCACCGACTACGTATGCATATGTGTGCGTGCAGCTTATAATATAAAG
TAAAGAGATTCTTAATTATAGATTGGTATTAATTATAATTAACTGATAGGGATGCAATCATTTTG
ATTCTCTAACACTAACACATCATGTGTGCATTATCATCAGCTTTCGTAATTTTCTGGACTACAAT
CTAACCCCTAATCGAATTTGTATTTTAATACAATGTGCCTTCGACTTGTATATTTATTAAGGGTT
TGAATCCTGACGTTTATGAATAGAGTAAATTAAGTTGAGAGGGTCGTATATGCCTTTGCAGTATC
CTATTT
Found at i:3102710 original size:28 final size:28
Alignment explanation
Indices: 3102670--3102725 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3102660 AAAAGAAGTA
*
3102670 TCCATCTACCTTTTGTCTATTAATTTTC
1 TCCATCTACCTTTTGTCCATTAATTTTC
3102698 TCCATCTACCTTTTGTCCATTAATTTTC
1 TCCATCTACCTTTTGTCCATTAATTTTC
3102726 ATTGTTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.52
Consensus pattern (28 bp):
TCCATCTACCTTTTGTCCATTAATTTTC
Found at i:3102716 original size:15 final size:15
Alignment explanation
Indices: 3102670--3102717 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3102660 AAAAGAAGTA
3102670 TCCATCTACCTTTTG
1 TCCATCTACCTTTTG
* * *
3102685 TCTAT-TA-ATTTTC
1 TCCATCTACCTTTTG
3102698 TCCATCTACCTTTTG
1 TCCATCTACCTTTTG
3102713 TCCAT
1 TCCAT
3102718 TAATTTTCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
15 13 0.52
ACGTcount: A:0.17, C:0.29, G:0.04, T:0.50
Consensus pattern (15 bp):
TCCATCTACCTTTTG
Found at i:3117999 original size:29 final size:26
Alignment explanation
Indices: 3117931--3117994 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
3117921 AAAAACAAAT
3117931 GCACCGAAAGTGCATTGGATTATTAG
1 GCACCGAAAGTGCATTGGATTATTAG
3117957 GCACCGAAAGTGCATTGGATTATTAG
1 GCACCGAAAGTGCATTGGATTATTAG
3117983 GCACCGAAAGTG
1 GCACCGAAAGTG
3117995 GTGCAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (26 bp):
GCACCGAAAGTGCATTGGATTATTAG
Found at i:3120718 original size:78 final size:78
Alignment explanation
Indices: 3120589--3120748 Score: 320
Period size: 78 Copynumber: 2.1 Consensus size: 78
3120579 GGTGATATTA
3120589 ACAACGGAGGGAGTATTCTCTTGAAAAAGGCGAACCGTAGCCAACTCATCGGGTTGTAACTTCCG
1 ACAACGGAGGGAGTATTCTCTTGAAAAAGGCGAACCGTAGCCAACTCATCGGGTTGTAACTTCCG
3120654 AGGAGGGGTTACC
66 AGGAGGGGTTACC
3120667 ACAACGGAGGGAGTATTCTCTTGAAAAAGGCGAACCGTAGCCAACTCATCGGGTTGTAACTTCCG
1 ACAACGGAGGGAGTATTCTCTTGAAAAAGGCGAACCGTAGCCAACTCATCGGGTTGTAACTTCCG
3120732 AGGAGGGGTTACC
66 AGGAGGGGTTACC
3120745 ACAA
1 ACAA
3120749 AGGCTGAGGC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (78 bp):
ACAACGGAGGGAGTATTCTCTTGAAAAAGGCGAACCGTAGCCAACTCATCGGGTTGTAACTTCCG
AGGAGGGGTTACC
Found at i:3125481 original size:19 final size:19
Alignment explanation
Indices: 3125459--3125499 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3125449 TTATTAGTCA
3125459 TTACTCAACTCATTATTTG
1 TTACTCAACTCATTATTTG
* *
3125478 TTACTCGACTTATTATTTG
1 TTACTCAACTCATTATTTG
3125497 TTA
1 TTA
3125500 AACTCACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.51
Consensus pattern (19 bp):
TTACTCAACTCATTATTTG
Found at i:3126389 original size:327 final size:327
Alignment explanation
Indices: 3125795--3126447 Score: 1198
Period size: 327 Copynumber: 2.0 Consensus size: 327
3125785 AGATGGCGTA
*
3125795 GAGTGAGCAACGGCGGGTGCGTGTGAGGAGCGATCAACGACATGTGAGTAAGAGGTTTGAGAGTG
1 GAGTGAGCAACGGCGGCTGCGTGTGAGGAGCGATCAACGACATGTGAGTAAGAGGTTTGAGAGTG
* * *
3125860 CTAGAGGTGGAGCGGTGAGAACAGATCAGACGTCGATGAACTTTTCTGTCTTTGTCAATAATGTG
66 CAAGAGGTGGAGCAGTGAGAACAGATCAGACGTCGATGAACTTTTATGTCTTTGTCAATAATGTG
3125925 AGCAAGAGGATTCATCCGTCATCTCTTAAGGAAGCTTTCATGGAATATGGTGTAGTGTCTGATGT
131 AGCAAGAGGATTCATCCGTCATCTCTTAAGGAAGCTTTCATGGAATATGGTGTAGTGTCTGATGT
3125990 GTTCATAGCATTTAGAAGCAGAAGGAGACTTTACGATAAATCCAATTTTGCGTTCGTGAGGTTCA
196 GTTCATAGCATTTAGAAGCAGAAGGAGACTTTACGATAAATCCAATTTTGCGTTCGTGAGGTTCA
*
3126055 AAAGCAAGCAAGAAGCTAGAGTAGCGGTCAGGAAGGCCGACGGGCGGCTGATGGATGGGTTCAAA
261 AAAGCAAGCAAAAAGCTAGAGTAGCGGTCAGGAAGGCCGACGGGCGGCTGATGGATGGGTTCAAA
3126120 AG
326 AG
*
3126122 GAGTGAGCAACGGCGGCTGCGTGTGAGGAGCGATCAACGGCATGTGAGTAAGAGGTTTGAGAGTG
1 GAGTGAGCAACGGCGGCTGCGTGTGAGGAGCGATCAACGACATGTGAGTAAGAGGTTTGAGAGTG
3126187 CAAGAGGTGGAGCAGTGAGAACAGATCAGACGTCGATGAACTTTTATGTCTTTGTCAATAATGTG
66 CAAGAGGTGGAGCAGTGAGAACAGATCAGACGTCGATGAACTTTTATGTCTTTGTCAATAATGTG
*
3126252 AGCAAGAGGATTCATCTGTCATCTCTTAAGGAAGCTTTCATGGAATATGGTGTAGTGTCTGATGT
131 AGCAAGAGGATTCATCCGTCATCTCTTAAGGAAGCTTTCATGGAATATGGTGTAGTGTCTGATGT
* * *
3126317 GTTCATATCATTTAGAAGCATAAGGAGACTTTACGATAAATCCACTTTTGCGTTCGTGAGGTTCA
196 GTTCATAGCATTTAGAAGCAGAAGGAGACTTTACGATAAATCCAATTTTGCGTTCGTGAGGTTCA
* *
3126382 AAAGCAAGCAAAAAGTTAGAGTAGCGGTCAGGAAGGCCGATGGGCGGCTGATGGATGGGTTCAAA
261 AAAGCAAGCAAAAAGCTAGAGTAGCGGTCAGGAAGGCCGACGGGCGGCTGATGGATGGGTTCAAA
3126447 A
326 A
3126448 TTAAAGTCTA
Statistics
Matches: 314, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
327 314 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (327 bp):
GAGTGAGCAACGGCGGCTGCGTGTGAGGAGCGATCAACGACATGTGAGTAAGAGGTTTGAGAGTG
CAAGAGGTGGAGCAGTGAGAACAGATCAGACGTCGATGAACTTTTATGTCTTTGTCAATAATGTG
AGCAAGAGGATTCATCCGTCATCTCTTAAGGAAGCTTTCATGGAATATGGTGTAGTGTCTGATGT
GTTCATAGCATTTAGAAGCAGAAGGAGACTTTACGATAAATCCAATTTTGCGTTCGTGAGGTTCA
AAAGCAAGCAAAAAGCTAGAGTAGCGGTCAGGAAGGCCGACGGGCGGCTGATGGATGGGTTCAAA
AG
Found at i:3129446 original size:13 final size:13
Alignment explanation
Indices: 3129428--3129452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3129418 AAAGTTGTGG
3129428 TTGTAAACATTAA
1 TTGTAAACATTAA
3129441 TTGTAAACATTA
1 TTGTAAACATTA
3129453 TTTAATTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TTGTAAACATTAA
Found at i:3129611 original size:6 final size:5
Alignment explanation
Indices: 3129576--3129625 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
3129566 ATATTCATTA
* *
3129576 TTATT ATTATT TTATT TTATT TTATT ATATT TATATT TATTTT TTATT
1 TTATT -TTATT TTATT TTATT TTATT TTATT T-TATT T-TATT TTATT
3129624 TT
1 TT
3129626 TAATAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
5 24 0.62
6 15 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Done.