Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009628.1 Corchorus capsularis cultivar CVL-1 contig09649, 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: 30147
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6829 original size:19 final size:18
Alignment explanation
Indices: 6802--6843 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6792 TGAGTAATTT
*
6802 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
*
6820 TATAAATAAAAATTTAATA
1 T-TAAATAAAAATATAATA
6839 TTAAA
1 TTAAA
6844 ACAATTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:8295 original size:19 final size:19
Alignment explanation
Indices: 8273--8329 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
8263 CAGCTGGTTC
8273 GAGCCATATCAGTCGGCCT
1 GAGCCATATCAGTCGGCCT
*
8292 GAGCC-TA-CA--CGGAC-
1 GAGCCATATCAGTCGGCCT
* *
8306 GAGCCAAATTAGTCGGCCT
1 GAGCCATATCAGTCGGCCT
8325 GAGCC
1 GAGCC
8330 TATTCGGACG
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
14 5 0.17
15 5 0.17
16 1 0.03
17 2 0.07
18 6 0.21
19 10 0.34
ACGTcount: A:0.25, C:0.32, G:0.28, T:0.16
Consensus pattern (19 bp):
GAGCCATATCAGTCGGCCT
Found at i:8309 original size:33 final size:33
Alignment explanation
Indices: 8272--8345 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
8262 TCAGCTGGTT
8272 CGAGCCATATCAGTCGGCCTGAGCCTACACGGA
1 CGAGCCATATCAGTCGGCCTGAGCCTACACGGA
* * **
8305 CGAGCCAAATTAGTCGGCCTGAGCCTATTCGGA
1 CGAGCCATATCAGTCGGCCTGAGCCTACACGGA
8338 CGAGCCAT
1 CGAGCCAT
8346 GTTAACCACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (33 bp):
CGAGCCATATCAGTCGGCCTGAGCCTACACGGA
Found at i:22362 original size:33 final size:33
Alignment explanation
Indices: 22264--22511 Score: 185
Period size: 33 Copynumber: 7.4 Consensus size: 33
22254 CAAACAGCCT
* * * *
22264 GAGTTGCCTAAGCCAGAATTGCCGAAAA-CTCCC
1 GAGTTGCCAAAGCCTGAATTGCC-AAAAGTTCCG
** * *
22297 GAGTTGCCAAAAGTGCCAAAACTGCCCAAAGTTCCG
1 GAGTTGCC-AAA--GCCTGAATTGCCAAAAGTTCCG
* *
22333 GAGTTGTCAAAGCCTGAATTGCCTAAAGTTCCG
1 GAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCG
* * * * * *
22366 GAATTACCCAAGCCTGAAATGCCAAAAGTTTCA
1 GAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCG
* * *
22399 GAGTTGCCAAAACCTGAATTGCCGAAAGTTCCA
1 GAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCG
* * * *
22432 GAATTGCCTAAA-CCTGAAATGCCAAAAATGCCG
1 GAGTTGCC-AAAGCCTGAATTGCCAAAAGTTCCG
* * *
22465 GAGTTGCCAAAGCCTGAATTTCCCAAAGTTCCC
1 GAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCG
**
22498 GAGTTATCAAAGCC
1 GAGTTGCCAAAGCC
22512 GGAGTTACCT
Statistics
Matches: 168, Mismatches: 41, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
32 3 0.02
33 134 0.80
34 5 0.03
35 6 0.04
36 20 0.12
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (33 bp):
GAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCG
Found at i:22415 original size:66 final size:66
Alignment explanation
Indices: 22319--22496 Score: 230
Period size: 66 Copynumber: 2.7 Consensus size: 66
22309 GTGCCAAAAC
* * * * *
22319 TGCCCAAAGTTCCGGAGTTGTCAAAGCCTGAATTGCCTAAAGTTCCGGAATTACCCAAGCCTGAA
1 TGCCAAAAGTTCCGGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCCAGAATTACCCAAACCTGAA
22384 A
66 A
* * * * * *
22385 TGCCAAAAGTTTCAGAGTTGCCAAAACCTGAATTGCCGAAAGTTCCAGAATTGCCTAAACCTGAA
1 TGCCAAAAGTTCCGGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCCAGAATTACCCAAACCTGAA
22450 A
66 A
* * *
22451 TGCCAAAAATGCCGGAGTTGCCAAAGCCTGAATTTCCCAAAGTTCC
1 TGCCAAAAGTTCCGGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCC
22497 CGAGTTATCA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 95 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (66 bp):
TGCCAAAAGTTCCGGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCCAGAATTACCCAAACCTGAA
A
Found at i:22577 original size:33 final size:33
Alignment explanation
Indices: 22534--22851 Score: 321
Period size: 33 Copynumber: 9.6 Consensus size: 33
22524 ATTAGAAGCC
* * *
22534 AAAGTCCCAGAGTTACCAAAGCCTGAATTGCCT
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* * *
22567 AAAGTTCCAGAATTACCAAAGGCTGAATTGCCA
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* * * *
22600 AAAGTTCCGGAGTTGCCCAAGCTTGAATTGCCG
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* * *
22633 AAAGTTCCGGAGTTGCCAAAACCTGAATTGCCG
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* * * *
22666 AAAGTTCCGGAGCTGCCCAAGCATGAATTGCCA
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
*** *
22699 AAAACCCCAGAGTTGCCAAAGCCTGAATTGCCT
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* * * * *
22732 AAAGTTCCCGAGTTTCCCAAGTCTGAATTTCCA
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* * * *
22765 AAAGTTTCTGAGCTGCCAAAGCCTGAATTACCA
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
** *
22798 AAAGTTCTTGAGTTGTCAAAGCCTGAATTGCCA
1 AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
* *
22831 AAAGTTCCCGAGTTACCAAAG
1 AAAGTTCCAGAGTTGCCAAAG
22852 TCGGAGTTGC
Statistics
Matches: 233, Mismatches: 52, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 233 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (33 bp):
AAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCA
Found at i:22721 original size:210 final size:210
Alignment explanation
Indices: 22322--22721 Score: 523
Period size: 210 Copynumber: 1.9 Consensus size: 210
22312 CCAAAACTGC
* * ** * *
22322 CCAAAGTTCCGGAGTTGTCAAAGCCTGAATTGCCTAAAGTTCCGGAATTACCCAAGCCTGAAATG
1 CCAAAGTCCCAGAGTTACCAAAGCCTGAATTGCCTAAAGTTCCAGAATTACCAAAGCCTGAAATG
* *
22387 CCAAAAGTTTCAGAGTTGCCAAAACCTGAATTGCCGAAAGTTCCAGAATTGCCTAAACCTGAAAT
66 CCAAAAGTTCCAGAGTTGCCAAAACCTGAATTGCCGAAAGTTCCAGAATTGCCAAAACCTGAAAT
* * *** *
22452 GCCAAAAATGCCGGAGTTGCCAAAGCCTGAATTTCCCAAAGTTCCCGAGTTATCAAAGCCGGAGT
131 GCCAAAAATGCCGGAGCTGCCAAAGCATGAATTTCCCAAAAACCCCGAGTTACCAAAGCCGGAGT
22517 TACCTAAATTAGAAG
196 TACCTAAATTAGAAG
* *
22532 CCAAAGTCCCAGAGTTACCAAAGCCTGAATTGCCTAAAGTTCCAGAATTACCAAAGGCTGAATTG
1 CCAAAGTCCCAGAGTTACCAAAGCCTGAATTGCCTAAAGTTCCAGAATTACCAAAGCCTGAAATG
* * * * * * *
22597 CCAAAAGTTCCGGAGTTGCCCAAGCTTGAATTGCCGAAAGTTCCGGAGTTGCCAAAACCTGAATT
66 CCAAAAGTTCCAGAGTTGCCAAAACCTGAATTGCCGAAAGTTCCAGAATTGCCAAAACCTGAAAT
* * * * * *
22662 GCCGAAAGTTCCGGAGCTGCCCAAGCATGAA-TTGCCAAAAACCCCAGAGTTGCCAAAGCC
131 GCCAAAAATGCCGGAGCTGCCAAAGCATGAATTTCCCAAAAACCCC-GAGTTACCAAAGCC
22722 TGAATTGCCT
Statistics
Matches: 160, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
209 10 0.06
210 150 0.94
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (210 bp):
CCAAAGTCCCAGAGTTACCAAAGCCTGAATTGCCTAAAGTTCCAGAATTACCAAAGCCTGAAATG
CCAAAAGTTCCAGAGTTGCCAAAACCTGAATTGCCGAAAGTTCCAGAATTGCCAAAACCTGAAAT
GCCAAAAATGCCGGAGCTGCCAAAGCATGAATTTCCCAAAAACCCCGAGTTACCAAAGCCGGAGT
TACCTAAATTAGAAG
Found at i:22882 original size:243 final size:243
Alignment explanation
Indices: 22633--23258 Score: 772
Period size: 243 Copynumber: 2.6 Consensus size: 243
22623 TGAATTGCCG
* * * * *
22633 AAAGTTCCGGAGTTGCCAAAACCTGAATTGCCGAAAGTTCCGGAGCTGCCCAAGCATGAATTGCC
1 AAAGTTCCAGAGTTGCCAAAACCTGAATTGCCTAAAGTTCCCGAGTTGCCCAAGCCTGAATTGCC
** * * **
22698 AAAAACCCCAGAGTTGCCAAAGCCTGAATTGCCTAAAGTTCCCGAGTTTCCCAAGTCTGAATTTC
66 AAAAATTCCAGAGTTGCCAAAGCCTGAATTGCCTAAAGTTCCTGAGTTGCCCAAACCTGAATTTC
* * * ** *
22763 CAAAAGTTTCTGAGCTGCCAAAGCCTGAATTACCAAAAGTTCTTGAGTTGTCAAAG-CCTGAATT
131 CAAAAGTTCCCGAGCTACCAAAGCCTGAATTACCAAAAGTTCCAGAGTTGCCAAAGACC-GAATT
* *
22827 GCCAAA-AGTTCCCGAGTTACCAAAGTCGGAGTTGCCTAAATTAGAAGCT
195 GCCAAAGA-TTCCCGAGTTACCAAAGCCGGAGTTACCTAAATTAGAAGCT
** * *
22876 AAAGTTCCAGAGTTGCCAAAACCTGAATTGCCTAAAGTTCTTGAGTTGTCTAAGCCTGAATTGCC
1 AAAGTTCCAGAGTTGCCAAAACCTGAATTGCCTAAAGTTCCCGAGTTGCCCAAGCCTGAATTGCC
* * *
22941 AAAAGTTCCTGAGTTGCCCAAGCCTGAATTGCCTAAAGTTCCTGAGTTGCCCAAACCTGAATTTC
66 AAAAATTCCAGAGTTGCCAAAGCCTGAATTGCCTAAAGTTCCTGAGTTGCCCAAACCTGAATTTC
* * *
23006 CAAAAGTTCCCGAGTTACCAAAGCCTGAATTACCGAAAGTTCCAGAGTTGCCAAAGACCGAATTT
131 CAAAAGTTCCCGAGCTACCAAAGCCTGAATTACCAAAAGTTCCAGAGTTGCCAAAGACCGAATTG
* * * * *
23071 CCCAAGATTCCTGAGTTGCCAAAGCCTGAGTTACCTAAATTAGAAGGT
196 CCAAAGATTCCCGAGTTACCAAAGCCGGAGTTACCTAAATTAGAAGCT
* * * * *
23119 AAAGTTCCAGAGTTTCCAAAGA-CTGATTTACCTAAAGTTCCCGAATTGCCCAAGCCTGAATTAC
1 AAAGTTCCAGAGTTGCCAAA-ACCTGAATTGCCTAAAGTTCCCGAGTTGCCCAAGCCTGAATTGC
** * * ** * *
23183 CGGAAATTCCAGAGTTACCAAAACCTGAATTGCCTAAAGTTCCTGAGTTATCCAAACCAGAATTA
65 CAAAAATTCCAGAGTTGCCAAAGCCTGAATTGCCTAAAGTTCCTGAGTTGCCCAAACCTGAATTT
*
23248 CCAAAAATTCC
130 CCAAAAGTTCC
23259 AAAAACTGAA
Statistics
Matches: 326, Mismatches: 54, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
243 322 0.99
244 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (243 bp):
AAAGTTCCAGAGTTGCCAAAACCTGAATTGCCTAAAGTTCCCGAGTTGCCCAAGCCTGAATTGCC
AAAAATTCCAGAGTTGCCAAAGCCTGAATTGCCTAAAGTTCCTGAGTTGCCCAAACCTGAATTTC
CAAAAGTTCCCGAGCTACCAAAGCCTGAATTACCAAAAGTTCCAGAGTTGCCAAAGACCGAATTG
CCAAAGATTCCCGAGTTACCAAAGCCGGAGTTACCTAAATTAGAAGCT
Found at i:22914 original size:33 final size:33
Alignment explanation
Indices: 22874--23109 Score: 262
Period size: 33 Copynumber: 7.2 Consensus size: 33
22864 AAATTAGAAG
* *
22874 CTAAAGTTCCAGAGTTGCCAAAACCTGAATTGC
1 CTAAAGTTCCTGAGTTGCCAAAGCCTGAATTGC
* * *
22907 CTAAAGTTCTTGAGTTGTCTAAGCCTGAATTGC
1 CTAAAGTTCCTGAGTTGCCAAAGCCTGAATTGC
* *
22940 CAAAAGTTCCTGAGTTGCCCAAGCCTGAATTGC
1 CTAAAGTTCCTGAGTTGCCAAAGCCTGAATTGC
*
22973 CTAAAGTTCCTGAGTTGCCCAAA-CCTGAATTTC
1 CTAAAGTTCCTGAGTTG-CCAAAGCCTGAATTGC
* * * *
23006 CAAAAGTTCCCGAGTTACCAAAGCCTGAATTAC
1 CTAAAGTTCCTGAGTTGCCAAAGCCTGAATTGC
* * *
23039 CGAAAGTTCCAGAGTTGCCAAAGACC-GAATTTC
1 CTAAAGTTCCTGAGTTGCCAAAG-CCTGAATTGC
* * *
23072 C-CAAGATTCCTGAGTTGCCAAAGCCTGAGTTAC
1 CTAAAG-TTCCTGAGTTGCCAAAGCCTGAATTGC
23105 CTAAA
1 CTAAA
23110 TTAGAAGGTA
Statistics
Matches: 172, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
32 10 0.06
33 154 0.90
34 8 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (33 bp):
CTAAAGTTCCTGAGTTGCCAAAGCCTGAATTGC
Found at i:22972 original size:15 final size:16
Alignment explanation
Indices: 22888--23011 Score: 67
Period size: 15 Copynumber: 7.6 Consensus size: 16
22878 AGTTCCAGAG
22888 TTGCCAAAA-CCTGAA
1 TTGCCAAAAGCCTGAA
* * *
22903 TTGCCTAAAGTTCTTGAG
1 TTGCCAAAAG--CCTGAA
* *
22921 TTGTC-TAAGCCTGAA
1 TTGCCAAAAGCCTGAA
*
22936 TTGCCAAAAGTTCCTGAG
1 TTGCCAAAAG--CCTGAA
*
22954 TTGCC-CAAGCCTGAA
1 TTGCCAAAAGCCTGAA
* *
22969 TTGCCTAAAGTTCCTGAG
1 TTGCCAAAAG--CCTGAA
*
22987 TTGCCCAAA-CCTGAA
1 TTGCCAAAAGCCTGAA
*
23002 TTTCCAAAAG
1 TTGCCAAAAG
23012 TTCCCGAGTT
Statistics
Matches: 81, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
15 38 0.47
16 6 0.07
17 6 0.07
18 31 0.38
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (16 bp):
TTGCCAAAAGCCTGAA
Found at i:22973 original size:111 final size:111
Alignment explanation
Indices: 22778--22977 Score: 310
Period size: 111 Copynumber: 1.8 Consensus size: 111
22768 GTTTCTGAGC
*
22778 TGCCAAAGCCTGAATTACCAAAAGTTCTTGAGTTGTCAAAGCCTGAATTGCCAAAAGTTCCCGAG
1 TGCCAAAACCTGAATTACCAAAAGTTCTTGAGTTGTCAAAGCCTGAATTGCCAAAAGTTCCCGAG
* *
22843 TTACCAAAGTCGGAGTTGCCTAAATTAGAAGCTAAAGTTCCAGAGT
66 TTACCAAAGCCGGAATTGCCTAAATTAGAAGCTAAAGTTCCAGAGT
* * * *
22889 TGCCAAAACCTGAATTGCCTAAAGTTCTTGAGTTGTCTAAGCCTGAATTGCCAAAAGTTCCTGAG
1 TGCCAAAACCTGAATTACCAAAAGTTCTTGAGTTGTCAAAGCCTGAATTGCCAAAAGTTCCCGAG
* * *
22954 TTGCCCAAGCCTGAATTGCCTAAA
66 TTACCAAAGCCGGAATTGCCTAAA
22978 GTTCCTGAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 79 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (111 bp):
TGCCAAAACCTGAATTACCAAAAGTTCTTGAGTTGTCAAAGCCTGAATTGCCAAAAGTTCCCGAG
TTACCAAAGCCGGAATTGCCTAAATTAGAAGCTAAAGTTCCAGAGT
Found at i:23138 original size:111 final size:111
Alignment explanation
Indices: 23008--23220 Score: 259
Period size: 111 Copynumber: 1.9 Consensus size: 111
22998 TGAATTTCCA
* * * *
23008 AAAGTTCCCGAGTTACCAAAGCCTGAATTACCGAAAGTTCCAGAGTTGCCAAAGACC-GAATTTC
1 AAAGTTCCAGAGTTACCAAAGACTGAATTACCGAAAGTTCCAGAATTGCCAAAG-CCTGAATTAC
* * * *
23072 C-CAAGATTCCTGAGTTGCCAAAGCCTGAGTTACCTAAATTAGAAGGT
65 CGCAA-ATTCCAGAGTTACCAAAACCTGAATTACCTAAATTAGAAGGT
* * * * *
23119 AAAGTTCCAGAGTTTCCAAAGACTGATTTACCTAAAGTTCCCGAATTGCCCAAGCCTGAATTACC
1 AAAGTTCCAGAGTTACCAAAGACTGAATTACCGAAAGTTCCAGAATTGCCAAAGCCTGAATTACC
* *
23184 GGAAATTCCAGAGTTACCAAAACCTGAATTGCCTAAA
66 GCAAATTCCAGAGTTACCAAAACCTGAATTACCTAAA
23221 GTTCCTGAGT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
110 2 0.02
111 81 0.95
112 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (111 bp):
AAAGTTCCAGAGTTACCAAAGACTGAATTACCGAAAGTTCCAGAATTGCCAAAGCCTGAATTACC
GCAAATTCCAGAGTTACCAAAACCTGAATTACCTAAATTAGAAGGT
Found at i:23240 original size:33 final size:33
Alignment explanation
Indices: 23118--23259 Score: 119
Period size: 33 Copynumber: 4.3 Consensus size: 33
23108 AATTAGAAGG
* *
23118 TAAAGTTCCAGAGTT-TCCAAAGACTGATTTACC
1 TAAAGTTCCAGAGTTATCCAAA-CCTGAATTACC
* * ** *
23151 TAAAGTTCCCGAATTGCCCAAGCCTGAATTACC
1 TAAAGTTCCAGAGTTATCCAAACCTGAATTACC
* *
23184 GGAAA-TTCCAGAGTTA-CCAAAACCTGAATTGCC
1 -TAAAGTTCCAGAGTTATCC-AAACCTGAATTACC
* *
23217 TAAAGTTCCTGAGTTATCCAAACCAGAATTACC
1 TAAAGTTCCAGAGTTATCCAAACCTGAATTACC
* *
23250 AAAAATTCCA
1 TAAAGTTCCA
23260 AAAACTGAAT
Statistics
Matches: 85, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
32 5 0.06
33 71 0.84
34 9 0.11
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (33 bp):
TAAAGTTCCAGAGTTATCCAAACCTGAATTACC
Found at i:23246 original size:66 final size:66
Alignment explanation
Indices: 23123--23259 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 66
23113 GAAGGTAAAG
* * * * * **
23123 TTCCAGAGTTTCCAAAGACTGATTTACCTAAAGTTCCCGAATTGCCCAAGCCTGAATTACCGGAA
1 TTCCAGAGTTACCAAAGACTGAATTACCTAAAGTTCCCGAATTACCCAAACCAGAATTACCAAAA
23188 A
66 A
* * * *
23189 TTCCAGAGTTACCAAA-ACCTGAATTGCCTAAAGTTCCTGAGTTATCCAAACCAGAATTACCAAA
1 TTCCAGAGTTACCAAAGA-CTGAATTACCTAAAGTTCCCGAATTACCCAAACCAGAATTACCAAA
23253 AA
65 AA
23255 TTCCA
1 TTCCA
23260 AAAACTGAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 58 0.98
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (66 bp):
TTCCAGAGTTACCAAAGACTGAATTACCTAAAGTTCCCGAATTACCCAAACCAGAATTACCAAAA
A
Found at i:23249 original size:144 final size:144
Alignment explanation
Indices: 22974--23249 Score: 339
Period size: 144 Copynumber: 1.9 Consensus size: 144
22964 CTGAATTGCC
* * *
22974 TAAAGTTCCTGAGTTGCCCAAACCTGAATTTCCAAAAGTTCCCGAGTTACCAAAGCCTGAATTAC
1 TAAAGTTCCAGAGTTGCCCAAAACTGAATTTCCAAAAGTTCCCGAATTACCAAAGCCTGAATTAC
* * * * *
23039 CGAAAGTTCCAGAGTTGCCAAAGACCGAATTTCCCAAGATTCCTGAGTTGCCAAAGCCTGAGTTA
66 CGAAAGTTCCAGAGTTACCAAAGACCGAATTGCCAAAGATTCCTGAGTTGCCAAAGCCAGAATTA
23104 CCTAAATTAGAAGG
131 CCTAAATTAGAAGG
* * * *
23118 TAAAGTTCCAGAGTT-TCCAAAGACTG-ATTTACCTAAAGTTCCCGAATTGCCCAAGCCTGAATT
1 TAAAGTTCCAGAGTTGCCCAAA-ACTGAATTT-CCAAAAGTTCCCGAATTACCAAAGCCTGAATT
*
23181 ACCGGAAA-TTCCAGAGTTACCAAA-ACCTGAATTGCCTAAAG-TTCCTGAGTTATCCAAA-CCA
64 ACC-GAAAGTTCCAGAGTTACCAAAGACC-GAATTGCC-AAAGATTCCTGAGTT-GCCAAAGCCA
23242 GAATTACC
125 GAATTACC
23250 AAAAATTCCA
Statistics
Matches: 113, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
143 12 0.11
144 89 0.79
145 12 0.11
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (144 bp):
TAAAGTTCCAGAGTTGCCCAAAACTGAATTTCCAAAAGTTCCCGAATTACCAAAGCCTGAATTAC
CGAAAGTTCCAGAGTTACCAAAGACCGAATTGCCAAAGATTCCTGAGTTGCCAAAGCCAGAATTA
CCTAAATTAGAAGG
Found at i:23318 original size:57 final size:57
Alignment explanation
Indices: 23185--23319 Score: 141
Period size: 57 Copynumber: 2.4 Consensus size: 57
23175 TGAATTACCG
* * * ** * *
23185 GAAATT-CCAGAGTTACCAAAACCTGAATTGCCTAAAGTTCCTGAGTTATCCAAACC
1 GAAATTACCAGAGTTACCAAAAACTGAATTACCCAAAGTTCCAAAATTACCCAAACC
* * *
23241 -AGAATTACCAAAAATT-CCAAAAACTGAATTACCCAAAGTTCCAAAATTACCCAAGCC
1 GA-AATTACC-AGAGTTACCAAAAACTGAATTACCCAAAGTTCCAAAATTACCCAAACC
23298 GAAATTACCAGAGTTACCAAAA
1 GAAATTACCAGAGTTACCAAAA
23320 CCTTAAGCGC
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
55 1 0.02
56 8 0.13
57 48 0.77
58 5 0.08
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.21
Consensus pattern (57 bp):
GAAATTACCAGAGTTACCAAAAACTGAATTACCCAAAGTTCCAAAATTACCCAAACC
Done.