Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018505.1 Corchorus olitorius cultivar O-4 contig18538, 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: 40779
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3970 original size:117 final size:113
Alignment explanation
Indices: 3743--4082 Score: 459
Period size: 117 Copynumber: 2.9 Consensus size: 113
3733 TTCCAGTTAT
* *
3743 TGGCATTTTGGGGAGAAACGCCCCTATATATTAGTCTTCATTTTTACCCAATTTGCATTTCCCGA
1 TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCC--
* * * * *
3808 AAAAAAAAAATAAATATGGAGGCATTTTTTATCCTGAAACGCCCCAATTTGG
64 -AGAAAAAATTAAATATGGGGGC-GTTTTTATCCTGAAACCCCCCAATTTGG
* * *
3860 TGGCATTTTGGGGAGAAATGCCCCTATATGTTAGTCTTAATTTTTACACAATTTGTATTTCCCAG
1 TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCCAG
3925 AAAAGAATTTAAATATGGGGGCGTTTTTCATCCTGAAACACCCCC-ATTTGG
66 AAAA-AA-TTAAATATGGGGGCGTTTTT-ATCCTGAAAC-CCCCCAATTTGG
* * *
3976 TGGCGTTTT-GGGAGAAACGCCCCTATATGTTAGTTTTCATTTTTACCCAATTTGTATTTCCCGG
1 TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCCAG
*
4040 AAAAAATTAAATATGGGGGCGTTTTTATCCTCAAACGCCCCCA
66 AAAAAATTAAATATGGGGGCGTTTTTATCCTGAAAC-CCCCCA
4083 TTTAGCAGCG
Statistics
Matches: 200, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
112 14 0.07
113 20 0.10
114 7 0.04
115 61 0.31
116 36 0.18
117 62 0.31
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (113 bp):
TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCCAG
AAAAAATTAAATATGGGGGCGTTTTTATCCTGAAACCCCCCAATTTGG
Found at i:4027 original size:115 final size:113
Alignment explanation
Indices: 3743--4085 Score: 481
Period size: 115 Copynumber: 3.0 Consensus size: 113
3733 TTCCAGTTAT
* *
3743 TGGCATTTTGGGGAGAAACGCCCCTATATATTAGTCTTCATTTTTACCCAATTTGCATTTCCCGA
1 TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCC--
* * * * *
3808 AAAAAAAAAATAAATATGGAGGCATTTTTTATCCTGAAACGCCCCAATTTGG
64 -AGAAAAAATTAAATATGGGGGC-GTTTTTATCCTGAAACGCCCCCATTTGG
* * *
3860 TGGCATTTTGGGGAGAAATGCCCCTATATGTTAGTCTTAATTTTTACACAATTTGTATTTCCCAG
1 TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCCAG
*
3925 AAAAGAATTTAAATATGGGGGCGTTTTTCATCCTGAAACACCCCCATTTGG
66 AAAA-AA-TTAAATATGGGGGCGTTTTT-ATCCTGAAACGCCCCCATTTGG
* * *
3976 TGGCGTTTT-GGGAGAAACGCCCCTATATGTTAGTTTTCATTTTTACCCAATTTGTATTTCCCGG
1 TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCCAG
*
4040 AAAAAATTAAATATGGGGGCGTTTTTATCCTCAAACGCCCCCATTT
66 AAAAAATTAAATATGGGGGCGTTTTTATCCTGAAACGCCCCCATTT
4086 AGCAGCGTTT
Statistics
Matches: 204, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
112 18 0.09
113 20 0.10
114 7 0.03
115 61 0.30
116 40 0.20
117 58 0.28
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (113 bp):
TGGCATTTTGGGGAGAAACGCCCCTATATGTTAGTCTTCATTTTTACCCAATTTGTATTTCCCAG
AAAAAATTAAATATGGGGGCGTTTTTATCCTGAAACGCCCCCATTTGG
Found at i:6784 original size:41 final size:41
Alignment explanation
Indices: 6738--6815 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
6728 CAAATAAAGG
*
6738 AAATAAATAATTCG-TAAATGA-ACAAACTAAAAGAAAATAGA
1 AAATAAATAA-CCGATAAAT-ATACAAACTAAAAGAAAATAGA
*
6779 AAATAAATAACCGATAAATATACTAACTAAAAGAAAA
1 AAATAAATAACCGATAAATATACAAACTAAAAGAAAA
6816 GAAAGCACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.09
41 30 0.91
ACGTcount: A:0.64, C:0.09, G:0.08, T:0.19
Consensus pattern (41 bp):
AAATAAATAACCGATAAATATACAAACTAAAAGAAAATAGA
Found at i:14001 original size:21 final size:21
Alignment explanation
Indices: 13975--14015 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13965 TGCTAGCCGT
* *
13975 GCCTTCCTCCGTGTCATCCGC
1 GCCTTCCTCCGCGCCATCCGC
*
13996 GCCTTCTTCCGCGCCATCCG
1 GCCTTCCTCCGCGCCATCCG
14016 AGCCAAATGC
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:0.05, C:0.49, G:0.20, T:0.27
Consensus pattern (21 bp):
GCCTTCCTCCGCGCCATCCGC
Found at i:18514 original size:21 final size:21
Alignment explanation
Indices: 18485--18529 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
18475 TTGGAACTCA
18485 TTGAATTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
*
18506 TTGAGTTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
18527 TTG
1 TTG
18530 GTTGATTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGAATTCAAAATTAGGGTTC
Found at i:18737 original size:21 final size:21
Alignment explanation
Indices: 18699--18739 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18689 AGGGCTTGAA
*
18699 AACCTTGCTCAAGCGCGGCCC
1 AACCTTGCCCAAGCGCGGCCC
* *
18720 AACCTTGCCCAGGTGCGGCC
1 AACCTTGCCCAAGCGCGGCC
18740 TACCTTAGAA
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:0.17, C:0.41, G:0.27, T:0.15
Consensus pattern (21 bp):
AACCTTGCCCAAGCGCGGCCC
Found at i:19003 original size:2 final size:2
Alignment explanation
Indices: 18996--19040 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18986 TGTTGGTAAT
18996 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19038 CA C
1 CA C
19041 CAATTGAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:23460 original size:21 final size:21
Alignment explanation
Indices: 23427--23480 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
23417 CTCCACCTGG
*
23427 GCACCCACATGG-TTGCCTTGA
1 GCACCCACGTGGTTTG-CTTGA
*
23448 GCACCCATGTGGTTTGCTTGA
1 GCACCCACGTGGTTTGCTTGA
* *
23469 GAACCCAGGTGG
1 GCACCCACGTGG
23481 GCAGTGTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.24
Consensus pattern (21 bp):
GCACCCACGTGGTTTGCTTGA
Found at i:23551 original size:76 final size:76
Alignment explanation
Indices: 23414--23563 Score: 171
Period size: 76 Copynumber: 2.0 Consensus size: 76
23404 ACAAGGACCC
* *
23414 CGACTCCACCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
23479 GGGCAGTGTCA
66 GGGCAGTGTCA
* ** * **
23490 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCACCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
23552 GATGGGCTGTGT
63 GATGGGCAGTGT
23564 GTTATTTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
75 4 0.06
76 52 0.84
77 6 0.10
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:32291 original size:30 final size:30
Alignment explanation
Indices: 32257--32781 Score: 567
Period size: 30 Copynumber: 17.7 Consensus size: 30
32247 AATCTCCAAA
*
32257 TGACACCAGAAGTTGTCATGATCTTGCTAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
32287 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
32317 TGACACCAGAAGTTGTCATTATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
32347 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
32377 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
32407 TGACACCAGAAGTTGTCATGCTCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * * *
32437 TAACACTAGAAGTTGTCAATGGTCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT
* *
32468 TG--ACCAGAAGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAAT
* * *
32499 AGACA-CATGAAGATGTCAT-A-ATT-CAAT
1 TGACACCA-GAAGTTGTCATGATCTTGCAAT
*
32526 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
32556 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
32586 TGACACCAGAAGTTGTCAAGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
32616 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
32646 TTACACCAGAAGTTGTCATGGTCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * * *
32676 TG--ACTAGAGGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAAT
* ** * * *
32707 AGACACTTGATGATGTCA--A-ATT-CAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
32733 TGACACCAGAAGTTGTCAT-A-ATT-CAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
32760 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
32782 TTTACTTTTC
Statistics
Matches: 431, Mismatches: 45, Indels: 39
0.84 0.09 0.08
Matches are distributed among these distances:
26 17 0.04
27 47 0.11
28 24 0.06
29 14 0.03
30 276 0.64
31 28 0.06
32 3 0.01
33 22 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:32621 original size:209 final size:205
Alignment explanation
Indices: 32313--32779 Score: 765
Period size: 209 Copynumber: 2.3 Consensus size: 205
32303 CATGGTCTTG
*
32313 CAATTGACACCAGAAGTTGTCATTATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAATT
1 CAATTGACACCAGAAGTTGTCA-T-TCTTGCAATTGACACCAGAAGTTGTCATGCTCTTGCAATT
* *
32378 GACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCATGCTCTTACAATTAACAC
64 GACACCAGAAGTTGTCAAGCTCTTGCAATTGACACCAGAAGTTGTCATGATCTTACAATTAACAC
*
32443 TAGAAGTTGTCAATGGTCTTACAATTGACCAGAAGTTGTCATGATAAATTTCCAATAGACACATG
129 CAGAAGTTGTC-ATGGTCTTACAATTGACCAGAAGTTGTCATGATAAATTTCCAATAGACACATG
32508 AAGATGTCATAATT
193 AAGATGTCA-AATT
32522 CAATTGACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCATGCTCTTGCAATT
1 CAATTGACACCAGAAGTTGTCAT--TCTTGCAATTGACACCAGAAGTTGTCATGCTCTTGCAATT
* *
32587 GACACCAGAAGTTGTCAAGCTCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTTACAC
64 GACACCAGAAGTTGTCAAGCTCTTGCAATTGACACCAGAAGTTGTCATGATCTTACAATTAACAC
* * *
32652 CAGAAGTTGTCATGGTCTTACAATTGACTAGAGGTTGTCATGATAAATTTCCAATAGACACTTGA
129 CAGAAGTTGTCATGGTCTTACAATTGACCAGAAGTTGTCATGATAAATTTCCAATAGACACATGA
*
32717 TGATGTCAAATT
194 AGATGTCAAATT
**
32729 CAATTGACACCAGAAGTTGTCATAATT-CAATTGACACCAGAAGTTGTCATG
1 CAATTGACACCAGAAGTTGTCATTCTTGCAATTGACACCAGAAGTTGTCATG
32780 ATTTTACTTT
Statistics
Matches: 244, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
204 24 0.10
205 2 0.01
207 27 0.11
208 59 0.24
209 132 0.54
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (205 bp):
CAATTGACACCAGAAGTTGTCATTCTTGCAATTGACACCAGAAGTTGTCATGCTCTTGCAATTGA
CACCAGAAGTTGTCAAGCTCTTGCAATTGACACCAGAAGTTGTCATGATCTTACAATTAACACCA
GAAGTTGTCATGGTCTTACAATTGACCAGAAGTTGTCATGATAAATTTCCAATAGACACATGAAG
ATGTCAAATT
Found at i:32732 original size:26 final size:27
Alignment explanation
Indices: 32718--32778 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
32708 GACACTTGAT
32718 GATGTCA-AATTCAATTGACACCAGAA
1 GATGTCATAATTCAATTGACACCAGAA
*
32744 GTTGTCATAATTCAATTGACACCAGAA
1 GATGTCATAATTCAATTGACACCAGAA
*
32771 GTTGTCAT
1 GATGTCAT
32779 GATTTTACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.18
27 27 0.82
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (27 bp):
GATGTCATAATTCAATTGACACCAGAA
Found at i:37559 original size:143 final size:143
Alignment explanation
Indices: 37292--37573 Score: 388
Period size: 143 Copynumber: 2.0 Consensus size: 143
37282 AATTGTTTCA
* * * * *
37292 AATTTGTTTATATATAAACGGATTTAGAGCGTTAATTCGCTTTGTATCCATATATCACAATCTAA
1 AATTCGTTTATATATAAACGGATTCAGAGCGTTAATTCGATTTGGATCCATATATCACAATCCAA
* * * * *
37357 GTCCAAATTCGGACGGATCAAATATCCGCCTTGGAGATTCAAACGGCAATTGTCTGATACACAAA
66 GTCCAAATTCGGACGGATCAAATATCCACCTCGGAGATCCAAACGACAATTGTCCGATACACAAA
*
37422 TGGTTGGAGCGTT
131 TGGTCGGAGCGTT
37435 AATTCGTTTATATATAAACGGATTCAGAGCGTTAATTC-ATTCTGGATCCATATATCACAATCCA
1 AATTCGTTTATATATAAACGGATTCAGAGCGTTAATTCGATT-TGGATCCATATATCACAATCCA
* * * * *
37499 AGTCCGAATTCGGACGGAT-ATGATATCCATCTCGTAGATCCAAACGACAATTGTCCGATACATA
65 AGTCCAAATTCGGACGGATCA-AATATCCACCTCGGAGATCCAAACGACAATTGTCCGATACACA
37563 AATGGTCGGAG
129 AATGGTCGGAG
37574 AGCTGAGACA
Statistics
Matches: 121, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
142 3 0.02
143 118 0.98
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (143 bp):
AATTCGTTTATATATAAACGGATTCAGAGCGTTAATTCGATTTGGATCCATATATCACAATCCAA
GTCCAAATTCGGACGGATCAAATATCCACCTCGGAGATCCAAACGACAATTGTCCGATACACAAA
TGGTCGGAGCGTT
Found at i:37807 original size:210 final size:209
Alignment explanation
Indices: 37403--37819 Score: 622
Period size: 210 Copynumber: 2.0 Consensus size: 209
37393 ATTCAAACGG
* * *
37403 CAATTGTCTGATACACAAATGGTTGGAGCGTTAATTCGTTTATATATAAACGGATTCAGAGCGTT
1 CAATTGTCCGATACACAAATGGTCGGAGCGTTAATTCGTTTATATATAAACGGATCCAGAGCGTT
* * *
37468 AATTCATTCTGGATCCATATATCACAATCCAAGTCCGAATTCGGACGGATATGATATCCATCTCG
66 AATACATTCTGGATCCATATATCACAATCCAAGTCCGAATTCAGACGGATAGGATATCCATCTCG
*
37533 TAGATCCAAACGACAATTGTCCGATACATAAATGGTCGGAGAGCTGAGACAAAAAAAGTTCAATT
131 AAGATCCAAACGACAATTGTCCGATACATAAATGGTCGGAGAGCTGAGACAAAAAAAGTTCAATT
37598 TTGTTAAAAAAAAAA
196 TTG-TAAAAAAAAAA
* * *
37613 CAATTGTCCGATACATAAATGGTCGGAGTGTTAATTCGTTTATATATAAACGGATCCGGAGCGTT
1 CAATTGTCCGATACACAAATGGTCGGAGCGTTAATTCGTTTATATATAAACGGATCCAGAGCGTT
* * * * *
37678 AATACGCTTC-GTATCCATATATCACAATCCAAGTCATGGATTCAGACGGATCGGATATCCATCT
66 AATAC-ATTCTGGATCCATATATCACAATCCAAGTC-CGAATTCAGACGGATAGGATATCCATCT
* * * *
37742 CGAAGATCCAAACGGCAATTGTTCGATACATAAATGGTCGGAGAGCTGTGACACAAAAA-TTCAA
129 CGAAGATCCAAACGACAATTGTCCGATACATAAATGGTCGGAGAGCTGAGACAAAAAAAGTTCAA
37806 TTTTGTAAAAAAAA
194 TTTTGTAAAAAAAA
37820 GAAAGGAAAA
Statistics
Matches: 186, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
209 9 0.05
210 97 0.52
211 80 0.43
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (209 bp):
CAATTGTCCGATACACAAATGGTCGGAGCGTTAATTCGTTTATATATAAACGGATCCAGAGCGTT
AATACATTCTGGATCCATATATCACAATCCAAGTCCGAATTCAGACGGATAGGATATCCATCTCG
AAGATCCAAACGACAATTGTCCGATACATAAATGGTCGGAGAGCTGAGACAAAAAAAGTTCAATT
TTGTAAAAAAAAAA
Found at i:39155 original size:2 final size:2
Alignment explanation
Indices: 39148--39196 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
39138 CTGGCAACCA
* * *
39148 AT AT AT AT AGG AT -T AT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39190 AT AT AT A
1 AT AT AT A
39197 CACTAGTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:39185 original size:18 final size:18
Alignment explanation
Indices: 39164--39199 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39154 ATAGGATTAT
39164 ATATATATATATATACAC
1 ATATATATATATATACAC
39182 ATATATATATATATACAC
1 ATATATATATATATACAC
39200 TAGTCTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATATATATATACAC
Found at i:39398 original size:17 final size:18
Alignment explanation
Indices: 39362--39398 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39352 CTTTTCTATG
*
39362 AAAATGAGTATACGTTTT
1 AAAATGAGTAAACGTTTT
39380 AAAATGAGTAAAC-TTTT
1 AAAATGAGTAAACGTTTT
39397 AA
1 AA
39399 GATTTCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (18 bp):
AAAATGAGTAAACGTTTT
Found at i:39577 original size:22 final size:22
Alignment explanation
Indices: 39549--39785 Score: 98
Period size: 22 Copynumber: 11.0 Consensus size: 22
39539 TATATTATTT
* *
39549 TGATAACCTCTCTAAGAAATTG
1 TGATAACCTCACTATGAAATTG
* *
39571 TGATAACCTCCCTGTGAAACTT-
1 TGATAACCTCACTATGAAA-TTG
* *
39593 TGATAACCACACTATGAAATTT
1 TGATAACCTCACTATGAAATTG
* * *
39615 TGATATCATC-CTATGAAATTT
1 TGATAACCTCACTATGAAATTG
* * * *
39636 TGATAAGCACACTATAAAACTG
1 TGATAACCTCACTATGAAATTG
39658 TGATAACCT--CTAT-AGAATAT-
1 TGATAACCTCACTATGA-AAT-TG
** *
39678 TGATAAATTCCCTAT-AGAATT-
1 TGATAACCTCACTATGA-AATTG
* * * *
39699 TGATAAGCACAATATGAAATTTT
1 TGATAACCTCACTATGAAA-TTG
* * *
39722 TG-TAACCACATTATGAAATTT
1 TGATAACCTCACTATGAAATTG
* * * *
39743 TGACAACCACATTATGAAATTT
1 TGATAACCTCACTATGAAATTG
*
39765 TGAT-AGCTACACTATGAAATT
1 TGATAACCT-CACTATGAAATT
39786 TCGATAATCT
Statistics
Matches: 170, Mismatches: 33, Indels: 24
0.75 0.15 0.11
Matches are distributed among these distances:
19 1 0.01
20 13 0.08
21 40 0.24
22 112 0.66
23 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TGATAACCTCACTATGAAATTG
Found at i:39786 original size:22 final size:21
Alignment explanation
Indices: 39585--39792 Score: 133
Period size: 22 Copynumber: 9.7 Consensus size: 21
39575 AACCTCCCTG
*
39585 TGAAACTTTGATAACCACACTA
1 TGAAATTTTGATAA-CACACTA
*
39607 TGAAATTTTGATATCATC-CTA
1 TGAAATTTTGATAACA-CACTA
39628 TGAAATTTTGATAAGCACACTA
1 TGAAATTTTGATAA-CACACTA
* * * *
39650 TAAAACTGTGATAAC-CTCTA
1 TGAAATTTTGATAACACACTA
* *
39670 T-AGAATATTGATAA-ATTCCCTA
1 TGA-AATTTTGATAACA--CACTA
*
39692 T-AGAA-TTTGATAAGCACAATA
1 TGA-AATTTTGATAA-CACACTA
*
39713 TGAAATTTTTG-TAACCACATTA
1 TGAAA-TTTTGATAA-CACACTA
* *
39735 TGAAATTTTGACAACCACATTA
1 TGAAATTTTGATAA-CACACTA
*
39757 TGAAATTTTGATAGCTACACTA
1 TGAAATTTTGATAAC-ACACTA
*
39779 TGAAATTTCGATAA
1 TGAAATTTTGATAA
39793 TCTGCAAAGT
Statistics
Matches: 150, Mismatches: 22, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 13 0.09
21 39 0.26
22 92 0.61
23 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAATTTTGATAACACACTA
Done.