Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006012.1 Hibiscus syriacus cultivar Beakdansim tig00014180_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: 85554
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4019 original size:81 final size:80
Alignment explanation
Indices: 3927--4405 Score: 635
Period size: 81 Copynumber: 6.0 Consensus size: 80
3917 GTATTTTAAC
* * * ** * *
3927 CAAAGGCATTTAGCCTTTCATCTAACATGCATAATTGACACTTTTCTACCAATTGCATAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAAC-TGCATAATTGACACATTTCTGTCAAATGCACAGCTAGG
* *
3992 CAAATAATCTTTTACT
65 CCATTAATCTTTTACT
* * *
4008 CAAAGGTATTTAACCTTTCATCTAATTGACATAATTGACACATATCTCTCAAATGCACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTG-CATAATTGACACATTTCTGTCAAATGCACAGCTAGG
4073 CCATTAATCTTTTACT
65 CCATTAATCTTTTACT
* * ** *
4089 CAAAGGTATTTAACCTTTCATCAAACTAGCATAATTGACACCTTTCAATCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACACATTTCTGTCAAATGCACAGCTAGG
*
4154 CCATTAATATTTTACT
65 CCATTAATCTTTTACT
* * * * *
4170 CAAAGGTATTTATCATTTCATATAACTGCATAATTGACACATTTCTGTCAAATGCACTGTTAGGC
1 CAAAGGTATTTAACCTTTCATCTAACTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGC
4235 CATTAATCTTTTACT
66 CATTAATCTTTTACT
4250 CAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTGTC-AA---ACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTG-CATAATTGACACATTTCTGTCAAATGCACAGCTAGG
4311 CCATTAATCTTTTACT
65 CCATTAATCTTTTACT
*
4327 CAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACA-TTCATGTCAAATGCACAGCTAG
1 CAAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACACATTTC-TGTCAAATGCACAGCTAG
* *
4391 GCGAATAATCTTTTA
64 GCCATTAATCTTTTA
4406 TTTAAAACAA
Statistics
Matches: 351, Mismatches: 38, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
76 3 0.01
77 66 0.19
78 3 0.01
80 75 0.21
81 203 0.58
82 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (80 bp):
CAAAGGTATTTAACCTTTCATCTAACTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGC
CATTAATCTTTTACT
Found at i:4246 original size:161 final size:161
Alignment explanation
Indices: 3927--4405 Score: 639
Period size: 161 Copynumber: 3.0 Consensus size: 161
3917 GTATTTTAAC
* * * * * *
3927 CAAAGGCATTTAGCCTTTCATCTAAC-ATGCATAATTGACACTTTTCTACCAATTGCATAGCTAG
1 CAAAGGTATTTAACCTTTCATCTAACTA-GCATAATTGACACATTTCTATCAAATGCACAGCTAG
* * * * *
3991 GCAAATAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGACATAATTGACACATATCTC
65 GCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTG-CATAATTGACACATTTCTG
4056 TCAAATGCACAGCTAGGCCATTAATCTTTTACT
129 TCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * * *
4089 CAAAGGTATTTAACCTTTCATCAAACTAGCATAATTGACACCTTTCAATCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTATCAAATGCACAGCTAGG
* * * *
4154 CCATTAATATTTTACTCAAAGGTATTTATCATTTCATATAACTGCATAATTGACACATTTCTGTC
66 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCATAATTGACACATTTCTGTC
* *
4219 AAATGCACTGTTAGGCCATTAATCTTTTACT
131 AAATGCACAGCTAGGCCATTAATCTTTTACT
*
4250 CAAAGGTATTTAACCTTTCATCTAACT-GACATAATTGACACATTTCTGTC-AA---ACAGCTAG
1 CAAAGGTATTTAACCTTTCATCTAACTAG-CATAATTGACACATTTCTATCAAATGCACAGCTAG
*
4310 GCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACA-TTCAT
65 GCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACACATTTC-T
* *
4374 GTCAAATGCACAGCTAGGCGAATAATCTTTTA
128 GTCAAATGCACAGCTAGGCCATTAATCTTTTA
4406 TTTAAAACAA
Statistics
Matches: 279, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
157 50 0.18
158 42 0.15
160 3 0.01
161 92 0.33
162 91 0.33
163 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (161 bp):
CAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTATCAAATGCACAGCTAGG
CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCATAATTGACACATTTCTGTC
AAATGCACAGCTAGGCCATTAATCTTTTACT
Found at i:15681 original size:44 final size:44
Alignment explanation
Indices: 15633--15721 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
15623 AGATTTGTAC
15633 TATAAGTTATTTAATATTTAATATGTATTATATTAAACAACCTA
1 TATAAGTTATTTAATATTTAATATGTATTATATTAAACAACCTA
15677 TATAAGTTATTTAATATTTAATATGTATTATATTAAACAACCTA
1 TATAAGTTATTTAATATTTAATATGTATTATATTAAACAACCTA
15721 T
1 T
15722 TATCTAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (44 bp):
TATAAGTTATTTAATATTTAATATGTATTATATTAAACAACCTA
Found at i:17936 original size:23 final size:23
Alignment explanation
Indices: 17873--17929 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
17863 ATTAGGTAGT
17873 GCTTATATAATGTAATAGATGGC
1 GCTTATATAATGTAATAGATGGC
* *
17896 GATTATATATTGTAATAGATGGC
1 GCTTATATAATGTAATAGATGGC
17919 GCTTATATAAT
1 GCTTATATAAT
17930 AAAATAGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (23 bp):
GCTTATATAATGTAATAGATGGC
Found at i:18159 original size:23 final size:23
Alignment explanation
Indices: 18109--18159 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
18099 AATAACATAT
* *
18109 TAGGTAGCGCTTATAAAACATAA
1 TAGGTAGCACTTATAAAACAAAA
* * *
18132 GAGGTAGCACTTATATAATAAAA
1 TAGGTAGCACTTATAAAACAAAA
18155 TAGGT
1 TAGGT
18160 TAATTACTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (23 bp):
TAGGTAGCACTTATAAAACAAAA
Found at i:18662 original size:198 final size:199
Alignment explanation
Indices: 18273--19003 Score: 1065
Period size: 199 Copynumber: 3.7 Consensus size: 199
18263 ATATTAGGTT
* * * * *** * * *
18273 TTGATACATTATGTTGACCTATTTTCTAATTATAGGGGTATATTTCTATCGGTTTCATTGTAAAG
1 TTGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGTTACATTGTAAAT
* *
18338 TTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACAATTTTAAATGTATCG
66 TTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCG
* *
18403 AAACTTTAT-ACGTGCACCTCGTTGGGCATTCATTCTGGACTAAAAGTATCGACACAAATTTAAA
131 ACACTTTATGA-GTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAA
18467 AAGTG
195 AAGTG
* *
18472 TTGATACATTATGTAGACCTATTTTCTCATAAAACTAGTATATTTTTACCGGTTACATTGTAAAT
1 TTGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGTTACATTGTAAAT
* *
18537 TTACCTATTACATTATAATTATAGGTTTCGATG-TTTTGGGATCGATATAATTTTAAATGTATCC
66 TTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCG
* * * *
18601 ACACGTTATGAGTGCACCTCGTTGGGCATTCATTCTGGGCAAAAAGTATCGACATAAATTTATAA
131 ACACTTTATGAGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAA
*
18666 AGCG
196 AGTG
* * *
18670 TCGATACATTATGTTGACCTATTTTGTCATAAAACCAGTATATTTCTACCGGTTACATTGTAAAT
1 TTGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGTTACATTGTAAAT
*
18735 TTACCTATTACATTATAATTATAGGTTTCAATGTTTTTGGGATCGATACAATTTTAAATGTATCG
66 TTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCG
* * *
18800 ACACTTTATGAGTGCACCTCGTTTGGCATTCATTCTGGACAAAACGTATCGACACAAATTTAGAA
131 ACACTTTATGAGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAA
18865 AGTG
196 AGTG
* * *
18869 TTCATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGTTATATTGTAAAT
1 TTGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGTTACATTGTAAAT
* * * *
18934 ATACCTATTACATTGTAATTATAGGTTTTGATGTTTTTGGGATTGATAC--TTTTAACAAATGTA
66 TTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTTT---AAATGTA
18997 TCGACAC
128 TCGACAC
19004 ATTTGTTTAC
Statistics
Matches: 479, Mismatches: 48, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
197 4 0.01
198 181 0.38
199 280 0.58
200 14 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (199 bp):
TTGATACATTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGTTACATTGTAAAT
TTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCG
ACACTTTATGAGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAA
AGTG
Found at i:23034 original size:18 final size:17
Alignment explanation
Indices: 23013--23071 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
23003 TGATTTGCTT
23013 AGAAGAAGCGATTGGTTG
1 AGAAGAAGCG-TTGGTTG
*
23031 AGAAGGAG-GTTGTTGTTG
1 AGAAGAAGCGTTG--GTTG
23049 AGAAG-AGC-TTGGTTG
1 AGAAGAAGCGTTGGTTG
23064 AGAAGAAG
1 AGAAGAAG
23072 TTTGAACAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 9 0.25
16 5 0.14
17 6 0.17
18 16 0.44
ACGTcount: A:0.32, C:0.03, G:0.41, T:0.24
Consensus pattern (17 bp):
AGAAGAAGCGTTGGTTG
Found at i:23063 original size:15 final size:15
Alignment explanation
Indices: 23024--23069 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
23014 GAAGAAGCGA
*
23024 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
23040 TTGTTGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
23057 TTGGTTGAGAAGA
1 TTGGTTGAGAAGA
23070 AGTTTGAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 6 0.22
18 8 0.30
ACGTcount: A:0.26, C:0.02, G:0.41, T:0.30
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:23823 original size:200 final size:200
Alignment explanation
Indices: 23370--24528 Score: 1576
Period size: 200 Copynumber: 5.8 Consensus size: 200
23360 TGTAATTTAA
* * * * *
23370 AAAAAGTATAGACACAAATTTAAAAAGTATCAATACAATATGTAGACATATTTTCTCATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * * *
23435 GGTATATTTCTATCGGTTACATTGTAAATTTACCTATTATATTATAATTATAGGTTTAGATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTT
* * * *
23500 TTGGGATCGATACAATTT--TAAATGTATCGATACTTTATGTGTGCACCTCGTTGGGAATTCATT
131 TTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATT
23563 CTGGAC
195 CTGGAC
*
23569 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACTTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
* *
23634 GACATATTTATACTGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTT
* * * **
23699 TTGGGATCGATACTTTTAAAAAATTTATCGACACTTTATGTGTGCACCTCGTCAGGCATTCATTC
131 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
23764 TGGAC
196 TGGAC
* * * * ** *
23769 AAAAAATATCAACACATATTTAAAAAGTATTGATACATTATGTAGATGTATTTTCTCATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
* *
23834 GCTATATTTATACCGGTTACATTGTAAATTTACCTATTATATTGTAATTATCGGTTTCT-ATGTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTT-TGATGTT
* * *
23898 TCTGGGATAGATACTTTTAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATT
130 TTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATT
23963 CTGGAC
195 CTGGAC
* * * * * * *
23969 AACAAGTATCGACACAAATATAGAAAGTGTTGATACGTTATGTAGACCTATTTTCTCATAAAATC
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * *
24034 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATTGGCTTTAATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTT
* *
24099 TTGGGATCGATACTTTTAATAAATGTATAGACAATTTATGCGTGCACCTCGTTGGGCATTCATTC
131 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
24164 TGGAC
196 TGGAC
*
24169 AAAAAAGTATCGACACAAATTTAGAAAA-TGTCGATACATTATGTAGACCTATTTTCTCATAAAA
1 -AAAAAGTATCGACACAAATTTA-AAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAA
* * *
24233 CTGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTTGATGT
64 CCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGT
* * * * * * *
24298 TTTTGTGATCGATACTTTTAATAACTATATCGACACTTTGTGCGTGCAACTTGTTGGGCATTCCT
129 TTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCAT
24363 TCTGGAC
194 TCTGGAC
* *
24370 AAAAAGTATCGAAATAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * *
24435 G------GTATA-----TACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTCGATGTTT
66 GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTT
*
24489 TTGAGATCGATACTTTTAA-AAGATGTATCGACACTTTATG
131 TTGGGATCGATACTTTTAATAA-ATGTATCGACACTTTATG
24529 TTGACCTATT
Statistics
Matches: 859, Mismatches: 93, Indels: 26
0.88 0.10 0.03
Matches are distributed among these distances:
188 2 0.00
189 80 0.09
194 3 0.00
198 3 0.00
199 134 0.16
200 458 0.53
201 176 0.20
202 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (200 bp):
AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTCATAAAACC
GATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTT
TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
TGGAC
Found at i:24268 original size:20 final size:20
Alignment explanation
Indices: 24243--24281 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24233 CTGATATATT
*
24243 TTTACCGGTTACATTGTAAA
1 TTTACCGATTACATTGTAAA
*
24263 TTTACCTATTACATTGTAA
1 TTTACCGATTACATTGTAA
24282 TTATCAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTACCGATTACATTGTAAA
Found at i:24688 original size:128 final size:128
Alignment explanation
Indices: 24441--24715 Score: 317
Period size: 128 Copynumber: 2.1 Consensus size: 128
24431 AACCGGTATA
* *
24441 TACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTCGATGTTTTTGAGATCGATACTTTT
1 TACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTCTTGAGATCGATACTTTT
* * * * **
24506 AAAAGATGTATCGACACTTTATGTTGACCTATTTTCTAATTAAACAGGTATATTTCT-ACCTGT
66 AAAAGATCTATCGACACATTATGTTGACCTATTTTCTAATTAAAAAAGTATATTT-TAACCACT
* ** *
24569 TACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTTATGTTCTTGGGATCGATACAATT
1 TACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTCTTGAGATCGATAC--TT
* * * * *
24634 TTAAAATATCT-T-GATACATTATGTTTA-CTAATTTTGTCAA-TAAAAAAGTGTATTTTAACCA
64 TTAAAAGATCTATCGACACATTATGTTGACCT-ATTTTCT-AATTAAAAAAGTATATTTTAACCA
24695 CT
127 CT
24697 TACATTGTAAATTTACCTA
1 TACATTGTAAATTTACCTA
24716 ATACTTTAAA
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
127 3 0.02
128 108 0.86
129 3 0.02
130 11 0.09
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (128 bp):
TACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTCTTGAGATCGATACTTTT
AAAAGATCTATCGACACATTATGTTGACCTATTTTCTAATTAAAAAAGTATATTTTAACCACT
Found at i:27422 original size:25 final size:25
Alignment explanation
Indices: 27388--27437 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27378 CTCATCGCTT
27388 CCTTTTGTTATTCTTGTGTCTCATG
1 CCTTTTGTTATTCTTGTGTCTCATG
27413 CCTTTTGTTATTCTTGTGTCTCATG
1 CCTTTTGTTATTCTTGTGTCTCATG
27438 GAAGCTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.08, C:0.20, G:0.16, T:0.56
Consensus pattern (25 bp):
CCTTTTGTTATTCTTGTGTCTCATG
Found at i:30381 original size:37 final size:37
Alignment explanation
Indices: 30322--30425 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
30312 CCTTTTCGTC
30322 CTACTAGGATTC-AACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
30358 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
30395 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
30426 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 10 0.17
37 49 0.83
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:31280 original size:4 final size:4
Alignment explanation
Indices: 31267--31304 Score: 67
Period size: 4 Copynumber: 9.2 Consensus size: 4
31257 TATATATTAA
31267 TATT TCATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT TATT TATT T
31305 TTCCTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:31358 original size:26 final size:24
Alignment explanation
Indices: 31309--31359 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
31299 TTATTTTTCC
*
31309 TTTTATTTTATTTTTTTTACTTAT
1 TTTTATTTTATTTTTTTCACTTAT
*
31333 TTTTATTCTTCATTTTTTTCATTTAT
1 TTTTATT-TT-ATTTTTTTCACTTAT
31359 T
1 T
31360 CATTTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
26 14 0.61
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTATTTTATTTTTTTCACTTAT
Found at i:39995 original size:3 final size:3
Alignment explanation
Indices: 39987--40026 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
39977 TATCTGGAAC
* *
39987 TCT TCT TCT TTT TCT TCT TCT TCT TCT TCC T-T TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
40027 CCGTGTGCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:47644 original size:32 final size:34
Alignment explanation
Indices: 47606--47687 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
47596 GATATATCAA
*
47606 TGAAAAGTTGTTGAA-GATG-ATTAATTGACAAC
1 TGAAAAGTTGATGAATGATGCATTAATTGACAAC
* * *
47638 TGAAAAGTTGCTGAAATGGTGCATTAATTGACCAC
1 TGAAAAGTTGATG-AATGATGCATTAATTGACAAC
47673 TGAAAAGTTGATGAA
1 TGAAAAGTTGATGAA
47688 ATAGTACATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 12 0.28
33 2 0.05
34 5 0.12
35 24 0.56
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (34 bp):
TGAAAAGTTGATGAATGATGCATTAATTGACAAC
Found at i:47669 original size:35 final size:35
Alignment explanation
Indices: 47625--47698 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
47615 GTTGAAGATG
* * *
47625 ATTAATTGACAACTGAAAAGTTGCTGAAATGGTGC
1 ATTAATTGACAACTGAAAAGTTGATGAAATAGTAC
*
47660 ATTAATTGACCACTGAAAAGTTGATGAAATAGTAC
1 ATTAATTGACAACTGAAAAGTTGATGAAATAGTAC
47695 ATTA
1 ATTA
47699 TGAGATGACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (35 bp):
ATTAATTGACAACTGAAAAGTTGATGAAATAGTAC
Found at i:60944 original size:26 final size:26
Alignment explanation
Indices: 60915--60968 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
60905 CTGAATGAAA
60915 TTATTCTGGAAAAGTTGTTCAGTCTC
1 TTATTCTGGAAAAGTTGTTCAGTCTC
60941 TTATTCTGGAAAAGTTGTTCAGTCTC
1 TTATTCTGGAAAAGTTGTTCAGTCTC
60967 TT
1 TT
60969 CTTCAATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (26 bp):
TTATTCTGGAAAAGTTGTTCAGTCTC
Found at i:69138 original size:17 final size:17
Alignment explanation
Indices: 69113--69150 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
69103 GCGTGCAAAC
69113 AAAAAAAG-TAAAAAAG
1 AAAAAAAGTTAAAAAAG
*
69129 AAAAATAAGTTTAAAAAG
1 AAAAA-AAGTTAAAAAAG
69147 AAAA
1 AAAA
69151 GAGAGACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAAAAAGTTAAAAAAG
Found at i:78463 original size:16 final size:16
Alignment explanation
Indices: 78444--78483 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
78434 CTTGCCCCCT
78444 TCCCTTTCCTTCTCCC
1 TCCCTTTCCTTCTCCC
78460 TCCCTTTCCTTCTCCC
1 TCCCTTTCCTTCTCCC
78476 TCCCTTTC
1 TCCCTTTC
78484 TTACGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (16 bp):
TCCCTTTCCTTCTCCC
Found at i:79054 original size:195 final size:194
Alignment explanation
Indices: 78814--79247 Score: 591
Period size: 195 Copynumber: 2.2 Consensus size: 194
78804 ATTAAAATTT
* * * *
78814 GTATCGATACTTTTCTAAGTATATGCACCAAATTATCGATACTTTAGGAATTTTAAAAAAATT-C
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAA-TTTAAAAAAATTGC
* * * *
78878 AATAATAGTGCCTATAAAATATCGATACTTTATAAACATGTATCGATACATGGCAATATAACATG
65 AATAATAGCGCCTATAAAATATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAG
*
78943 TAAAAATATGACAAAAACTGATTTCAATATGACAAAACCGATAAAGAACTACCAAATATATTGAA
130 TAAAAATATGAC-AAAACCGATTTCAATATGACAAAACCGATAAAGAACTACCAAATATATTGAA
79008 G
194 G
* *
79009 GTATCGATACTTTTATAAGTATATGTATCATAGTATCGATACTTTAGGAATTTAAAAGAATTGCA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCA
* * *
79074 ATAGTAGCGCCTATAAAGTATCGATACTTTAGAGACATGTATCGATACATGACAATATAACAAGT
66 ATAATAGCGCCTATAAAATATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
* * * * * ** * ** *
79139 TAAAATATGACAAAACCGATTTTAATATTACAAAATCGGTAAAGCGCTATCGGATATGTTGAAG
131 AAAAATATGACAAAACCGATTTCAATATGACAAAACCGATAAAGAACTACCAAATATATTGAAG
* * *
79203 GTATCGATAATTTAATAAGTATATGTATCATATTATCAATACTTT
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTT
79248 TAAAACAAAA
Statistics
Matches: 209, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
194 94 0.45
195 115 0.55
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (194 bp):
GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCA
ATAATAGCGCCTATAAAATATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
AAAAATATGACAAAACCGATTTCAATATGACAAAACCGATAAAGAACTACCAAATATATTGAAG
Found at i:79940 original size:20 final size:20
Alignment explanation
Indices: 79912--79949 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
79902 AATTTTTTTA
*
79912 TGAATAGTGAACAGTACCGG
1 TGAACAGTGAACAGTACCGG
79932 TGAACAGTGAACAGTACC
1 TGAACAGTGAACAGTACC
79950 CATGCACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
TGAACAGTGAACAGTACCGG
Found at i:79958 original size:20 final size:20
Alignment explanation
Indices: 79911--79959 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
79901 GAATTTTTTT
* *
79911 ATGAATAGTGAACAGTACCG
1 ATGAACAGTGAACAGTACCC
*
79931 GTGAACAGTGAACAGTACCC
1 ATGAACAGTGAACAGTACCC
*
79951 ATGCACAGT
1 ATGAACAGT
79960 AGGGGAAACG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
ATGAACAGTGAACAGTACCC
Done.