Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004977.1 Hibiscus syriacus cultivar Beakdansim tig00011173_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: 57858
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:194 original size:2 final size:2
Alignment explanation
Indices: 187--266 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
177 CTTGAATGTT
*
187 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA GA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
267 GTTTGAATAG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1037 original size:21 final size:21
Alignment explanation
Indices: 1005--1060 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
995 ACACTTGGGA
*
1005 TGTACCGATACACCTAAAGAG
1 TGTACTGATACACCTAAAGAG
* * *
1026 TTTATTGATACACCTAGAGAG
1 TGTACTGATACACCTAAAGAG
1047 TGTACTGATACACC
1 TGTACTGATACACC
1061 CACACTCCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (21 bp):
TGTACTGATACACCTAAAGAG
Found at i:7593 original size:31 final size:31
Alignment explanation
Indices: 7555--7632 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
7545 TTAAAAAACG
7555 TAAGTTTTGGTCACTTACTTTATCATTTTAT
1 TAAGTTTTGGTCACTTACTTTATCATTTTAT
* *
7586 TAAGTTTTAGTCACTTACTTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACTTTATCATTTTAT
*
7617 CAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
7633 GGACATGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.53
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACTTTATCATTTTAT
Found at i:8880 original size:31 final size:31
Alignment explanation
Indices: 8842--8916 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
8832 CGTCCAATTA
*
8842 ACCAAAACTTAATAAAACAGTAACGAAAGTG
1 ACCAAAACTTAATAAAACAATAACGAAAGTG
* * *
8873 ACTAAAACTTAATAAAATAATAACGTAAGTG
1 ACCAAAACTTAATAAAACAATAACGAAAGTG
8904 ACCAAAAC-TAATA
1 ACCAAAACTTAATA
8917 TTTTTAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.13
31 34 0.87
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (31 bp):
ACCAAAACTTAATAAAACAATAACGAAAGTG
Found at i:9059 original size:15 final size:15
Alignment explanation
Indices: 9039--9068 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9029 TACTATCAAC
9039 AAACCATTAAAAATT
1 AAACCATTAAAAATT
9054 AAACCATTAAAAATT
1 AAACCATTAAAAATT
9069 TATGACTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
AAACCATTAAAAATT
Found at i:26055 original size:22 final size:22
Alignment explanation
Indices: 26025--26076 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
26015 TTTGATAGTT
*
26025 GTGGTTCCTAGGTCCTATATTA
1 GTGGGTCCTAGGTCCTATATTA
26047 GTGGGTCCTAGGTCCTATATTA
1 GTGGGTCCTAGGTCCTATATTA
26069 GTGGGTCC
1 GTGGGTCC
26077 GAGTCGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.37
Consensus pattern (22 bp):
GTGGGTCCTAGGTCCTATATTA
Found at i:27005 original size:15 final size:15
Alignment explanation
Indices: 26985--27015 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26975 GTTTAGGTTC
26985 GTTTTCAAAACAAAG
1 GTTTTCAAAACAAAG
*
27000 GTTTTCAAATCAAAG
1 GTTTTCAAAACAAAG
27015 G
1 G
27016 AAATCTAAGC
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:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (15 bp):
GTTTTCAAAACAAAG
Found at i:33380 original size:25 final size:25
Alignment explanation
Indices: 33346--33397 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
33336 TCATTCCTGA
*
33346 TTTCGAAGTCTTTGGCCTCACTTTT
1 TTTCAAAGTCTTTGGCCTCACTTTT
33371 TTTCAAAGTCTTTGGCCTCACTTTT
1 TTTCAAAGTCTTTGGCCTCACTTTT
33396 TT
1 TT
33398 CTAGTTGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (25 bp):
TTTCAAAGTCTTTGGCCTCACTTTT
Found at i:40373 original size:25 final size:25
Alignment explanation
Indices: 40339--40390 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
40329 TCATTCCTGA
*
40339 TTTCGAAGTCTTTGGCCTCACTTTT
1 TTTCAAAGTCTTTGGCCTCACTTTT
40364 TTTCAAAGTCTTTGGCCTCACTTTT
1 TTTCAAAGTCTTTGGCCTCACTTTT
40389 TT
1 TT
40391 CTAGTTGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (25 bp):
TTTCAAAGTCTTTGGCCTCACTTTT
Found at i:43451 original size:13 final size:13
Alignment explanation
Indices: 43433--43459 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43423 ATCTATAGGA
43433 CCTTCATCCTCTT
1 CCTTCATCCTCTT
43446 CCTTCATCCTCTT
1 CCTTCATCCTCTT
43459 C
1 C
43460 TCCCCAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.44
Consensus pattern (13 bp):
CCTTCATCCTCTT
Found at i:48495 original size:229 final size:229
Alignment explanation
Indices: 48093--48551 Score: 765
Period size: 229 Copynumber: 2.0 Consensus size: 229
48083 ATCCACTTAC
48093 CATTGACGAGTTTGAAATGAGCCATTCGAAGAGATGAATCATCAATCTTATTTACTAGAGAAAAA
1 CATTGACGAGTTTGAAATGAGCCATTCGAAGAGATGAATCATCAATCTTATTTACTAGAGAAAAA
* * * * *
48158 TGAATAACTATGGAGCAATTTATATTCTCCTTGATAAAGATATGACTTAGGATGAAATTGTAGTA
66 TGAATAACTACGGAGCAATTTATATTCTCCTTAATAAAGACATGACTTAAGATGAAACTGTAGTA
* *
48223 AAATAAGGTGACCATATAGGTAAGACGGTTTTTGACGATGTAAACTAGGTAGATAAAAATTATCT
131 AAATAAGGTGACCATATAGGTAAGACGGTTATTGACAATGTAAACTAGGTAGATAAAAATTATCT
* *
48288 AAGCAAGATTAATGCATTGTCTAGTGCAGAAGCA
196 AAGCAAGATAAATGCATTGTCTAGTACAGAAGCA
**
48322 CATTGACGAGTTTGAAATGAGCCATTCGAAGAGATGAATCATCAATCTTATTTACTAGAGGGAAA
1 CATTGACGAGTTTGAAATGAGCCATTCGAAGAGATGAATCATCAATCTTATTTACTAGAGAAAAA
* * *
48387 TGAATATCTACGGATCAATTTATATTCTCCTTAATAAAGACATGACTTAAGATGCAACTGTAGTA
66 TGAATAACTACGGAGCAATTTATATTCTCCTTAATAAAGACATGACTTAAGATGAAACTGTAGTA
* *
48452 AAGTGAGGTGACCATATAGGTAAGACGGTTATTGACAATGTAAACTAGGTAGATAAAAATTATCT
131 AAATAAGGTGACCATATAGGTAAGACGGTTATTGACAATGTAAACTAGGTAGATAAAAATTATCT
*
48517 AAGCAAGATAAATGCATTGTCTAGTACGGAAGCA
196 AAGCAAGATAAATGCATTGTCTAGTACAGAAGCA
48551 C
1 C
48552 TAAATCCACA
Statistics
Matches: 213, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
229 213 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (229 bp):
CATTGACGAGTTTGAAATGAGCCATTCGAAGAGATGAATCATCAATCTTATTTACTAGAGAAAAA
TGAATAACTACGGAGCAATTTATATTCTCCTTAATAAAGACATGACTTAAGATGAAACTGTAGTA
AAATAAGGTGACCATATAGGTAAGACGGTTATTGACAATGTAAACTAGGTAGATAAAAATTATCT
AAGCAAGATAAATGCATTGTCTAGTACAGAAGCA
Found at i:49018 original size:20 final size:20
Alignment explanation
Indices: 48985--49029 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
48975 TCTTAGGGCA
**
48985 CATTTAGGTTCATATAGA-TG
1 CATTTAGGAGCATATA-ATTG
49005 CATTTAGGAGCATATAATTG
1 CATTTAGGAGCATATAATTG
49025 CATTT
1 CATTT
49030 GGTGGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (20 bp):
CATTTAGGAGCATATAATTG
Found at i:50273 original size:421 final size:421
Alignment explanation
Indices: 49482--50330 Score: 1324
Period size: 421 Copynumber: 2.0 Consensus size: 421
49472 AAAGGGGGGG
* *
49482 GGGTAAAAGTTTCCATTTTTTATTTTTAAATAATCTTGGTGGTAACCTGCATAGCCAATCTAAAG
1 GGGTAAAAGTTTCCATTTTTTATTTTTAAATAATCTTGGTGGTAAACTCCATAGCCAATCTAAAG
** * * *
49547 AGAGTGGCGTGCTATGCATCCGAGAGGAGCTAGCCACTAAGGTGACATTCATGGTGGTATGAGGA
66 AGAACGACATGCTATGCATCCGAGAAGAGCTAGCCACTAAGGTGACATTCATGGTGGTATGAGGA
* *
49612 GCTACTGGAAACTGGCATTGGGAGTTTTTCCTATACCCTTATGCTTTTATTTTTACTCGATTTAT
131 GCTACTCGAAACTGGCATTGGGAGTTTTTCCTATACCCTTATGCTTTTATTTTTACTAGATTTAT
* * * *
49677 TGGTTTATGTATAAACGATTATTCTCTTGAATATTTTGAACCCCATCATGAACTAAACTTTATTT
196 TGGGTTATATAGAAACGATTATTCTCTTGAATATTTTGAACCCCACCATGAACTAAACTTTATTT
* *
49742 GGTGTGGGTTCTCTTAGATGACTGAGTTTTTGTTTTAATGAATGATTTCAAATTTTATGTTTACC
261 GGTGTGGGTTCTCTTAGATGACTGAGTTTTTGTTTTAATGAACGATTTCAAATTTTATGTCTACC
* *
49807 TATTTCTTTTTCTAATTGTGCTTAATTACTTAAGATTGTAGGAGGCATGAAAGTGTCCATTTCTT
326 TATTTCTTTTTCTAATTGTGCTTAATTACTTAAGATGGCAGGAGGCATGAAAGTGTCCATTTCTT
49872 AAGTATATTACTTAGTTTTTGAGAGAAAATA
391 AAGTATATTACTTAGTTTTTGAGAGAAAATA
* * * * * *
49903 GGGTAAAATTTTCCATTTTTTCTTTTTACATATTCTTGGTTGTAAACTCCATAGCCAATCTAGAG
1 GGGTAAAAGTTTCCATTTTTTATTTTTAAATAATCTTGGTGGTAAACTCCATAGCCAATCTAAAG
* * * *
49968 AGAACGACATGCTATGCATCTGAGAAGAGCTAGCTAGTAAGGTGACATTCATGGTGGTCTGAGGA
66 AGAACGACATGCTATGCATCCGAGAAGAGCTAGCCACTAAGGTGACATTCATGGTGGTATGAGGA
*
50033 GCTAC-CGACAACTGGCATTGGGAGTTTTTTCTATACCCTTATGCTTTTATTTTTACTAGATTTA
131 GCTACTCGA-AACTGGCATTGGGAGTTTTTCCTATACCCTTATGCTTTTATTTTTACTAGATTTA
* *
50097 TTGGGTTGTATAGAAAGGATTATTCTCTTGAATATTTTGAA-CCCACCATGAACTAAACTTTATT
195 TTGGGTTATATAGAAACGATTATTCTCTTGAATATTTTGAACCCCACCATGAACTAAACTTTATT
* * * *
50161 TGGTGTGGGTTCTCTTGGATGATTGAGTTTTTTGTTTTAATTAACGATTTCAATTTTTATGTCTA
260 TGGTGTGGGTTCTCTTAGATGACTGAG-TTTTTGTTTTAATGAACGATTTCAAATTTTATGTCTA
* *
50226 CCTATTTGTTTTTCTCATTGTGCTTAATTACTTAAGATGGCAGGAGGCATGAAAGTGTCCATTTC
324 CCTATTTCTTTTTCTAATTGTGCTTAATTACTTAAGATGGCAGGAGGCATGAAAGTGTCCATTTC
*
50291 TTAAGTATATTACTTAGTTTTTGAGAGAAACTA
389 TTAAGTATATTACTTAGTTTTTGAGAGAAAATA
*
50324 GGTTAAA
1 GGGTAAA
50331 GATGCTTAGT
Statistics
Matches: 388, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
420 49 0.13
421 339 0.87
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (421 bp):
GGGTAAAAGTTTCCATTTTTTATTTTTAAATAATCTTGGTGGTAAACTCCATAGCCAATCTAAAG
AGAACGACATGCTATGCATCCGAGAAGAGCTAGCCACTAAGGTGACATTCATGGTGGTATGAGGA
GCTACTCGAAACTGGCATTGGGAGTTTTTCCTATACCCTTATGCTTTTATTTTTACTAGATTTAT
TGGGTTATATAGAAACGATTATTCTCTTGAATATTTTGAACCCCACCATGAACTAAACTTTATTT
GGTGTGGGTTCTCTTAGATGACTGAGTTTTTGTTTTAATGAACGATTTCAAATTTTATGTCTACC
TATTTCTTTTTCTAATTGTGCTTAATTACTTAAGATGGCAGGAGGCATGAAAGTGTCCATTTCTT
AAGTATATTACTTAGTTTTTGAGAGAAAATA
Done.