Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008563.1 Hibiscus syriacus cultivar Beakdansim tig00111473_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: 653500
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 3 of 3
Found at i:608629 original size:2 final size:2
Alignment explanation
Indices: 608622--608653 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
608612 AAGTCTTGTG
608622 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
608654 CGTACAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:609040 original size:13 final size:13
Alignment explanation
Indices: 609022--609062 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
609012 GAGTAAACTT
609022 TTTTATTTATTTA
1 TTTTATTTATTTA
609035 TTTTATTT-TTCTA
1 TTTTATTTATT-TA
609048 TTTTA--TATTTA
1 TTTTATTTATTTA
609059 TTTT
1 TTTT
609063 CTCTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.27
12 4 0.15
13 15 0.58
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:609052 original size:18 final size:20
Alignment explanation
Indices: 609031--609072 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
609021 TTTTTATTTA
609031 TTTAT-TTTATTTT-TCTAT
1 TTTATATTTATTTTCTCTAT
*
609049 TTTATATTTATTTTCTCTTT
1 TTTATATTTATTTTCTCTAT
609069 TTTA
1 TTTA
609073 AATGAGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATATTTATTTTCTCTAT
Found at i:637286 original size:44 final size:44
Alignment explanation
Indices: 637223--637309 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
637213 TGCATGCTTT
* *
637223 ATGCTATTTGTTCTAACTCAAGTGTCTAATGTTAGAACACCTTC
1 ATGCTATTTGTTCCAACTCAAGTGTATAATGTTAGAACACCTTC
637267 ATGCTATTTGTTCCAACTCAAGTGTATAATGTTAGAACACCTT
1 ATGCTATTTGTTCCAACTCAAGTGTATAATGTTAGAACACCTT
637310 GCTTTATCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (44 bp):
ATGCTATTTGTTCCAACTCAAGTGTATAATGTTAGAACACCTTC
Found at i:642093 original size:28 final size:26
Alignment explanation
Indices: 642062--642167 Score: 104
Period size: 28 Copynumber: 3.8 Consensus size: 26
642052 TATTATTTTT
* *
642062 AAAATATATAAATTTAAATTAAGATA
1 AAAAAATATATATTTAAATTAAGATA
* *
642088 AAAAAATATATTCTTTAAGTTAAGATA
1 AAAAAATATA-TATTTAAATTAAGATA
*
642115 ATAATAAATATATTTTTAAATTAAGATA
1 A-AA-AAATATATATTTAAATTAAGATA
*
642143 AAAATAATAGATATTTTAAAGTTAA
1 AAAA-AATATATA-TTTAAA-TTAA
642168 TATATGAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
26 10 0.15
27 22 0.33
28 23 0.35
29 11 0.17
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (26 bp):
AAAAAATATATATTTAAATTAAGATA
Found at i:642207 original size:60 final size:56
Alignment explanation
Indices: 642074--642209 Score: 154
Period size: 57 Copynumber: 2.4 Consensus size: 56
642064 AATATATAAA
*
642074 TTTAAATTAAGATAAAAA-AATATATTCTTTAAGTTAAGATAATAATAAATATATT
1 TTTAAATTAAGATAAAAATAATATATTCTTAAAGTTAAGATAATAATAAATATATT
* *
642129 TTTAAATTAAGATAAAAATAATAGATATT-TTAAAGTTAATAT-ATGAATAAA-ATTTT
1 TTTAAATTAAGATAAAAATAAT--ATATTCTTAAAGTTAAGATAAT-AATAAATATATT
642185 ATTTAATAAGTTAAGATAAAAATAA
1 -TTT-A-AA-TTAAGATAAAAATAA
642210 AATCTATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
55 18 0.26
56 9 0.13
57 20 0.29
58 6 0.09
59 2 0.03
60 15 0.21
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.39
Consensus pattern (56 bp):
TTTAAATTAAGATAAAAATAATATATTCTTAAAGTTAAGATAATAATAAATATATT
Found at i:642209 original size:31 final size:29
Alignment explanation
Indices: 642073--642227 Score: 126
Period size: 28 Copynumber: 5.3 Consensus size: 29
642063 AAATATATAA
*
642073 ATTTAAA-TTAAGATAAAAA-AATATATT
1 ATTTAAAGTTAAGATAAAAATAAAATATT
* *
642100 CTTT-AAGTTAAGATAATAATAAATATATT
1 ATTTAAAGTTAAGATAAAAATAAA-ATATT
642129 -TTTAAA-TTAAGATAAAAATAATAGATA-T
1 ATTTAAAGTTAAGATAAAAATAA-A-ATATT
* ** *
642157 -TTTAAAGTTAATATATGAATAAAATTTT
1 ATTTAAAGTTAAGATAAAAATAAAATATT
642185 ATTTAATAAGTTAAGATAAAAATAAAATCTATT
1 ATTT-A-AAGTTAAGATAAAAATAAAA--TATT
*
642218 TTTTAAAGTT
1 ATTTAAAGTT
642228 CAAATATATA
Statistics
Matches: 102, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.02
27 16 0.16
28 28 0.27
29 26 0.25
30 1 0.01
31 22 0.22
32 1 0.01
33 6 0.06
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (29 bp):
ATTTAAAGTTAAGATAAAAATAAAATATT
Found at i:644034 original size:19 final size:21
Alignment explanation
Indices: 643999--644040 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
643989 TGAGGAAGAG
*
643999 AATATTTTTGAAGGAGA-GAA
1 AATATTTTTCAAGGAGATGAA
644019 AATATTTTTCAA-GAGATGAA
1 AATATTTTTCAAGGAGATGAA
644039 AA
1 AA
644041 GTTCTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (21 bp):
AATATTTTTCAAGGAGATGAA
Found at i:644514 original size:190 final size:189
Alignment explanation
Indices: 644154--644564 Score: 553
Period size: 190 Copynumber: 2.2 Consensus size: 189
644144 TCAAATAGAT
* * *
644154 AATAATATATTTTAATTTGAAAT-GTTCAAAAGATAAATATCCTTTTGCAATTCAAACTTAAATA
1 AATAATATA-TTTAATTTGCAATAGTT-AAAAGATAAATATCCTTTTACAATTCAAACTTAAACA
* * * * * *
644218 GGTATTATTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGCTATAAATAT
64 GATATTATTTAATTTGAAACATACAAAAATATATAATTATCTTTAATATTCAAAACTAAAAAGAT
* *
644283 AACAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTTATATTCAAATTA
129 AACAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATCCAAATTA
* *
644344 AATAATATATTTAATTTGCAATAGTTAAAAGATAAA-CTCCTTTTACTATTCAAACTTAAACA-A
1 AATAATATATTTAATTTGCAATAGTTAAAAGATAAATATCCTTTTACAATTCAAACTTAAACAGA
*
644407 TATTATTTTTAATTTGAAACATACAAAAATATATAATTATCTTTTAATGA-TCAAAATTAAAAAG
66 TATTA--TTTAATTTGAAACATACAAAAATATATAATTATC-TTTAAT-ATTCAAAACTAAAAAG
* *
644471 ATAACAAATATCTTTTTAAATTGACTTATTAAAAGAGTAATTATCCTACTAATATCCAAATTA
127 ATAACAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATCCAAATTA
* *
644534 AA-AATTATCTTTTAATTTGCAATAGTAAAAA
1 AATAA-TAT-ATTTAATTTGCAATAGTTAAAA
644565 AGAATATAAA
Statistics
Matches: 196, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
187 5 0.03
188 22 0.11
189 56 0.29
190 92 0.47
191 21 0.11
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (189 bp):
AATAATATATTTAATTTGCAATAGTTAAAAGATAAATATCCTTTTACAATTCAAACTTAAACAGA
TATTATTTAATTTGAAACATACAAAAATATATAATTATCTTTAATATTCAAAACTAAAAAGATAA
CAAATACCTTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATCCAAATTA
Found at i:647215 original size:52 final size:52
Alignment explanation
Indices: 647153--647258 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
647143 GTAAAGGACC
**
647153 AAACGCACTTAATTAAAAAATCGGTAACCAAAGTTGATCAAACCGAAAACAA
1 AAACGCACTTAATTAAAAAATAAGTAACCAAAGTTGATCAAACCGAAAACAA
*
647205 AAACGCACTTAATTAAAAAATAAGTAATCAAAGTTGATCAAACCGAAAACAA
1 AAACGCACTTAATTAAAAAATAAGTAACCAAAGTTGATCAAACCGAAAACAA
647257 AA
1 AA
647259 GGGACTAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.18
Consensus pattern (52 bp):
AAACGCACTTAATTAAAAAATAAGTAACCAAAGTTGATCAAACCGAAAACAA
Found at i:651338 original size:27 final size:28
Alignment explanation
Indices: 651287--651344 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
651277 TCACATTGCT
*
651287 TAACAAAAAAATTGATGTCGATGTTTGA
1 TAACAAAAAAATTGATGTCGATGTTTAA
*
651315 TAACAAAAAAA-TGATTTC-ATTGTTTAA
1 TAACAAAAAAATTGATGTCGA-TGTTTAA
651342 TAA
1 TAA
651345 TTAAAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 15 0.56
28 11 0.41
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (28 bp):
TAACAAAAAAATTGATGTCGATGTTTAA
Found at i:653387 original size:24 final size:24
Alignment explanation
Indices: 653355--653412 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
653345 GTTTACAAAA
653355 GAATACTCATTTTCCTTAAAGTTC
1 GAATACTCATTTTCCTTAAAGTTC
653379 GAATACTCATTTTCCTTAAAGTTC
1 GAATACTCATTTTCCTTAAAGTTC
653403 GAATACTCAT
1 GAATACTCAT
653413 GTGTAAAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (24 bp):
GAATACTCATTTTCCTTAAAGTTC
Done.