Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009615.1 Hibiscus syriacus cultivar Beakdansim tig00117001_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: 259590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:220126 original size:422 final size:418
Alignment explanation
Indices: 219619--220499 Score: 1556
Period size: 422 Copynumber: 2.1 Consensus size: 418
219609 ACCAGACCCG
* *
219619 ACCCGACCCGACTCGAAATAATAAACAAAA-A---TTATTTAATAAAAACAGTGAATTAATCCGA
1 ACCCGACCCAACCCGAAATAATAAA-AAAATATTTTTATTTAATAAAAACAGTGAATTAATCCGA
* *
219680 CCCGACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTGAACCCGACCCGAAT
65 ACCGACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTGAACCCGACCCAAAT
* ** *
219745 ATTACACTTAAAAAACCTGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATAT
130 ATTACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAAATTCATCAGACCCGACCCGAATAT
219810 ATGAATTAGAAATCAAACCCGACCCGACCCGAAATAATAAAAAATTATATTTATTTAAGTGACTT
195 ATGAATTAGAAATCAAACCCGACCCGACCCGAAATAATAAAAAATTATATTTATTTAAGTGACTT
*
219875 AATCCAATCCGACCTGAATTATATATATTTTCGGGTCGGTCCG-TTTTTTTCACCCTAAACCCGA
260 AATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGTTTTTTTTCACCCTAAACCCGA
*
219939 CCCGACCCGAATATCACACTTAAAAAAACCCGATCTGACCCGACCAAAATAAAGTTTCACCCGAC
325 CCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTTT----C-AC
220004 CCGACCCGACCCGACCCGAATATATGAATTAGAA
385 CCGACCCGACCCGACCCGAATATATGAATTAGAA
*
220038 ACCCGACCCAACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGAATTAATCCGAA
1 ACCCGACCCAACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGAATTAATCCGAA
220103 CCGACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTGAACCCGACCCAAATA
66 CCGACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTGAACCCGACCCAAATA
220168 TTACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAAATTCATCAGACCCGACCCGAATATA
131 TTACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAAATTCATCAGACCCGACCCGAATATA
*
220233 TGAATTATAAATCAAACCCGACCCGACCCGAAATAATAAAAAATTATATTTATTTAAGTGACTTA
196 TGAATTAGAAATCAAACCCGACCCGACCCGAAATAATAAAAAATTATATTTATTTAAGTGACTTA
220298 ATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGTTTTTTTTCACCCTAAACCCGAC
261 ATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGTTTTTTTTCACCCTAAACCCGAC
220363 CCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTTTCACCCGACC
326 CCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTTTCACCCGACC
220428 CGACCCGACCCGAATATATGAATTAGAA
391 CGACCCGACCCGAATATATGAATTAGAA
*
220456 ACCCGACCCAACCCGAAATAATAAAAAAATATTTTTATTCAATA
1 ACCCGACCCAACCCGAAATAATAAAAAAATATTTTTATTTAATA
220500 TATAAATAAG
Statistics
Matches: 443, Mismatches: 14, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
418 81 0.18
419 25 0.06
422 260 0.59
423 77 0.17
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (418 bp):
ACCCGACCCAACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGAATTAATCCGAA
CCGACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTGAACCCGACCCAAATA
TTACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAAATTCATCAGACCCGACCCGAATATA
TGAATTAGAAATCAAACCCGACCCGACCCGAAATAATAAAAAATTATATTTATTTAAGTGACTTA
ATCCAACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGTTTTTTTTCACCCTAAACCCGAC
CCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTTTCACCCGACC
CGACCCGACCCGAATATATGAATTAGAA
Found at i:223251 original size:2 final size:2
Alignment explanation
Indices: 223244--223273 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
223234 ATAGCAAACC
223244 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
223274 CCGCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:226363 original size:2 final size:2
Alignment explanation
Indices: 226356--226394 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
226346 ATAATTGCTT
226356 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
226395 TACTGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:230331 original size:30 final size:30
Alignment explanation
Indices: 230295--230361 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
230285 ATAAAGTATG
* *
230295 CAAAAGTTCAAGGACCAAAAGGGTAATTTT
1 CAAAAGTTCAAGGACCAAAACGATAATTTT
* *
230325 CAAAAGTTTAAGGACCAAAACTATAATTTT
1 CAAAAGTTCAAGGACCAAAACGATAATTTT
230355 CAAAAGT
1 CAAAAGT
230362 CATGTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (30 bp):
CAAAAGTTCAAGGACCAAAACGATAATTTT
Found at i:231555 original size:19 final size:21
Alignment explanation
Indices: 231522--231560 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
231512 TAGAAATTAA
*
231522 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
231542 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
231561 ACTATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:233348 original size:24 final size:23
Alignment explanation
Indices: 233307--233372 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
233297 ACGCAAGTGA
233307 AAATAAATAAAAACATTACAAACT
1 AAATAAATAAAAACATTA-AAACT
*
233331 AAAT-AATAAAATCAATTAAAAC-
1 AAATAAATAAAAAC-ATTAAAACT
* * *
233353 AATTGAATAGAAACATTAAA
1 AAATAAATAAAAACATTAAA
233373 TACAAATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 9 0.25
23 19 0.53
24 8 0.22
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.23
Consensus pattern (23 bp):
AAATAAATAAAAACATTAAAACT
Found at i:233938 original size:21 final size:21
Alignment explanation
Indices: 233887--233940 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
233877 GTGGTAATGG
233887 CATCTGAACCGATTGCAGTGA
1 CATCTGAACCGATTGCAGTGA
** * * * *
233908 TGTTTAAACCGATTGCGGTGC
1 CATCTGAACCGATTGCAGTGA
233929 CATCTGAACCGA
1 CATCTGAACCGA
233941 CAATGTACCT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (21 bp):
CATCTGAACCGATTGCAGTGA
Found at i:235793 original size:64 final size:65
Alignment explanation
Indices: 235724--235884 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 65
235714 GTGCACTAAG
* *
235724 TGTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCC-TGAGTGCATCGATGCATGGT
1 TGTGCATCGATACATAAAATGCATTCGATGTTTTCATAAAA-CCTTGAGTGCATCGATGCATGGT
235787 -
65 A
*
235787 TGGTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGT
1 T-GTGCATCGATACATAAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGT
235852 A
65 A
* * *
235853 TATGCATCGATTCATGAAATGCATTCGATGTT
1 TGTGCATCGATACATAAAATGCATTCGATGTT
235885 CAATTTATTC
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 1 0.01
64 34 0.39
65 52 0.59
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (65 bp):
TGTGCATCGATACATAAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTA
Found at i:235924 original size:65 final size:64
Alignment explanation
Indices: 235725--235934 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 64
235715 TGCACTAAGT
* * *
235725 GTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCC-TGAGTGCATCGATGCATGGTT
1 GTGCATCGATACATCAAATGCATTCGATG-TTTCATAAAA-CCATGAGTGCATCGATGCATGGTT
235788 G
64 G
*
235789 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATACATCAAATGCATTCGATG-TTTCATAAAACCATGAGTGCATCGATGCATGGT-T
235854 -
64 G
* * * * **
235854 ATGCATCGATTCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATACATCAAATGCATTCGATGTTTC-A-TAAAACCATGAGTGCATCGATGCATGG-T
235917 TG
63 TG
*
235919 GTGCATCGGTACATCA
1 GTGCATCGATACATCA
235935 CTTTGAAAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 52 0.42
65 69 0.55
66 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATACATCAAATGCATTCGATGTTTCATAAAACCATGAGTGCATCGATGCATGGTTG
Found at i:241926 original size:20 final size:20
Alignment explanation
Indices: 241891--241931 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
241881 TTTGATCATG
*
241891 ATATTTCCATATGCATGTAT
1 ATATTTCCATATGCATATAT
241911 ATATTT-CATATGGCATATAT
1 ATATTTCCATAT-GCATATAT
241931 A
1 A
241932 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
ATATTTCCATATGCATATAT
Found at i:245850 original size:17 final size:17
Alignment explanation
Indices: 245830--245872 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
245820 ACCGTTGGAA
245830 CACTTAGTGCATTGGTG
1 CACTTAGTGCATTGGTG
245847 CACTTAGTGCATTGGTG
1 CACTTAGTGCATTGGTG
*
245864 CACTAAGTG
1 CACTTAGTG
245873 TGCATCGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (17 bp):
CACTTAGTGCATTGGTG
Found at i:247749 original size:21 final size:21
Alignment explanation
Indices: 247725--247777 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
247715 AAGAAATATT
* *
247725 CATTTTAAGTAGCAAAATTAA
1 CATTTTAAGTAGAAAAAATAA
*
247746 CATTTCTGA-TA-AAAAAATAA
1 CATTT-TAAGTAGAAAAAATAA
247766 CATTTTAAGTAG
1 CATTTTAAGTAG
247778 TGTTCTATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 2 0.08
20 14 0.56
21 7 0.28
22 2 0.08
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (21 bp):
CATTTTAAGTAGAAAAAATAA
Found at i:250791 original size:20 final size:20
Alignment explanation
Indices: 250766--250816 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
250756 CACAGAATGT
250766 AAGATTACCAGTGAAAATAA
1 AAGATTACCAGTGAAAATAA
*
250786 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAAAATAA
*
250806 AAGATTGCCAG
1 AAGATTACCAG
250817 GGAATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGAAAATAA
Found at i:253085 original size:46 final size:46
Alignment explanation
Indices: 253018--253109 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
253008 CCTTTTACTC
253018 CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
1 CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
253064 CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
1 CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
253110 TCTCAAAGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (46 bp):
CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
Found at i:256460 original size:29 final size:29
Alignment explanation
Indices: 256399--256532 Score: 115
Period size: 29 Copynumber: 4.5 Consensus size: 29
256389 GCACAACCCA
* * ***
256399 AGGTCGCCAAGCACTCCAAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTTGT
256428 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTTGT
** * * *
256457 AGGTCGCCAAACAATCCCGGCGACCAAGATGGT
1 AGGTCGCCATGCACTCCCAGCGACC----TTGT
* * *
256490 AGGTCGCCATGTACGCCCAGCGACCTTAT
1 AGGTCGCCATGCACTCCCAGCGACCTTGT
256519 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
256533 GCCGGCGTCC
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
29 60 0.73
33 22 0.27
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.16
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTTGT
Found at i:256727 original size:13 final size:13
Alignment explanation
Indices: 256713--256758 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
256703 TGCAAAGTGT
*
256713 CATAGCTTCGTGT
1 CATAGCTTCGTGC
256726 CATAGCTTCGTGC
1 CATAGCTTCGTGC
* *
256739 CCTAGCTTCGAGC
1 CATAGCTTCGTGC
256752 CATAGCT
1 CATAGCT
256759 GCTCCCTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.30
Consensus pattern (13 bp):
CATAGCTTCGTGC
Found at i:257200 original size:21 final size:21
Alignment explanation
Indices: 257175--257218 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
257165 AATTTAGTTA
257175 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
257196 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
257217 AT
1 AT
257219 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:257232 original size:28 final size:29
Alignment explanation
Indices: 257195--257251 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
257185 TAGTATAAAT
*
257195 TATTAGTTTGTTAGTTTAAGT-TATATTA
1 TATTAATTTGTTAGTTTAAGTATATATTA
257223 TATTAATTTGTTAGTTTAAGTATATATTA
1 TATTAATTTGTTAGTTTAAGTATATATTA
257252 GATATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (29 bp):
TATTAATTTGTTAGTTTAAGTATATATTA
Done.