Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007188.1 Hibiscus syriacus cultivar Beakdansim tig00018934_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: 283786
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:247408 original size:21 final size:18
Alignment explanation
Indices: 247363--247396 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
247353 GTTTTTTTAT
247363 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
247380 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
247397 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:247516 original size:15 final size:17
Alignment explanation
Indices: 247490--247521 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
247480 TTCTATGGGA
247490 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
247506 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
247522 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:256741 original size:18 final size:18
Alignment explanation
Indices: 256718--256758 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
256708 AGGCATTTTA
* * *
256718 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGATTGT
256736 TCCTCTGCTCGTGATTGT
1 TCCTCTGCTCGTGATTGT
256754 TCCTC
1 TCCTC
256759 GTGTTGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.29, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGATTGT
Found at i:258414 original size:23 final size:22
Alignment explanation
Indices: 258332--258415 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
258322 AAGAACCTCC
* *
258332 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
* *
258353 AGGGAGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
258376 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
258398 AGGGGCGTATCGATTCCC
1 AGGGG-GAATCGATTCCC
258416 TCTACACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.32
22 6 0.11
23 30 0.57
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:262227 original size:22 final size:21
Alignment explanation
Indices: 262185--262224 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
262175 AAGACTGTTT
262185 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
262206 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
262225 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:263691 original size:19 final size:20
Alignment explanation
Indices: 263654--263692 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
263644 CGTTGATCAG
263654 GGGGGGAATCGGTACTCCCTT
1 GGGGGGAATCGGTA-TCCCTT
263675 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
263693 CCGAGCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGGTATCCCTT
Found at i:264330 original size:25 final size:24
Alignment explanation
Indices: 264290--264347 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
264280 AAAAGCCCAA
* *
264290 TGTATTAGTACATTTGTTGCACTCT
1 TGTATTAGTACATTTG-GGCACTCG
*
264315 TGTATTAGTATC-TTTGGGTACTCG
1 TGTATTAGTA-CATTTGGGCACTCG
264339 TGTATTAGT
1 TGTATTAGT
264348 GCAATTATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.48
25 14 0.48
26 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (24 bp):
TGTATTAGTACATTTGGGCACTCG
Found at i:264478 original size:25 final size:24
Alignment explanation
Indices: 264441--264495 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
264431 ATCCCATTGA
* *
264441 ATTAGTACATTTGTTGCACTCTTGT
1 ATTAGTACATTTG-GGCACTCGTGT
*
264466 ATTAGTATC-TTTGGGTACTCGTGT
1 ATTAGTA-CATTTGGGCACTCGTGT
264490 ATTAGT
1 ATTAGT
264496 GCAATTATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 14 0.54
25 11 0.42
26 1 0.04
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (24 bp):
ATTAGTACATTTGGGCACTCGTGT
Found at i:264541 original size:48 final size:48
Alignment explanation
Indices: 264489--264597 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
264479 GGTACTCGTG
** * *
264489 TATTAGTGCAATTATGCACTCCTGTATCAGTGTATTTGTCCACTCCTA
1 TATTAGTGCAATTATGCACTCCAATATCAGTGCATTCGTCCACTCCTA
* * * * * *
264537 TATTAGTACTAA-TGTGTACTCCAATATTAGTGCATTCGTGCACTCCTG
1 TATTAGTGC-AATTATGCACTCCAATATCAGTGCATTCGTCCACTCCTA
264585 TATTAGTGCAATT
1 TATTAGTGCAATT
264598 TGTACTATTG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
47 2 0.04
48 44 0.92
49 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (48 bp):
TATTAGTGCAATTATGCACTCCAATATCAGTGCATTCGTCCACTCCTA
Found at i:264758 original size:48 final size:48
Alignment explanation
Indices: 264506--264771 Score: 148
Period size: 48 Copynumber: 5.5 Consensus size: 48
264496 GCAATTATGC
* * * * * *
264506 ACTCCTGTATCAGTGTATTTGTCCACTCCTATATTAGTA-CTAATGTGT
1 ACTCTTGTATTAGTGCATTCGTGCACTCCTATATTAGTACCT-TTGTGT
*** * * **
264554 ACTCCAATATTAGTGCATTCGTGCACTCCTGTATTAGTGCAATT-TGT
1 ACTCTTGTATTAGTGCATTCGTGCACTCCTATATTAGTACCTTTGTGT
* * * * * * *
264601 ACTATTGGATTTAGAGCATCCGTGCACTCCTA-ATTCTATTACATTCGTGT
1 ACTCTTGTA-TTAGTGCATTCGTGCACTCCTATA-T-TAGTACCTTTGTGT
** * * * * * *
264651 ACTCGAGTATTAATGTATTTGTTGCACTCCTTTATTAGTGCC-TTGTTGC
1 ACTCTTGTATTAGTGCATTCG-TGCACTCCTATATTAGTACCTTTG-TGT
*
264700 ACT-TTAGTATTAGTGCATTCGTGCACTCCTATGTTAGTACCTTTGTGT
1 ACTCTT-GTATTAGTGCATTCGTGCACTCCTATATTAGTACCTTTGTGT
264748 ACTCTTGTATTTAGTAG-ATTCGTG
1 ACTCTTGTA-TTAGT-GCATTCGTG
264772 TACTTTTAGC
Statistics
Matches: 158, Mismatches: 47, Indels: 25
0.69 0.20 0.11
Matches are distributed among these distances:
47 8 0.05
48 79 0.50
49 51 0.32
50 19 0.12
51 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (48 bp):
ACTCTTGTATTAGTGCATTCGTGCACTCCTATATTAGTACCTTTGTGT
Found at i:267573 original size:24 final size:24
Alignment explanation
Indices: 267515--267578 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
267505 GCATAAAAGC
* * *
267515 ACTAACATAGGAGTACCCAAAGGT
1 ACTAATATAGTAGTGCCCAAAGGT
267539 ACTAATATAGTAGTGCCCAAAGGT
1 ACTAATATAGTAGTGCCCAAAGGT
267563 ACTAATATAGTAGTGC
1 ACTAATATAGTAGTGC
267579 AACAAATGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (24 bp):
ACTAATATAGTAGTGCCCAAAGGT
Found at i:271686 original size:22 final size:22
Alignment explanation
Indices: 271661--271704 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
271651 CCATTAGCTT
271661 TAAATTCAAATAT-CAAATAACA
1 TAAA-TCAAATATCCAAATAACA
**
271683 TAAATCAGGTATCCAAATAACA
1 TAAATCAAATATCCAAATAACA
271705 ATTCTCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (22 bp):
TAAATCAAATATCCAAATAACA
Found at i:273603 original size:184 final size:184
Alignment explanation
Indices: 273277--273664 Score: 604
Period size: 184 Copynumber: 2.1 Consensus size: 184
273267 TTTTCTAATT
* * * *
273277 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAATTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATATATAAT
273341 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
* * *
273406 GGATCTTAAATTATTAATTGAGTTTTAAATTGTTTGGGGTTAGCCCAAATGTTA
131 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
*
273460 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AATTTACAATTAATTT-AAATAATATATA
* * *
273524 ATTATAAAATAAAAAATTT-ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTACAAGTT
64 ATTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTT
* *
273587 ATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
128 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
273644 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
273665 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
183 13 0.07
184 142 0.76
185 25 0.13
186 8 0.04
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
Found at i:274978 original size:3 final size:3
Alignment explanation
Indices: 274970--275051 Score: 128
Period size: 3 Copynumber: 27.3 Consensus size: 3
274960 ATATTAATTG
* * *
274970 ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT ATA ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
275018 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
275052 AATATATTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:275060 original size:12 final size:11
Alignment explanation
Indices: 274960--275051 Score: 89
Period size: 12 Copynumber: 7.8 Consensus size: 11
274950 TTTTTTACCC
274960 ATATTAATTGATT
1 ATATT-ATT-ATT
274973 ATTATTATTATT
1 A-TATTATTATT
274985 ATA--ATTATT
1 ATATTATTATT
*
274994 ATTATTATTATA
1 A-TATTATTATT
275006 ATAATTATTATT
1 AT-ATTATTATT
275018 ATTATTATTATT
1 A-TATTATTATT
275030 ATCATTATTATT
1 AT-ATTATTATT
275042 ATTATTATTA
1 A-TATTATTA
275052 AATATATTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 17
0.78 0.02 0.19
Matches are distributed among these distances:
9 7 0.10
10 2 0.03
11 4 0.06
12 46 0.67
13 6 0.09
14 4 0.06
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (11 bp):
ATATTATTATT
Found at i:275201 original size:16 final size:16
Alignment explanation
Indices: 275178--275218 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
275168 CCTAATCCCT
275178 AGCCGCCTCTGCCTCCC
1 AGCCGCCTCTGCCT-CC
275195 A-CCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
275210 AGCCGCCTC
1 AGCCGCCTC
275219 AATGGTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.13
16 19 0.83
17 1 0.04
ACGTcount: A:0.07, C:0.59, G:0.17, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Done.