Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008538.1 Hibiscus syriacus cultivar Beakdansim tig00111425_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: 61064
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:130 original size:17 final size:15
Alignment explanation
Indices: 84--133 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
74 TATCATTTTG
84 TTATA-TATTATATA
1 TTATATTATTATATA
*
98 TTATTTTAATTTATATA
1 TTATATT-A-TTATATA
115 TTAATATTATTA-ATA
1 TT-ATATTATTATATA
130 TTAT
1 TTAT
134 TTCTTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.20
15 6 0.20
16 4 0.13
17 10 0.33
18 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:1248 original size:2 final size:2
Alignment explanation
Indices: 1226--1291 Score: 93
Period size: 2 Copynumber: 33.5 Consensus size: 2
1216 ATGTATTATT
1226 TA TA CTA TA GTA TA TA T- 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 TA TA TA TA TA TA
1269 TA TA TA TA TA TA T- TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1292 TTTTTTTCTC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.05
2 52 0.88
3 4 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1413 original size:2 final size:2
Alignment explanation
Indices: 1406--1459 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
1396 ATTTATTTAT
*
1406 TA TA TA TA T- TA T- TA TA T- TT TA TA TA TA -A 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
1444 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
1460 TACTTATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1419 original size:12 final size:12
Alignment explanation
Indices: 1402--1469 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
1392 CTTTATTTAT
1402 TTATTATATATA
1 TTATTATATATA
1414 TTATTATAT-T-
1 TTATTATATATA
1424 TTA-TATATAATA
1 TTATTATAT-ATA
1436 TATATATATATATA
1 T-TAT-TATATATA
*
1450 TATATAATAT-TA
1 T-TATTATATATA
1462 CTTATTAT
1 -TTATTAT
1470 TTTTTTTCGT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
9 5 0.11
10 3 0.06
11 2 0.04
12 17 0.36
13 7 0.15
14 8 0.17
15 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (12 bp):
TTATTATATATA
Found at i:1427 original size:19 final size:21
Alignment explanation
Indices: 1405--1459 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1395 TATTTATTTA
1405 TTATATATATTAT-TATAT-T
1 TTATATATATTATATATATAT
*
1424 TTATATATAATATATATATAT
1 TTATATATATTATATATATAT
* *
1445 ATATATATATAATAT
1 TTATATATATTATAT
1460 TACTTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATATATTATATATATAT
Found at i:13621 original size:105 final size:105
Alignment explanation
Indices: 12958--13613 Score: 1034
Period size: 105 Copynumber: 6.4 Consensus size: 105
12948 AGGTTTTACC
* *
12958 CAGAGTCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
13023 ACGAAGGGACCGCTGATTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * *
13056 CAGGGCCAATTTCAACTTCACAACGAAGGAAATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
13121 ACGAAGGGACCGCTGGTTGTCAATAAACAATT-TC--A--
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
13156 -AG-GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
13219 ACGAAGGGACCGCTGGTTATCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
13259 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
13324 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
13364 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
13429 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * ** * *
13469 TAGAGCCAATCTCAACTTCACAACGAAGGATATCAGACTCCAGACAATGCAAGTTCAACTTTACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
13534 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
13574 TAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
13614 GGGACAATAC
Statistics
Matches: 521, Mismatches: 24, Indels: 19
0.92 0.04 0.03
Matches are distributed among these distances:
98 170 0.33
99 6 0.01
100 1 0.00
101 1 0.00
104 3 0.01
105 340 0.65
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:14131 original size:13 final size:13
Alignment explanation
Indices: 14113--14151 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
14103 TATCATTTTG
14113 TTATATTATATAA
1 TTATATTATATAA
*
14126 TTATATTGTATAA
1 TTATATTATATAA
14139 TTATA-TATATAA
1 TTATATTATATAA
14151 T
1 T
14152 ATTATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (13 bp):
TTATATTATATAA
Found at i:14134 original size:21 final size:22
Alignment explanation
Indices: 14110--14165 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
14100 TTTTATCATT
*
14110 TTGTTATATTATATA-ATTATA
1 TTGTTATATTATATATATAATA
14131 TTG-TATAATTATATATATAATA
1 TTGTTAT-ATTATATATATAATA
*
14153 TTATTAATATTAT
1 TTGTT-ATATTAT
14166 TTCTTTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 11 0.38
22 7 0.24
23 6 0.21
24 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TTGTTATATTATATATATAATA
Found at i:15379 original size:17 final size:18
Alignment explanation
Indices: 15348--15390 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
15338 TCTTGTTCTT
15348 TATATATTTCATTC-TATTG
1 TATATATTT-ATTCTTA-TG
15367 TATATATTT-TTCTTATG
1 TATATATTTATTCTTATG
15384 TATATAT
1 TATATAT
15391 ATACGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.52
18 2 0.09
19 9 0.39
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATATTTATTCTTATG
Found at i:15532 original size:2 final size:2
Alignment explanation
Indices: 15449--15512 Score: 87
Period size: 2 Copynumber: 31.5 Consensus size: 2
15439 TTTATTTATT
15449 TA TA CTA TA GTA TA T- 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 TA TA TA TA TA TA
15492 TA TA TA TA TA TA CT- TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA T
15513 TTTTTTCGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.04
2 50 0.88
3 5 0.09
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19260 original size:29 final size:28
Alignment explanation
Indices: 19209--19267 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
19199 CAGTCTATTA
* *
19209 AAATGTTCAAAGGTAGACTGAGTTGGTGG
1 AAATGTTCAAAGATAGACCGAGTT-GTGG
*
19238 AAATGTTCAAAGATTGACCGAGTTGTGG
1 AAATGTTCAAAGATAGACCGAGTTGTGG
19266 AA
1 AA
19268 GGATGTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.27
Consensus pattern (28 bp):
AAATGTTCAAAGATAGACCGAGTTGTGG
Found at i:23297 original size:32 final size:32
Alignment explanation
Indices: 23255--23343 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
23245 AATGTTTTTT
23255 TATAT-TAACATTTATTTGAACATAATATCTAA
1 TATATATAACATTTATTTGAACATAATAT-TAA
* * **
23287 TA-ATATAACATTTATTCGAACATGATATTTT
1 TATATATAACATTTATTTGAACATAATATTAA
* *
23318 TATATATAATATTTATTTGAATATAA
1 TATATATAACATTTATTTGAACATAA
23344 CTTCTATAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 5 0.11
32 42 0.89
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATATAACATTTATTTGAACATAATATTAA
Found at i:32913 original size:2 final size:2
Alignment explanation
Indices: 32906--32936 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32896 AAATATTCTA
*
32906 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32937 AAATGATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58242 original size:22 final size:21
Alignment explanation
Indices: 58217--58259 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
58207 AACCGACCGA
58217 ACCGAATTAATTCGGTTCGGTT
1 ACCGAATTAATTCGG-TCGGTT
*
58239 ACCGAATTAGTTCGGTCGGTT
1 ACCGAATTAATTCGGTCGGTT
58260 TAAGGTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
ACCGAATTAATTCGGTCGGTT
Found at i:58656 original size:175 final size:174
Alignment explanation
Indices: 58337--58696 Score: 562
Period size: 174 Copynumber: 2.0 Consensus size: 174
58327 ATTAAATTTT
* *
58337 AAATATTAAATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAAAATTT
1 AAATATTAAATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAAAATTT
*
58402 AAGATCCAATAACTTTTAAACTTAAATCAATATTAATAATTAAAAAATTATATAAATTTTTTATT
66 AAGATCCAATAACTTTTAAACTTAAATCAATATTAATAATTAAAAAATTATATAAAATTTTTATT
58467 TTATAATATATATTTAAATTATTTGTAAATGTTTTTAATTAAAA
131 TTATAATATATATTTAAATTATTTGTAAATGTTTTTAATTAAAA
58511 AAATATTAAATATTATATATAACATATGAGCT-AAGCCCAAACCATTTAAAACCCAATTAATAAT
1 AAATATTAAATATTATATATAACATATGAGCTCAA-CCCAAACCATTTAAAACCCAATTAA-AAT
* *
58575 TTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTATCTAAAATTTTT
64 TTAAGATCCAATAACTTTTAAACTTAAATCAATATTAA-TAATTAAAAAATTATATAAAATTTTT
* * * *
58640 ATTTTATAATTATATTTATTAAATTAATTATAAACTTTTTTTGAATT-AAA
128 ATTTTATAA-TATATAT-TTAAATTATTTGTAAA-TGTTTTT-AATTAAAA
58690 AAATATT
1 AAATATT
58697 TATTTTATAT
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
173 2 0.01
174 55 0.32
175 41 0.24
176 32 0.19
177 6 0.04
178 14 0.08
179 16 0.09
180 4 0.02
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (174 bp):
AAATATTAAATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAAAATTT
AAGATCCAATAACTTTTAAACTTAAATCAATATTAATAATTAAAAAATTATATAAAATTTTTATT
TTATAATATATATTTAAATTATTTGTAAATGTTTTTAATTAAAA
Found at i:58849 original size:15 final size:15
Alignment explanation
Indices: 58829--58857 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58819 AAAAAAAATT
58829 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
58844 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
58858 CGGTCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Done.