Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008543.1 Hibiscus syriacus cultivar Beakdansim tig00111432_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: 282078
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 3 of 3
Found at i:262018 original size:60 final size:60
Alignment explanation
Indices: 261887--262024 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
261877 GCGCTTTGAA
* * * *
261887 AATCGCATTGCGATAGTCAGCATCTCGTTGCTATAGTCAGAATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCACGTTGCGATAGTCAGAATCGCATTGCGATAGTCAG
* * * * *
261947 AATCTCGTTGCGATAGTCAGAATCACGTTGCGATAGTCATAATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCACGTTGCGATAGTCAGAATCGCATTGCGATAGT-CAG
*
262007 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
262025 GGAAAATCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 64 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCACGTTGCGATAGTCAGAATCGCATTGCGATAGTCAG
Found at i:263654 original size:3 final size:3
Alignment explanation
Indices: 263646--263682 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
263636 CGTTTGTTAA
263646 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
263683 TACATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:264074 original size:21 final size:20
Alignment explanation
Indices: 264050--264089 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
264040 TCTAATCATG
*
264050 CCATAAAACAAAGAGAGATCA
1 CCATAAAAAAAAGAG-GATCA
264071 CCATAAAAAAAAGAGGATC
1 CCATAAAAAAAAGAGGATC
264090 GAAGGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.17, G:0.15, T:0.10
Consensus pattern (20 bp):
CCATAAAAAAAAGAGGATCA
Found at i:265133 original size:30 final size:30
Alignment explanation
Indices: 265044--265145 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
265034 CTTAACTTTA
* * *
265044 TTTTTATTATTTTATTCCTTTAACTTTCTA
1 TTTTTATTATTTTAGTCCTTTAAATTTCTG
*
265074 TTTTTATTATTTTAGTCATTTAAATTTCTG
1 TTTTTATTATTTTAGTCCTTTAAATTTCTG
* * *
265104 TTTTTGTTGTTTTAGTCCTGTAAATTTCTG
1 TTTTTATTATTTTAGTCCTTTAAATTTCTG
* *
265134 TTATTACTATTT
1 TTTTTATTATTT
265146 ATTCCCTTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.64
Consensus pattern (30 bp):
TTTTTATTATTTTAGTCCTTTAAATTTCTG
Found at i:268513 original size:21 final size:21
Alignment explanation
Indices: 268484--268536 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
268474 ATTCTGACTA
268484 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
268505 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
268526 TCGCAATGCGA
1 TCGCATTGCGA
268537 ATACATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:268572 original size:41 final size:40
Alignment explanation
Indices: 268526--268619 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
268516 TTTTCCTAAT
*
268526 TCGCAATGCGAATACATAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACATAAATCGCAACGCGAATAT-GAAAA
* * * *
268567 TCGCAATGCGATTACGTAAATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACATAAATCGCAACGCGAATATGAAAA
268607 TCGCAATGCGAAT
1 TCGCAATGCGAAT
268620 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 16 0.34
41 31 0.66
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACATAAATCGCAACGCGAATATGAAAA
Found at i:268599 original size:61 final size:60
Alignment explanation
Indices: 268526--268639 Score: 165
Period size: 61 Copynumber: 1.9 Consensus size: 60
268516 TTTTCCTAAT
*
268526 TCGCAATGCGAATACATAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACATAAATCGCAACGCGAATCT-GAAAATCGCAATGCGATTACGTAAA
** * **
268587 TCGCAATGCGAATATGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACATAAATCGCAACGCGAATCTGAAAATCGCAATGCGATT
268640 TACATAGCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 16 0.34
61 31 0.66
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (60 bp):
TCGCAATGCGAATACATAAATCGCAACGCGAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:268629 original size:20 final size:20
Alignment explanation
Indices: 268526--268637 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
268516 TTTTCCTAAT
**
268526 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATATGTAAA
* * *
268546 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATAT-GTAAA
* *
268567 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATATGTAAA
268587 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
* *
268607 TCGCAATGCGAATCTG-ACTA
1 TCGCAATGCGAATATGTA-AA
268627 TCGCAATGCGA
1 TCGCAATGCGA
268638 TTTACATAGC
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 61 0.80
21 14 0.18
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:268846 original size:22 final size:22
Alignment explanation
Indices: 268820--268881 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
268810 ACATCCGTCC
268820 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
* *
268842 TCATCTCCGACGATATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
*
268864 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
268882 TTCACGGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:269294 original size:20 final size:20
Alignment explanation
Indices: 269251--269314 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
269241 CGATTCTTGC
** *
269251 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
*
269271 GTTGCGATAGTCATTTTCTT
1 GTTGCGATAGTCATTTTCGT
**
269291 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
269311 GTTG
1 GTTG
269315 TGATTTAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:269319 original size:20 final size:20
Alignment explanation
Indices: 269266--269320 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
269256 GATAGTCAAA
* **
269266 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
269286 TTCTTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
269306 TTCGTGTTGTGATTT
1 TTCGTGTTGCGATTT
269321 AAAGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.15, G:0.22, T:0.53
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:271223 original size:20 final size:20
Alignment explanation
Indices: 271196--271247 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
271186 AGAATAGTTT
* *
271196 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATA
*
271216 ATTATCGCAACGCGAAAATA
1 ACTATCGCAACGCGAAAATA
271236 ACTATCGCAACG
1 ACTATCGCAACG
271248 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATA
Found at i:271325 original size:20 final size:20
Alignment explanation
Indices: 271300--271370 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
271290 CAATGCGAAA
*
271300 TTTCGCATTGTGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
271320 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
*
271340 TTTCGCGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
*
271360 TTTCGCGTTGC
1 TTTCGCATTGC
271371 AATTTTAAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
TTTCGCATTGCGATAGTCAT
Found at i:271897 original size:18 final size:19
Alignment explanation
Indices: 271858--271899 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
271848 CTCACCTGTC
271858 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
271879 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
271897 ATC
1 ATC
271900 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:273545 original size:33 final size:34
Alignment explanation
Indices: 273508--273579 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
273498 ATGACTATCG
*
273508 CAACGAGAGAATCGTAATGCG-AAATGAAAATCA
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCA
* *
273541 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCA
273575 CAACG
1 CAACG
273580 CGAAACTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
CAACGAGAGAATCGCAATGCGAAAATGAAAATCA
Found at i:273660 original size:20 final size:19
Alignment explanation
Indices: 273588--273726 Score: 111
Period size: 20 Copynumber: 7.1 Consensus size: 19
273578 CGCGAAACTA
**
273588 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATAGTC
*
273607 ATTTTCGCATTGCGATTCACTC
1 A-TTTCGCATTGCGA-T-AGTC
*
273629 ATGTCG--TTGCGATAGTC
1 ATTTCGCATTGCGATAGTC
273646 ATTTCCGCATTGCGATAGTC
1 ATTT-CGCATTGCGATAGTC
* *
273666 AATTCCGCGTTGCGATAGTC
1 -ATTTCGCATTGCGATAGTC
**
273686 ATTTCTGTGTTGCGATAGTC
1 ATTTC-GCATTGCGATAGTC
* *
273706 ATATTCGCGTTGCGATTGTC
1 AT-TTCGCATTGCGATAGTC
273726 A
1 A
273727 AATGAATGTC
Statistics
Matches: 100, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
17 6 0.06
18 3 0.03
19 11 0.11
20 66 0.66
21 11 0.11
22 3 0.03
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTC
Found at i:273688 original size:40 final size:40
Alignment explanation
Indices: 273633--273726 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
273623 TCACTCATGT
273633 CGTTGCGATAGTCATTTCCGCATTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCCGCATTGCGATAGTCATATT-CG
* **
273673 CGTTGCGATAGTCATTTCTGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGCATTGCGATAGTCATATTCG
*
273713 CGTTGCGATTGTCA
1 CGTTGCGATAGTCA
273727 AATGAATGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 46 0.94
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCATTGCGATAGTCATATTCG
Found at i:276558 original size:12 final size:13
Alignment explanation
Indices: 276541--276569 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
276531 ATTTGTTTAA
276541 GAAATT-ATTTTT
1 GAAATTGATTTTT
276553 GAAATTGATTTTT
1 GAAATTGATTTTT
276566 GAAA
1 GAAA
276570 AACTTACTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
GAAATTGATTTTT
Found at i:276605 original size:31 final size:32
Alignment explanation
Indices: 276567--276647 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 32
276557 TTGATTTTTG
276567 AAAAACTTACTCCCCCTTACTATAGCACATC-
1 AAAAACTTACTCCCCCTTACTATAGCACATCT
276598 AAAAACTTACTCCCCCTTACTATAGCACATCT
1 AAAAACTTACTCCCCCTTACTATAGCACATCT
* * *
276630 ATAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
276648 TTTGTTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 31 0.67
32 15 0.33
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.31
Consensus pattern (32 bp):
AAAAACTTACTCCCCCTTACTATAGCACATCT
Found at i:278998 original size:17 final size:17
Alignment explanation
Indices: 278976--279010 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
278966 AACTCATATC
278976 AAAATTAATTATGTTCA
1 AAAATTAATTATGTTCA
278993 AAAATTAATTATGTTCA
1 AAAATTAATTATGTTCA
279010 A
1 A
279011 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
AAAATTAATTATGTTCA
Done.