Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006035.1 Hibiscus syriacus cultivar Beakdansim tig00014245_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: 53782
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2126 original size:26 final size:26
Alignment explanation
Indices: 2076--2127 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2066 ATGGTATGAC
**
2076 GTGGCAGTTTCTAGAAGGTCCAGTCA
1 GTGGCAGTTTCTAGAAAATCCAGTCA
*
2102 GTGGCAGTTTCTAGAAAATCTAGTCA
1 GTGGCAGTTTCTAGAAAATCCAGTCA
2128 ACGCGCCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (26 bp):
GTGGCAGTTTCTAGAAAATCCAGTCA
Found at i:5750 original size:28 final size:28
Alignment explanation
Indices: 5710--5766 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5700 GTTTTTGTCT
5710 TCCCAGTTTCAAAGGAGGGAGCCAACTA
1 TCCCAGTTTCAAAGGAGGGAGCCAACTA
5738 TCCCAGTTTCAAAGGAGGGAGCCAACTA
1 TCCCAGTTTCAAAGGAGGGAGCCAACTA
5766 T
1 T
5767 GGACAAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (28 bp):
TCCCAGTTTCAAAGGAGGGAGCCAACTA
Found at i:13517 original size:2 final size:2
Alignment explanation
Indices: 13506--13538 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13496 TTTCTCAATC
13506 TA TA -A 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
13539 AAACAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:14149 original size:13 final size:13
Alignment explanation
Indices: 14131--14175 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
14121 GTCATAAATC
*
14131 TATGACACGCATT
1 TATGACACACATT
14144 TATGACACACATT
1 TATGACACACATT
***
14157 TATGATGTACATT
1 TATGACACACATT
14170 TATGAC
1 TATGAC
14176 TCGCATTGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TATGACACACATT
Found at i:15566 original size:10 final size:10
Alignment explanation
Indices: 15551--15576 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15541 AAATGCATTA
15551 CAAAACTAGG
1 CAAAACTAGG
15561 CAAAACTAGG
1 CAAAACTAGG
15571 CAAAAC
1 CAAAAC
15577 AATGGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.15, T:0.08
Consensus pattern (10 bp):
CAAAACTAGG
Found at i:15843 original size:22 final size:22
Alignment explanation
Indices: 15815--15872 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
15805 AGACGGGAGT
*
15815 ATGTGTATGTATGATATGA-AA
1 ATGTGTATGTATGATACGAGAA
15836 GATGTGTA--TATGATACGAGAA
1 -ATGTGTATGTATGATACGAGAA
*
15857 ATGTTTATGTATGATA
1 ATGTGTATGTATGATA
15873 GTTGTATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 15 0.48
21 2 0.06
22 14 0.45
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (22 bp):
ATGTGTATGTATGATACGAGAA
Found at i:19275 original size:14 final size:14
Alignment explanation
Indices: 19256--19292 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
19246 ATAAATTAGT
19256 GTGTGTCATCGTTC
1 GTGTGTCATCGTTC
19270 GTGTGTCATCGTTC
1 GTGTGTCATCGTTC
19284 GTGTGTCAT
1 GTGTGTCAT
19293 TAAATGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.19, G:0.30, T:0.43
Consensus pattern (14 bp):
GTGTGTCATCGTTC
Found at i:21717 original size:16 final size:18
Alignment explanation
Indices: 21685--21717 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
21675 ATAAATAAAC
21685 TATAGTAAAGCATTTCAA
1 TATAGTAAAGCATTTCAA
21703 TATA-TAAAG-ATTTCA
1 TATAGTAAAGCATTTCA
21718 TAATAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (18 bp):
TATAGTAAAGCATTTCAA
Found at i:25689 original size:15 final size:15
Alignment explanation
Indices: 25669--25751 Score: 64
Period size: 15 Copynumber: 6.3 Consensus size: 15
25659 GTTTGTTTTT
25669 AACATTATCAATATC
1 AACATTATCAATATC
25684 AACATTAT---TATC
1 AACATTATCAATATC
*
25696 --C-TTATCAATACC
1 AACATTATCAATATC
25708 AACATTAT---TATC
1 AACATTATCAATATC
*
25720 --C-TTATCAATACC
1 AACATTATCAATATC
25732 AACATTATCAATATC
1 AACATTATCAATATC
25747 AACAT
1 AACAT
25752 GCTCATCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 24
0.65 0.05 0.30
Matches are distributed among these distances:
9 8 0.15
10 2 0.04
12 13 0.25
14 2 0.04
15 27 0.52
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (15 bp):
AACATTATCAATATC
Found at i:25705 original size:24 final size:24
Alignment explanation
Indices: 25673--25739 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
25663 GTTTTTAACA
*
25673 TTATCAATATCAACATTATTATCC
1 TTATCAATACCAACATTATTATCC
25697 TTATCAATACCAACATTATTATCC
1 TTATCAATACCAACATTATTATCC
25721 TTATCAATACCAACATTAT
1 TTATCAATACCAACATTAT
25740 CAATATCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (24 bp):
TTATCAATACCAACATTATTATCC
Found at i:31908 original size:18 final size:18
Alignment explanation
Indices: 31881--31915 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31871 CACCTAAAAC
31881 CATTTGATTTTAATAAAT
1 CATTTGATTTTAATAAAT
* *
31899 CATTTTATTTTACTAAA
1 CATTTGATTTTAATAAA
31916 ATACCAATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
CATTTGATTTTAATAAAT
Found at i:32299 original size:29 final size:30
Alignment explanation
Indices: 32266--32322 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
32256 TTGCTTTTTA
32266 AGTTTAGTGCCTAACGTT-TATTCCGTTCT
1 AGTTTAGTGCCTAACGTTGTATTCCGTTCT
* * *
32295 AGTTTGGTGTCTAACGTTGTATTTCGTT
1 AGTTTAGTGCCTAACGTTGTATTCCGTT
32323 ATTCAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (30 bp):
AGTTTAGTGCCTAACGTTGTATTCCGTTCT
Found at i:35393 original size:31 final size:31
Alignment explanation
Indices: 35355--35419 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
35345 GAACCTAGAC
*
35355 AAAGGTTGGGCACCAAAGT-GGAAAACAATTT
1 AAAGGTTGGGCACCAAA-TCGAAAAACAATTT
35386 AAAGGTTGGGCACCAAATCGAAAAACAATTT
1 AAAGGTTGGGCACCAAATCGAAAAACAATTT
35417 AAA
1 AAA
35420 TTGGAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (31 bp):
AAAGGTTGGGCACCAAATCGAAAAACAATTT
Found at i:37066 original size:15 final size:15
Alignment explanation
Indices: 37048--37078 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37038 TGTTTAACAA
37048 ACAAATCAAATAACC
1 ACAAATCAAATAACC
*
37063 ACAAGTCAAATAACC
1 ACAAATCAAATAACC
37078 A
1 A
37079 ATATTCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.26, G:0.03, T:0.13
Consensus pattern (15 bp):
ACAAATCAAATAACC
Found at i:40304 original size:33 final size:31
Alignment explanation
Indices: 40245--40305 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
40235 ATTAATTATA
* * *
40245 TATTATTATTATTATTATTCTCTTATATATT
1 TATTATTATAATTATTATTATATTATATATT
40276 TATTATATATAATATATTATTATATTATAT
1 TATTAT-TATAAT-TATTATTATATTATAT
40306 TTACAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.24
32 5 0.20
33 14 0.56
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTATTATAATTATTATTATATTATATATT
Found at i:40305 original size:31 final size:29
Alignment explanation
Indices: 40232--40308 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
40222 GTCCGTTTTG
*
40232 ATTATTA-ATTATATATTATTATTATTATT
1 ATTATTATATTATAT-TTATTATTATAATT
*
40261 ATTCTCT-TA-TATATTTATTATATATAATAT
1 ATTAT-TATATTATATTTATTAT-TATAAT-T
40291 ATTATTATATTATATTTA
1 ATTATTATATTATATTTA
40309 CAAATATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
28 7 0.18
29 15 0.38
30 9 0.23
31 8 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTATTATATTATATTTATTATTATAATT
Found at i:43034 original size:18 final size:18
Alignment explanation
Indices: 43011--43047 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43001 CCAATGAAGG
43011 GCATCATAATGAAAATCC
1 GCATCATAATGAAAATCC
43029 GCATCATAATGAAAATCC
1 GCATCATAATGAAAATCC
43047 G
1 G
43048 AGGATAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (18 bp):
GCATCATAATGAAAATCC
Found at i:49519 original size:14 final size:12
Alignment explanation
Indices: 49454--49533 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
49444 TGTCAGTTTT
49454 TATTAT-TATATA
1 TATTATATAT-TA
*
49466 TATTAT-TGTTA
1 TATTATATATTA
49477 TTATTAT-TATTA
1 -TATTATATATTA
* *
49489 TCTTACATATT-
1 TATTATATATTA
*
49500 TATTATATATAA
1 TATTATATATTA
49512 TA-TATTATATTA
1 TATTA-TATATTA
49524 TATT-TATATT
1 TATTATATATT
49534 TACAAATACT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
11 22 0.40
12 32 0.58
13 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (12 bp):
TATTATATATTA
Found at i:52240 original size:3 final size:3
Alignment explanation
Indices: 52232--52264 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
52222 TTCACTTCAC
52232 ATA ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52265 CATTGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:52257 original size:8 final size:8
Alignment explanation
Indices: 52235--52264 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
52225 ACTTCACATA
52235 ATAATAAT
1 ATAATAAT
52243 AATAATAAT
1 -ATAATAAT
52252 ATAATAAT
1 ATAATAAT
52260 ATAAT
1 ATAAT
52265 CATTGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Done.