Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003767.1 Hibiscus syriacus cultivar Beakdansim tig00008068_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: 63245
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:691 original size:22 final size:21
Alignment explanation
Indices: 651--691 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
641 ATTTTAAATA
* *
651 ATTTTTATAAATATTATATTT
1 ATTTATATAAATATAATATTT
672 ATTTATATAAAATATAATAT
1 ATTTATAT-AAATATAATAT
692 AACATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTATATAAATATAATATTT
Found at i:4325 original size:126 final size:126
Alignment explanation
Indices: 4049--4396 Score: 513
Period size: 126 Copynumber: 2.8 Consensus size: 126
4039 TGCTTGGTCC
* * *
4049 TTTTGAACCATTTCATAGAAAATTTGCCTATGTGACAGTTATTCTATTTTTATATTATAATGTGG
1 TTTTGAACCATTTCATAGAAAAGTTGCCTATGTGGCAGTTATTCTATTTTGATATTATAATGTGG
* *
4114 CCATGAGGAATTTT-ATGCAAGAGAAATAAAGAACTGTGTCATGTAAGTACATTACTAGAT
66 GCATGAGGAATTTTGATGCAAGAGAAAAAAAGAACTGTGTCATGTAAGTACATTACTAGAT
* * *
4174 TTTTTAACTATTTCATAGAAAAGTTGCCTATGTGGCAGTTATTCTATTTTGATATTATTATGTGG
1 TTTTGAACCATTTCATAGAAAAGTTGCCTATGTGGCAGTTATTCTATTTTGATATTATAATGTGG
* * * *
4239 GCATGAAGAATTTTGATGCAACAGAAAGAAAGAACTGTGTCCTGTAAGTACATTACTAG-T
66 GCATGAGGAATTTTGATGCAAGAGAAAAAAAGAACTGTGTCATGTAAGTACATTACTAGAT
* * * * *
4299 TTTTCGAACCATTTCATAGAAGAGTTGTCTATGTGGCAGTTTTTCTAGTTTGATATTATCATGTG
1 TTTT-GAACCATTTCATAGAAAAGTTGCCTATGTGGCAGTTATTCTATTTTGATATTATAATGTG
4364 GGCATGAGGAA-TTTGATGCAAGAGAAAAAAAGA
65 GGCATGAGGAATTTTGATGCAAGAGAAAAAAAGA
4397 TAGAGTCTTT
Statistics
Matches: 200, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
125 96 0.48
126 104 0.52
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (126 bp):
TTTTGAACCATTTCATAGAAAAGTTGCCTATGTGGCAGTTATTCTATTTTGATATTATAATGTGG
GCATGAGGAATTTTGATGCAAGAGAAAAAAAGAACTGTGTCATGTAAGTACATTACTAGAT
Found at i:10557 original size:18 final size:18
Alignment explanation
Indices: 10534--10568 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
10524 TTGTCAGCAT
10534 GTTGCAAGTCGAATCCTA
1 GTTGCAAGTCGAATCCTA
10552 GTTGCAAGTCGAATCCT
1 GTTGCAAGTCGAATCCT
10569 CCAATCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
GTTGCAAGTCGAATCCTA
Found at i:11468 original size:20 final size:20
Alignment explanation
Indices: 11441--11498 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
11431 TTTGGTTTAC
11441 AGAATGTAAGATTA-CTAGTG
1 AGAATGTAAGATTATC-AGTG
*
11461 ATAATGTAAGATTATCAGTG
1 AGAATGTAAGATTATCAGTG
*
11481 GGAATGTAAGATTATCAG
1 AGAATGTAAGATTATCAG
11499 GGAATAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (20 bp):
AGAATGTAAGATTATCAGTG
Found at i:14966 original size:45 final size:45
Alignment explanation
Indices: 14915--15000 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
14905 AAGCTCCTCA
* * *
14915 GATAAAGGCAAAGGAGCAGAACCTATCAAAACTGTTAAAAAAGGG
1 GATAAAGGAAAAGGAGCAGAACCAACCAAAACTGTTAAAAAAGGG
*
14960 GATAAAGGAAAAGGAGCAGAACCAACCAAATCTGTTAAAAA
1 GATAAAGGAAAAGGAGCAGAACCAACCAAAACTGTTAAAAA
15001 TCCATAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.13
Consensus pattern (45 bp):
GATAAAGGAAAAGGAGCAGAACCAACCAAAACTGTTAAAAAAGGG
Found at i:15012 original size:45 final size:45
Alignment explanation
Indices: 14913--15012 Score: 101
Period size: 45 Copynumber: 2.2 Consensus size: 45
14903 CCAAGCTCCT
* * * * *
14913 CAGATAAAGGCAAAGGAGCAGAACCTATCAAAACTGTTAAAAAAG
1 CAGAAAAAGGAAAAGGAGCAGAACCAACCAAAACTGTTAAAAAAC
** * * *
14958 GGGATAAAGGAAAAGGAGCAGAACCAACCAAATCTGTTAAAAATC
1 CAGAAAAAGGAAAAGGAGCAGAACCAACCAAAACTGTTAAAAAAC
*
15003 CATAAAAAGG
1 CAGAAAAAGG
15013 CAGAGGACCG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (45 bp):
CAGAAAAAGGAAAAGGAGCAGAACCAACCAAAACTGTTAAAAAAC
Found at i:20827 original size:21 final size:22
Alignment explanation
Indices: 20802--20863 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
20792 TTAAACAATT
20802 AAAATAAATTATTAAAA-G-TA
1 AAAATAAATTATTAAAATGTTA
* * *
20822 ATAAATTATTTTTTAAGAATGTTA
1 A-AAATAAATTATTAA-AATGTTA
*
20846 AAATTAAATTATTAAAAT
1 AAAATAAATTATTAAAAT
20864 AAAATGTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.35
22 5 0.16
23 11 0.35
24 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAATAAATTATTAAAATGTTA
Found at i:22874 original size:20 final size:18
Alignment explanation
Indices: 22849--22895 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
22839 TTTGGTTCAC
*
22849 GGAATATAAGATTACCAGT
1 GGAATATAAGATTAACA-T
*
22868 GGGAATAAAAGATTAACAT
1 -GGAATATAAGATTAACAT
22887 GGAATATAA
1 GGAATATAA
22896 TTACTGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 15 0.62
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.23
Consensus pattern (18 bp):
GGAATATAAGATTAACAT
Found at i:26326 original size:3 final size:3
Alignment explanation
Indices: 26320--26365 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
26310 AGAAATGAGG
* * *
26320 GAA GAA GAA GGA GAA AAA GAA AAA GAA TGAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA
26366 ATTGTTGCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:33462 original size:25 final size:25
Alignment explanation
Indices: 33428--33477 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
33418 TTTCGGGATC
33428 AACACAATGTGGGTGTGATTGATTG
1 AACACAATGTGGGTGTGATTGATTG
33453 AACACAATGTGGGTGTGATTGATTG
1 AACACAATGTGGGTGTGATTGATTG
33478 CTAACATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (25 bp):
AACACAATGTGGGTGTGATTGATTG
Found at i:34449 original size:15 final size:15
Alignment explanation
Indices: 34431--34460 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34421 TATATTATGG
34431 AAAATATTAATTTAT
1 AAAATATTAATTTAT
*
34446 AAAATATTTATTTAT
1 AAAATATTAATTTAT
34461 TTAGAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATATTAATTTAT
Found at i:34539 original size:18 final size:19
Alignment explanation
Indices: 34516--34562 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
34506 TTTCTTCAAT
34516 ATTAAAAATAAATATAT-A
1 ATTAAAAATAAATATATGA
*
34534 ATTAAAAATTAATATATGA
1 ATTAAAAATAAATATATGA
*
34553 TTTAAAAATA
1 ATTAAAAATA
34563 GGATATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTAAAAATAAATATATGA
Found at i:34772 original size:15 final size:14
Alignment explanation
Indices: 34742--34839 Score: 60
Period size: 15 Copynumber: 7.0 Consensus size: 14
34732 TATTTATATA
*
34742 AATAATAATAAGAAT
1 AATAA-AATAATAAT
34757 AATAAAAGTAATAAT
1 AATAAAA-TAATAAT
34772 AATAAAATAAT-AT
1 AATAAAATAATAAT
**
34785 TGT-AAATAATAATT
1 AATAAAATAATAA-T
*
34799 AA-AAAAT-ATAGT
1 AATAAAATAATAAT
* *
34811 ATTAAAATATAAAAT
1 AATAAAATA-ATAAT
* *
34826 ATTAAAAAAATAAT
1 AATAAAATAATAAT
34840 CAAAAATGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
12 9 0.14
13 12 0.18
14 15 0.23
15 29 0.45
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (14 bp):
AATAAAATAATAAT
Found at i:34792 original size:23 final size:23
Alignment explanation
Indices: 34736--34811 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
34726 TATATTTATT
34736 TATA-TAAATAATAATAAGAATAA
1 TATAGTAAATAATAATAA-AATAA
*
34759 TAAAAGT-AATAATAATAAAATAA
1 T-ATAGTAAATAATAATAAAATAA
*
34782 TATTGTAAATAATAATTAAAA-AA
1 TATAGTAAATAATAA-TAAAATAA
34805 TATAGTA
1 TATAGTA
34812 TTAAAATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 3 0.07
23 23 0.51
24 18 0.40
25 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TATAGTAAATAATAATAAAATAA
Found at i:34797 original size:3 final size:3
Alignment explanation
Indices: 34742--34783 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
34732 TATTTATATA
*
34742 AAT AAT AAT AAG AAT AAT AA- AAGT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
34784 TTGTAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.12
3 28 0.82
4 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:35011 original size:2 final size:2
Alignment explanation
Indices: 35004--35047 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
34994 ATTTACCTAA
35004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35046 AT
1 AT
35048 GCTGATAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36072 original size:3 final size:3
Alignment explanation
Indices: 36058--36140 Score: 116
Period size: 3 Copynumber: 28.0 Consensus size: 3
36048 TTTGTATCTG
* *
36058 TAA TAA -AA TAA TAA TAA TAA TAT TAA TAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
36105 TAA TAA TAG TAA TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
36141 AAAAAACCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
2 3 0.04
3 67 0.94
4 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40784 original size:33 final size:33
Alignment explanation
Indices: 40712--40784 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
40702 CATGGCCACT
* *
40712 CGCTTTGATCACGTTCTTCATGAGGTTGATACC
1 CGCTTTGATCAAGTTCTTCATCAGGTTGATACC
** * *
40745 TACTTTGATCAAGTTCTTTATCATGTTGATACC
1 CGCTTTGATCAAGTTCTTCATCAGGTTGATACC
40778 CGCTTTG
1 CGCTTTG
40785 GTGCCGTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (33 bp):
CGCTTTGATCAAGTTCTTCATCAGGTTGATACC
Found at i:45655 original size:20 final size:23
Alignment explanation
Indices: 45624--45669 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
45614 ATATATATAA
45624 TTTTAGTAATTTA-A-ATTTTAT
1 TTTTAGTAATTTATATATTTTAT
45645 TTTTAGT-ATTTATATATTTTAT
1 TTTTAGTAATTTATATATTTTAT
45667 TTT
1 TTT
45670 AAATAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 8 0.35
22 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTAGTAATTTATATATTTTAT
Found at i:45666 original size:22 final size:22
Alignment explanation
Indices: 45624--45686 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
45614 ATATATATAA
45624 TTTTAGTAATTTA-A-ATTTTAT
1 TTTTAGT-ATTTATATATTTTAT
45645 TTTTAGTATTTATATATTTTAT
1 TTTTAGTATTTATATATTTTAT
* * *
45667 TTTAAATAGTT-TATATTTTA
1 TTTTAGTATTTATATATTTTA
45687 AATAGTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 5 0.14
21 17 0.46
22 15 0.41
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTAGTATTTATATATTTTAT
Found at i:45683 original size:16 final size:16
Alignment explanation
Indices: 45664--45700 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
45654 TTATATATTT
45664 TATTTTAAATAGTTTA
1 TATTTTAAATAGTTTA
*
45680 TATTTTAAATAGTTTT
1 TATTTTAAATAGTTTA
45696 TATTT
1 TATTT
45701 AAAAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TATTTTAAATAGTTTA
Found at i:48558 original size:33 final size:34
Alignment explanation
Indices: 48521--48591 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
48511 CCTAAAATGT
* *
48521 TATTTTTTTCTACCGAAAATATTAATAT-TAAAA
1 TATTTTTTTCTACCAAAAATATTAATATCGAAAA
** *
48554 TATTTTTTTCTGTCAAAAATGTTAATATCGAAAA
1 TATTTTTTTCTACCAAAAATATTAATATCGAAAA
48588 TATT
1 TATT
48592 CATTTTAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (34 bp):
TATTTTTTTCTACCAAAAATATTAATATCGAAAA
Found at i:54252 original size:30 final size:30
Alignment explanation
Indices: 54183--54260 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
54173 TATGAACCTT
* *
54183 TTTTCTCAAATTGGTATCTGAAATTGGAAA
1 TTTTCTCAAATTGGTACCTGAAATTAGAAA
*
54213 TAATTCTCAAATTGGTACCT-AAACTTAGAAA
1 T-TTTCTCAAATTGGTACCTGAAA-TTAGAAA
54244 TTTTCTCAAATTGGTAC
1 TTTTCTCAAATTGGTAC
54261 TTGATGGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (30 bp):
TTTTCTCAAATTGGTACCTGAAATTAGAAA
Done.