Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000103.1 Hibiscus syriacus cultivar Beakdansim tig00000187_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: 47333
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5326 original size:30 final size:30
Alignment explanation
Indices: 5238--5330 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
5228 GGAGGACCTA
* * * *
5238 TCCAGAGGTCACACAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
5267 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
5297 TCCAGAGGTCATAAAGATCCTC-GTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
5327 TCCA
1 TCCA
5331 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
29 17 0.29
30 41 0.71
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:5361 original size:31 final size:31
Alignment explanation
Indices: 5319--5417 Score: 139
Period size: 31 Copynumber: 3.2 Consensus size: 31
5309 AAAGATCCTC
*
5319 GTAAACTGTCCATATGTTCCTTAGAACATAG
1 GTAAACTGTCCATATGTTCCGTAGAACATAG
* *
5350 GTATACTGTCCATATG-TCTCGAAG-ACATAG
1 GTAAACTGTCCATATGTTC-CGTAGAACATAG
5380 GTAAAACTGTCCATATGTTCCGTAGAACATAG
1 GT-AAACTGTCCATATGTTCCGTAGAACATAG
5412 GTAAAC
1 GTAAAC
5418 CCGACTCTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 10 0.17
31 39 0.66
32 10 0.17
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (31 bp):
GTAAACTGTCCATATGTTCCGTAGAACATAG
Found at i:6254 original size:2 final size:2
Alignment explanation
Indices: 6247--6307 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
6237 ATACAATTCC
6247 TA TA TA TA TA TA TA 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
6289 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
6308 CTAACTCATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6805 original size:21 final size:21
Alignment explanation
Indices: 6781--6825 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6771 TGTTGTTCGT
* *
6781 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6802 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6823 TTG
1 TTG
6826 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9582 original size:30 final size:30
Alignment explanation
Indices: 9523--9611 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
9513 CCCGGAGGAC
* * *
9523 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
9552 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
9582 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
9612 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:9647 original size:31 final size:31
Alignment explanation
Indices: 9607--9707 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
9597 AAAGATCCTC
*
9607 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
9638 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
9669 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
9701 GGTAAAC
1 GGTAAAC
9708 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:10543 original size:2 final size:2
Alignment explanation
Indices: 10536--10602 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
10526 TATACATTCC
10536 TA TA TA TA TA TA TA 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
10578 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10603 CTAACTCATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11099 original size:21 final size:21
Alignment explanation
Indices: 11075--11119 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11065 TGTTGTTCGT
* *
11075 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
11096 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
11117 TTG
1 TTG
11120 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:12405 original size:12 final size:12
Alignment explanation
Indices: 12388--12422 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12378 GTCATCTTTT
12388 TCCTCTCTTCTC
1 TCCTCTCTTCTC
*
12400 TCCTCTCTTTTC
1 TCCTCTCTTCTC
*
12412 TCCTCTATTCT
1 TCCTCTCTTCT
12423 TTATCTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (12 bp):
TCCTCTCTTCTC
Found at i:12810 original size:36 final size:36
Alignment explanation
Indices: 12770--12841 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
12760 AGTGAGGTAA
*
12770 CACATAAGTAACTCCCATTTACCATATGTGAGCCAT
1 CACATAAGTAACTCCCATTTACCATATGGGAGCCAT
12806 CACATAAGTAACTCCCATTTACCATATGGGAGCCAT
1 CACATAAGTAACTCCCATTTACCATATGGGAGCCAT
12842 AAGACTATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (36 bp):
CACATAAGTAACTCCCATTTACCATATGGGAGCCAT
Found at i:13324 original size:20 final size:19
Alignment explanation
Indices: 13295--13358 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
13285 AACCGGTAAT
13295 GATA-CTAAGGCTAGTATC
1 GATACCTAAGGCTAGTATC
* *
13313 GATACCCTAAGGCCAATATC
1 GATA-CCTAAGGCTAGTATC
13333 GATA-CTGACAGGCTCAGTATC
1 GATACCT-A-AGGCT-AGTATC
13354 GATAC
1 GATAC
13359 TGACGTCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.17
19 1 0.03
20 20 0.56
21 9 0.25
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (19 bp):
GATACCTAAGGCTAGTATC
Found at i:13639 original size:22 final size:22
Alignment explanation
Indices: 13614--13685 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
13604 TTCTCTTTCC
13614 CAGTGCGATGGCACTTTAGTAT
1 CAGTGCGATGGCACTTTAGTAT
* *
13636 CAGTGTGAAT-GCACTTTTGTAT
1 CAGTGCG-ATGGCACTTTAGTAT
13658 CAGT--GATGCAGCACTTTAGTAT
1 CAGTGCGATG--GCACTTTAGTAT
*
13680 TAGTGC
1 CAGTGC
13686 TAAGACACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
22 35 0.88
23 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (22 bp):
CAGTGCGATGGCACTTTAGTAT
Found at i:24632 original size:14 final size:14
Alignment explanation
Indices: 24609--24646 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
24599 TCTGTCTATA
*
24609 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
24622 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
24637 TGCAGGGATT
1 TGCAGGGATT
24647 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:25533 original size:28 final size:29
Alignment explanation
Indices: 25496--25554 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
25486 AGTTAGGGTG
* *
25496 AACTTGAACTTATAAAATTTT-AGGGACA
1 AACTTAAACTTATAAAATTTTAAGAGACA
25524 AACTTAAACTTATAAAATTTTAAGAGACA
1 AACTTAAACTTATAAAATTTTAAGAGACA
25553 AA
1 AA
25555 AACAGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (29 bp):
AACTTAAACTTATAAAATTTTAAGAGACA
Found at i:26551 original size:21 final size:21
Alignment explanation
Indices: 26525--26592 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
26515 AACCGTTTGA
* *
26525 CTCTTATTCTTCTTCTTCCTC
1 CTCTTACTCTTCCTCTTCCTC
26546 CTCTTACTCTTCCTCTTCCTCTTC
1 CTCTTACTCTTCCTCTT-C-C-TC
*
26570 CTCTTCCTCTTCCTCTTCCTC
1 CTCTTACTCTTCCTCTTCCTC
26591 CT
1 CT
26593 TCTAGAGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 19 0.46
22 2 0.05
23 2 0.05
24 18 0.44
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (21 bp):
CTCTTACTCTTCCTCTTCCTC
Found at i:26555 original size:6 final size:6
Alignment explanation
Indices: 26544--26590 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
26534 TTCTTCTTCC
*
26544 TCCTCT TACTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
26591 CTTCTAGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTCT
Found at i:29704 original size:30 final size:29
Alignment explanation
Indices: 29655--29719 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29645 GTCGAGTGAC
** *
29655 CATTTTGTAACAATGATAACGTTAATGAT
1 CATTTTGTAACAACAATAACATTAATGAT
*
29684 CATTTTGTAACAAACAATAACATTAGTGAT
1 CATTTTGTAAC-AACAATAACATTAATGAT
29714 CGATTT
1 C-ATTT
29720 GTGACTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 11 0.37
30 15 0.50
31 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (29 bp):
CATTTTGTAACAACAATAACATTAATGAT
Found at i:37443 original size:16 final size:16
Alignment explanation
Indices: 37419--37461 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
37409 TCAAGTCGAG
* *
37419 TCGATCTCAGCAATAC
1 TCGAGCTCAACAATAC
37435 TCGAGCTCAACAATAC
1 TCGAGCTCAACAATAC
37451 TCGAGCTCAAC
1 TCGAGCTCAAC
37462 TCGGCTCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.21
Consensus pattern (16 bp):
TCGAGCTCAACAATAC
Found at i:38344 original size:19 final size:20
Alignment explanation
Indices: 38320--38357 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38310 CAAAATGACC
*
38320 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
38339 CAATTTCAACACTCTAACA
1 CAATTTCAACACTCTAACA
38358 ATAATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:39296 original size:29 final size:30
Alignment explanation
Indices: 39241--39297 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
39231 CCCTAAATTT
* * *
39241 TTTCAAAACTTTATACTTTGGTTACTAAAC
1 TTTCAAAACTTTACACTATGGTCACTAAAC
39271 TTTCAAAA-TTTACACTATGGTCACTAA
1 TTTCAAAACTTTACACTATGGTCACTAA
39298 CCAAAATTCT
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:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTCAAAACTTTACACTATGGTCACTAAAC
Found at i:43004 original size:2 final size:2
Alignment explanation
Indices: 42997--43033 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42987 TAAAAATGGT
42997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43034 TACACGTGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45320 original size:23 final size:23
Alignment explanation
Indices: 45252--45312 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
45242 ACATTTTATA
45252 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
45275 CGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
45298 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
45313 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:45685 original size:13 final size:13
Alignment explanation
Indices: 45667--45697 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
45657 AAGCATTTAG
45667 AGTTTTCTTTAAA
1 AGTTTTCTTTAAA
*
45680 AGTTTTCTTTATA
1 AGTTTTCTTTAAA
45693 AGTTT
1 AGTTT
45698 AAAGCCTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (13 bp):
AGTTTTCTTTAAA
Done.