Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003976.1 Hibiscus syriacus cultivar Beakdansim tig00008635_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: 59981
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2060 original size:30 final size:31
Alignment explanation
Indices: 2001--2076 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1991 CAACATCAGA
* *
2001 TACCAATCTAAGAATTTTTTTAAAGTTTAA-G
1 TACCAATTTGAGAATTTTTTT-AAGTTTAAGG
*
2032 TACTAATTTGAGAATTTGTTTT-AGTTTAAGG
1 TACCAATTTGAGAATTT-TTTTAAGTTTAAGG
2063 TACCAATTTGAGAA
1 TACCAATTTGAGAA
2077 AAGAATAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.18
31 28 0.72
32 4 0.10
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (31 bp):
TACCAATTTGAGAATTTTTTTAAGTTTAAGG
Found at i:6834 original size:11 final size:11
Alignment explanation
Indices: 6797--6851 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
6787 TTTATTAAAC
*
6797 TATTATAAAAT
1 TATTATCAAAT
* *
6808 TATCATTAAAT
1 TATTATCAAAT
6819 T-TTATCAAAT
1 TATTATCAAAT
*
6829 TATTAT-AAAA
1 TATTATCAAAT
6839 TATTTATCAAAT
1 TA-TTATCAAAT
6851 T
1 T
6852 TAATGAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 13 0.37
11 18 0.51
12 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTATCAAAT
Found at i:6851 original size:32 final size:31
Alignment explanation
Indices: 6774--6852 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
6764 TAAAAATCGT
*
6774 AAATTTTATTAAA-TTTATTAAACTATTATA
1 AAATTTTATTAAATTTTATCAAACTATTATA
* *
6804 AAATTATCATTAAATTTTATCAAATTATTATA
1 AAATT-TTATTAAATTTTATCAAACTATTATA
*
6836 AAATATTTATCAAATTT
1 AAAT-TTTATTAAATTT
6853 AATGAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.12
31 7 0.17
32 28 0.68
33 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTTTATTAAATTTTATCAAACTATTATA
Found at i:13561 original size:14 final size:14
Alignment explanation
Indices: 13542--13579 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
13532 AATCATCCGT
*
13542 TAAATATTTTTTTA
1 TAAATATTTTTATA
13556 TAAATATTTTTATA
1 TAAATATTTTTATA
13570 TCAAA-ATTTT
1 T-AAATATTTT
13580 CTGTTCACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TAAATATTTTTATA
Found at i:22065 original size:2 final size:2
Alignment explanation
Indices: 22054--22101 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
22044 TCGAAGTTAG
22054 TA TA -A 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
22095 TA TA TA T
1 TA TA TA T
22102 TAATAACAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24668 original size:18 final size:18
Alignment explanation
Indices: 24645--24682 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
24635 AATTTAATCA
24645 CATAATCAAAGTCA-TAAT
1 CATAATCAAA-TCATTAAT
24663 CATAATCAAATCATTAAT
1 CATAATCAAATCATTAAT
24681 CA
1 CA
24683 ACCTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (18 bp):
CATAATCAAATCATTAAT
Found at i:27794 original size:2 final size:2
Alignment explanation
Indices: 27787--27829 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
27777 TAGTAATTTC
27787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27827 AT A
1 AT A
27830 ATTATCAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32710 original size:21 final size:21
Alignment explanation
Indices: 32680--32732 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
32670 TGGTTCAACC
32680 TAAATTTTTTTGAT-TTTTTAT
1 TAAA-TTTTTTGATATTTTTAT
*
32701 TAAATGTTTTTGGTATTTTTAT
1 TAAAT-TTTTTGATATTTTTAT
*
32723 TTAATTTTTT
1 TAAATTTTTT
32733 AAATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 11 0.39
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.70
Consensus pattern (21 bp):
TAAATTTTTTGATATTTTTAT
Found at i:40446 original size:14 final size:14
Alignment explanation
Indices: 40427--40458 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40417 CGTTCGTGAA
40427 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
40441 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
40455 CGTT
1 CGTT
40459 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:40475 original size:24 final size:24
Alignment explanation
Indices: 40428--40478 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
40418 GTTCGTGAAC
* *
40428 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
40452 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
40476 GTT
1 GTT
40479 TAACCCAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:41525 original size:16 final size:16
Alignment explanation
Indices: 41500--41558 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
41490 CCAACGTTTA
41500 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
41516 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
41532 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
41548 TGTTCGTTTAT
1 TGTTCGTTTAT
41559 TTATTAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:41664 original size:14 final size:16
Alignment explanation
Indices: 41624--41664 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
41614 AAAAAAAATT
*
41624 TGTTCGTTTATATTCG
1 TGTTCATTTATATTCG
*
41640 TGTTCATTTATGTTCG
1 TGTTCATTTATATTCG
41656 T-TT-ATTTAT
1 TGTTCATTTAT
41665 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 15 0.65
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATATTCG
Found at i:41923 original size:29 final size:29
Alignment explanation
Indices: 41881--41937 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
41871 AGTGTTTGTC
**
41881 GTAGGTCGCCATGCTTTCAGGGCGACCTT
1 GTAGGTCGCCATGCACTCAGGGCGACCTT
*
41910 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCAGGGCGACCT
41938 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.32, G:0.32, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCAGGGCGACCTT
Found at i:42029 original size:29 final size:29
Alignment explanation
Indices: 41996--42051 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
41986 TCCCAACACA
*
41996 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
42025 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
42052 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:42095 original size:23 final size:23
Alignment explanation
Indices: 42069--42114 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
42059 CTCGGTTGCC
*
42069 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
*
42092 CTCGGCTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
42115 TTCGAATGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.41, G:0.24, T:0.24
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:42128 original size:23 final size:23
Alignment explanation
Indices: 42077--42122 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42067 CCCTCGGATT
**
42077 CCCTCGCATAGCTCGCTCGGCTG
1 CCCTCGCATAGCTCGCTCGAATG
*
42100 CCCTCGCATAGCTCGTTCGAATG
1 CCCTCGCATAGCTCGCTCGAATG
42123 GTCTCGGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.39, G:0.24, T:0.24
Consensus pattern (23 bp):
CCCTCGCATAGCTCGCTCGAATG
Found at i:42129 original size:33 final size:33
Alignment explanation
Indices: 42092--42168 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
42082 GCATAGCTCG
* * *
42092 CTCGGCTGCCCTCGCATAGCTCGTTCGAATGGT
1 CTCGGATGCCCTCGCATAGCTCGGTCGAATGGC
* *
42125 CTCGGATGCTCTCGCATAGCTCGGTCGGATGGC
1 CTCGGATGCCCTCGCATAGCTCGGTCGAATGGC
42158 CTCGGATGCCC
1 CTCGGATGCCC
42169 AACGTGTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.25
Consensus pattern (33 bp):
CTCGGATGCCCTCGCATAGCTCGGTCGAATGGC
Found at i:46372 original size:60 final size:58
Alignment explanation
Indices: 46262--46375 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 58
46252 ACAATCAAGT
* * *
46262 GATCATTTTAACTTTTAATAGTCAAGAGACATATCAAAGCAACATTCTATAATTAGAG
1 GATCATTTTAACTTTTAACAGTCAAGAGACATATCAAAACAACATCCTATAATTAGAG
* *
46320 GATCATTTTGTAACTTTTAACAGTCAATGA-ACTTTAT-AAAACAATATCCTATAATT
1 GATCA-TTT-TAACTTTTAACAGTCAA-GAGAC-ATATCAAAACAACATCCTATAATT
46376 GCCACCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
58 5 0.11
59 3 0.06
60 34 0.72
61 5 0.11
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (58 bp):
GATCATTTTAACTTTTAACAGTCAAGAGACATATCAAAACAACATCCTATAATTAGAG
Found at i:48368 original size:14 final size:13
Alignment explanation
Indices: 48322--48365 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
48312 GAGTCTCGGA
48322 TTTAATATATTCAC
1 TTTAAT-TATTCAC
* *
48336 TTTAATTATTAAAA
1 TTTAATTATT-CAC
48350 TTTAATTATTCAC
1 TTTAATTATTCAC
48363 TTT
1 TTT
48366 TAAATATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTAATTATTCAC
Found at i:48379 original size:28 final size:28
Alignment explanation
Indices: 48321--48385 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
48311 TGAGTCTCGG
* *
48321 ATTTAATATATTCACTTTAATTATTAAA
1 ATTTAATATATTCACTTTAAATATCAAA
*
48349 ATTTAAT-TATTCACTTTTAAATATCATA
1 ATTTAATATATTCAC-TTTAAATATCAAA
*
48377 ATTAAATAT
1 ATTTAATAT
48386 TTAAAGTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 23 0.74
29 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTAATATATTCACTTTAAATATCAAA
Found at i:49016 original size:2 final size:2
Alignment explanation
Indices: 48955--49003 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
48945 ATTGAAATTG
48955 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
48997 AT AT AT A
1 AT AT AT A
49004 GGGTAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51985 original size:13 final size:13
Alignment explanation
Indices: 51962--51994 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
51952 TTCCCATTAC
51962 AGACGTGCATATGA
1 AGAC-TGCATATGA
51976 AGACTGCATATGA
1 AGACTGCATATGA
51989 AGACTG
1 AGACTG
51995 TTCAACTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (13 bp):
AGACTGCATATGA
Found at i:55535 original size:25 final size:23
Alignment explanation
Indices: 55498--55546 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
55488 TCACATTCAG
55498 ATTTCTTTAAAAATATTTCAAATAAT
1 ATTTCTTTAAAAA-ATTT-AAA-AAT
*
55524 ATTT-TTTTAAAAATTTAAAAAT
1 ATTTCTTTAAAAAATTTAAAAAT
55546 A
1 A
55547 ACATATGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.18
23 3 0.14
24 4 0.18
25 7 0.32
26 4 0.18
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTCTTTAAAAAATTTAAAAAT
Found at i:55547 original size:25 final size:26
Alignment explanation
Indices: 55498--55547 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
55488 TCACATTCAG
**
55498 ATTTCTTTAAAAATATTTCAAATAAT
1 ATTTCTTTAAAAATATTAAAAATAAT
*
55524 ATTTTTTTAAAAAT-TTAAAAATAA
1 ATTTCTTTAAAAATATTAAAAATAA
55548 CATATGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTCTTTAAAAATATTAAAAATAAT
Done.