Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007557.1 Hibiscus syriacus cultivar Beakdansim tig00021264_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: 96959
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:7851 original size:13 final size:13
Alignment explanation
Indices: 7833--7858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7823 TAAATAGTGC
7833 ACAAATATAAATT
1 ACAAATATAAATT
7846 ACAAATATAAATT
1 ACAAATATAAATT
7859 GAGTATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ACAAATATAAATT
Found at i:10278 original size:18 final size:18
Alignment explanation
Indices: 10247--10281 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10237 GGATTCAATA
**
10247 TAATAATTTTAATTTTAT
1 TAATAATTGAAATTTTAT
10265 TAATAATTGAAATTTTA
1 TAATAATTGAAATTTTA
10282 AGTTAAAAAA
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAATAATTGAAATTTTAT
Found at i:10667 original size:23 final size:21
Alignment explanation
Indices: 10630--10683 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
10620 CGGTTCAACC
*
10630 TAAATTTTTT-TTATTTTTTAT
1 TAAATTTTTTAGTA-TTTTTAT
10651 TAAATGTTTTTAGTATTTTTAT
1 TAAAT-TTTTTAGTATTTTTAT
*
10673 TTAATTTTTTA
1 TAAATTTTTTA
10684 AATAATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.38
22 16 0.55
23 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TAAATTTTTTAGTATTTTTAT
Found at i:17111 original size:144 final size:144
Alignment explanation
Indices: 16876--17163 Score: 425
Period size: 144 Copynumber: 2.0 Consensus size: 144
16866 GCAGTAAAAG
**
16876 ATGTGAGTACTGGAAATGTTAATGGAGGAAGTATTTCTGCTGCTACAAACTCTAATGCAGTATCA
1 ATGTGAGTACTGGAAATGTTAATGGAGGAAGTATTTCTGCAACTACAAACTCTAATGCAGTATCA
* * * * * *
16941 TATGGGACTTGTCCTGGAAGATAAAAAGTTTGTTCTGATAATGTGGATGTTTAGGTGACTAAACA
66 GATGGGACTTATCCTGGAAGAGAAAAAGTTTGTTATGATAAGGTGGATGTTCAGGTGACTAAACA
*
17006 GATTGATAAAGAGA
131 AATTGATAAAGAGA
* * * *
17020 ATGTGAGTACTGTAAATGTTAATGGTGGAAGTATTTCTGCAACTACAAACTCTAATGTAGTGTCA
1 ATGTGAGTACTGGAAATGTTAATGGAGGAAGTATTTCTGCAACTACAAACTCTAATGCAGTATCA
*
17085 GATGGGATTTATCCTGGTAA-AGAAAAAGTTTGTTATGATAAGGTGGATGTTCAGGTGACTAAAC
66 GATGGGACTTATCCTGG-AAGAGAAAAAGTTTGTTATGATAAGGTGGATGTTCAGGTGACTAAAC
*
17149 AAATTGATCAAGAGA
130 AAATTGATAAAGAGA
17164 GAGCTATCAC
Statistics
Matches: 128, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
144 126 0.98
145 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (144 bp):
ATGTGAGTACTGGAAATGTTAATGGAGGAAGTATTTCTGCAACTACAAACTCTAATGCAGTATCA
GATGGGACTTATCCTGGAAGAGAAAAAGTTTGTTATGATAAGGTGGATGTTCAGGTGACTAAACA
AATTGATAAAGAGA
Found at i:21074 original size:18 final size:18
Alignment explanation
Indices: 21043--21077 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21033 CGATTCAATA
**
21043 TAATAATTTTAATTTTAT
1 TAATAATTGAAATTTTAT
21061 TAATAATTGAAATTTTA
1 TAATAATTGAAATTTTA
21078 AGTTAAAAAA
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAATAATTGAAATTTTAT
Found at i:40077 original size:21 final size:21
Alignment explanation
Indices: 40051--40106 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
40041 TTATGGGTTG
40051 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATATTCAA
40072 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATATTCAA
40093 TGTGCATCGATGCA
1 TGTGCATCGATGCA
40107 CTCTAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGCATCGATGCATATTCAA
Found at i:40866 original size:18 final size:19
Alignment explanation
Indices: 40843--40879 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40833 GAGCCCTGAG
40843 ATATATGA-AAGAGAAAGT
1 ATATATGACAAGAGAAAGT
*
40861 ATATATGACAAGTGAAAGT
1 ATATATGACAAGAGAAAGT
40880 GAATCATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.22, T:0.24
Consensus pattern (19 bp):
ATATATGACAAGAGAAAGT
Found at i:41011 original size:18 final size:18
Alignment explanation
Indices: 40988--41035 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
40978 GGATCTACGC
40988 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
*
41006 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACACAGT
41024 GGTCCTTCGGGA
1 GGTCCTTCGGGA
41036 TAAATTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (18 bp):
GGTCCTTCGGGACACAGT
Found at i:44628 original size:13 final size:13
Alignment explanation
Indices: 44610--44636 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44600 TTTTAAGATC
44610 ATACTTAACCTTT
1 ATACTTAACCTTT
44623 ATACTTAACCTTT
1 ATACTTAACCTTT
44636 A
1 A
44637 GTTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (13 bp):
ATACTTAACCTTT
Found at i:49723 original size:2 final size:2
Alignment explanation
Indices: 49716--49743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49706 ATTTAAAAAT
49716 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
49744 GAACATGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53238 original size:23 final size:23
Alignment explanation
Indices: 53201--53264 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
53191 CATCTTGTAT
*
53201 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAA
* * *
53224 AATTGCACCGTAGTGCCGCGTAA
1 AAATGCACCGAAGTGCCACGTAA
53247 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
53265 TATAAGGTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAA
Found at i:53660 original size:2 final size:2
Alignment explanation
Indices: 53653--53682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53643 ATGTCTTATC
53653 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
53683 TCACATGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53851 original size:25 final size:26
Alignment explanation
Indices: 53821--53869 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
53811 ATGCCCTGAT
53821 TAATAACTTATATCATAT-ATATATA
1 TAATAACTTATATCATATCATATATA
53846 TAATAACTTATATCATATCATATA
1 TAATAACTTATATCATATCATATA
53870 GCTTATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATAACTTATATCATATCATATATA
Found at i:57581 original size:63 final size:63
Alignment explanation
Indices: 57403--57584 Score: 229
Period size: 63 Copynumber: 2.9 Consensus size: 63
57393 GATAGTAGTA
* * ** * * *
57403 AGGAAAAGCTTTTGATGGAAGGGGAAAACATCAGCAAACAGAATGGAAAGAACAGGATAACAG
1 AGGAAAAGTTTTTGAAGGAAGGGGAAAATGTAAGCAAACAGAATGGAAAGAAGAGGAGAACAG
* * *
57466 AGGAAACGTTTTTGAATGAAGGGGAAAATGTAAGCAAAAAGAATGGAAAGAAGAGGAGAACAG
1 AGGAAAAGTTTTTGAAGGAAGGGGAAAATGTAAGCAAACAGAATGGAAAGAAGAGGAGAACAG
* ** * *
57529 AGGAAAAGTTTTTGAAGGAAGGGGACAATGTTTGCAATCAGAATGTAAAGAAGAGG
1 AGGAAAAGTTTTTGAAGGAAGGGGAAAATGTAAGCAAACAGAATGGAAAGAAGAGG
57585 GGAGGGGATG
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 101 1.00
ACGTcount: A:0.46, C:0.07, G:0.31, T:0.16
Consensus pattern (63 bp):
AGGAAAAGTTTTTGAAGGAAGGGGAAAATGTAAGCAAACAGAATGGAAAGAAGAGGAGAACAG
Found at i:66351 original size:29 final size:29
Alignment explanation
Indices: 66306--66463 Score: 203
Period size: 29 Copynumber: 5.4 Consensus size: 29
66296 GACCCGACCC
* *
66306 GGGTGCTATTTTTGTAAATATTTTTAAAA
1 GGGTGTTATTTTAGTAAATATTTTTAAAA
66335 GGGTGTTATTTTAGTAAATATTTTTAAAA
1 GGGTGTTATTTTAGTAAATATTTTTAAAA
*
66364 GGGTGTTATTTTTGTAAATATTTTTAAAA
1 GGGTGTTATTTTAGTAAATATTTTTAAAA
* *
66393 -AGTGTTATTTTTGTAAATATTTTTAAAA
1 GGGTGTTATTTTAGTAAATATTTTTAAAA
* * *
66421 TGTTGTTAGTTTCA-TAAATATTTTTAAAA
1 GGGTGTTA-TTTTAGTAAATATTTTTAAAA
*
66450 AGGTGTTAGTTTTA
1 GGGTGTTA-TTTTA
66464 ATTCTGTTAG
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
28 27 0.23
29 86 0.74
30 3 0.03
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (29 bp):
GGGTGTTATTTTAGTAAATATTTTTAAAA
Found at i:66428 original size:57 final size:57
Alignment explanation
Indices: 66306--66462 Score: 215
Period size: 57 Copynumber: 2.7 Consensus size: 57
66296 GACCCGACCC
* * *
66306 GGGTGCTATTTTTGTAAATATTTTTAAAAGGGTGTTATTTTAGTAAATATTTTTAAAA
1 GGGTGTTATTTTTGTAAATATTTTTAAAA-AGTGTTATTTTTGTAAATATTTTTAAAA
66364 GGGTGTTATTTTTGTAAATATTTTTAAAAAGTGTTATTTTTGTAAATATTTTTAAAA
1 GGGTGTTATTTTTGTAAATATTTTTAAAAAGTGTTATTTTTGTAAATATTTTTAAAA
* * * ** *
66421 TGTTGTTAGTTTCATAAATATTTTTAAAAAGGTGTTAGTTTT
1 GGGTGTTATTTTTGTAAATATTTTTAAAAA-GTGTTATTTTT
66463 AATTCTGTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
57 51 0.57
58 38 0.43
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (57 bp):
GGGTGTTATTTTTGTAAATATTTTTAAAAAGTGTTATTTTTGTAAATATTTTTAAAA
Found at i:88312 original size:4 final size:4
Alignment explanation
Indices: 88303--88339 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
88293 CTAAAAACAA
*
88303 AAAT AAAT AAAT AAAT AAAT AATAT AAAT AACT AAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT
88340 GTAATAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:88346 original size:17 final size:16
Alignment explanation
Indices: 88303--88339 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
88293 CTAAAAACAA
88303 AAATAAATAAATAAAT
1 AAATAAATAAATAAAT
*
88319 AAATAATATAAATAACT
1 AAATAA-ATAAATAAAT
88336 AAAT
1 AAAT
88340 GTAATAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAATAAATAAAT
Found at i:88542 original size:33 final size:35
Alignment explanation
Indices: 88416--88644 Score: 238
Period size: 34 Copynumber: 6.6 Consensus size: 35
88406 CAAAAATCGC
**
88416 TTTTAAAAA-TATATATTATACGTTTTCAAAATCG
1 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
* * * * *
88450 TTTTAAGAAAACCATATACTATAAGTTTTCAAAACCGTG
1 TTTT-A-AAAACTATATATTATACGTTTTCAAAA--TTA
88489 TTTT---AACTATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
88521 TTTTAAAAACT-T-TATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
* * * ***
88554 TTTTTAAAAACTATGTACTATATGTTTTCAAAACCG
1 -TTTTAAAAACTATATATTATACGTTTTCAAAATTA
88590 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
*
88625 -TTTAAAAACTATATACTATA
1 TTTTAAAAACTATATATTATA
88645 TATGTTTTTT
Statistics
Matches: 162, Mismatches: 22, Indels: 22
0.79 0.11 0.11
Matches are distributed among these distances:
32 5 0.03
33 21 0.13
34 57 0.35
35 35 0.22
36 20 0.12
37 19 0.12
39 5 0.03
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATACGTTTTCAAAATTA
Found at i:88551 original size:104 final size:105
Alignment explanation
Indices: 88416--88644 Score: 324
Period size: 104 Copynumber: 2.2 Consensus size: 105
88406 CAAAAATCGC
*
88416 TTTTAAAAA-TATATATTATACGTTTTCAAAATCGTTTTAAGAAAACCATATACTATAAGTTTTC
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCATTTTAA-AAAACCATATACTATAAGTTTTC
*
88480 AAAACCGTGTTT-TAACTATATATTATACGTTTTCAAAATTA
65 AAAACCGT-TTTAAAACTATATATTATACGTTTTCAAAATTA
* * * * *
88521 TTTTAAAAACT-T-TATTATACGTTTTCAAAATTATTTTTAAAAACTATGTACTATATGTTTTCA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCATTTTAAAAAACCATATACTATAAGTTTTCA
88584 AAACCGTTTTAAAAACTATATATTATACGTTTTCAAAATTA
66 AAACCGTTTT-AAAACTATATATTATACGTTTTCAAAATTA
*
88625 -TTTAAAAACTATATACTATA
1 TTTTAAAAACTATATATTATA
88645 TATGTTTTTT
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
102 3 0.03
103 38 0.34
104 53 0.48
105 16 0.14
106 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (105 bp):
TTTTAAAAACTATATATTATACGTTTTCAAAATCATTTTAAAAAACCATATACTATAAGTTTTCA
AAACCGTTTTAAAACTATATATTATACGTTTTCAAAATTA
Found at i:88652 original size:71 final size:69
Alignment explanation
Indices: 88417--88644 Score: 250
Period size: 69 Copynumber: 3.3 Consensus size: 69
88407 AAAAATCGCT
* * *
88417 TTTAAAAA-TATATATTATACGTTTTCAAAATCGTTTTAAGAAAACCATATACTATAAGTTTTCA
1 TTTAAAAACTATATATTATACGTTTTCAAAATCGTTTT-A-AAAACTATATATTATACGTTTTCA
* *
88481 AAACCGTG
64 AAA--TTA
* **
88489 TTT--TAACTATATATTATACGTTTTCAAAATTATTTTAAAAACT-T-TATTATACGTTTTCAAA
1 TTTAAAAACTATATATTATACGTTTTCAAAATCGTTTTAAAAACTATATATTATACGTTTTCAAA
88550 ATTA
66 ATTA
* * * *
88554 TTTTTAAAAACTATGTACTATATGTTTTCAAAACCGTTTTAAAAACTATATATTATACGTTTTCA
1 --TTTAAAAACTATATATTATACGTTTTCAAAATCGTTTTAAAAACTATATATTATACGTTTTCA
88619 AAATTA
64 AAATTA
*
88625 TTTAAAAACTATATACTATA
1 TTTAAAAACTATATATTATA
88645 TATGTTTTTT
Statistics
Matches: 133, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
65 1 0.01
67 19 0.14
68 1 0.01
69 57 0.43
70 4 0.03
71 48 0.36
72 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (69 bp):
TTTAAAAACTATATATTATACGTTTTCAAAATCGTTTTAAAAACTATATATTATACGTTTTCAAA
ATTA
Done.