Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002737.1 Hibiscus syriacus cultivar Beakdansim tig00005642_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: 55817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4669 original size:2 final size:2
Alignment explanation
Indices: 4662--4703 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4652 CACTATACTA
4662 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
4704 CAAAATAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8497 original size:20 final size:20
Alignment explanation
Indices: 8456--8498 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
8446 TATAGTTTTC
*
8456 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAACA
*
8476 AAAACAACA-ATTTAAAAACA
1 AAAACAACATAATT-AAAACA
8496 AAA
1 AAA
8499 TATTTTCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACAACATAATTAAAACA
Found at i:8769 original size:2 final size:2
Alignment explanation
Indices: 8762--8799 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
8752 TTACCCGGAT
8762 TA TA TA TA -A TA TA -A T- 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 TA TA T
8800 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9461 original size:21 final size:22
Alignment explanation
Indices: 9407--9469 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
9397 CCCTTGGGGG
* *
9407 GTATCAATACACATTAAAGGAAT
1 GTATCGATACACATTCAAGG-AT
* *
9430 GTATAGGTACACATTCAAGG-T
1 GTATCGATACACATTCAAGGAT
*
9451 GTATCGATACATA-TCAAGG
1 GTATCGATACACATTCAAGG
9470 GGGTATGGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 6 0.18
21 11 0.33
23 16 0.48
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (22 bp):
GTATCGATACACATTCAAGGAT
Found at i:17769 original size:18 final size:16
Alignment explanation
Indices: 17744--17777 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
17734 CTACTCATGG
17744 TGTTTATGTTACTTTTA
1 TGTTTATGTTA-TTTTA
17761 TGTTATATGTTATTTTA
1 TGTT-TATGTTATTTTA
17778 AAGGCTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.65
Consensus pattern (16 bp):
TGTTTATGTTATTTTA
Found at i:22453 original size:15 final size:15
Alignment explanation
Indices: 22433--22464 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22423 TTCATGGGGT
22433 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
*
22448 AAGAAGAAAATGTCA
1 AAGAAGAAAACGTCA
22463 AA
1 AA
22465 AAAGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.09, G:0.19, T:0.09
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:28828 original size:2 final size:2
Alignment explanation
Indices: 28821--28850 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28811 TCAATCTACA
28821 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
28851 TTACGAAATA
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:30102 original size:13 final size:13
Alignment explanation
Indices: 30084--30108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30074 TAAGATTTTG
30084 AAATTTTGAAATC
1 AAATTTTGAAATC
30097 AAATTTTGAAAT
1 AAATTTTGAAAT
30109 TACTCCCCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AAATTTTGAAATC
Found at i:30787 original size:12 final size:12
Alignment explanation
Indices: 30770--30798 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
30760 TTGTTGTGCT
30770 TGCTCTTCGGGC
1 TGCTCTTCGGGC
30782 TGCTCTTCGGGC
1 TGCTCTTCGGGC
30794 TGCTC
1 TGCTC
30799 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (12 bp):
TGCTCTTCGGGC
Found at i:32424 original size:20 final size:21
Alignment explanation
Indices: 32379--32439 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
32369 TTCCCCTGTG
32379 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
32402 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
*
32422 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
32440 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 3 0.08
23 13 0.36
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:36270 original size:21 final size:21
Alignment explanation
Indices: 36246--36285 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36236 GAGTTTGTTT
*
36246 TCATTTTTAAATTTTAAAACA
1 TCATTTATAAATTTTAAAACA
*
36267 TCATTTATATATTTTAAAA
1 TCATTTATAAATTTTAAAA
36286 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TCATTTATAAATTTTAAAACA
Found at i:42194 original size:14 final size:14
Alignment explanation
Indices: 42130--42197 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
42120 AGTCCAGTCA
*
42130 CTGAGTCAAATCGAT
1 CTGAGTCAACTCG-T
* * * *
42145 CGGAGTTAACCCAT
1 CTGAGTCAACTCGT
*
42159 CTGAGTCAACTAGGT
1 CTGAGTCAACT-CGT
*
42174 CTAAGTCAACTCGT
1 CTGAGTCAACTCGT
42188 CTGAGTCAAC
1 CTGAGTCAAC
42198 CCGTTGACTT
Statistics
Matches: 39, Mismatches: 13, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
14 20 0.51
15 19 0.49
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:42219 original size:14 final size:14
Alignment explanation
Indices: 42200--42226 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42190 GAGTCAACCC
42200 GTTGACTTTGACCA
1 GTTGACTTTGACCA
42214 GTTGACTTTGACC
1 GTTGACTTTGACC
42227 GAAAAGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (14 bp):
GTTGACTTTGACCA
Found at i:47282 original size:27 final size:27
Alignment explanation
Indices: 47252--47304 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
47242 AGATTTATAG
*
47252 AAAT-GCCCTTAAAGTTTAAAATGACCA
1 AAATAGCCC-TAAAGTGTAAAATGACCA
*
47279 AAATATCCCTAAAGTGTAAAATGACC
1 AAATAGCCCTAAAGTGTAAAATGACC
47305 TAAAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (27 bp):
AAATAGCCCTAAAGTGTAAAATGACCA
Done.