Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003048.1 Hibiscus syriacus cultivar Beakdansim tig00006351_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: 57607
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:92 original size:18 final size:19
Alignment explanation
Indices: 66--107 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
56 GTTTACATTA
*
66 TGTTGCGAAAT-AATATTG
1 TGTTTCGAAATAAATATTG
84 TGTTTCGAAATAAATATTG
1 TGTTTCGAAATAAATATTG
103 TGTTT
1 TGTTT
108 TGAATTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (19 bp):
TGTTTCGAAATAAATATTG
Found at i:174 original size:20 final size:20
Alignment explanation
Indices: 149--199 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
139 TAAACGCGCT
* *
149 TTGCGAATTTGACTTCTTTG
1 TTGCGAATTTGACTTATGTG
169 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
189 TTGCGAATTTG
1 TTGCGAATTTG
200 GAAAATCGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:2188 original size:24 final size:24
Alignment explanation
Indices: 2156--2211 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2146 CTATTCTTTC
2156 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
2180 GCTTCAATTGAGCTCGAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
2204 GCTTCAAT
1 GCTTCAAT
2212 CGAACTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:3293 original size:20 final size:21
Alignment explanation
Indices: 3249--3294 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3239 TGTGGGTGTT
** *
3249 TAATGCTGGAAATTGATGTTT
1 TAATGCTGGAAATTGAAATTA
3270 TAATGCT-GAAATTGAAATTA
1 TAATGCTGGAAATTGAAATTA
3290 TAATG
1 TAATG
3295 TTGTTTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (21 bp):
TAATGCTGGAAATTGAAATTA
Found at i:6068 original size:23 final size:23
Alignment explanation
Indices: 6031--6075 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6021 TTTAAGTTAA
** *
6031 TTTTGGTTCGGGTTACTTTTGAC
1 TTTTGGTTCAAGTTAATTTTGAC
6054 TTTTGGTTCAAGTTAATTTTGA
1 TTTTGGTTCAAGTTAATTTTGA
6076 TATCAGTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.22, T:0.53
Consensus pattern (23 bp):
TTTTGGTTCAAGTTAATTTTGAC
Found at i:6145 original size:32 final size:32
Alignment explanation
Indices: 6104--6168 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
6094 TCGATAATGG
6104 TTGATTTTCATTTCGCTAAATTTTGGATCAGT
1 TTGATTTTCATTTCGCTAAATTTTGGATCAGT
6136 TTGATTTTCATTTCGCTAAATTTTGGATCAGT
1 TTGATTTTCATTTCGCTAAATTTTGGATCAGT
6168 T
1 T
6169 ATGGGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (32 bp):
TTGATTTTCATTTCGCTAAATTTTGGATCAGT
Found at i:7122 original size:2 final size:2
Alignment explanation
Indices: 7117--7158 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
7107 ACACACACAC
*
7117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7159 GTCCAGAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10594 original size:46 final size:46
Alignment explanation
Indices: 10527--10617 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
10517 TACCGTTTGC
10527 AAAATGAAACGGTAAAGAATATACATCTGTATTTCATTTTTCATAA
1 AAAATGAAACGGTAAAGAATATACATCTGTATTTCATTTTTCATAA
10573 AAAATGAAACGGTAAAGAATATACATCTGTATTTCATTTTTCATA
1 AAAATGAAACGGTAAAGAATATACATCTGTATTTCATTTTTCATA
10618 GATTTATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (46 bp):
AAAATGAAACGGTAAAGAATATACATCTGTATTTCATTTTTCATAA
Found at i:12779 original size:24 final size:24
Alignment explanation
Indices: 12723--12772 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12713 TTGTTTACTT
* * *
12723 TAATTTAATATATAATATTATTAA
1 TAATTAAATATATAATAATATAAA
12747 TAATTAAATATATAATAATAGTAAA
1 TAATTAAATATATAATAATA-TAAA
12772 T
1 T
12773 CATAAATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATTAAATATATAATAATATAAA
Found at i:14659 original size:13 final size:13
Alignment explanation
Indices: 14638--14680 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
14628 ATGATAGAAG
14638 TAATAAAATAAAA
1 TAATAAAATAAAA
*
14651 TAGTAAAATAAAA
1 TAATAAAATAAAA
*
14664 TAATAAATATACAA
1 TAATAAA-ATAAAA
14678 TAA
1 TAA
14681 AATAAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
TAATAAAATAAAA
Found at i:17759 original size:31 final size:32
Alignment explanation
Indices: 17720--17810 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 32
17710 AGAGTCGAGA
17720 GTTACCTATGTCTTTCGAGACATATGGACAAT
1 GTTACCTATGTCTTTCGAGACATATGGACAAT
* * * * *
17752 -TTACCTATGCCCTTCAAGACATATTGACAGT
1 GTTACCTATGTCTTTCGAGACATATGGACAAT
* *
17783 GTTACTTATGTTCTTTGGA-ACATATGGA
1 GTTACCTATG-TCTTTCGAGACATATGGA
17811 TAGGTCATTC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
31 26 0.57
32 16 0.35
33 4 0.09
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (32 bp):
GTTACCTATGTCTTTCGAGACATATGGACAAT
Found at i:18844 original size:21 final size:21
Alignment explanation
Indices: 18820--18935 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
18810 TACCCCTACG
*
18820 AGTATCAATACTACCCTTGGC
1 AGTATCGATACTACCCTTGGC
* *
18841 AGTATCGACACTGACACATT-G-
1 AGTATCGATACT-AC-CCTTGGC
* *** *
18862 AGTATCGATACT-GCAGGGGT
1 AGTATCGATACTACCCTTGGC
*
18882 AGTATCAATACTACCCTTGGC
1 AGTATCGATACTACCCTTGGC
18903 AGTATCGATACTACCCTTGGC
1 AGTATCGATACTACCCTTGGC
*
18924 AGTGTCGATACT
1 AGTATCGATACT
18936 TCCAGTCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
18 2 0.03
19 1 0.01
20 11 0.15
21 55 0.73
22 3 0.04
23 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTACCCTTGGC
Found at i:21221 original size:32 final size:32
Alignment explanation
Indices: 21093--21223 Score: 163
Period size: 32 Copynumber: 4.1 Consensus size: 32
21083 ACTGATACTC
* * * *
21093 ATGTGCATTATCTGAATGTAAACATGACCATA
1 ATGTGCATTATATGAATGCAAACCTAACCATA
* * * *
21125 CTATGCATTATTTGAATGCAAACCTAGCCATA
1 ATGTGCATTATATGAATGCAAACCTAACCATA
* *
21157 CTATGCATTATATGAATGCAAACCTAACCATA
1 ATGTGCATTATATGAATGCAAACCTAACCATA
*
21189 ATGTGCATTATATGAATGCACACCTAACCATA
1 ATGTGCATTATATGAATGCAAACCTAACCATA
21221 ATG
1 ATG
21224 CGTATTATTA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 87 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (32 bp):
ATGTGCATTATATGAATGCAAACCTAACCATA
Found at i:22406 original size:19 final size:20
Alignment explanation
Indices: 22361--22410 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
22351 ATGTGCCAAC
22361 AGTATCGATACTAACCCTTG
1 AGTATCGATACTAACCCTTG
* * *
22381 GGTATCGATGCTCACCC-TG
1 AGTATCGATACTAACCCTTG
22400 AGTATCGATAC
1 AGTATCGATAC
22411 CAAAACTAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTAACCCTTG
Found at i:22491 original size:20 final size:20
Alignment explanation
Indices: 22466--22517 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
22456 CCTGTAGGGA
22466 GTATCGATACTCTACCCTGG
1 GTATCGATACTCTACCCTGG
* **
22486 GTATCGATATTCTACGTTGG
1 GTATCGATACTCTACCCTGG
22506 GTATCGATACTC
1 GTATCGATACTC
22518 CTGTAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (20 bp):
GTATCGATACTCTACCCTGG
Found at i:27427 original size:20 final size:21
Alignment explanation
Indices: 27402--27442 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27392 CTTTTGAAAG
* *
27402 CAAAATTAGATTTT-AAAAAT
1 CAAAATGAAATTTTGAAAAAT
27422 CAAAATGAAATTTTGAAAAAT
1 CAAAATGAAATTTTGAAAAAT
27443 GATTTTGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
CAAAATGAAATTTTGAAAAAT
Found at i:28226 original size:14 final size:14
Alignment explanation
Indices: 28209--28235 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28199 TGACTTGGAT
28209 TTATTGAATTTCAA
1 TTATTGAATTTCAA
28223 TTATTGAATTTCA
1 TTATTGAATTTCA
28236 TGTGCTACTA
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:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TTATTGAATTTCAA
Found at i:30548 original size:22 final size:24
Alignment explanation
Indices: 30508--30551 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
30498 GATAGTGTAA
30508 CAGTTAAAATATTTTATGATTTTT
1 CAGTTAAAATATTTTATGATTTTT
30532 CAGTT-AAATA-TTTATGATTT
1 CAGTTAAAATATTTTATGATTT
30552 AATATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (24 bp):
CAGTTAAAATATTTTATGATTTTT
Found at i:40298 original size:19 final size:19
Alignment explanation
Indices: 40249--40298 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
40239 AATATCTATG
40249 TAAT-TTTAATTTATTTTT
1 TAATATTTAATTTATTTTT
*
40267 TAATA-ATACATTTATTTTT
1 TAATATTTA-ATTTATTTTT
*
40286 TATTATTTAATTT
1 TAATATTTAATTT
40299 CTTAACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.23
19 18 0.69
20 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATATTTAATTTATTTTT
Found at i:40461 original size:22 final size:23
Alignment explanation
Indices: 40404--40464 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
40394 GTTTGCCTCT
*
40404 TAATGGAATCATTCAGCGCTGAA
1 TAATTGAATCATTCAGCGCTGAA
*
40427 TAATTCAA-CATTCAGCGCTGAA
1 TAATTGAATCATTCAGCGCTGAA
* *
40449 T-GTTGAATTATTCAGC
1 TAATTGAATCATTCAGC
40465 ATTCAGCACG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 4 0.12
22 22 0.69
23 6 0.19
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (23 bp):
TAATTGAATCATTCAGCGCTGAA
Found at i:44344 original size:55 final size:55
Alignment explanation
Indices: 44247--44747 Score: 826
Period size: 55 Copynumber: 9.1 Consensus size: 55
44237 ATATCTTCGT
* * *
44247 CAATCGTGTCTGCTCCCTATTT-TTCAGAGAGTATAAGACTCGAACGAT-TCTCGA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAA
* *
44301 TAATCGTGCCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* *
44356 CAATCGTGTCTGTTCCCTATTTGTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
44411 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
44466 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
** * *
44521 CAATTATGTCTGCTCCTTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTTAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* * *
44576 CAATCGTGTCTGCTCCCTATTTCTTCAAAGAGTACGAGACTCGAATAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* * *
44631 CAATTGTGTTTGCTCCCTATTTCTTAAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
44686 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
44741 CAATCGT
1 CAATCGT
44748 TGGGAAACCT
Statistics
Matches: 414, Mismatches: 31, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
54 20 0.05
55 393 0.95
56 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (55 bp):
CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
Found at i:45684 original size:7 final size:8
Alignment explanation
Indices: 45671--45721 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
45661 GAACCCTTCT
45671 TTTTTTCA
1 TTTTTTCA
*
45679 TTTTTCCA
1 TTTTTTCA
45687 TTTTTT-A
1 TTTTTTCA
*
45694 TTTTTTTA
1 TTTTTTCA
*
45702 TTTTTTTA
1 TTTTTTCA
45710 TTTTTTCA
1 TTTTTTCA
45718 TTTT
1 TTTT
45722 CACTCATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
7 7 0.18
8 32 0.82
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Done.