Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000610.1 Hibiscus syriacus cultivar Beakdansim tig00001184_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: 58289
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:6320 original size:16 final size:16
Alignment explanation
Indices: 6295--6327 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6285 AATCAATACA
6295 AATATTTAAAT-ATTT
1 AATATTTAAATAATTT
6310 AATATTTTAAATAATTT
1 AATA-TTTAAATAATTT
6327 A
1 A
6328 TTTAGGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTTAAATAATTT
Found at i:7927 original size:35 final size:38
Alignment explanation
Indices: 7888--7957 Score: 103
Period size: 35 Copynumber: 1.9 Consensus size: 38
7878 GTTTAAGATA
7888 AAATATATTA-TTTAA-TCA-TTTAAAATA-TAATAAAT
1 AAATATATTATTTTAACT-ATTTTAAAATATTAATAAAT
7923 AAATATATTATTTTAACTATTTTAAAATATTAATA
1 AAATATATTATTTTAACTATTTTAAAATATTAATA
7958 TATACGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 10 0.32
36 6 0.19
37 10 0.32
38 5 0.16
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (38 bp):
AAATATATTATTTTAACTATTTTAAAATATTAATAAAT
Found at i:8711 original size:17 final size:17
Alignment explanation
Indices: 8689--8722 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
8679 TAATTATATA
8689 TTAAATCTTTTA-AAATT
1 TTAAAT-TTTTATAAATT
8706 TTAAATTTTTATAAATT
1 TTAAATTTTTATAAATT
8723 AAATTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTTTTATAAATT
Found at i:9103 original size:67 final size:64
Alignment explanation
Indices: 9020--9145 Score: 173
Period size: 67 Copynumber: 1.9 Consensus size: 64
9010 ACTAAAGTTC
*
9020 AAAAACACTAGATTTAATTATTAAACTTCTGAATTACTTTTTTTTTATCAGTTATTCAATTAAAT
1 AAAAACACTAGATTTAATTATTAAACTTCTGAATTAC---TTTTTTATCAGTTACTCAATTAAAT
9085 TA
63 TA
** *
9087 AAAAACACTCAG-TTTAATTATTAAGTTTTTGAATTACTTTTTTATCAGTTACTCAATTA
1 AAAAACACT-AGATTTAATTATTAAACTTCTGAATTACTTTTTTATCAGTTACTCAATTA
9146 TTGAATAGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
64 21 0.39
67 31 0.57
68 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (64 bp):
AAAAACACTAGATTTAATTATTAAACTTCTGAATTACTTTTTTATCAGTTACTCAATTAAATTA
Found at i:12600 original size:16 final size:15
Alignment explanation
Indices: 12570--12598 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12560 CATCTGAAAC
12570 GTTTATTTTTAAAAG
1 GTTTATTTTTAAAAG
12585 GTTTATTTTTAAAA
1 GTTTATTTTTAAAA
12599 AGAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
GTTTATTTTTAAAAG
Found at i:14539 original size:18 final size:18
Alignment explanation
Indices: 14516--14550 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14506 ACTGAATATT
14516 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
14534 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
14551 GCTAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:21347 original size:18 final size:18
Alignment explanation
Indices: 21324--21358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21314 ACTGAATATT
*
21324 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
21342 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
21359 GATAATACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:24946 original size:15 final size:15
Alignment explanation
Indices: 24926--24965 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
24916 TCTCGATTAC
24926 ATCCACTTTGGCTTT
1 ATCCACTTTGGCTTT
*
24941 ATCCACTTTGGTTTT
1 ATCCACTTTGGCTTT
24956 ATCCACTTTG
1 ATCCACTTTG
24966 ATGCCTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (15 bp):
ATCCACTTTGGCTTT
Found at i:27368 original size:21 final size:20
Alignment explanation
Indices: 27339--27378 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27329 GTATCAAGGT
27339 TTTTATTGAAGCCATGAAATC
1 TTTTATTGAAGCCAT-AAATC
* *
27360 TTTTGTTGAGGCCATAAAT
1 TTTTATTGAAGCCATAAAT
27379 TCATGCAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTTATTGAAGCCATAAATC
Found at i:31308 original size:21 final size:21
Alignment explanation
Indices: 31282--31321 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31272 CAGAACCCCA
*
31282 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
31303 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
31322 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:31350 original size:19 final size:20
Alignment explanation
Indices: 31304--31363 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
31294 TTCCCCTGTG
31304 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
31327 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
31346 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
31364 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:40667 original size:12 final size:12
Alignment explanation
Indices: 40652--40682 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40642 TATTATTATT
40652 ATTTTTATTTTA
1 ATTTTTATTTTA
*
40664 ATTTTAATTTTA
1 ATTTTTATTTTA
40676 ATTTTTA
1 ATTTTTA
40683 CAGGCCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:40809 original size:16 final size:16
Alignment explanation
Indices: 40784--40815 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40774 TTTGAAACCC
*
40784 TACGATTTCCAATCGT
1 TACGAATTCCAATCGT
40800 TACGAATTCCAATCGT
1 TACGAATTCCAATCGT
40816 AGCCGTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (16 bp):
TACGAATTCCAATCGT
Found at i:42784 original size:5 final size:5
Alignment explanation
Indices: 42774--42805 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
42764 ATTGGTAATT
42774 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
42806 TATTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:46124 original size:23 final size:22
Alignment explanation
Indices: 46098--46148 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
46088 AGGGAATCAG
46098 TTCCCATTCAAAGGGGGAAACGA
1 TTCCCATTC-AAGGGGGAAACGA
* * *
46121 TTCCCCCTTCAAGGGGGTATCGA
1 TT-CCCATTCAAGGGGGAAACGA
46144 TTCCC
1 TTCCC
46149 TTTGCACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 15 0.62
24 6 0.25
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (22 bp):
TTCCCATTCAAGGGGGAAACGA
Found at i:51834 original size:18 final size:19
Alignment explanation
Indices: 51807--51843 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
51797 AAAATTGTTG
*
51807 TTTTTAATTAAAATTAATA
1 TTTTTAATTAAAAATAATA
51826 TTTTT-ATTAAAAATAATA
1 TTTTTAATTAAAAATAATA
51844 AGTATGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTAATTAAAAATAATA
Done.