Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007536.1 Hibiscus syriacus cultivar Beakdansim tig00021093_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: 27265
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:2402 original size:18 final size:18
Alignment explanation
Indices: 2371--2412 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
2361 AAATTTAAAA
2371 GAAAATATATAAATACTAT
1 GAAAATATATAAATA-TAT
2390 GAAAATA-ATAAATATAT
1 GAAAATATATAAATATAT
*
2407 AAAAAT
1 GAAAAT
2413 TTGAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
GAAAATATATAAATATAT
Found at i:2940 original size:23 final size:25
Alignment explanation
Indices: 2900--2948 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
2890 GAGAAAAAGA
*
2900 AAAAAATTTATATATATTTATAAAT
1 AAAAAATTTATATATATTTAGAAAT
*
2925 AAAATATTTAT-T-TATTTAGAAAT
1 AAAAAATTTATATATATTTAGAAAT
2948 A
1 A
2949 TCAGAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAAAATTTATATATATTTAGAAAT
Found at i:4459 original size:3 final size:3
Alignment explanation
Indices: 4453--4506 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
4443 ATTATTTTTT
*
4453 TAA TAA TAA TATA TAA TAA -ATA TAA T-A TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
4498 TAA TAA TAA
1 TAA TAA TAA
4507 ATGGGTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 3 0.07
3 38 0.84
4 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4480 original size:14 final size:14
Alignment explanation
Indices: 4463--4500 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
4453 TAATAATAAT
4463 ATATAATAAATATA
1 ATATAATAAATATA
*
4477 ATATAATAATTATA
1 ATATAATAAATATA
4491 ATAATAATAA
1 AT-ATAATAA
4501 TAATAAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAATAAATATA
Found at i:6331 original size:20 final size:21
Alignment explanation
Indices: 6293--6331 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
6283 AAAAAAATTA
**
6293 TATATAAATTTTATTATAAAG
1 TATATAAATTTTAAAATAAAG
6314 TATATAAA-TTTAAAATAA
1 TATATAAATTTTAAAATAA
6332 TAAAACAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TATATAAATTTTAAAATAAAG
Found at i:6723 original size:11 final size:11
Alignment explanation
Indices: 6707--6736 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
6697 GAACGCTTGG
6707 CCGTCTCTCTC
1 CCGTCTCTCTC
6718 CCGTCTCTCTC
1 CCGTCTCTCTC
6729 CCGTCTCT
1 CCGTCTCT
6737 AGCCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.53, G:0.10, T:0.37
Consensus pattern (11 bp):
CCGTCTCTCTC
Found at i:8314 original size:113 final size:112
Alignment explanation
Indices: 8116--8421 Score: 483
Period size: 113 Copynumber: 2.7 Consensus size: 112
8106 GATTAAAATT
* *
8116 AACTTATTCTTCCTTCTTCAGTTGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTCGATCCA
1 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGT-GATCCA
* *
8181 TCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATG
65 TCAAGTGATGGATTTGAGCAAAAGATTAAACAAGCTCTTCTCATTATG
8229 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA
1 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-TGATCCA
8294 TCAAGTGATGGATTTGAGCAAAAGATTAAACAAGCTCTTCTCATTATG
65 TCAAGTGATGGATTTGAGCAAAAGATTAAACAAGCTCTTCTCATTATG
* * *
8342 AACTTCTTCTTCATTCTTCAGACGAGTTCTTCTCATTATGAACTCTT-TCTGGAAATGTTGATCC
1 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAG-TGATCC
*
8406 AT--TGTGATGGATTTGA
64 ATCAAGTGATGGATTTGA
8422 ATCTTTGCTA
Statistics
Matches: 182, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
111 13 0.07
113 166 0.91
114 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (112 bp):
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGATCCAT
CAAGTGATGGATTTGAGCAAAAGATTAAACAAGCTCTTCTCATTATG
Found at i:9548 original size:18 final size:19
Alignment explanation
Indices: 9520--9597 Score: 88
Period size: 19 Copynumber: 3.9 Consensus size: 19
9510 TTTACAAAAT
9520 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
*
9540 -AAAAATAAATTGAATCTC
1 AAAAAATAAATTGAATTTC
9558 AAAAAATAAATTGAATTT-
1 AAAAAATAAATTGAATTTC
9576 AGAGAAAATAAACTTAGAATTT
1 A-A-AAAATAAA-TT-GAATTT
9598 ATTAATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.29
19 20 0.39
20 8 0.16
21 2 0.04
22 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:9948 original size:9 final size:8
Alignment explanation
Indices: 9926--9981 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
9916 ATCTTGACCC
9926 TCTTTTTT
1 TCTTTTTT
* *
9934 TATTTTCT
1 TCTTTTTT
9942 TCTTTTTT
1 TCTTTTTT
9950 TCTTTTTTT
1 TC-TTTTTT
9959 TCTCTTTATT
1 TCT-TTT-TT
9969 TCATTTTTT
1 TC-TTTTTT
9978 TCTT
1 TCTT
9982 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 17 0.43
9 15 0.38
10 7 0.17
11 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:9948 original size:17 final size:17
Alignment explanation
Indices: 9928--9981 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
9918 CTTGACCCTC
*
9928 TTTTTTTATTTTCTTCT
1 TTTTTTTATTTTTTTCT
9945 TTTTTTCT-TTTTTTTCT
1 TTTTTT-TATTTTTTTCT
*
9962 CTTTATTTCATTTTTTTCT
1 -TTT-TTTTATTTTTTTCT
9981 T
1 T
9982 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 14 0.45
18 5 0.16
19 12 0.39
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTATTTTTTTCT
Found at i:9961 original size:20 final size:20
Alignment explanation
Indices: 9931--9982 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
9921 GACCCTCTTT
*
9931 TTTTATTTTCTTCTTTTTTTC
1 TTTT-TTTTCTTCTTTATTTC
9952 TTTTTTTTC-TCTTTATTTC
1 TTTTTTTTCTTCTTTATTTC
*
9971 ATTTTTTTCTTC
1 TTTTTTTTCTTC
9983 AAGCATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 17 0.61
20 7 0.25
21 4 0.14
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTTCTTCTTTATTTC
Found at i:13506 original size:9 final size:9
Alignment explanation
Indices: 13491--13523 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
13481 GAAAAATAAT
13491 GAATGTAAA
1 GAATGTAAA
*
13500 AAATGTAAA
1 GAATGTAAA
13509 GAATGTAAA
1 GAATGTAAA
13518 GAATGT
1 GAATGT
13524 TTGCCATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (9 bp):
GAATGTAAA
Found at i:20581 original size:16 final size:15
Alignment explanation
Indices: 20560--20589 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20550 TTAATACTTG
20560 AAAATAAAAACAAAAA
1 AAAATAAAAA-AAAAA
20576 AAAATAAAAAAAAA
1 AAAATAAAAAAAAA
20590 TAATATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAATAAAAAAAAAA
Found at i:22821 original size:3 final size:3
Alignment explanation
Indices: 22813--22883 Score: 69
Period size: 3 Copynumber: 24.0 Consensus size: 3
22803 TTTGGGTCTG
*
22813 TAA TAA TAA CTTAA TTAA TAA TAA TAA TAA T-A TAA TAG TAA -AA TAA
1 TAA TAA TAA --TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
22859 -AA TAA TAT TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
22884 AAAACAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 43 0.74
4 4 0.07
5 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22885 original size:30 final size:30
Alignment explanation
Indices: 22829--22885 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
22819 TAACTTAATT
*
22829 AATAATAATAATAATATAATAGTAAAATAA
1 AATAATAATAATAATATAATAATAAAATAA
*
22859 AATAATATTAATAATA-ATATAATAAAA
1 AATAATAATAATAATATA-ATAATAAAA
22886 AACAAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (30 bp):
AATAATAATAATAATATAATAATAAAATAA
Found at i:27140 original size:14 final size:15
Alignment explanation
Indices: 27108--27140 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27098 ATACATATAC
27108 TTTATAGTATAACTA
1 TTTATAGTATAACTA
*
27123 TTTATAGT-TAAGTA
1 TTTATAGTATAACTA
27137 TTTA
1 TTTA
27141 AAAAACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (15 bp):
TTTATAGTATAACTA
Done.