Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000677.1 Hibiscus syriacus cultivar Beakdansim tig00001313_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: 88990
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8376 original size:22 final size:23
Alignment explanation
Indices: 8351--8405 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
8341 TTATTTTATA
* *
8351 TATTTATTTACTATTGTTTAG-T
1 TATTTATTTACTACTATTTAGTT
* *
8373 TATTTACTTATTACTATTTAGTTT
1 TATTTATTTACTACTATTTAG-TT
8397 TATTTATTT
1 TATTTATTT
8406 GTCATGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.65
24 9 0.35
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (23 bp):
TATTTATTTACTACTATTTAGTT
Found at i:18706 original size:17 final size:17
Alignment explanation
Indices: 18668--18706 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
18658 AAATTGAATG
*
18668 AAAAAATAAAAAATATA
1 AAAAAATAAAAAATAAA
18685 AAAAAAT-AAAAATAAA
1 AAAAAATAAAAAATAAA
*
18701 ATAAAA
1 AAAAAA
18707 GGGGGTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAATAAAAAATAAA
Found at i:19445 original size:24 final size:24
Alignment explanation
Indices: 19418--19488 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
19408 ATGGGCAGAG
*
19418 TGATAGCCAAATAGTACATGGACT
1 TGATAGCCAAATAGTACAAGGACT
*
19442 TGATAGCCAAATAGTACAGGGACT
1 TGATAGCCAAATAGTACAAGGACT
* *
19466 TGATTGCCAAATAATACAAGGAC
1 TGATAGCCAAATAGTACAAGGAC
19489 CTGACTGCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (24 bp):
TGATAGCCAAATAGTACAAGGACT
Found at i:20575 original size:12 final size:12
Alignment explanation
Indices: 20558--20586 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20548 ATTAGATTAC
20558 TATAACTATATA
1 TATAACTATATA
20570 TATAACTATATA
1 TATAACTATATA
20582 TATAA
1 TATAA
20587 TAGTATTTTT
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAACTATATA
Found at i:22011 original size:2 final size:2
Alignment explanation
Indices: 22004--22119 Score: 100
Period size: 2 Copynumber: 59.5 Consensus size: 2
21994 TACATACATG
22004 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
* * * * *
22046 TA T- TA T- TT TA AA TGA TA T- TA TA AA TA TT TA TGA -A TA TA TGG
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T-A TA TA TA T-A
* *
22087 TA -A TT TA TA -A TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22120 TATTTTTGGA
Statistics
Matches: 92, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
1 6 0.07
2 82 0.89
3 4 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24701 original size:2 final size:2
Alignment explanation
Indices: 24694--24751 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
24684 TTATTTAGAA
24694 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
24736 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
24752 GAAAAATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25101 original size:16 final size:16
Alignment explanation
Indices: 25081--25123 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
25071 AAAGTCCATT
25081 AAAAATAAAACTTT-A
1 AAAAATAAAACTTTCA
25096 ACAAAATAAAA-TTTCA
1 A-AAAATAAAACTTTCA
25112 AAATAATAAAAC
1 AAA-AATAAAAC
25124 AATTTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAAACTTTCA
Found at i:30819 original size:21 final size:21
Alignment explanation
Indices: 30793--30837 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30783 GATTTCTGGG
* *
30793 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
30814 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
30835 CAA
1 CAA
30838 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:31210 original size:2 final size:2
Alignment explanation
Indices: 31203--31257 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
31193 CATGAGTTAG
31203 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
31245 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
31258 GGAATTGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32071 original size:32 final size:32
Alignment explanation
Indices: 32030--32126 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
32020 GAGTCGAGGG
32030 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
32062 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
32093 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
32125 TT
1 TT
32127 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:32102 original size:31 final size:31
Alignment explanation
Indices: 32029--32129 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
32019 AGAGTCGAGG
32029 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
32060 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
32092 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
32123 GTTTACC
1 GTTTACC
32130 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:32161 original size:30 final size:30
Alignment explanation
Indices: 32117--32190 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
32107 AAGGAACATA
32117 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
32148 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
32178 TGGATAGTTACCG
1 TGGACAGTTACCG
32191 GGGTATGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 35 0.83
31 7 0.17
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:32211 original size:29 final size:30
Alignment explanation
Indices: 32125--32213 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
32115 TATGGACAGT
* * *
32125 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATATGTATGACCTCTGGATAG
* *
32155 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATATGTATGACCTCTGGATAG
* *
32185 TTACCG-GGGTATGTGTGACCTCTGGATAG
1 TTACCGAGGATATGTATGACCTCTGGATAG
32214 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 19 0.35
30 35 0.65
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATATGTATGACCTCTGGATAG
Found at i:53445 original size:59 final size:59
Alignment explanation
Indices: 53370--53765 Score: 621
Period size: 59 Copynumber: 6.7 Consensus size: 59
53360 TGGCACTAAC
* * *
53370 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGTCACTTTG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* *
53429 TGTGCTAAAATTTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* * * *
53488 TGTACTAAAATGTTAAGAAATTCATACAAAGTGTATGAATTTTCGTATAGGGCACTTTG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* *
53547 TGTGCTAAAATGTTAAAAAAATCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* * *
53606 TGTGCTAAAATATTAAAAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTCG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* * *
53665 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
* *
53724 TGTGCTAAAATGTTAAAAAATTCATTCTAAGTGTATGAATTT
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT
53766 ATGTATTGGG
Statistics
Matches: 313, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 313 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (59 bp):
TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCG
Found at i:54386 original size:45 final size:45
Alignment explanation
Indices: 54294--54387 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
54284 GATGTATAAC
* *
54294 AATGTATAATAATGTATAAAAGGCATGAATGAATGTCATAAATGA
1 AATGTATAATAATGTATAAAAGGCATGAAAGAATGTCAAAAATGA
* *
54339 AATGTATAATAGTGTATAAAAGGCATGAAAGGATG-CAAAAATGGA
1 AATGTATAATAATGTATAAAAGGCATGAAAGAATGTCAAAAAT-GA
54384 AATG
1 AATG
54388 GCATAATGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 6 0.14
45 38 0.86
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (45 bp):
AATGTATAATAATGTATAAAAGGCATGAAAGAATGTCAAAAATGA
Found at i:58548 original size:18 final size:19
Alignment explanation
Indices: 58515--58552 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
58505 TAACTCAAAG
58515 TTAAATATTATTTTAAGTAA
1 TTAAATATTATTTTAA-TAA
58535 TTAAAT-TT-TTTTAATAA
1 TTAAATATTATTTTAATAA
58552 T
1 T
58553 ATCATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 2 0.11
20 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTAAATATTATTTTAATAA
Found at i:58866 original size:16 final size:16
Alignment explanation
Indices: 58845--58875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58835 TAATTTCAAA
*
58845 AAATAAAAAGTAAATC
1 AAATAAAAAATAAATC
58861 AAATAAAAAATAAAT
1 AAATAAAAAATAAAT
58876 AAGACATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATAAAAAATAAATC
Found at i:62161 original size:21 final size:19
Alignment explanation
Indices: 62125--62176 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
62115 TATTTATTTA
*
62125 AATATT-ATACATTATATATT
1 AATATTAATA-ATTATA-AAT
62145 AATATTAATAATATATAAAT
1 AATATTAATAAT-TATAAAT
62165 ATATATTAATAA
1 A-ATATTAATAA
62177 AAAAATGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTAATAATTATAAAT
Found at i:75363 original size:23 final size:24
Alignment explanation
Indices: 75310--75360 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
75300 CTTTATTTTC
* * *
75310 TTTTCTTCTTTTTGAGTGCTTGAA
1 TTTTCTTCTTTTGGAGTACTTCAA
75334 TTTTCTTCTTTTGGAGTACTTCAA
1 TTTTCTTCTTTTGGAGTACTTCAA
75358 TTT
1 TTT
75361 CTTTGCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTACTTCAA
Found at i:77526 original size:2 final size:2
Alignment explanation
Indices: 77519--77562 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
77509 TGAAAGTGGA
77519 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
77561 AT
1 AT
77563 GTTGGTGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79323 original size:21 final size:17
Alignment explanation
Indices: 79279--79321 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
79269 CTTGAGTATG
79279 AGGTGAATGTATTTTAA
1 AGGTGAATGTATTTTAA
79296 AGGTGAATGTATTTTAA
1 AGGTGAATGTATTTTAA
*
79313 AGGTTAATG
1 AGGTGAATG
79322 AACATGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (17 bp):
AGGTGAATGTATTTTAA
Found at i:80054 original size:11 final size:11
Alignment explanation
Indices: 80038--80062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80028 TACAAAAAAA
80038 GAAGTGCAAGT
1 GAAGTGCAAGT
80049 GAAGTGCAAGT
1 GAAGTGCAAGT
80060 GAA
1 GAA
80063 AGAAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:80128 original size:24 final size:22
Alignment explanation
Indices: 80086--80143 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
80076 ATAAAAAAAA
* *
80086 TCAACAAAG-AAATTGAAGCAC
1 TCAAAAAAGAAAATTCAAGCAC
80107 TCTAAAAGAAGAAAATTCAAGCAC
1 TC-AAAA-AAGAAAATTCAAGCAC
80131 TCAAAAAAGAAAA
1 TCAAAAAAGAAAA
80144 AAAGAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 10 0.31
23 7 0.22
24 13 0.41
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.14
Consensus pattern (22 bp):
TCAAAAAAGAAAATTCAAGCAC
Found at i:84215 original size:11 final size:11
Alignment explanation
Indices: 84201--84225 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
84191 TTACAAAAAA
84201 GAAGTGCAAGT
1 GAAGTGCAAGT
84212 GAAGTGCAAGT
1 GAAGTGCAAGT
84223 GAA
1 GAA
84226 AGAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:84281 original size:24 final size:24
Alignment explanation
Indices: 84248--84298 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
84238 ATCAACAAAT
* *
84248 AAATTGAAGCACTCCAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAGA
84272 AAATTCAAGCACTCAAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAGA
84296 AAA
1 AAA
84299 GAAAAGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.12
Consensus pattern (24 bp):
AAATTCAAGCACTCAAAAAGAAGA
Done.