Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005007.1 Hibiscus syriacus cultivar Beakdansim tig00011237_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: 60846
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:4716 original size:2 final size:2
Alignment explanation
Indices: 4709--4745 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4699 AGTTATATCA
*
4709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4746 AGAATGGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6359 original size:39 final size:39
Alignment explanation
Indices: 6303--6458 Score: 186
Period size: 39 Copynumber: 4.0 Consensus size: 39
6293 ACTAACTACC
** * * * * *
6303 GCATGCTCCTCAACTTTGTGCTCAGGGTATGTCCTTACT
1 GCATGCTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
* * *
6342 GCATGCTCCTCTGCTTTGTACATATGATAAGACCTTACT
1 GCATGCTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
*
6381 GCATACTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
1 GCATGCTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
* * *
6420 GCAGGCTCCTCTGCTTTGTGCACAAGGTAAGCCCTTACT
1 GCATGCTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
6459 AGGTGTACAT
Statistics
Matches: 100, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 100 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (39 bp):
GCATGCTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
Found at i:11371 original size:18 final size:18
Alignment explanation
Indices: 11343--11394 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
11333 TTCGACCATT
11343 GATCG-TGACCATTGACC
1 GATCGTTGACCATTGACC
11360 GATCGTTGACCATTGACC
1 GATCGTTGACCATTGACC
*
11378 GACCGTTGACCATTGAC
1 GATCGTTGACCATTGAC
11395 TTTGACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (18 bp):
GATCGTTGACCATTGACC
Found at i:11874 original size:197 final size:198
Alignment explanation
Indices: 11638--12045 Score: 653
Period size: 197 Copynumber: 2.0 Consensus size: 198
11628 AGTTAGATTC
11638 GGTGTTT-CCGTCTGTCAGATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTA
1 GGTGTTTCCCGTCTGTCA-ATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTA
*
11702 AATTATTAAATAAAGGTTAATATTATTCATATTATGATTCCAATATAAATTTTCTGATT-TATGA
65 AATTATTAAATAAAGGTTAATA-TATTCATATTATGATTCCAATATAAA-TTTCTGATTCTAGGA
*
11766 TCTAGCATTGCCGC-TCGTGATCGACAAACTCAGTAGTAAGCTTTCGTATCAGACTACTTAGATC
128 TCTAGCATTGCCGCATCGTGATCGACAAACTCAGTAGTAAGCTTCCGTATCAGACTACTTAGATC
11830 GATATA
193 GATATA
*
11836 GGTGTTTCCCGTCTGTC-ATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTTCGTAA
1 GGTGTTTCCCGTCTGTCAATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTAA
* * *
11900 ATTATTTAATAAAGGTTAATATATTCATATTATGATTCCAATATAGATTTCTTATTCGTAGGATC
66 ATTATTAAATAAAGGTTAATATATTCATATTATGATTCCAATATAAATTTCTGATTC-TAGGATC
* *
11965 TAGCATTGCCGCTGATCGTGATCGACAAACTCAGTAGTAGGCTTCCTTATCAGACTACTTAGATC
130 TAGCATTGCCGC--ATCGTGATCGACAAACTCAGTAGTAAGCTTCCGTATCAGACTACTTAGATC
12030 GATATA
193 GATATA
12036 GGTGTCTTCC
1 GGTGT-TTCC
12046 TGTTAGTGTT
Statistics
Matches: 195, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
195 8 0.04
196 25 0.13
197 84 0.43
198 7 0.04
199 9 0.05
200 58 0.30
201 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (198 bp):
GGTGTTTCCCGTCTGTCAATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTAA
ATTATTAAATAAAGGTTAATATATTCATATTATGATTCCAATATAAATTTCTGATTCTAGGATCT
AGCATTGCCGCATCGTGATCGACAAACTCAGTAGTAAGCTTCCGTATCAGACTACTTAGATCGAT
ATA
Found at i:12476 original size:37 final size:36
Alignment explanation
Indices: 12427--12546 Score: 123
Period size: 39 Copynumber: 3.2 Consensus size: 36
12417 TCGGGGTAGT
* *
12427 CCTTATGTAGGCTCCTGTTTTGTGCACAAGATAAGA
1 CCTTATGCAGGCTCCTGCTTTGTGCACAAGATAAGA
* *
12463 CCTTACTGCAGGCTCCTCTGCTTTGTGCACAGGATATGA
1 CCTTA-TGCAGGCT-C-CTGCTTTGTGCACAAGATAAGA
* * *
12502 CCTTATCGCAGGCTCCTATGCTTTGTGCACAGGGTAAGC
1 CCTTAT-GCAGGCTCC--TGCTTTGTGCACAAGATAAGA
12541 CCTTAT
1 CCTTAT
12547 TAGGTGTACA
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
36 5 0.07
37 8 0.11
38 3 0.04
39 55 0.77
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (36 bp):
CCTTATGCAGGCTCCTGCTTTGTGCACAAGATAAGA
Found at i:12491 original size:39 final size:39
Alignment explanation
Indices: 12445--12546 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
12435 AGGCTCCTGT
*
12445 TTTGTGCACAAGATAAGACCTTA-CTGCAGGCTCCTCTGC
1 TTTGTGCACAAGATAAGACCTTATC-GCAGGCTCCTATGC
* *
12484 TTTGTGCACAGGATATGACCTTATCGCAGGCTCCTATGC
1 TTTGTGCACAAGATAAGACCTTATCGCAGGCTCCTATGC
* * *
12523 TTTGTGCACAGGGTAAGCCCTTAT
1 TTTGTGCACAAGATAAGACCTTAT
12547 TAGGTGTACA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 55 0.98
40 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (39 bp):
TTTGTGCACAAGATAAGACCTTATCGCAGGCTCCTATGC
Found at i:17217 original size:43 final size:44
Alignment explanation
Indices: 17097--17221 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 44
17087 ATCTACCTCA
* * * *
17097 TTCTATGATAGAATCAAATAAAATAAGATTATGTTGATTCAAATAC
1 TTCTATGA-AGAATCAAACAAAATAA-CTAATGTTGATCCAAATAC
* * * * *
17143 TTCTGTGAAGAATCAAGCAGAATGAC-AATGTTGATCCAAATCC
1 TTCTATGAAGAATCAAACAAAATAACTAATGTTGATCCAAATAC
*
17186 TTCTATGAAGAATCAAACAAAAT-ACTGATGTTGATC
1 TTCTATGAAGAATCAAACAAAATAACTAATGTTGATC
17222 TGCCTCTTTC
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 2 0.03
43 43 0.66
45 13 0.20
46 7 0.11
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (44 bp):
TTCTATGAAGAATCAAACAAAATAACTAATGTTGATCCAAATAC
Found at i:18511 original size:12 final size:12
Alignment explanation
Indices: 18495--18602 Score: 84
Period size: 13 Copynumber: 9.1 Consensus size: 12
18485 CCCTTTTTTA
*
18495 TTTTCCTTTT-T
1 TTTTTCTTTTCT
*
18506 TCTTTCTTTTCT
1 TTTTTCTTTTCT
18518 TTTTTCTTTTCCT
1 TTTTTCTTTT-CT
*
18531 TTTAT-TTTTC-
1 TTTTTCTTTTCT
18541 -TTTTCTTTTCCT
1 TTTTTCTTTT-CT
18553 TTTCTT-TTTATCT
1 TTT-TTCTTT-TCT
*
18566 TCTTTCTTTTC-
1 TTTTTCTTTTCT
*
18577 TTCTTCTTTTCT
1 TTTTTCTTTTCT
18589 TTTTTCCTTTTCT
1 TTTTT-CTTTTCT
18602 T
1 T
18603 CTTCAAGTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 19 0.25
12 22 0.29
13 26 0.34
14 3 0.04
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:18516 original size:5 final size:5
Alignment explanation
Indices: 18503--18591 Score: 76
Period size: 5 Copynumber: 16.8 Consensus size: 5
18493 TATTTTCCTT
*
18503 TTTTC -TTTC TTTTC TTTTTTC TTTTCC TTTTAT TTTTC TTTTC TTTTCC
1 TTTTC TTTTC TTTTC --TTTTC TTTT-C TTTT-C TTTTC TTTTC TTTT-C
18552 TTTTC TTTT- TATCTTC -TTTC TTTTC TTCTTC TTTTC TTTT
1 TTTTC TTTTC T-T-TTC TTTTC TTTTC TT-TTC TTTTC TTTT
18592 TTCCTTTTCT
Statistics
Matches: 71, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
4 8 0.11
5 37 0.52
6 21 0.30
7 5 0.07
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:18519 original size:29 final size:29
Alignment explanation
Indices: 18487--18549 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
18477 TCTTTAACCC
18487 CTTTTTTATTTTCCTTTT-TTCTTTCTTTT
1 CTTTTTTATTTTCCTTTTATT-TTTCTTTT
*
18516 CTTTTTTCTTTTCCTTTTATTTTTCTTTT
1 CTTTTTTATTTTCCTTTTATTTTTCTTTT
18545 CTTTT
1 CTTTT
18550 CCTTTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (29 bp):
CTTTTTTATTTTCCTTTTATTTTTCTTTT
Found at i:18521 original size:16 final size:15
Alignment explanation
Indices: 18495--18605 Score: 82
Period size: 16 Copynumber: 7.0 Consensus size: 15
18485 CCCTTTTTTA
*
18495 TTTTCCTTTTTTCTT
1 TTTTTCTTTTTTCTT
18510 TCTTTTCTTTTTTCTT
1 T-TTTTCTTTTTTCTT
18526 TTCCTTT-TATTTTTCTT
1 TT--TTTCT-TTTTTCTT
*
18543 TTCTTT-TCCTTTTCTT
1 TT-TTTCT-TTTTTCTT
* *
18559 TTTATCTTCTTTCTT
1 TTTTTCTTTTTTCTT
*
18574 TTCTTCTTCTTTTCTT
1 TTTTTCTT-TTTTCTT
*
18590 TTTTCCTTTTCTTCTT
1 TTTTTCTTTT-TTCTT
18606 CAAGTATATT
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
15 18 0.23
16 47 0.60
17 13 0.17
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:30218 original size:69 final size:69
Alignment explanation
Indices: 30107--30240 Score: 234
Period size: 69 Copynumber: 1.9 Consensus size: 69
30097 ATCTTGGGCA
* *
30107 GGTTTATGTAAAAGCTTTTTACTTCGATACAATCCACCCAATATGAATACAC-AGCTACATAATG
1 GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGA-CTACATAATG
30171 ATGTG
65 ATGTG
30176 GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGACTACATAATGA
1 GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGACTACATAATGA
30241 CATTGCAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 61 0.98
70 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (69 bp):
GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGACTACATAATGA
TGTG
Found at i:35534 original size:24 final size:24
Alignment explanation
Indices: 35489--35538 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
35479 TGGTGGTTGG
35489 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
35513 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
35537 TT
1 TT
35539 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:40928 original size:24 final size:24
Alignment explanation
Indices: 40883--40932 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40873 TGGTGGTTGG
40883 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
40907 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
40931 TT
1 TT
40933 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:53249 original size:18 final size:18
Alignment explanation
Indices: 53220--53264 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
53210 ATATAAATAT
* *
53220 AAATGTAAATGAATATTAA
1 AAATG-AAATGAAAATGAA
*
53239 TAATGAAATGAAAATGAA
1 AAATGAAATGAAAATGAA
53257 AAATGAAA
1 AAATGAAA
53265 AAATGCATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.24
Consensus pattern (18 bp):
AAATGAAATGAAAATGAA
Found at i:53253 original size:24 final size:22
Alignment explanation
Indices: 53204--53256 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
53194 AAGCTTTAAT
* *
53204 AAATTAATATAAATATAAATGT
1 AAATGAATATAAATATAAATGA
*
53226 AAATGAATATTAATAATGAAATGA
1 AAATGAATATAAAT-AT-AAATGA
53250 AAATGAA
1 AAATGAA
53257 AAATGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 12 0.46
23 2 0.08
24 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (22 bp):
AAATGAATATAAATATAAATGA
Found at i:55422 original size:19 final size:19
Alignment explanation
Indices: 55398--55442 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
55388 TTGGAGTAAA
55398 CTGGAGTAAACTCGGTTCT
1 CTGGAGTAAACTCGGTTCT
55417 CTGGAGTAAACTCGGTTCT
1 CTGGAGTAAACTCGGTTCT
55436 CTTGGAG
1 C-TGGAG
55443 CCCTCAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (19 bp):
CTGGAGTAAACTCGGTTCT
Found at i:59406 original size:80 final size:79
Alignment explanation
Indices: 59184--59472 Score: 398
Period size: 80 Copynumber: 3.6 Consensus size: 79
59174 AAAAGGGGAG
** * * * * *
59184 CCAACCTAAGGATATACCTTGGATCTACCCAAGGACATCCTTAGATTCGTAGGGTTACCTTAAGT
1 CCAACCTAAGGATATACCTTGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACCTTATGC
* * *
59249 ACACAGCTAAGGTAA
65 ACACAACAAAGGAAA
* *
59264 CCAACCTAAGGATGTACCTTGGGCCTATCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCA
1 CCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCA
*
59329 CATAACAAAGGAAA
66 CACAACAAAGGAAA
* * *
59343 CCAAACTAAGGATATACCTTGGGACCTACCCAAGATATCCCTAGGTCCGTAGGGTTACATTATGC
1 CCAACCTAAGGATATACCTTGGG-CCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGC
*
59408 ACACAACAAAGGGAA
65 ACACAACAAAGGAAA
*
59423 CTAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCGTA
1 CCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCGTA
59473 AGGACTTACA
Statistics
Matches: 185, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
79 85 0.46
80 100 0.54
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (79 bp):
CCAACCTAAGGATATACCTTGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCA
CACAACAAAGGAAA
Done.