Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005850.1 Hibiscus syriacus cultivar Beakdansim tig00013733_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: 61504
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4010 original size:17 final size:18
Alignment explanation
Indices: 3988--4025 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3978 TGTAGGAGTC
3988 TTTCTT-TTCTCTT-TTGT
1 TTTCTTCTT-TCTTGTTGT
4005 TTTCTTCTTTCTTGTTGT
1 TTTCTTCTTTCTTGTTGT
4023 TTT
1 TTT
4026 TTGTTGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTCTTCTTTCTTGTTGT
Found at i:4411 original size:33 final size:33
Alignment explanation
Indices: 4369--4437 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
4359 GTTGATGAAT
*
4369 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
4402 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
4435 GAA
1 GAA
4438 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:4442 original size:13 final size:12
Alignment explanation
Indices: 4423--4519 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
4413 TTATTGGCGT
4423 GATATGGTGATG
1 GATATGGTGATG
4435 GAATATGGTGAT-
1 G-ATATGGTGATG
*
4447 GATATAGGCG-T-
1 GATAT-GGTGATG
4458 GATAATGGTGATG
1 GAT-ATGGTGATG
4471 GACTATGGTGAT-
1 GA-TATGGTGATG
*
4483 GATATAGGCG-T-
1 GATAT-GGTGATG
*
4494 GATAATGGAGATG
1 GAT-ATGGTGATG
4507 GATTATGGTGATG
1 GA-TATGGTGATG
4520 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:4478 original size:36 final size:36
Alignment explanation
Indices: 4408--4520 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
4398 AATGGAAGGA
* *
4408 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
4443 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
4479 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
4515 TGATGA
1 TGATGA
4521 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:10569 original size:4 final size:5
Alignment explanation
Indices: 10541--10566 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10531 ACTCAAAAAG
10541 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
10567 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:13623 original size:24 final size:24
Alignment explanation
Indices: 13588--13638 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13578 TCACTTCAAG
* *
13588 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGAATCAAGAAACATGACTT
* *
13612 TTGAAGAATCAATAAACGTGACTT
1 TTGAAGAATCAAGAAACATGACTT
13636 TTG
1 TTG
13639 GTGATCCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACATGACTT
Found at i:18609 original size:36 final size:36
Alignment explanation
Indices: 18562--18633 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
18552 CATATCATAA
*
18562 TATGGTGATGATATTGGCATGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
*
18598 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
18634 AGATTGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.35, T:0.32
Consensus pattern (36 bp):
TATGGTGATGATATAGGCATGATAATGGTGATGGAC
Found at i:23089 original size:36 final size:36
Alignment explanation
Indices: 23025--23101 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
23015 GATATGGTGG
* * * *
23025 TGGAATATGGTGATTATATAGGCGTGATAATGGA-GA
1 TGGACTATGGTGATGATAAAGGCATGATAAT-GATGA
23061 TGGACTATGGTGATGATAAAGGCATGATAATGATGA
1 TGGACTATGGTGATGATAAAGGCATGATAATGATGA
23097 TGGAC
1 TGGAC
23102 AGATTGTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (36 bp):
TGGACTATGGTGATGATAAAGGCATGATAATGATGA
Found at i:25295 original size:33 final size:33
Alignment explanation
Indices: 25253--25321 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
25243 GTTGATGAAT
*
25253 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-CATGAAATGGTAATG
* * *
25286 GAAGGATGATGTTATTGGCATGATATGGTGATG
1 GAAGGATGATGTTAATGGCATGAAATGGTAATG
25319 GAA
1 GAA
25322 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGAAATGGTAATG
Found at i:25362 original size:36 final size:36
Alignment explanation
Indices: 25292--25404 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
25282 AATGGAAGGA
* * *
25292 TGATGTTATTGGCATGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
25327 TGATGATATAGGCGTGATAATGGTGATGTACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
25363 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
25399 TGATGA
1 TGATGA
25405 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 15 0.22
36 54 0.78
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:25403 original size:13 final size:12
Alignment explanation
Indices: 25305--25404 Score: 57
Period size: 13 Copynumber: 8.3 Consensus size: 12
25295 TGTTATTGGC
25305 ATGA-TATGGTG
1 ATGATTATGGTG
*
25316 ATGGAATATGGTG
1 AT-GATTATGGTG
*
25329 ATGA-TATAGGCG
1 ATGATTAT-GGTG
*
25341 -TGATAATGGTG
1 ATGATTATGGTG
*
25352 ATGTACTATGGTG
1 ATG-ATTATGGTG
*
25365 ATGA-TATAGGCG
1 ATGATTAT-GGTG
* *
25377 -TGATAATGGAG
1 ATGATTATGGTG
25388 ATGGATTATGGTG
1 AT-GATTATGGTG
25401 ATGA
1 ATGA
25405 AAATAGTATC
Statistics
Matches: 69, Mismatches: 10, Indels: 19
0.70 0.10 0.19
Matches are distributed among these distances:
11 20 0.29
12 20 0.29
13 29 0.42
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
ATGATTATGGTG
Found at i:29553 original size:23 final size:23
Alignment explanation
Indices: 29525--29579 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
29515 GTGATGGAAT
29525 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
29548 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
29571 ATGGAGATG
1 ATGGTGATG
29580 GATTATGGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:37005 original size:20 final size:19
Alignment explanation
Indices: 36982--37039 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
36972 ATGGTCTTAA
*
36982 GAAATGAATATATAATAAAG
1 GAAATGAAAATA-AATAAAG
*
37002 GAAATGAAAATAAATAATAA
1 GAAATGAAAATAAATAA-AG
37022 G-AATG-AAATGAAATAAAG
1 GAAATGAAAAT-AAATAAAG
37040 AAAGGATAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.15
19 15 0.45
20 13 0.39
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.21
Consensus pattern (19 bp):
GAAATGAAAATAAATAAAG
Found at i:39279 original size:19 final size:21
Alignment explanation
Indices: 39255--39306 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
39245 CAGCCACAAG
*
39255 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
39274 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
39295 CATGTATTTTCA
1 CATGTATTTTCA
39307 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:40013 original size:17 final size:17
Alignment explanation
Indices: 39991--40039 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
39981 AATTGGAATG
39991 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAA-AT
40008 CAAAAAGAAA-AAAAAT
1 CAAAAAGAAAGAAAAAT
40024 CAAAATAG-AAGAAAAA
1 CAAAA-AGAAAGAAAAA
40040 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.03
16 11 0.38
17 17 0.59
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAAT
Found at i:61304 original size:55 final size:53
Alignment explanation
Indices: 61217--61320 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 53
61207 GATGGAAATA
*
61217 ATAATATGATAATTTACTAACATGTGAATGAATGCTTATGATAGAATAGAATGT
1 ATAATATGATAATTTACTAACATGTGAATGAATAC-TATGATAGAATAGAATGT
61271 ATAA-ATGATAATTTATACTAACATGTGAATGAATACTATGATAGAATAGA
1 ATAATATGATAA-TT-TACTAACATGTGAATGAATACTATGATAGAATAGA
61321 CATTATTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
53 7 0.15
54 20 0.43
55 20 0.43
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (53 bp):
ATAATATGATAATTTACTAACATGTGAATGAATACTATGATAGAATAGAATGT
Done.