Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002405.1 Hibiscus syriacus cultivar Beakdansim tig00004922_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: 100295
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:16443 original size:17 final size:18
Alignment explanation
Indices: 16403--16443 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
16393 ATATTACTTT
*
16403 TAAAATTTTTATTTATAA
1 TAAAATTCTTATTTATAA
*
16421 T-TAATTCTTATTT-TAA
1 TAAAATTCTTATTTATAA
16437 TAAAATT
1 TAAAATT
16444 ATAAATTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.21
17 14 0.74
18 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAAATTCTTATTTATAA
Found at i:28479 original size:15 final size:15
Alignment explanation
Indices: 28456--28506 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
28446 CGCCCCACAT
* *
28456 CCGCACCGCATCCAC
1 CCGCCCCGCATCCGC
28471 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
* *
28486 CCTCCCCACATCCGC
1 CCGCCCCGCATCCGC
28501 CCGCCC
1 CCGCCC
28507 AACTAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.12, C:0.67, G:0.14, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:29659 original size:16 final size:16
Alignment explanation
Indices: 29638--29668 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29628 GAATCTGTGA
29638 AGGAATTGAAATCTGT
1 AGGAATTGAAATCTGT
29654 AGGAATTGAAATCTG
1 AGGAATTGAAATCTG
29669 AATCTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
AGGAATTGAAATCTGT
Found at i:30245 original size:27 final size:28
Alignment explanation
Indices: 30203--30270 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
30193 CCTAAACCCG
* * *
30203 AACCCAACCCGAATATTACAC-TTAAAA
1 AACCCGACCCGAATATCAAACTTTAAAA
*
30230 AACCCGACCCGGATATCAAACTTTAAAA
1 AACCCGACCCGAATATCAAACTTTAAAA
*
30258 AACCCGATCCGAA
1 AACCCGACCCGAA
30271 CCCGAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.44, C:0.31, G:0.09, T:0.16
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACTTTAAAA
Found at i:30283 original size:29 final size:30
Alignment explanation
Indices: 30251--30318 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
30241 GATATCAAAC
30251 TTTAAAAAACCCGA-TCCGAA-CCCGAA-TTT
1 TTTAAAAAACCCGACT-C-AATCCCGAATTTT
*
30280 TTTAAAAAATCCGACTCAATCCCGAATTTT
1 TTTAAAAAACCCGACTCAATCCCGAATTTT
30310 TTTAAAAAA
1 TTTAAAAAA
30319 AAATCCGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 2 0.06
29 20 0.57
30 13 0.37
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (30 bp):
TTTAAAAAACCCGACTCAATCCCGAATTTT
Found at i:34731 original size:6 final size:6
Alignment explanation
Indices: 34722--34747 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34712 GGAATCAGAT
34722 GAAGTG GAAGTG GAAGTG GAAGTG GA
1 GAAGTG GAAGTG GAAGTG GAAGTG GA
34748 GCTAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
GAAGTG
Found at i:36196 original size:60 final size:58
Alignment explanation
Indices: 36100--36275 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 58
36090 ATGTCCCTAG
*
36100 ACTATGATCCTCATTCTAAATTGATACCTAAACTTTTAAATATTCTATTTTCATCCTCAA
1 ACTATGAT-ATCATTCTAAATTGAT-CCTAAACTTTTAAATATTCTATTTTCATCCTCAA
* * * * * *
36160 ACTATGATATTCATTCTAAATTGGTCCTTGAGCTTTTGAATATTCTAATTTCATCCTCAG
1 ACTATGATA-TCATTCTAAATTGATCC-TAAACTTTTAAATATTCTATTTTCATCCTCAA
* * * * *
36220 ACTACGACCATCATTCTAAATTGCTCCCCAAACTTTTAAATATTCCATTTTCATCC
1 ACTATGA-TATCATTCTAAATTGAT-CCTAAACTTTTAAATATTCTATTTTCATCC
36276 AAAGTTCATC
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 2 0.02
60 91 0.95
61 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (58 bp):
ACTATGATATCATTCTAAATTGATCCTAAACTTTTAAATATTCTATTTTCATCCTCAA
Found at i:36692 original size:19 final size:20
Alignment explanation
Indices: 36677--36744 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
36667 TTTTTTAATT
36677 TAATTATAAATATTT-ATAA
1 TAATTATAAATATTTAATAA
36696 TAATTATAAATATTT-ATAA
1 TAATTATAAATATTTAATAA
* *
36715 T-ATTATGATATTATTTAATTA
1 TAATTAT-A-AATATTTAATAA
36736 TAATT-TAAA
1 TAATTATAAA
36745 CGATTTTCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.12
19 22 0.52
20 7 0.17
21 5 0.12
22 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (20 bp):
TAATTATAAATATTTAATAA
Found at i:36695 original size:10 final size:9
Alignment explanation
Indices: 36680--36718 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
36670 TTTAATTTAA
36680 TTATAAATAT
1 TTAT-AATAT
*
36690 TTATAATAA
1 TTATAATAT
36699 TTATAAATAT
1 TTAT-AATAT
36709 TTATAATAT
1 TTATAATAT
36718 T
1 T
36719 ATGATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTATAATAT
Found at i:39191 original size:16 final size:16
Alignment explanation
Indices: 39170--39206 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
39160 CATTAATTTA
*
39170 AATTTAAGCATTATAT
1 AATTTAAGCATTAAAT
*
39186 AATTTAATCATTAAAT
1 AATTTAAGCATTAAAT
39202 AATTT
1 AATTT
39207 TTATAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTTAAGCATTAAAT
Found at i:44468 original size:21 final size:20
Alignment explanation
Indices: 44426--44468 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
44416 TGATCTTAAT
* **
44426 TTAAATTTAATTAAAATTTA
1 TTAAATTAAATTAAAAAATA
44446 TTAAATTGAAATTAAAAAATA
1 TTAAATT-AAATTAAAAAATA
44467 TT
1 TT
44469 TGTAATCAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAAATTAAATTAAAAAATA
Found at i:47237 original size:15 final size:15
Alignment explanation
Indices: 47214--47244 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47204 CTTTTTCTTC
*
47214 TTGTGTCATTCATTA
1 TTGTCTCATTCATTA
47229 TTGTCTCATTCATTA
1 TTGTCTCATTCATTA
47244 T
1 T
47245 AAAAGCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (15 bp):
TTGTCTCATTCATTA
Found at i:53341 original size:26 final size:25
Alignment explanation
Indices: 53307--53358 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
53297 TGCAGATAAA
* *
53307 TATTTTAAATATTTAATTAATAAAAG
1 TATTCTAAATATTTAAATAA-AAAAG
*
53333 TATTCTAAATGTTTAAATAAAAAAG
1 TATTCTAAATATTTAAATAAAAAAG
53358 T
1 T
53359 TATACTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
TATTCTAAATATTTAAATAAAAAAG
Found at i:66506 original size:8 final size:8
Alignment explanation
Indices: 66493--66534 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
66483 CCCAGTCCCT
66493 CCTCTCTC
1 CCTCTCTC
66501 CCTCTCTC
1 CCTCTCTC
66509 CCTCTC-C
1 CCTCTCTC
66516 CTCTCCTTCTC
1 C-CT-C-TCTC
66527 CCTCTCTC
1 CCTCTCTC
66535 AAATAATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 2 0.07
8 20 0.67
9 2 0.07
10 4 0.13
11 2 0.07
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
CCTCTCTC
Found at i:76012 original size:15 final size:15
Alignment explanation
Indices: 75992--76039 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
75982 TTTCCTTATT
75992 CTTCTCATTCCCCTC
1 CTTCTCATTCCCCTC
* *
76007 CTTCTCCTCCCCCTC
1 CTTCTCATTCCCCTC
*
76022 CTTCTCATTCTCCTC
1 CTTCTCATTCCCCTC
76037 CTT
1 CTT
76040 TTTCTTCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.04, C:0.54, G:0.00, T:0.42
Consensus pattern (15 bp):
CTTCTCATTCCCCTC
Found at i:88709 original size:41 final size:41
Alignment explanation
Indices: 88652--88730 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
88642 GACATTCTGT
88652 TACATAGATCCTGAATATCAACAAACGGGCATGCTAACAAC
1 TACATAGATCCTGAATATCAACAAACGGGCATGCTAACAAC
88693 TACATAGATCCTGAATATCAACAAACGGGCATGCTAAC
1 TACATAGATCCTGAATATCAACAAACGGGCATGCTAAC
88731 TAAATCAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (41 bp):
TACATAGATCCTGAATATCAACAAACGGGCATGCTAACAAC
Found at i:90081 original size:17 final size:16
Alignment explanation
Indices: 90059--90091 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
90049 ATATTTTATC
90059 AATAATAAATTTTAAAT
1 AATAATAAA-TTTAAAT
90076 AATAATAAATTTAAAT
1 AATAATAAATTTAAAT
90092 TGATGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTAAAT
Found at i:98314 original size:9 final size:9
Alignment explanation
Indices: 98300--98360 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
98290 CCCCGACCCG
98300 ATTATATAT
1 ATTATATAT
98309 ATTATATAT
1 ATTATATAT
98318 A-TATATAT
1 ATTATATAT
98326 A-TA-ATAT
1 ATTATATAT
* *
98333 TTTATATTT
1 ATTATATAT
*
98342 TTTATAT-T
1 ATTATATAT
98350 AATTATATAT
1 -ATTATATAT
98360 A
1 A
98361 AATATTTTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
7 4 0.09
8 13 0.29
9 27 0.60
10 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATATAT
Found at i:98384 original size:12 final size:12
Alignment explanation
Indices: 98367--98391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
98357 TATAAATATT
98367 TTCGGGTTTGGG
1 TTCGGGTTTGGG
98379 TTCGGGTTTGGG
1 TTCGGGTTTGGG
98391 T
1 T
98392 ATAATATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.48, T:0.44
Consensus pattern (12 bp):
TTCGGGTTTGGG
Done.