Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005475.1 Hibiscus syriacus cultivar Beakdansim tig00012551_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: 61869
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7377 original size:18 final size:18
Alignment explanation
Indices: 7354--7414 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
7344 ATCAGGGTCG
*
7354 GCGGGCTCTTCTGCTTCA
1 GCGGGCTCTTCTACTTCA
7372 GCGGGCTCTTCTACTTCA
1 GCGGGCTCTTCTACTTCA
7390 GCGGGCTCTTCTACTTCA
1 GCGGGCTCTTCTACTTCA
7408 GCGGGCT
1 GCGGGCT
7415 GGGGACTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.08, C:0.33, G:0.28, T:0.31
Consensus pattern (18 bp):
GCGGGCTCTTCTACTTCA
Found at i:17631 original size:18 final size:19
Alignment explanation
Indices: 17594--17631 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17584 ACTCGACGTG
*
17594 TTCACTAGATAAATATAAT
1 TTCACTAGATAAATAAAAT
*
17613 TTCATTAGA-AAATAAAAT
1 TTCACTAGATAAATAAAAT
17631 T
1 T
17632 AATAAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
TTCACTAGATAAATAAAAT
Found at i:26442 original size:24 final size:24
Alignment explanation
Indices: 26410--26458 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
26400 CTCATTGGAA
26410 AATTAATTCATAGATATTAGTCTT
1 AATTAATTCATAGATATTAGTCTT
26434 AATTAATTCATAGATATTAGTCTT
1 AATTAATTCATAGATATTAGTCTT
26458 A
1 A
26459 CATAAATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (24 bp):
AATTAATTCATAGATATTAGTCTT
Found at i:28453 original size:84 final size:83
Alignment explanation
Indices: 28265--28454 Score: 208
Period size: 84 Copynumber: 2.3 Consensus size: 83
28255 TAATTTTATC
* * * * *
28265 TTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTTTTATTA
1 TTTAAGAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATGA
28330 TATTTTATCTTATAATTGT
66 TA-TTTATCTTATAATTGT
* * * *
28349 TTTAGGAATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGATATTA-TTTTATGA
1 TTTAAGAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATGA
*
28413 -A-TTATCTT-TAGGTTGTT
66 TATTTATCTTATA-ATTG-T
28430 TTTAAGAATTTGAAGGCTATAAATA
1 TTTAAGAATTT-AA-G-TATAAATA
28455 CCCTCTCAGG
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 2 0.02
80 10 0.11
81 11 0.12
82 2 0.02
83 8 0.09
84 61 0.65
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (83 bp):
TTTAAGAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATGA
TATTTATCTTATAATTGT
Found at i:34547 original size:6 final size:5
Alignment explanation
Indices: 34522--34586 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
34512 GCGGCAACCC
* * **
34522 ATTTT GTTTT ATTTT CATTTT AATTTC GCTTT ATTTTTT ATTTT A-TTT
1 ATTTT ATTTT ATTTT -ATTTT -ATTTT ATTTT A-TT-TT ATTTT ATTTT
34570 ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT AT
34587 CAGATGCTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
4 4 0.09
5 28 0.60
6 12 0.26
7 3 0.06
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:34576 original size:14 final size:14
Alignment explanation
Indices: 34557--34583 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34547 TCGCTTTATT
34557 TTTTATTTTATTTA
1 TTTTATTTTATTTA
34571 TTTTATTTTATTT
1 TTTTATTTTATTT
34584 TATCAGATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:37190 original size:8 final size:8
Alignment explanation
Indices: 37152--37199 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
37142 AAACTCCCTT
37152 TTATATTTA
1 TTAT-TTTA
*
37161 TTACTATTA
1 TTA-TTTTA
*
37170 TTA-TTTG
1 TTATTTTA
37177 TTATTTTA
1 TTATTTTA
37185 TTATTTTA
1 TTATTTTA
37193 TTATTTT
1 TTATTTT
37200 CCTTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 5 0.15
8 18 0.55
9 9 0.27
10 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATTTTA
Found at i:38891 original size:42 final size:42
Alignment explanation
Indices: 38832--39193 Score: 510
Period size: 42 Copynumber: 8.6 Consensus size: 42
38822 AAAGAGCCTG
* *
38832 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
38874 GGGAAACTGTAAGGCTTACCCTTGTACACAGCAAAAGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
38916 -GGAGAACTGTAAGGCTTACCCTTGTACACAAAAAAGTAACCT
1 GGGA-AACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
38958 GGGAAATTGTAAGGGTTACCCTTGTACACAACAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
39000 GGGAAACTATAAGGCTTACCCTTGTACAAAACAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* * *
39042 GGGAAACTGTAGGGCTTACCCTTGTACACAAAAAAGGGACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
39084 GGGAAACTATAAGGCCTACCCTTGTACACAACAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
39126 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAGCCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* * *
39168 GCAGTAACGGTAAGGACTTACCCTTG
1 G-GGAAACTGTAAGG-CTTACCCTTG
39194 CACATAGCAG
Statistics
Matches: 285, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
41 3 0.01
42 259 0.91
43 13 0.05
44 10 0.04
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (42 bp):
GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
Found at i:41967 original size:42 final size:42
Alignment explanation
Indices: 41883--42227 Score: 431
Period size: 42 Copynumber: 8.1 Consensus size: 42
41873 AGGTTTTATT
* * * * * *
41883 CTTGCACATAGCAAAAGAGCCTGAGGAAAATGTAAGGTTTACC
1 CTTGCACACAACAAAGGAACCTG-GGAAACTGTAAGGCTTACC
*
41926 CTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* * * *
41968 CTTGCACACATCAAAGGAACCT-AGAGAACTATAAGACTTACC
1 CTTGCACACAACAAAGGAACCTGGGA-AACTGTAAGGCTTACC
* * **
42010 CTTGTACACAACAAAGTAACCTGGGAAACTGTAAGATTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* *
42052 CTTGTACACAACAAAGGAACATGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
*
42094 CTTGTACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
*
42136 CTTGTACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* * * *
42178 CTTGCACACAACAAGGGAGCCTGCGGTAACGGTAAGGACTTACC
1 CTTGCACACAACAAAGGAACCTG-GGAAACTGTAAGG-CTTACC
*
42222 GTTGCA
1 CTTGCA
42228 TATAGCAGAG
Statistics
Matches: 272, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
41 2 0.01
42 226 0.83
43 33 0.12
44 11 0.04
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (42 bp):
CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
Found at i:44891 original size:18 final size:18
Alignment explanation
Indices: 44847--44893 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
44837 GTCACAACCC
44847 GACCCGACCCGACCCATT
1 GACCCGACCCGACCCATT
* **
44865 TACCCGACCCGACCTGTT
1 GACCCGACCCGACCCATT
*
44883 GACCTGACCCG
1 GACCCGACCCG
44894 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGACCCATT
Found at i:44903 original size:7 final size:7
Alignment explanation
Indices: 44891--44929 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
44881 TTGACCTGAC
44891 CCGTTGA
1 CCGTTGA
44898 CCGTTGA
1 CCGTTGA
44905 CCGTTGA
1 CCGTTGA
44912 CCCGTTGA
1 -CCGTTGA
44920 CCGTTGA
1 CCGTTGA
44927 CCG
1 CCG
44930 GCGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:44916 original size:15 final size:15
Alignment explanation
Indices: 44891--44938 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
44881 TTGACCTGAC
44891 CCGTTGA-CCGTTGA
1 CCGTTGACCCGTTGA
44905 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
44920 CCGTTGACCGGCGTTGA
1 CCGTTGACC--CGTTGA
44937 CC
1 CC
44939 ACTGTTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.23
15 16 0.52
17 8 0.26
ACGTcount: A:0.12, C:0.33, G:0.29, T:0.25
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:46939 original size:24 final size:23
Alignment explanation
Indices: 46912--46998 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
46902 ATTTCCGAAT
*
46912 TGAATTCTGTTCTGATACGTTACC
1 TGAATTCTGTTCTGATAC-TGACC
* * *
46936 TGAATTCTGTTATGATTCTGATC
1 TGAATTCTGTTCTGATACTGACC
* **
46959 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGACC
*
46983 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
46999 TTCTGATATC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 17 0.33
24 35 0.67
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:46966 original size:47 final size:48
Alignment explanation
Indices: 46915--47005 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
46905 TCCGAATTGA
*
46915 ATTCTGTTCTGATA-C-GTTACCTGAATTCTGTTATGA-TTCTGATCTGG
1 ATTCTGTTCTGATATCTGATA--TGAATTCTGTTATGATTTCTGATCTGG
*
46962 ATTCTGTTCTGATATCTGATATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGATATGAATTCTGTTATGATTTCTGAT
47006 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 28 0.72
48 8 0.21
49 3 0.08
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGATATGAATTCTGTTATGATTTCTGATCTGG
Found at i:47003 original size:24 final size:24
Alignment explanation
Indices: 46936--47007 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
46926 ATACGTTACC
*
46936 TGAATTCTGTTATGA-TTCTGATC
1 TGAATTCTGTTATGATTTCTGATA
* * *
46959 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTATGATTTCTGATA
*
46983 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
47007 T
1 T
47008 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 13 0.32
24 28 0.68
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:49256 original size:20 final size:20
Alignment explanation
Indices: 49215--49256 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
49205 AGGGAAGGAC
*
49215 AATTTTAAGAACTTTGAGAG
1 AATTTTAAGAACTTTGAAAG
*
49235 AATTTTAA-AACATTTTAAAG
1 AATTTTAAGAAC-TTTGAAAG
49255 AA
1 AA
49257 GACCCAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (20 bp):
AATTTTAAGAACTTTGAAAG
Found at i:57544 original size:22 final size:22
Alignment explanation
Indices: 57519--57560 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
57509 CAAACGCAAG
57519 TTTGAACCGAGTTCGACTTCAA
1 TTTGAACCGAGTTCGACTTCAA
*
57541 TTTGAATCGAGTTCGACTTC
1 TTTGAACCGAGTTCGACTTC
57561 GAGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (22 bp):
TTTGAACCGAGTTCGACTTCAA
Found at i:57579 original size:23 final size:22
Alignment explanation
Indices: 57526--57573 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
57516 AAGTTTGAAC
*
57526 CGAGTTCGACTTCAATTTGAAT
1 CGAGTTCGACTTCAATTTAAAT
*
57548 CGAGTTCGACTTCGAGTTTAAAT
1 CGAGTTCGACTTC-AATTTAAAT
57571 CGA
1 CGA
57574 AGTCGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (22 bp):
CGAGTTCGACTTCAATTTAAAT
Done.