Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000331.1 Hibiscus syriacus cultivar Beakdansim tig00000615_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: 73537
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4632 original size:21 final size:21
Alignment explanation
Indices: 4606--4682 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
4596 GTAGAGACAG
4606 CAAAGAGAAGCAGCGGCAGCA
1 CAAAGAGAAGCAGCGGCAGCA
4627 CAAAGAGAAGCAGCGGCAGCA
1 CAAAGAGAAGCAGCGGCAGCA
* *
4648 CAAAGAGAAACAGCGGCATCA
1 CAAAGAGAAGCAGCGGCAGCA
4669 CAAAGAGAAGCAGC
1 CAAAGAGAAGCAGC
4683 ATATCAGCAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.45, C:0.23, G:0.30, T:0.01
Consensus pattern (21 bp):
CAAAGAGAAGCAGCGGCAGCA
Found at i:5149 original size:43 final size:43
Alignment explanation
Indices: 5086--5423 Score: 279
Period size: 43 Copynumber: 7.9 Consensus size: 43
5076 TGTTTTTAGC
*
5086 AAAAACGCCGCAAAAAATCAATACCTATTGCGGCGTTTGTGAG
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGTGAG
** * * * * * **
5129 AAAAACGCATCAAAACATCAAAATCTACTACGATGTTTGTG-G
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGTGAG
* * * * *
5171 AATAAACACCGCAAAACATCAACATCTACTGCGGCGTTTGTG-G
1 AA-AAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGTGAG
* * *
5214 AAAAACGCCGTAAAACATCAACACCTATTGCGGCGTTT-TAGAG
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGT-GAG
* * * * * *
5257 AAAAACGCCACTATATATCATTACCTATTGCGGCGTTTATCTA-
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGT-GAG
* * * * **
5300 AAAAACGCTGCTAAATATCAATACCTATTGCGGCATTTTTCTG
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGTGAG
* * * * * *
5343 ACAAACGCCGCTAAATATCAACACCTATTGTGGCGTTTGTCAC
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGTGAG
* *
5386 ACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
1 AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTT
5424 TTTGTTTAAA
Statistics
Matches: 243, Mismatches: 47, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.00
42 36 0.15
43 204 0.84
44 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCAAAATATCAATACCTATTGCGGCGTTTGTGAG
Found at i:30023 original size:17 final size:17
Alignment explanation
Indices: 29997--30043 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
29987 ATCTTCTTTA
29997 TTTTCACTAT-AAATTACT
1 TTTTC-CTATCAAATTA-T
*
30015 TTTTCCTATCCAATTAT
1 TTTTCCTATCAAATTAT
30032 TTTTCC-ATCAAA
1 TTTTCCTATCAAA
30044 AACCCCCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 10 0.38
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTCCTATCAAATTAT
Found at i:34144 original size:25 final size:24
Alignment explanation
Indices: 34059--34145 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 24
34049 TTTATTTTAA
*
34059 AAAAT-ATAAATATTATATTATATT
1 AAAATAATAAATATTA-ATTTTATT
* *
34083 ATAA-AATAAATATT--TTCATTTTT
1 AAAATAATAAATATTAATT--TTATT
*
34106 AAAATAATTTAATATTAATTTTATT
1 AAAATAA-TAAATATTAATTTTATT
34131 AAAATATATAAATAT
1 AAAATA-ATAAATAT
34146 ACTAATATCA
Statistics
Matches: 48, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
21 2 0.04
23 6 0.12
24 14 0.29
25 23 0.48
26 1 0.02
27 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATAATAAATATTAATTTTATT
Found at i:39252 original size:72 final size:72
Alignment explanation
Indices: 39158--39296 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 72
39148 AGAACAAAGT
* * * * * *
39158 AAAATTTTTAGTGAGTTTAACGAGCAA-AGAATTGAGTTTAGCAACAAGTTTTTTTAACGAGCAC
1 AAAATTTTTAATGAGCTTAACGAACAACA-AATCGAGTTGAACAACAA-TTTTTTTAACGAGCAC
39222 GAGTCGAAC
64 GAGTCGAAC
* *
39231 AAAA-TTTTAATGAGCTTAACGAACAACAAATCGGGTTGAACAATAATTTTTTTAACGAGCACGA
1 AAAATTTTTAATGAGCTTAACGAACAACAAATCGAGTTGAACAACAATTTTTTTAACGAGCACGA
39295 GT
66 GT
39297 TGAGCACTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
71 20 0.35
72 32 0.56
73 5 0.09
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (72 bp):
AAAATTTTTAATGAGCTTAACGAACAACAAATCGAGTTGAACAACAATTTTTTTAACGAGCACGA
GTCGAAC
Found at i:39578 original size:170 final size:170
Alignment explanation
Indices: 39296--39639 Score: 555
Period size: 170 Copynumber: 2.0 Consensus size: 170
39286 CGAGCACGAG
* * * * *
39296 TTGAGCACTATCCAACTCACCATCGACTCGCTCAATAAGCACCATATTTCTATATCTGTCAAATT
1 TTGAGCACCATCCAACTCACCATCGACTCGCTCAATAAACACCATAGTTCCATATATGTCAAATT
*
39361 AAAAAGAATACATATGTTATGGCATGTGGTGCATATTTGTAAAAGTTTGTGGTAAGCTGCAAGAA
66 AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAAGTTTGTGGTAAGCTGCAAGAA
39426 TTTAAATGGTGACACATAAACCACCATTTTCAA-ATAAAGA
131 TTTAAATGGTGACACATAAACCACCATTTTCAACA-AAAGA
* * * *
39466 TTGAGCACCATCTAATTCACCATCGACTCGCTCGATAAACACCATAGTTCCATATATGTCAGATT
1 TTGAGCACCATCCAACTCACCATCGACTCGCTCAATAAACACCATAGTTCCATATATGTCAAATT
*
39531 AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAAGTTTGTGGTAAGCTGCAATAA
66 AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAAGTTTGTGGTAAGCTGCAAGAA
* *
39596 TTTAAATGTTGACACATGAACCACCATTTTCAACAAAAGA
131 TTTAAATGGTGACACATAAACCACCATTTTCAACAAAAGA
39636 TTGA
1 TTGA
39640 AGCATCTTAT
Statistics
Matches: 160, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
170 159 0.99
171 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (170 bp):
TTGAGCACCATCCAACTCACCATCGACTCGCTCAATAAACACCATAGTTCCATATATGTCAAATT
AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAAGTTTGTGGTAAGCTGCAAGAA
TTTAAATGGTGACACATAAACCACCATTTTCAACAAAAGA
Found at i:50185 original size:2 final size:2
Alignment explanation
Indices: 50178--50216 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
50168 TCTCCTCTTC
50178 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT ACT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT
50217 TTGGAGTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:59743 original size:13 final size:13
Alignment explanation
Indices: 59740--59781 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
59730 CGTTGACCCT
*
59740 ACCCGACCTGTTG
1 ACCCGACCCGTTG
59753 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
59766 A-CCGTACCTGTTG
1 ACCCG-ACCCGTTG
59779 ACC
1 ACC
59782 GTTGACCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 3 0.12
13 21 0.84
14 1 0.04
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:59743 original size:18 final size:18
Alignment explanation
Indices: 59717--59762 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
59707 ACCAGTCATA
59717 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
59735 ACCCTACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
59753 ACCCGACCCG
1 ACCCGACCCG
59763 TTGACCGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:59782 original size:13 final size:13
Alignment explanation
Indices: 59745--59796 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
59735 ACCCTACCCG
59745 ACCTGTTGACCCG-
1 ACCTGTTGA-CCGT
*
59758 ACCCGTTGACCGT
1 ACCTGTTGACCGT
59771 ACCTGTTGACCGTT
1 ACCTGTTGACCG-T
59785 GACC-GTTGACCG
1 -ACCTGTTGACCG
59797 ACGTTGACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 3 0.09
13 19 0.56
14 9 0.26
15 3 0.09
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (13 bp):
ACCTGTTGACCGT
Found at i:59785 original size:7 final size:7
Alignment explanation
Indices: 59760--59796 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
59750 TTGACCCGAC
59760 CCGTTGA
1 CCGTTGA
59767 CCG-T-A
1 CCGTTGA
59772 CCTGTTGA
1 CC-GTTGA
59780 CCGTTGA
1 CCGTTGA
59787 CCGTTGA
1 CCGTTGA
59794 CCG
1 CCG
59797 ACGTTGACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 3 0.11
6 2 0.07
7 19 0.70
8 3 0.11
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:62342 original size:24 final size:24
Alignment explanation
Indices: 62315--62409 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
62305 ATTTCCGACT
** *
62315 TGAATTCTGTTATGATAAATGACC
1 TGAATTCTGTTATGATATCTGATC
* *
62339 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTATGATATCTGATC
* *
62363 TGGATTCTGTTATGATATCTGTTC
1 TGAATTCTGTTATGATATCTGATC
* *
62387 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTATGATATCTGAT
62410 ATCTTCGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATATCTGATC
Found at i:62358 original size:12 final size:12
Alignment explanation
Indices: 62338--62407 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
62328 GATAAATGAC
*
62338 CTGAATTCTGTT
1 CTGATTTCTGTT
*
62350 CTGATTTCTGAT
1 CTGATTTCTGTT
62362 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
62374 ATGATATCTGTT
1 CTGATTTCTGTT
*
62386 CTGAATTCTGTT
1 CTGATTTCTGTT
*
62398 TTGATTTCTG
1 CTGATTTCTG
62408 ATATCTTCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:62406 original size:48 final size:48
Alignment explanation
Indices: 62301--62409 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
62291 AAATATTTTA
* *
62301 TCTGATTTCCGA-CTTGAATTCTGTTATGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTATGATAAATGACCTGAATTCTGT
** **
62349 TCTGATTTCTGATCTGGATTCTGTTATGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTATGATAAATGACCTGAATTCTGT
*
62397 TTTGATTTCTGAT
1 TCTGATTTCTGAT
62410 ATCTTCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTATGATAAATGACCTGAATTCTGT
Found at i:62576 original size:2 final size:2
Alignment explanation
Indices: 62569--62605 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
62559 GGGATGGGGG
62569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62606 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.