Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006020.1 Hibiscus syriacus cultivar Beakdansim tig00014208_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: 77585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1448 original size:22 final size:21
Alignment explanation
Indices: 1423--1465 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1413 TTTTTTCATT
*
1423 TTTTATTATTCTTATTAATTTA
1 TTTTATTATTATTATT-ATTTA
*
1445 TTTTTTTATTATTATTATTTA
1 TTTTATTATTATTATTATTTA
1466 AAATATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTATTATTATTATTATTTA
Found at i:1545 original size:23 final size:23
Alignment explanation
Indices: 1500--1556 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
1490 AGAACCCGAC
*
1500 CCAAACCCAAAACCTAGGCCCAAA
1 CCAAACCC-AAACCCAGGCCCAAA
* *
1524 GCAAACCCAAACCCAGGTCCAAA
1 CCAAACCCAAACCCAGGCCCAAA
1547 CCAAACCCAA
1 CCAAACCCAA
1557 CCAAGCCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.46, C:0.42, G:0.09, T:0.04
Consensus pattern (23 bp):
CCAAACCCAAACCCAGGCCCAAA
Found at i:9658 original size:90 final size:89
Alignment explanation
Indices: 9503--9679 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
9493 CCTAACACAC
* * *
9503 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTACTTAAATCTATA
1 CCTTTTAGAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
9568 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
9592 CCTTTTAGATCCAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTAGAGCCAAGTTACCCTAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTAT
9657 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
9680 TTCGGTATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 31 0.38
90 50 0.62
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (89 bp):
CCTTTTAGAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:13349 original size:46 final size:46
Alignment explanation
Indices: 13282--13374 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
13272 ATAAGTTTGA
*
13282 TTCGAGTTATTTGTTTTTGATCTCTTAGTATTTATGTTATAAATGG
1 TTCGAGTCATTTGTTTTTGATCTCTTAGTATTTATGTTATAAATGG
13328 TTCGAGTCATTTGTTTTTGATCTCTTAGTATTTATGTTATAAATGG
1 TTCGAGTCATTTGTTTTTGATCTCTTAGTATTTATGTTATAAATGG
13374 T
1 T
13375 GTTATCTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.54
Consensus pattern (46 bp):
TTCGAGTCATTTGTTTTTGATCTCTTAGTATTTATGTTATAAATGG
Found at i:13365 original size:23 final size:23
Alignment explanation
Indices: 13293--13365 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
13283 TCGAGTTATT
13293 TGTTTTTGATCTCTTAGTATTTA
1 TGTTTTTGATCTCTTAGTATTTA
* * *
13316 TGTTATAAATGGT-TC-GAGTCA-TT-
1 TGTT-T--TTGATCTCTTAGT-ATTTA
13339 TGTTTTTGATCTCTTAGTATTTA
1 TGTTTTTGATCTCTTAGTATTTA
13362 TGTT
1 TGTT
13366 ATAAATGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 6 0.17
23 12 0.33
24 6 0.17
25 3 0.08
26 3 0.08
ACGTcount: A:0.19, C:0.08, G:0.16, T:0.56
Consensus pattern (23 bp):
TGTTTTTGATCTCTTAGTATTTA
Found at i:14482 original size:15 final size:15
Alignment explanation
Indices: 14462--14496 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
14452 ATTAGCTGCC
14462 GGTTCATCAGGAACA
1 GGTTCATCAGGAACA
14477 GGTTCATCAGGAACA
1 GGTTCATCAGGAACA
14492 GGTTC
1 GGTTC
14497 CTTAATGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (15 bp):
GGTTCATCAGGAACA
Found at i:14698 original size:23 final size:23
Alignment explanation
Indices: 14645--14698 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
14635 AACAATGGAA
14645 ATATTAAAGTAAGAAAATTTACC
1 ATATTAAAGTAAGAAAATTTACC
*
14668 ATACTAAAGTAAGAAAATTTACC
1 ATATTAAAGTAAGAAAATTTACC
14691 GA-ATTAAA
1 -ATATTAAA
14699 ATTTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (23 bp):
ATATTAAAGTAAGAAAATTTACC
Found at i:16498 original size:20 final size:21
Alignment explanation
Indices: 16475--16544 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
16465 TATTATTTCA
16475 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
16495 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAAATATATATTT
*
16517 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAAATATATATTT
16539 AATTAA
1 AATTAA
16545 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 20 0.53
23 3 0.08
24 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:18692 original size:21 final size:23
Alignment explanation
Indices: 18653--18697 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
18643 TAAAAACAAG
18653 TAAAATATAAAACAAAATT-AAA
1 TAAAATATAAAACAAAATTGAAA
18675 TAAAA-ATACAAA-AAAATTGAAA
1 TAAAATATA-AAACAAAATTGAAA
18697 T
1 T
18698 CAATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
TAAAATATAAAACAAAATTGAAA
Found at i:18718 original size:16 final size:17
Alignment explanation
Indices: 18686--18721 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
18676 AAAAATACAA
*
18686 AAAAATTGAAATCAATT
1 AAAAATTGAAATAAATT
18703 AAAAA-TGAAATAAATT
1 AAAAATTGAAATAAATT
18719 AAA
1 AAA
18722 TATGGTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAAATTGAAATAAATT
Found at i:39585 original size:17 final size:16
Alignment explanation
Indices: 39553--39592 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
39543 CTTGTTGTTG
39553 TTCTTTCAACTTCTTT
1 TTCTTTCAACTTCTTT
*
39569 TTCTTTGCAATTTCTTT
1 TTCTTT-CAACTTCTTT
*
39586 TTTTTTC
1 TTCTTTC
39593 TTCTTCAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (16 bp):
TTCTTTCAACTTCTTT
Found at i:57984 original size:30 final size:31
Alignment explanation
Indices: 57948--58006 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
57938 TAAAGTTTGG
57948 AAAAGTTCA-AGGACCAAAAG-GATAATTTTC
1 AAAAGTTCAGAGGACCAAAAGTGA-AATTTTC
* *
57978 AAAAGTTTAGGGGACCAAAAGTGAAATTT
1 AAAAGTTCAGAGGACCAAAAGTGAAATTT
58007 AAAAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.32
31 15 0.60
32 2 0.08
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (31 bp):
AAAAGTTCAGAGGACCAAAAGTGAAATTTTC
Found at i:58022 original size:29 final size:31
Alignment explanation
Indices: 57958--58022 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
57948 AAAAGTTCAA
*
57958 GGACCAAAAGGATAATTTTCAAAAGTTTAGG
1 GGACCAAAAGGATAATTTTCAAAAATTTAGG
57989 GGACCAAAAGTGA-AA-TTT-AAAAATTTAGG
1 GGACCAAAAG-GATAATTTTCAAAAATTTAGG
*
58018 TGACC
1 GGACC
58023 CCATAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 14 0.45
30 3 0.10
31 12 0.39
32 2 0.06
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.25
Consensus pattern (31 bp):
GGACCAAAAGGATAATTTTCAAAAATTTAGG
Found at i:62759 original size:3 final size:3
Alignment explanation
Indices: 62751--62776 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
62741 CCACCTCTAT
62751 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
62777 AACCCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:65575 original size:22 final size:21
Alignment explanation
Indices: 65550--65593 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
65540 ATGTAAATTT
* *
65550 AAAGAAATATAAAGAATTGAAG
1 AAAGAAACATAAA-AATTCAAG
*
65572 AAAGTAACATAAAAATTCAAG
1 AAAGAAACATAAAAATTCAAG
65593 A
1 A
65594 TGATTAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.18
Consensus pattern (21 bp):
AAAGAAACATAAAAATTCAAG
Found at i:71519 original size:7 final size:7
Alignment explanation
Indices: 71507--71534 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
71497 AACTGATAGT
71507 TTAAATG
1 TTAAATG
71514 TTAAATG
1 TTAAATG
71521 TTAAATG
1 TTAAATG
71528 TTAAATG
1 TTAAATG
71535 CGTGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TTAAATG
Found at i:73592 original size:16 final size:16
Alignment explanation
Indices: 73563--73619 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
73553 TGAACAAATA
**
73563 AAAATATTTTAAATTC
1 AAAATATTAAAAATTC
73579 AAAATATTAAAAATT-
1 AAAATATTAAAAATTC
*
73594 -AAATA-TAAAAATACC
1 AAAATATTAAAAAT-TC
73609 AAAA-ATTAAAA
1 AAAATATTAAAA
73620 TTAAATTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 7 0.21
14 5 0.15
15 1 0.03
16 21 0.62
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAAAATTC
Found at i:73604 original size:22 final size:21
Alignment explanation
Indices: 73571--73624 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
73561 TAAAAATATT
* **
73571 TTAAATTCAAAATATTAAAAA
1 TTAAATTAAAAATACCAAAAA
73592 TTAAATATAAAAATACCAAAAA
1 TTAAAT-TAAAAATACCAAAAA
73614 TTAAAATTAAA
1 TT-AAATTAAA
73625 TTACTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 18 0.64
23 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (21 bp):
TTAAATTAAAAATACCAAAAA
Found at i:74305 original size:24 final size:22
Alignment explanation
Indices: 74278--74331 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
74268 GGTATTATTC
*
74278 TATTTAAGTTTATGAATATTTTTA
1 TATTTAA-TTTA-AAATATTTTTA
74302 TATTATGAATTTAAAATATTTTTA
1 TATT-T-AATTTAAAATATTTTTA
74326 T-TTTAA
1 TATTTAA
74332 AAAATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 2 0.07
22 1 0.04
23 2 0.07
24 15 0.56
25 5 0.19
26 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TATTTAATTTAAAATATTTTTA
Done.