Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003723.1 Hibiscus syriacus cultivar Beakdansim tig00007964_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: 62260
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:8346 original size:33 final size:33
Alignment explanation
Indices: 8287--8353 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
8277 ATGTATTCTC
8287 TTTAAAAAAAATCAATACATAAATATTAATATTT
1 TTTAAAAAAAATCAATACATAAATATT-ATATTT
* *
8321 TTTAAAAAAATAT-AAT-CTTATATATTATATTT
1 TTTAAAAAAA-ATCAATACATAAATATTATATTT
8353 T
1 T
8354 CGAGCTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.23
33 8 0.27
34 13 0.43
35 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (33 bp):
TTTAAAAAAAATCAATACATAAATATTATATTT
Found at i:9831 original size:21 final size:20
Alignment explanation
Indices: 9791--9832 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
9781 CCAACTTACA
*
9791 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
9811 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
9832 A
1 A
9833 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:9859 original size:20 final size:20
Alignment explanation
Indices: 9834--9872 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
9824 CTATTATTAG
9834 TTGTATGACAACTAATAATT
1 TTGTATGACAACTAATAATT
9854 TTGTATGACAACTAATAAT
1 TTGTATGACAACTAATAAT
9873 CTCCTACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
TTGTATGACAACTAATAATT
Found at i:14433 original size:23 final size:23
Alignment explanation
Indices: 14403--14468 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
14393 GTCACTTTTC
14403 AACCATTATTAG-TGCCAACTATG
1 AACCATTATT-GTTGCCAACTATG
*
14426 AACCATTATTGTTGCAAACTATG
1 AACCATTATTGTTGCCAACTATG
14449 AACCATTATTGTTGCCAACT
1 AACCATTATTGTTGCCAACT
14469 TACAATGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (23 bp):
AACCATTATTGTTGCCAACTATG
Found at i:24675 original size:3 final size:3
Alignment explanation
Indices: 24669--24698 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24659 CTCTCTTCTT
24669 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
24699 AGAGACTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:25946 original size:32 final size:32
Alignment explanation
Indices: 25910--25977 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
25900 AAGTTCACTC
* * *
25910 GTGAGTAAGAGGAAAATGGGTAAGTGTGATTG
1 GTGAGCAAGAGGAAAACGGGTAAGTGTCATTG
* *
25942 GTGAGCAAGAGGAGAACGGGTAAGTGTCCTTG
1 GTGAGCAAGAGGAAAACGGGTAAGTGTCATTG
25974 GTGA
1 GTGA
25978 ATCTTCGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.06, G:0.41, T:0.22
Consensus pattern (32 bp):
GTGAGCAAGAGGAAAACGGGTAAGTGTCATTG
Found at i:28261 original size:2 final size:2
Alignment explanation
Indices: 28254--28293 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28244 ATTTTCAATT
28254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28294 AAACAAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28585 original size:20 final size:20
Alignment explanation
Indices: 28562--28622 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
28552 ATATAAATTA
28562 TTTGAGTTTAATATTAGATT
1 TTTGAGTTTAATATTAGATT
* *
28582 TTT--GTGT-ATA-TAAATT
1 TTTGAGTTTAATATTAGATT
*
28598 ATTTGAGTTTAATATTGGATT
1 -TTTGAGTTTAATATTAGATT
28619 TTTG
1 TTTG
28623 TTAACCCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 3 0.10
19 3 0.10
20 10 0.32
21 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (20 bp):
TTTGAGTTTAATATTAGATT
Found at i:28590 original size:37 final size:37
Alignment explanation
Indices: 28540--28623 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
28530 ATTGTTGTCA
28540 AGATTTTTGTGTATATAAATTATTTGAGTTTAATATT
1 AGATTTTTGTGTATATAAATTATTTGAGTTTAATATT
28577 AGATTTTTGTGTATATAAATTATTTGAGTTTAATATT
1 AGATTTTTGTGTATATAAATTATTTGAGTTTAATATT
*
28614 GGATTTTTGT
1 AGATTTTTGT
28624 TAACCCTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (37 bp):
AGATTTTTGTGTATATAAATTATTTGAGTTTAATATT
Found at i:28602 original size:17 final size:17
Alignment explanation
Indices: 28545--28602 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
28535 TGTCAAGATT
28545 TTTGTGTATATAAATTA
1 TTTGTGTATATAAATTA
* *
28562 TTTGAGTTTAATATTAGATT-
1 TTT--GTGT-ATA-TAAATTA
28582 TTTGTGTATATAAATTA
1 TTTGTGTATATAAATTA
28599 TTTG
1 TTTG
28603 AGTTTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 5 0.16
17 10 0.31
18 3 0.09
19 3 0.09
20 6 0.19
21 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (17 bp):
TTTGTGTATATAAATTA
Found at i:30985 original size:4 final size:4
Alignment explanation
Indices: 30966--31000 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
30956 CATGTGCATG
30966 CCAT GCCAT ACCAT CCAT CCAT CCAT CCAT CCAT C
1 CCAT -CCAT -CCAT CCAT CCAT CCAT CCAT CCAT C
31001 ACCACCATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 21 0.72
5 8 0.28
ACGTcount: A:0.26, C:0.49, G:0.03, T:0.23
Consensus pattern (4 bp):
CCAT
Found at i:37402 original size:21 final size:20
Alignment explanation
Indices: 37378--37426 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
37368 TTCAAAATCA
* *
37378 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
37398 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
37418 -CTTTCAAAA
1 TTTTTCAAAA
37427 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:47280 original size:65 final size:65
Alignment explanation
Indices: 47122--47280 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 65
47112 GTTTAAGGTG
* * * **
47122 CATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTTAT
1 CATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTTAT
47185 A
65 A
* *
47186 CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTATG
1 CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTATA
*
47250 CATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 CATCGATGCATAAG-G-AGTGCATCGATGCAT
47281 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.71
65 22 0.27
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (65 bp):
CATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTATA
Found at i:47795 original size:18 final size:18
Alignment explanation
Indices: 47772--47806 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
47762 CTAGGAGATT
47772 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
47790 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
47807 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:51194 original size:65 final size:65
Alignment explanation
Indices: 51034--51194 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
51024 TTGTTTAAGG
* * * **
51034 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
51097 A
65 A
*
51098 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
51162 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
51195 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:51691 original size:18 final size:18
Alignment explanation
Indices: 51668--51702 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
51658 CTAGGAGATT
51668 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
51686 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
51703 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:53389 original size:20 final size:20
Alignment explanation
Indices: 53364--53401 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53354 CCCCCTTTGA
*
53364 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
53384 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
53402 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Done.