Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004291.1 Hibiscus syriacus cultivar Beakdansim tig00009414_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: 63315
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:47 original size:6 final size:6
Alignment explanation
Indices: 38--73 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28 CCTCCTCCTC
38 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
74 TCTCCTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCCTT
Found at i:1867 original size:28 final size:27
Alignment explanation
Indices: 1807--1865 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
1797 ACACACATTA
* *
1807 TAAACGAATTACTTCGACCTTATTCTC
1 TAAACGAATTACTTCGACATAATTCTC
1834 TAAACGTAATTACTTCGACATGAATTCTC
1 TAAACG-AATTACTTCGACAT-AATTCTC
1863 TAA
1 TAA
1866 CGAGAGTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 6 0.21
28 13 0.46
29 9 0.32
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (27 bp):
TAAACGAATTACTTCGACATAATTCTC
Found at i:7023 original size:30 final size:30
Alignment explanation
Indices: 6987--7047 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
6977 AAAGAAGTGG
*
6987 TAAACGAATCAAACTATCTAGTAATCTGCT
1 TAAACGAATCAAACTATCTAGTAATATGCT
*
7017 TAAACGAATCAAACTATCTTGTAATATGCT
1 TAAACGAATCAAACTATCTAGTAATATGCT
7047 T
1 T
7048 CGTTATACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (30 bp):
TAAACGAATCAAACTATCTAGTAATATGCT
Found at i:7440 original size:17 final size:18
Alignment explanation
Indices: 7399--7441 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
7389 TTTTATTGTT
* *
7399 TTTTTTTAATTATAAGCA
1 TTTTATTAATCATAAGCA
*
7417 TTATATTAATCATAA-CA
1 TTTTATTAATCATAAGCA
7434 TTTTATTA
1 TTTTATTA
7442 GTCTAATCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTTATTAATCATAAGCA
Found at i:7953 original size:33 final size:32
Alignment explanation
Indices: 7916--7991 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
7906 TTTAAAGATC
*
7916 TATTTAATTTACAAAAAAGTAA-AAATTATTTAA
1 TATTTAA-ATACAAAAAAGTAACAAATTA-TTAA
* *
7949 TATTTCAAATATAAAAAGGTAACAAATTATTAA
1 TATTT-AAATACAAAAAAGTAACAAATTATTAA
*
7982 TAATTAAATA
1 TATTTAAATA
7992 TGAAATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 5 0.14
33 24 0.65
34 8 0.22
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (32 bp):
TATTTAAATACAAAAAAGTAACAAATTATTAA
Found at i:8408 original size:17 final size:18
Alignment explanation
Indices: 8376--8409 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8366 AAAGTAGAAG
8376 ATTTATTTAAAATTAATT
1 ATTTATTTAAAATTAATT
*
8394 ATTTA-TTAAATTTAAT
1 ATTTATTTAAAATTAAT
8410 CATAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATTTAAAATTAATT
Found at i:9045 original size:17 final size:17
Alignment explanation
Indices: 9023--9055 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9013 TATTACGTAA
9023 TATTAAAATTATAATTT
1 TATTAAAATTATAATTT
9040 TATTAAAATTATAATT
1 TATTAAAATTATAATT
9056 ATAAAGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAAATTATAATTT
Found at i:15877 original size:47 final size:47
Alignment explanation
Indices: 15820--15920 Score: 186
Period size: 47 Copynumber: 2.2 Consensus size: 47
15810 TTAAAAATAT
*
15820 ATTTATAACCTTAATTATAATATGAGTAAAGTACATAAATAATTATG
1 ATTTATAACCTTAATTATAATAGGAGTAAAGTACATAAATAATTATG
15867 ATTTATAACCTTAATTATAATAGGAGTAAAGTACATAAATAATTATG
1 ATTTATAACCTTAATTATAATAGGAGTAAAGTACATAAATAATTATG
15914 A-TTATAA
1 ATTTATAA
15921 GTTGTTGTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 6 0.11
47 47 0.89
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (47 bp):
ATTTATAACCTTAATTATAATAGGAGTAAAGTACATAAATAATTATG
Found at i:21430 original size:2 final size:2
Alignment explanation
Indices: 21366--21411 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
21356 AATGAATTAA
21366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21407 AT AT A
1 AT AT A
21412 ATTTGTATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21762 original size:29 final size:28
Alignment explanation
Indices: 21724--21790 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
21714 AATTTAGACA
* *
21724 AAAATAAATATTTTATGTATACATTTTAAT
1 AAAA-AAATA-TTTAAGTACACATTTTAAT
* *
21754 AAAAAAATA-TTAAGTACATATTTTGAT
1 AAAAAAATATTTAAGTACACATTTTAAT
21781 AAAAAAATAT
1 AAAAAAATAT
21791 AATTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.72
29 5 0.16
30 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAAAAATATTTAAGTACACATTTTAAT
Found at i:22420 original size:16 final size:15
Alignment explanation
Indices: 22399--22428 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22389 TTAAAATATG
22399 TATTTAATATATTTCA
1 TATTTAATA-ATTTCA
22415 TATTTAATAATTTC
1 TATTTAATAATTTC
22429 GATTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTAATAATTTCA
Found at i:30367 original size:23 final size:22
Alignment explanation
Indices: 30335--30377 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
30325 CGCCATTATT
30335 ATATTATTTTAATAATAAAAAAC
1 ATATTATTTTAATAA-AAAAAAC
* *
30358 ATATTTTTTTATTAAAAAAA
1 ATATTATTTTAATAAAAAAA
30378 TTAACTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTATTTTAATAAAAAAAAC
Found at i:32113 original size:104 final size:103
Alignment explanation
Indices: 31934--32140 Score: 387
Period size: 104 Copynumber: 2.0 Consensus size: 103
31924 GAAACTTTAT
31934 TGATATTCATTTAAATGCCGTGAGCTTTTTTCCCTTGTTAGATTTTGACATACTGCTTCATTCAC
1 TGATATTCATTTAAATGCCGTGAGCTTTTTTCCCTTGTTAGATTTTGACATACTGCTTCATTCAC
*
31999 TCGTTTTGTGCTGTGCCTAGTTTAAGTTAATAATATAC
66 TCGTTTTGTGCTGTGCCTAGTTTAAGTTAATAACATAC
*
32037 TGATATTCATTTAAATGCTGTGAGCTTTTTTTCCCTTGTTAGATTTTGACATACTGCTTCATTCA
1 TGATATTCATTTAAATGCCGTGAGC-TTTTTTCCCTTGTTAGATTTTGACATACTGCTTCATTCA
32102 CTCGTTTTGTGCTGTGCCTAGTTTAAGTTAATAACATAC
65 CTCGTTTTGTGCTGTGCCTAGTTTAAGTTAATAACATAC
32141 ACCAAAACTC
Statistics
Matches: 101, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
103 24 0.24
104 77 0.76
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.45
Consensus pattern (103 bp):
TGATATTCATTTAAATGCCGTGAGCTTTTTTCCCTTGTTAGATTTTGACATACTGCTTCATTCAC
TCGTTTTGTGCTGTGCCTAGTTTAAGTTAATAACATAC
Found at i:35684 original size:2 final size:2
Alignment explanation
Indices: 35679--35714 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35669 ATAACTTCTC
35679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35715 TCCAATTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38804 original size:14 final size:15
Alignment explanation
Indices: 38771--38809 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
38761 ATTTTATTTG
*
38771 AATAAATTGTAATAT
1 AATAAATTATAATAT
*
38786 AATAAATTATTAT-T
1 AATAAATTATAATAT
38800 AATAAATTAT
1 AATAAATTAT
38810 CCTAATCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATAAATTATAATAT
Found at i:55989 original size:30 final size:30
Alignment explanation
Indices: 55953--56011 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
55943 CAAAGAAGTA
55953 GAAATTATTTCTGATTGATTAATTGTATAT
1 GAAATTATTTCTGATTGATTAATTGTATAT
55983 GAAATTATTTCTGATTGATTAATTGTATA
1 GAAATTATTTCTGATTGATTAATTGTATA
56012 GGTGGCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (30 bp):
GAAATTATTTCTGATTGATTAATTGTATAT
Found at i:61166 original size:31 final size:30
Alignment explanation
Indices: 61096--61168 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
61086 AATAATTTAG
*
61096 TCTTTTAATTTTTTATAAAAAATATTTAAT
1 TCTTTTATTTTTTTATAAAAAATATTTAAT
* * *
61126 TATACTTATTTTTATTATATAAAAT-TTTAAAT
1 TCT-TTTATTTTT-TTATAAAAAATATTT-AAT
61158 TCTTTTATTTT
1 TCTTTTATTTT
61169 GGATTACGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
30 2 0.06
31 17 0.50
32 15 0.44
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (30 bp):
TCTTTTATTTTTTTATAAAAAATATTTAAT
Found at i:61516 original size:31 final size:31
Alignment explanation
Indices: 61457--61548 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 31
61447 AGGGTACATG
*
61457 ATCCATAACATTATCAATCCGTTTGATTTTA
1 ATCCATAACATTATCAATCCGTTCGATTTTA
* ** *
61488 ATCCCTAACATTATTGATCGGTTCGATTTTA
1 ATCCATAACATTATCAATCCGTTCGATTTTA
* *
61519 GTCCTTCAACCATTATC--T-CGTTCGATTTTA
1 ATCCAT-AA-CATTATCAATCCGTTCGATTTTA
61549 GTCTCTCAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
30 11 0.22
31 31 0.62
32 2 0.04
33 6 0.12
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (31 bp):
ATCCATAACATTATCAATCCGTTCGATTTTA
Done.