Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007385.1 Hibiscus syriacus cultivar Beakdansim tig00019858_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: 79323
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:10697 original size:16 final size:16
Alignment explanation
Indices: 10676--10742 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
10666 GTCTCTAACG
10676 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
10692 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
10708 TTTATGTTCATGTTCG
1 TTTATGTTCGTGTTCA
10724 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
10738 TTTAT
1 TTTAT
10743 TAAATGAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:10715 original size:32 final size:32
Alignment explanation
Indices: 10674--10734 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
10664 GGGTCTCTAA
*
10674 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCATGTTCATTTATGTTCGTGTT
*
10706 CGTTTATGTTCATGTTCGTTTATGTTCGT
1 CGTTTATGTTCATGTTCATTTATGTTCGT
10735 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCATGTTCATTTATGTTCGTGTT
Found at i:22648 original size:13 final size:13
Alignment explanation
Indices: 22630--22654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22620 AAAACCTATA
22630 ATTATAATAATTT
1 ATTATAATAATTT
22643 ATTATAATAATT
1 ATTATAATAATT
22655 AAAATATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:25383 original size:21 final size:23
Alignment explanation
Indices: 25357--25401 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
25347 GGAAAATGGG
*
25357 AAATTA-TTGTCAAAATAA-TAT
1 AAATTACTTATCAAAATAACTAT
*
25378 AAATTACTTATCAATATAACTAT
1 AAATTACTTATCAAAATAACTAT
25401 A
1 A
25402 CACTGAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATTACTTATCAAAATAACTAT
Found at i:29040 original size:72 final size:72
Alignment explanation
Indices: 28955--29098 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
28945 CTGTCGTAAA
*
28955 ATTTTTAACAAAAAAAAAACGAGTTTGGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
1 ATTTTTAACAAAAAAAAAACGAGTCTGGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
29020 AATAGTC
66 AATAGTC
*
29027 ATTTTTAACAAAAAAAAAACGAGTCTGGAACATATGAATAGTAAGATTATAATTTGATAATTTTT
1 ATTTTTAACAAAAAAAAAACGAGTCTGGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
29092 AATAGTC
66 AATAGTC
29099 TATGGACTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (72 bp):
ATTTTTAACAAAAAAAAAACGAGTCTGGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
AATAGTC
Found at i:37489 original size:18 final size:18
Alignment explanation
Indices: 37463--37497 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37453 ATTTTTGATA
37463 TACACAAATCATTTTTTT
1 TACACAAATCATTTTTTT
*
37481 TACATAAATCATTTTTT
1 TACACAAATCATTTTTT
37498 ACACAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
TACACAAATCATTTTTTT
Found at i:43853 original size:24 final size:23
Alignment explanation
Indices: 43819--43865 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
43809 CATTTAAATG
* *
43819 ATAAACGAACACATATGAACGAAC
1 ATAAACAAACACA-ATAAACGAAC
43843 ATAAACAAACACAATAAACGAAC
1 ATAAACAAACACAATAAACGAAC
43866 GCAAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.11
Consensus pattern (23 bp):
ATAAACAAACACAATAAACGAAC
Found at i:43874 original size:37 final size:37
Alignment explanation
Indices: 43819--43923 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
43809 CATTTAAATG
* *
43819 ATAAACGAACACATATGAACGAACATAAACAAACACA
1 ATAAACGAACACAAATGAACGAACACAAACAAACACA
* * * *
43856 ATAAACGAACGCAAATGAATGAACGCAAACGAACACA
1 ATAAACGAACACAAATGAACGAACACAAACAAACACA
* *
43893 ATAAATGAACATAAATGAACGTAA-ACAAACA
1 ATAAACGAACACAAATGAACG-AACACAAACA
43924 TAAATGAACA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 53 0.96
38 2 0.04
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.11
Consensus pattern (37 bp):
ATAAACGAACACAAATGAACGAACACAAACAAACACA
Found at i:43888 original size:24 final size:23
Alignment explanation
Indices: 43858--43902 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
43848 CAAACACAAT
* *
43858 AAACGAACGCAAATGAATGAACGC
1 AAACGAACAC-AATAAATGAACGC
43882 AAACGAACACAATAAATGAAC
1 AAACGAACACAATAAATGAAC
43903 ATAAATGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.56, C:0.20, G:0.16, T:0.09
Consensus pattern (23 bp):
AAACGAACACAATAAATGAACGC
Found at i:43906 original size:10 final size:10
Alignment explanation
Indices: 43893--43935 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
43883 AACGAACACA
43893 ATAAATGAAC
1 ATAAATGAAC
43903 ATAAATGAAC
1 ATAAATGAAC
* **
43913 GTAAACAAAC
1 ATAAATGAAC
43923 ATAAATGAAC
1 ATAAATGAAC
43933 ATA
1 ATA
43936 GTTTTTTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:43910 original size:33 final size:30
Alignment explanation
Indices: 43873--43935 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 30
43863 AACGCAAATG
43873 AATGAACGCAAACGAACACAATAAATGAACATA
1 AATGAACGCAAAC-AA-AC-ATAAATGAACATA
*
43906 AATGAACGTAAACAAACATAAATGAACATA
1 AATGAACGCAAACAAACATAAATGAACATA
43936 GTTTTTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 13 0.45
31 2 0.07
32 2 0.07
33 12 0.41
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (30 bp):
AATGAACGCAAACAAACATAAATGAACATA
Found at i:53637 original size:17 final size:17
Alignment explanation
Indices: 53610--53651 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
53600 TTTTTTATTA
*
53610 TTAATTTTATTGATCAAT
1 TTAA-TTTATTAATCAAT
*
53628 TTAATTTATTAATTAAT
1 TTAATTTATTAATCAAT
53645 TTAATTT
1 TTAATTT
53652 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTAATTTATTAATCAAT
Found at i:63624 original size:28 final size:29
Alignment explanation
Indices: 63552--63624 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
63542 AATTTTTTAA
*
63552 AAAAATGATCAAAAAATATTATTAGACGTT
1 AAAAATGATCAAAAAA-ATTATTAGACGCT
* *
63582 AAAAAT-AACAAAAAAATTATTAGAGGCT
1 AAAAATGATCAAAAAAATTATTAGACGCT
*
63610 AAAAATGATCGAAAA
1 AAAAATGATCAAAAA
63625 TTTATAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.46
29 14 0.38
30 6 0.16
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (29 bp):
AAAAATGATCAAAAAAATTATTAGACGCT
Found at i:76177 original size:23 final size:23
Alignment explanation
Indices: 76126--76178 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
76116 ATCTAATACT
* *
76126 TAATATTTGAAGAATAAGTTTCA
1 TAATTTTTGAAGAATAAGATTCA
76149 -ATATTTTTGGAAGAATAA-ATTCA
1 TA-ATTTTT-GAAGAATAAGATTCA
76172 TAATTTT
1 TAATTTT
76179 CTTTTACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.04
23 14 0.56
24 10 0.40
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
TAATTTTTGAAGAATAAGATTCA
Done.