Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008993.1 Hibiscus syriacus cultivar Beakdansim tig00112369_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: 51225
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:6387 original size:31 final size:28
Alignment explanation
Indices: 6344--6426 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 28
6334 CTTTTTTTTT
*
6344 TTTTTGTAAAAATAAGTACCTAAAGTTATC
1 TTTTTGTCAAAATAAGTACCTAAAG-TA-C
* *
6374 TTTTTGGTCAAAATAACTACTTAAAGTAC
1 TTTTT-GTCAAAATAAGTACCTAAAGTAC
*
6403 TTTATGTCAAAAT-AGTTACCTAAA
1 TTTTTGTCAAAATAAG-TACCTAAA
6427 CTATTCAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.02
28 15 0.33
29 5 0.11
30 7 0.16
31 17 0.38
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
TTTTTGTCAAAATAAGTACCTAAAGTAC
Found at i:6426 original size:28 final size:30
Alignment explanation
Indices: 6352--6426 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 30
6342 TTTTTTTGTA
*
6352 AAAATAAGTACCTAAAGTTATCTTTTTGGTC
1 AAAAT-AGTACCTAAAGTTATCTTTATGGTC
* *
6383 AAAATAACTACTTAAAG-TA-CTTTAT-GTC
1 AAAAT-AGTACCTAAAGTTATCTTTATGGTC
6411 AAAATAGTTACCTAAA
1 AAAATAG-TACCTAAA
6427 CTATTCAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 15 0.39
29 5 0.13
30 2 0.05
31 15 0.39
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (30 bp):
AAAATAGTACCTAAAGTTATCTTTATGGTC
Found at i:10725 original size:2 final size:2
Alignment explanation
Indices: 10718--10747 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10708 TTTTACTAAT
10718 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
10748 CGAAAATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12711 original size:21 final size:21
Alignment explanation
Indices: 12687--12751 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
12677 GATATAACAA
*
12687 TTCACGGTACTGAAGTGGCGG
1 TTCACGGTACTGAAGTGGCAG
*
12708 TTCATGGTACTGAAGTGGCAG
1 TTCACGGTACTGAAGTGGCAG
* * *
12729 TTCACGATACTGACGTGGTAG
1 TTCACGGTACTGAAGTGGCAG
12750 TT
1 TT
12752 TAGGGTGGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (21 bp):
TTCACGGTACTGAAGTGGCAG
Found at i:19577 original size:22 final size:22
Alignment explanation
Indices: 19552--19593 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
19542 ATCAAATGAG
19552 GCATCTCTTGCAACAAAAATAC
1 GCATCTCTTGCAACAAAAATAC
19574 GCATCTCTTGCAACAAAAAT
1 GCATCTCTTGCAACAAAAAT
19594 GCAAAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (22 bp):
GCATCTCTTGCAACAAAAATAC
Found at i:20103 original size:29 final size:29
Alignment explanation
Indices: 20069--20127 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20059 CCTAAATTAA
20069 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
20098 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
20127 T
1 T
20128 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:24786 original size:29 final size:29
Alignment explanation
Indices: 24752--24810 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
24742 CCTAAATTAA
24752 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
24781 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
24810 T
1 T
24811 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:27665 original size:18 final size:18
Alignment explanation
Indices: 27639--27674 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27629 AACATTGTAT
*
27639 TCCAATGCTTCTGGCAAC
1 TCCAATGCTCCTGGCAAC
*
27657 TCCAGTGCTCCTGGCAAC
1 TCCAATGCTCCTGGCAAC
27675 CGTCGAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (18 bp):
TCCAATGCTCCTGGCAAC
Found at i:33617 original size:29 final size:27
Alignment explanation
Indices: 33571--33625 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
33561 AATACGTATA
33571 ATATATTTATTTTAAAAACTATATAAC
1 ATATATTTATTTTAAAAACTATATAAC
*
33598 ATATATTATATTTTCAAAAATTATATAA
1 ATATATT-TATTTT-AAAAACTATATAA
33626 TATGTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.28
28 6 0.24
29 12 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATTTATTTTAAAAACTATATAAC
Found at i:33624 original size:22 final size:22
Alignment explanation
Indices: 33598--33647 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
33588 ACTATATAAC
33598 ATATATTATATTTTCAAAAATT
1 ATATATTATATTTTCAAAAATT
* *
33620 ATATAATATGTTTTCAAAAATT
1 ATATATTATATTTTCAAAAATT
33642 ATATAT
1 ATATAT
33648 ACTATATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATATTATATTTTCAAAAATT
Found at i:33667 original size:29 final size:28
Alignment explanation
Indices: 33571--33668 Score: 77
Period size: 28 Copynumber: 3.6 Consensus size: 28
33561 AATACGTATA
33571 ATATATTTATTTTAAAAACTATATA-AC-
1 ATATATTTATTTTAAAAA-TATATATACT
*
33598 ATATATTATATTTTCAAAA-AT-TATA-T
1 ATATATT-TATTTTAAAAATATATATACT
* *
33624 A-ATATGT-TTTCAAAAATTATATATACT
1 ATATATTTATTTTAAAAA-TATATATACT
33651 ATATATGTT-TTTTAAAAA
1 ATATAT-TTATTTTAAAAA
33669 CTATTTTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
23 7 0.12
24 1 0.02
25 8 0.14
26 8 0.14
27 9 0.16
28 14 0.25
29 9 0.16
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
ATATATTTATTTTAAAAATATATATACT
Found at i:33699 original size:40 final size:40
Alignment explanation
Indices: 33630--33710 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 40
33620 ATATAATATG
33630 TTTTCAAAAATTATATATACTATATATGTTTTTTAAAAACTA
1 TTTTCAAAAATTATATATACTATATATG-TTTTT-AAAACTA
33672 TTTTC-AAAATTCATATATA-T-TATATGTTTTTAAAACTA
1 TTTTCAAAAATT-ATATATACTATATATGTTTTTAAAACTA
33710 T
1 T
33711 AAAATATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
38 8 0.21
39 5 0.13
40 6 0.16
41 7 0.18
42 12 0.32
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (40 bp):
TTTTCAAAAATTATATATACTATATATGTTTTTAAAACTA
Found at i:33751 original size:17 final size:17
Alignment explanation
Indices: 33714--33754 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
33704 AAACTATAAA
**
33714 ATATATTTTCAAAAATT
1 ATATATTTTCAAAAACC
33731 ATATATTTTCAAAAACC
1 ATATATTTTCAAAAACC
33748 ATATATT
1 ATATATT
33755 ATATACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATTTTCAAAAACC
Found at i:38064 original size:14 final size:14
Alignment explanation
Indices: 38028--38054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38018 ATTTATTTTT
38028 TAATTATATTTATA
1 TAATTATATTTATA
38042 TAATTATATTTAT
1 TAATTATATTTAT
38055 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:40655 original size:21 final size:21
Alignment explanation
Indices: 40631--40671 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40621 GATAAAAAAT
*
40631 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
40652 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
40672 TTTAACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:48816 original size:3 final size:3
Alignment explanation
Indices: 48802--48894 Score: 141
Period size: 3 Copynumber: 30.3 Consensus size: 3
48792 GTTTAAAAAA
*
48802 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
48848 TAT TAT TAT TAA TAT TAT TAT TAA TAT TAT TAT TAT TAAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
48894 T
1 T
48895 TACCACTACC
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
3 76 0.93
4 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Done.