Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002753.1 Hibiscus syriacus cultivar Beakdansim tig00005670_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: 48820
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5506 original size:13 final size:13
Alignment explanation
Indices: 5488--5513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5478 TTATCTTTTA
5488 GAGAAAATAACTT
1 GAGAAAATAACTT
5501 GAGAAAATAACTT
1 GAGAAAATAACTT
5514 ATAAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
GAGAAAATAACTT
Found at i:7632 original size:20 final size:20
Alignment explanation
Indices: 7607--7703 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
7597 CGTAACTCGA
*
7607 TTTCGAGTTGTGAATTTCAT
1 TTTCGAGTTGCGAATTTCAT
7627 TTTCGAGTTGCGAA-TTCGAT
1 TTTCGAGTTGCGAATTTC-AT
*
7647 TTTCGAGTTGCGATTTTCAT
1 TTTCGAGTTGCGAATTTCAT
* * **
7667 GTTGCGAATTGCGAATTGAAT
1 -TTTCGAGTTGCGAATTTCAT
* *
7688 TTTCGTGTTACGAATT
1 TTTCGAGTTGCGAATT
7704 GCGAATTCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.67
21 18 0.29
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTCAT
Found at i:7701 original size:27 final size:27
Alignment explanation
Indices: 7659--7730 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
7649 TCGAGTTGCG
* *
7659 ATTTTCATGTTGCGAATTGCGAATTGA
1 ATTTTCGTGTTGCGAATTGCGAATTCA
*
7686 ATTTTCGTGTTACGAATTGCGAATTCA
1 ATTTTCGTGTTGCGAATTGCGAATTCA
*
7713 ATTTTCGAGTTGCGAATT
1 ATTTTCGTGTTGCGAATT
7731 TTATTTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (27 bp):
ATTTTCGTGTTGCGAATTGCGAATTCA
Found at i:7736 original size:20 final size:20
Alignment explanation
Indices: 7607--7751 Score: 85
Period size: 20 Copynumber: 6.8 Consensus size: 20
7597 CGTAACTCGA
* *
7607 TTTCGAGTTGTGAATTTCAT
1 TTTCGAGTTGCGAATTTTAT
**
7627 TTTCGAGTTGCGAATTCGAT
1 TTTCGAGTTGCGAATTTTAT
7647 TTTCGAGTTGCG-ATTTTCAT
1 TTTCGAGTTGCGAATTTT-AT
* * *
7667 GTTGCGAATTGCGAATTGAATTTT
1 -TTTCGAGTTGCGAATT---TTAT
* **
7691 CGTGTTACGAATTGCGAATTCAAT
1 --T-TT-CGAGTTGCGAATTTTAT
7715 TTTCGAGTTGCGAATTTTAT
1 TTTCGAGTTGCGAATTTTAT
* * *
7735 TTTTGAGCTGCAAATTT
1 TTTCGAGTTGCGAATTT
7752 GAGTTGCAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
19 3 0.03
20 59 0.60
21 12 0.12
22 4 0.04
24 2 0.02
25 4 0.04
26 1 0.01
27 13 0.13
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.44
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTTAT
Found at i:10632 original size:24 final size:24
Alignment explanation
Indices: 10605--10675 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
10595 CCAAATCCGA
* *
10605 GTATTGACTAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAATTTCGG
*
10629 GTATAGACCAAGATCAAATTTCGG
1 GTATTGACCAAGATCAAATTTCGG
10653 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAATTTCG
10676 AATACTGACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAATTTCGG
Found at i:10684 original size:24 final size:24
Alignment explanation
Indices: 10634--10684 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
10624 TTCGGGTATA
** *
10634 GACCAAGATCAAATTTCGGGTATT
1 GACCAAGATCAAATTTCGAATACT
10658 GACCAAGATCAAATTTCGAATACT
1 GACCAAGATCAAATTTCGAATACT
10682 GAC
1 GAC
10685 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GACCAAGATCAAATTTCGAATACT
Found at i:11678 original size:20 final size:20
Alignment explanation
Indices: 11600--11682 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
11590 ATTCACGTAG
*
11600 GAATTCAAAAATCGAGTTGC
1 GAATTTAAAAATCGAGTTGC
** * * * *
11620 GAAAATGAAACTCGTGTTAC
1 GAATTTAAAAATCGAGTTGC
**
11640 GAA-TTAGAAAATCTTGTTGC
1 GAATTTA-AAAATCGAGTTGC
11660 GAATTTAAAAATCGAGTTGC
1 GAATTTAAAAATCGAGTTGC
11680 GAA
1 GAA
11683 AAAGAAATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
19 1 0.02
20 43 0.91
21 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (20 bp):
GAATTTAAAAATCGAGTTGC
Found at i:11689 original size:40 final size:42
Alignment explanation
Indices: 11645--11724 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
11635 GTTACGAATT
11645 AGAAAATCTTGTTGCG-AATT-TAAAAATCGAGTTGCGAAAA
1 AGAAAATCTTGTTGCGAAATTGTAAAAATCGAGTTGCGAAAA
* * *
11685 AGAAATTCTTGTTGCGAAATTGTCAAATTCGAGTTGCGAA
1 AGAAAATCTTGTTGCGAAATTGTAAAAATCGAGTTGCGAA
11725 TTCGACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 15 0.43
41 4 0.11
42 16 0.46
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (42 bp):
AGAAAATCTTGTTGCGAAATTGTAAAAATCGAGTTGCGAAAA
Found at i:11742 original size:20 final size:19
Alignment explanation
Indices: 11717--11807 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 19
11707 TCAAATTCGA
**
11717 GTTGCGAATTCGACTTTTGT
1 GTTGCGAATTCGA-AATTGT
*
11737 GTTGCGAATTCGAAAACTGT
1 GTTGCGAATTCG-AAATTGT
*
11757 GTTGCGAAATT-GGAATTCGT
1 GTTGCG-AATTCGAAATT-GT
*
11777 GTTGCGAATTCGAAATTGA
1 GTTGCGAATTCGAAATTGT
11796 GTTGCGAATTCG
1 GTTGCGAATTCG
11808 TTGGTTATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 20 0.33
20 35 0.58
21 5 0.08
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCGAAATTGT
Found at i:11743 original size:82 final size:79
Alignment explanation
Indices: 11654--11807 Score: 186
Period size: 82 Copynumber: 1.9 Consensus size: 79
11644 TAGAAAATCT
* *
11654 TGTTGCGAATTTAAAAA-TCGAGTTGCGAAAAAGAAATTCTTGTTGCGAAATT-GTCAAATTCGA
1 TGTTGCGAATTCAAAAACT-GAGTTGCGAAAAAGAAATTCGTGTTGCG-AATTCG--AAATT-GA
11717 GTTGCGAATTCGACTTTTG
61 GTTGCGAATTCGACTTTTG
* * ** *
11736 TGTTGCGAATTCGAAAACTGTGTTGCGAAATTGGAATTCGTGTTGCGAATTCGAAATTGAGTTGC
1 TGTTGCGAATTCAAAAACTGAGTTGCGAAAAAGAAATTCGTGTTGCGAATTCGAAATTGAGTTGC
11801 GAATTCG
66 GAATTCG
11808 TTGGTTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 14 0.22
80 5 0.08
81 4 0.06
82 39 0.62
83 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (79 bp):
TGTTGCGAATTCAAAAACTGAGTTGCGAAAAAGAAATTCGTGTTGCGAATTCGAAATTGAGTTGC
GAATTCGACTTTTG
Found at i:12143 original size:2 final size:2
Alignment explanation
Indices: 12136--12166 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12126 TATAACCTAT
12136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12167 TCAATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12264 original size:21 final size:21
Alignment explanation
Indices: 12222--12264 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12212 GTATATTCAA
*
12222 ATTTTTAGTAATTTAATTTTT
1 ATTTTTAGTAATTTAATATTT
*
12243 ATTTTTAG-AATTTTTATATTT
1 ATTTTTAGTAA-TTTAATATTT
12264 A
1 A
12265 ATATTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
ATTTTTAGTAATTTAATATTT
Found at i:12281 original size:23 final size:24
Alignment explanation
Indices: 12255--12309 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
12245 TTTTAGAATT
*
12255 TTTATATTTA-ATATTT-GAATAAC
1 TTTATATTTATA-ATTTAAAATAAC
12278 TTTATATTTATAATTTAAAATAAC
1 TTTATATTTATAATTTAAAATAAC
12302 TTT-TATTT
1 TTTATATTT
12310 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTATATTTATAATTTAAAATAAC
Found at i:36199 original size:73 final size:75
Alignment explanation
Indices: 36004--36210 Score: 258
Period size: 76 Copynumber: 2.8 Consensus size: 75
35994 ACATTATATT
* * * * *
36004 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAATTTAATTAAGTTTTAGGATATT
1 TTATCATTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGAATATT
* *
36069 ATTTTTATATT
65 ATTTTTAAATA
** *
36080 TTATCATTGTTTTAAATATTTTAGTCTAAATAAGTTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATCATTGTTTTAGGTATTTTAGTTTAAAT-AGTTTTAGTATTTTAATTAGGATTTAGAATATT
36145 A-TTTTAAATA
65 ATTTTTAAATA
* *
36155 TTATTA-T-TTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATCATTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
36211 AGATGTTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
72 6 0.05
73 38 0.33
74 1 0.01
75 12 0.11
76 56 0.49
77 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (75 bp):
TTATCATTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAATATTA
TTTTTAAATA
Found at i:36813 original size:17 final size:17
Alignment explanation
Indices: 36788--36821 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36778 CTTTATCCCA
*
36788 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
36805 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
36822 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:36926 original size:29 final size:28
Alignment explanation
Indices: 36877--36939 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
36867 TTTATTACTA
* *
36877 TTTTTAATTCATTATTTATTATTTTATTT
1 TTTTTAATTCATAATTAATTA-TTTATTT
*
36906 TTTTTAATTTATAATTAATTATTTATTT
1 TTTTTAATTCATAATTAATTATTTATTT
*
36934 ATTTTA
1 TTTTTA
36940 TACCTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTAATTCATAATTAATTATTTATTT
Found at i:45270 original size:83 final size:84
Alignment explanation
Indices: 45143--45380 Score: 243
Period size: 83 Copynumber: 2.9 Consensus size: 84
45133 ACGTTGCGGA
* * *
45143 TTAATCTATAGTGGCATTTTTTTCAACAAATGCCGCAACAGAGTAGTACTTTAG-ATGCGTTGTT
1 TTAATATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCA-GCGTTGTT
* *
45207 ATACAAACGCCGTAATAGGG
65 ATACAAACACCATAATAGGG
* ** *
45227 TTAATATATAGTGGCA-TTTTTTCAACAAATGCCGTAATTGAGTAGTAATTTAGCAGCGTTTTTA
1 TTAATATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCAGCGTTGTTA
*
45291 TACAAATACCATAATAGGG
66 TACAAACACCATAATAGGG
* * ** * * * * *
45310 TTCATCA-ATAGTGG-AGTTTTTTTAACAAACACTGCAATAGACTAGTACTTTAGC-GTCGTTTT
1 TTAAT-ATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCAG-CGTTGT
45372 TATACAAAC
64 TATACAAAC
45381 GTAGCAATGA
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
82 2 0.02
83 112 0.85
84 17 0.13
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (84 bp):
TTAATATATAGTGGCAGTTTTTTCAACAAATGCCGCAACAGAGTAGTAATTTAGCAGCGTTGTTA
TACAAACACCATAATAGGG
Found at i:45564 original size:39 final size:39
Alignment explanation
Indices: 45490--45568 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
45480 GTTTTTGATC
* * *
45490 AAACGCCGCAAAAGACTCTTACTTTACTGGTGTTTGTAT
1 AAACGCCGCAAAAGACTCTAAATTTACTGGCGTTTGTAT
* *
45529 AAACGCCGCTAAAGACTC-AAATTTTCGTGGCGTTTGTAT
1 AAACGCCGCAAAAGACTCTAAATTTAC-TGGCGTTTGTAT
45568 A
1 A
45569 CAAACGCTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (39 bp):
AAACGCCGCAAAAGACTCTAAATTTACTGGCGTTTGTAT
Found at i:45610 original size:41 final size:41
Alignment explanation
Indices: 45555--45678 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 41
45545 TCAAATTTTC
* *
45555 GTGGCGTTTGTATACAAACGCTGCTATAAACTCGTACTTTA
1 GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
* *
45596 GTGGAGTTTTTATACAAACACTGCTATAGACTCGTACTTTA
1 GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
* * * * *
45637 GTGGCGCTTTTATATAAACACCGCTATATACTTGTACTTTA
1 GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
45678 G
1 G
45679 CAATTTGTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
GTGGCGTTTTTATACAAACACTGCTATAAACTCGTACTTTA
Done.