Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009419.1 Hibiscus syriacus cultivar Beakdansim tig00113377_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: 22630
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1397 original size:30 final size:31
Alignment explanation
Indices: 1336--1406 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
1326 GAGCTGCTCA
1336 CGAGCTTCAGTTCAGGATTTCGAGTTCGAGT
1 CGAGCTTCAGTTCAGGATTTCGAGTTCGAGT
* *
1367 CGAG-TTCATTTCAGAGTTTTCGAGTT-GAGT
1 CGAGCTTCAGTTCAG-GATTTCGAGTTCGAGT
1397 CGAGC-TCAGT
1 CGAGCTTCAGT
1407 AATAAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (31 bp):
CGAGCTTCAGTTCAGGATTTCGAGTTCGAGT
Found at i:2451 original size:15 final size:15
Alignment explanation
Indices: 2433--2466 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2423 CATTATCACT
* *
2433 ACCATGATCACCATC
1 ACCATCATCACCACC
2448 ACCATCATCACCACC
1 ACCATCATCACCACC
2463 ACCA
1 ACCA
2467 ACACTTGACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.47, G:0.03, T:0.15
Consensus pattern (15 bp):
ACCATCATCACCACC
Found at i:16262 original size:16 final size:16
Alignment explanation
Indices: 16241--16271 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16231 TGCTATTAAC
16241 CCAAGTTTAAACTTTT
1 CCAAGTTTAAACTTTT
16257 CCAAGTTTAAACTTT
1 CCAAGTTTAAACTTT
16272 GACCTAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (16 bp):
CCAAGTTTAAACTTTT
Found at i:19288 original size:20 final size:20
Alignment explanation
Indices: 19263--19357 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
19253 AATTGAGAAA
*
19263 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
19283 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
19304 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
19324 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
19344 TTCGCAACGCGATA
1 ATCGCAACGCGATA
19358 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:19289 original size:41 final size:41
Alignment explanation
Indices: 19097--19274 Score: 338
Period size: 41 Copynumber: 4.3 Consensus size: 41
19087 CGATTTTCCC
19097 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
19138 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
19179 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
19220 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
19261 AAATCGCAATGCGA
1 AATTCGCAATGCGA
19275 TACTGACTAT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:19305 original size:41 final size:41
Alignment explanation
Indices: 19242--19337 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
19232 GAATAAGTAA
* * * *
19242 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-AAAAAATCGCAACGAGATACTGACT
* *
19283 ATCGCAATGCGATAATAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACT
*
19324 TTCGCAACGCGATA
1 ATCGCAACGCGATA
19338 CTGACTTTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACT
Found at i:19573 original size:22 final size:22
Alignment explanation
Indices: 19545--19588 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19535 CACTCTCTCA
19545 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
19567 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
19589 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:19877 original size:20 final size:20
Alignment explanation
Indices: 19852--19889 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19842 CGATTCTCTC
19852 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
19872 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
19890 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:21224 original size:18 final size:18
Alignment explanation
Indices: 21198--21242 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21188 TCCACTTCGG
*
21198 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
21216 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
21234 GAGCCATCA
1 GAGCCATCA
21243 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:21766 original size:19 final size:18
Alignment explanation
Indices: 21744--21840 Score: 68
Period size: 19 Copynumber: 5.6 Consensus size: 18
21734 GGAAATGGCT
21744 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
21763 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
21777 ATCGCAACGCGAAAATG-AA
1 ATCGCAA-GCG-AAATGAAA
*
21796 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
21810 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
21829 ATCGCAATGCGA
1 ATCGCAA-GCGA
21841 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 24
0.68 0.06 0.27
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 4 0.07
17 4 0.07
18 1 0.02
19 31 0.51
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:21779 original size:14 final size:14
Alignment explanation
Indices: 21760--21818 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
21750 ATGCGAAATG
21760 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21774 AAAATCGCAACGCGAAA
1 AAAATCGCAA--CG-AC
21791 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
21807 AAAATCGCAACG
1 AAAATCGCAACG
21819 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
16 4 0.11
17 4 0.11
19 9 0.24
ACGTcount: A:0.49, C:0.25, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:21789 original size:33 final size:33
Alignment explanation
Indices: 21744--21835 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
21734 GGAAATGGCT
*
21744 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
21777 ATCGCAACGCGAAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCG-AAATGAAAATCGCAACGACAAA
21810 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
21836 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
32 5 0.09
33 46 0.82
34 5 0.09
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:21852 original size:19 final size:18
Alignment explanation
Indices: 21836--21951 Score: 96
Period size: 19 Copynumber: 6.4 Consensus size: 18
21826 AAAATCGCAA
*
21836 TGCGATTTGTGTTTCGCGT
1 TGCGATTT-CGTTTCGCGT
21855 TGCGATTTCGTTTCGCGT
1 TGCGATTTCGTTTCGCGT
*
21873 TGCGATTT--TGT--CGT
1 TGCGATTTCGTTTCGCGT
* *
21887 TGCGATTTTCATTTCGCAT
1 TGCGA-TTTCGTTTCGCGT
* *
21906 TGCGATATCTATTTCGCGT
1 TGCGATTTC-GTTTCGCGT
* *
21925 TGCGATAGTCATTTCGCGT
1 TGCGAT-TTCGTTTCGCGT
21944 TGCGATTT
1 TGCGATTT
21952 TAAGTTTCGG
Statistics
Matches: 82, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 21 0.26
19 44 0.54
20 2 0.02
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (18 bp):
TGCGATTTCGTTTCGCGT
Found at i:21965 original size:38 final size:37
Alignment explanation
Indices: 21836--21967 Score: 127
Period size: 38 Copynumber: 3.6 Consensus size: 37
21826 AAAATCGCAA
*
21836 TGCGATTTGT-GTTTCGCGTTGCGATTTCGTTTCGCGT
1 TGCGATTT-TAGTTTCGCGTTGCGATTTCATTTCGCGT
*
21873 TGCGATTTT-G--T--CGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTAGTTTCGCGTTGCGA-TTTCATTTCGCGT
* *
21906 TGCGATATCTA-TTTCGCGTTGCGATAGTCATTTCGCGT
1 TGCGAT-TTTAGTTTCGCGTTGCGAT-TTCATTTCGCGT
21944 TGCGATTTTAAGTTTCG-GTTGCGA
1 TGCGATTTT-AGTTTCGCGTTGCGA
21968 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
32 8 0.10
33 17 0.22
34 3 0.04
36 3 0.04
37 11 0.14
38 32 0.41
39 5 0.06
ACGTcount: A:0.12, C:0.18, G:0.26, T:0.44
Consensus pattern (37 bp):
TGCGATTTTAGTTTCGCGTTGCGATTTCATTTCGCGT
Found at i:22041 original size:25 final size:24
Alignment explanation
Indices: 21983--22043 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
21973 AACTATTCTT
*
21983 CTTCTGGAATGTTTATATGTTGTC
1 CTTCTGGAATGTTTATATGTTGTA
**
22007 CTT-TTAAATGTTTATATAG-TGCTA
1 CTTCTGGAATGTTTATAT-GTTG-TA
22031 CTTCTGGAATGTT
1 CTTCTGGAATGTT
22044 ATCTGAGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 14 0.48
24 8 0.28
25 7 0.24
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.49
Consensus pattern (24 bp):
CTTCTGGAATGTTTATATGTTGTA
Done.