Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005148.1 Hibiscus syriacus cultivar Beakdansim tig00011594_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: 87556
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3906 original size:40 final size:40
Alignment explanation
Indices: 3851--3973 Score: 237
Period size: 40 Copynumber: 3.1 Consensus size: 40
3841 TGCAGATATG
3851 TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTTGGCTCC
1 TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTTGGCTCC
*
3891 TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTGGGCTCC
1 TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTTGGCTCC
3931 TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTTGGCTCC
1 TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTTGGCTCC
3971 TTA
1 TTA
3974 CGATATGCAG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (40 bp):
TTAGAAGCATTCCTTGTAACTAGAGCTTTGGCTTGGCTCC
Found at i:5260 original size:23 final size:23
Alignment explanation
Indices: 5232--5275 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5222 ATATATTCAT
5232 ATTTTAAAT-AAATCATTTTTATA
1 ATTTTAAATAAAAT-ATTTTTATA
*
5255 ATTTTAATTAAAATATTTTTA
1 ATTTTAAATAAAATATTTTTA
5276 ATATTCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTAAATAAAATATTTTTATA
Found at i:19338 original size:13 final size:13
Alignment explanation
Indices: 19317--19348 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19307 ATGGGGAAAA
*
19317 GTTGTTGATTTTG
1 GTTGCTGATTTTG
19330 GTTGCTGATTTTG
1 GTTGCTGATTTTG
19343 GTTGCT
1 GTTGCT
19349 ACGAAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.56
Consensus pattern (13 bp):
GTTGCTGATTTTG
Found at i:20905 original size:23 final size:22
Alignment explanation
Indices: 20834--20906 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 22
20824 TGTTCGCAAG
20834 CATGTTCAATTATATGTTCATGAA
1 CATGTTC-ATT-TATGTTCATGAA
**
20858 CATGTTTGTTTAATGTT--TGCAAA
1 CATGTTCATTT-ATGTTCATG--AA
20881 CATGTTCATTTAGTGTTCATGAA
1 CATGTTCATTTA-TGTTCATGAA
20904 CAT
1 CAT
20907 TTAACGAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 27 0.69
24 6 0.15
25 2 0.05
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (22 bp):
CATGTTCATTTATGTTCATGAA
Found at i:33402 original size:2 final size:2
Alignment explanation
Indices: 33397--33423 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33387 GTGTGTGTGT
33397 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
33424 TCACCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39462 original size:15 final size:15
Alignment explanation
Indices: 39442--39472 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39432 CAACATATAG
39442 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
39457 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
39472 A
1 A
39473 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:48971 original size:21 final size:21
Alignment explanation
Indices: 48945--48986 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
48935 TGCCGATTTT
48945 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
48966 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
48987 AACTTGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:49034 original size:33 final size:32
Alignment explanation
Indices: 48973--49083 Score: 161
Period size: 33 Copynumber: 3.4 Consensus size: 32
48963 TCGTAAACTT
48973 TATTTCAATTATCGAACTT-GAAGTTTTTAAG
1 TATTTCAATTATCGAACTTGGAAGTTTTTAAG
*
49004 TATTTGAATTTATCGAACTTGGAAGTTTTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
* * *
49037 TATTTGAATTTATCAAACTTGGAAGTATTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
49070 TATTTCAATTATCG
1 TATTTCAATTATCG
49084 TAAACTTTGT
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 7 0.10
32 16 0.22
33 50 0.68
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.45
Consensus pattern (32 bp):
TATTTCAATTATCGAACTTGGAAGTTTTTAAG
Found at i:49180 original size:15 final size:15
Alignment explanation
Indices: 49125--49181 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
49115 TTTAATAATA
*
49125 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
49140 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
49155 TAAAAAAAACCGGTTTTT
1 T---TAAAACCGGTTTTT
49173 TTAAAACCG
1 TTAAAACCG
49182 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 21 0.62
18 13 0.38
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:57296 original size:29 final size:30
Alignment explanation
Indices: 57264--57324 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
57254 TTTAGATATC
* *
57264 TATTTTGACT-AAAAAATAGTTTAAATACT
1 TATTTTAACTAAAAAAATACTTTAAATACT
57293 TATTTTAACTAAAAAAATACTTTAAATACT
1 TATTTTAACTAAAAAAATACTTTAAATACT
57323 TA
1 TA
57325 AACAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (30 bp):
TATTTTAACTAAAAAAATACTTTAAATACT
Found at i:58407 original size:2 final size:2
Alignment explanation
Indices: 58400--58424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58390 TACTCTAAAA
58400 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
58425 ATAAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65841 original size:56 final size:56
Alignment explanation
Indices: 65710--65957 Score: 208
Period size: 55 Copynumber: 4.6 Consensus size: 56
65700 TGACGAGCCT
* * * *
65710 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATC-TTCATAAAACGTGTCT
1 GCTCTCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTTAATAAAACGGGTCC
* * *
65765 ACTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGTCC
* * * * *
65821 GCTCTTTCTTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTTAATAAAACGGGTCC
* * * * * ** **
65876 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAA-CGAACTAGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGTCC
* *
65927 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTC
65958 AATCTTCAAC
Statistics
Matches: 160, Mismatches: 27, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
51 44 0.28
55 66 0.41
56 50 0.31
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (56 bp):
GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAATAAAACGGGTCC
Found at i:65932 original size:51 final size:51
Alignment explanation
Indices: 65872--66228 Score: 642
Period size: 51 Copynumber: 7.0 Consensus size: 51
65862 CAATAAACAG
* * *
65872 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
65923 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
65974 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
66025 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
66076 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
66127 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
66178 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
66229 CACTTTGTGA
Statistics
Matches: 297, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 297 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:66000 original size:102 final size:102
Alignment explanation
Indices: 65829--66227 Score: 663
Period size: 102 Copynumber: 3.9 Consensus size: 102
65819 CCGCTCTTTC
* ** ** * *
65829 TTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCTTTCAGG
1 TTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGA
65894 GAGTATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTA
62 GAGTATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTA
65935 TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
1 TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
*
66000 ATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTA
66 ATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTA
*
66037 TTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
1 TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
66102 ATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTA
66 ATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTA
*
66139 TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGT
1 TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
*
66204 ATAGGACTCAATCTTCAACAAACT
66 ATAGGACTCAATCTTCAACGAACT
66228 TCACTTTGTG
Statistics
Matches: 280, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
102 258 0.92
106 22 0.08
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (102 bp):
TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
ATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTA
Found at i:67510 original size:18 final size:18
Alignment explanation
Indices: 67481--67582 Score: 95
Period size: 18 Copynumber: 5.8 Consensus size: 18
67471 TTTATTTCTC
*
67481 TTTT-TTCATTTTCCCTT
1 TTTTCTTCATTTTTCCTT
*
67498 TTTT-TTCATTTTTCATT
1 TTTTCTTCATTTTTCCTT
**
67515 TTTTCTTCCCTTTTCCTT
1 TTTTCTTCATTTTTCCTT
**
67533 TTTTCTTTTTTTTTCCGTT
1 TTTTCTTCATTTTTCC-TT
*
67552 TTTTCCATCATTTTT-CTT
1 TTTT-CTTCATTTTTCCTT
67570 TTTTC-TCATTTTT
1 TTTTCTTCATTTTT
67583 TCTCTTTTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.11
17 20 0.28
18 29 0.41
19 7 0.10
20 7 0.10
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTTCTTCATTTTTCCTT
Found at i:67519 original size:26 final size:26
Alignment explanation
Indices: 67468--67516 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
67458 CTTGAACCCT
*
67468 CCTTTTATTTCTCTTTTTTCATTTTC
1 CCTTTTATTTCTCATTTTTCATTTTC
67494 CCTTTT-TTT-TCATTTTTCATTTT
1 CCTTTTATTTCTCATTTTTCATTTT
67517 TTCTTCCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 3 0.14
26 6 0.27
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.71
Consensus pattern (26 bp):
CCTTTTATTTCTCATTTTTCATTTTC
Found at i:67528 original size:25 final size:25
Alignment explanation
Indices: 67499--67553 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
67489 TTTTCCCTTT
*
67499 TTTTTCATTTTTCATTTTTTCTTCCC
1 TTTTCCATTTTTC-TTTTTTCTTCCC
* * *
67525 TTTTCCTTTTTTCTTTTTTTTTCCG
1 TTTTCCATTTTTCTTTTTTCTTCCC
67550 TTTT
1 TTTT
67554 TTCCATCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTCCATTTTTCTTTTTTCTTCCC
Found at i:77315 original size:44 final size:45
Alignment explanation
Indices: 77249--77345 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 45
77239 TTGTTATCCA
* *
77249 CAAAAAGAAATCCTAACTGCATGATATCTAATTCGCATGCTTATT
1 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTATT
* *
77294 CAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTGTT
1 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTATT
77338 CGAAAAAT
1 C-AAAAAT
77346 GAAAATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
44 32 0.68
45 15 0.32
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (45 bp):
CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTATT
Found at i:86938 original size:19 final size:19
Alignment explanation
Indices: 86910--86958 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
86900 TTAACTTTTT
86910 CTTTTATCTTTCATTATTAA
1 CTTTTATCTTTCATT-TTAA
*
86930 -TTTTCTCTTTCATTTTAA
1 CTTTTATCTTTCATTTTAA
*
86948 CTTTTACCTTT
1 CTTTTATCTTT
86959 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (19 bp):
CTTTTATCTTTCATTTTAA
Done.