Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006005.1 Hibiscus syriacus cultivar Beakdansim tig00014158_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: 182743
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:162406 original size:27 final size:28
Alignment explanation
Indices: 162354--162405 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
162344 TTATTCTACT
162354 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
162382 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
162406 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:162439 original size:11 final size:11
Alignment explanation
Indices: 162423--162462 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
162413 TCTTTCTTTT
162423 TATTATTCTTG
1 TATTATTCTTG
162434 TATTATTCTTG
1 TATTATTCTTG
* *
162445 TATTATTTTTA
1 TATTATTCTTG
162456 TATTATT
1 TATTATT
162463 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:162463 original size:11 final size:11
Alignment explanation
Indices: 162419--162463 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
162409 TTTCTCTTTC
162419 TTTT-TATTAT
1 TTTTGTATTAT
*
162429 TCTTGTATTAT
1 TTTTGTATTAT
*
162440 TCTTGTATTAT
1 TTTTGTATTAT
*
162451 TTTTATATTAT
1 TTTTGTATTAT
162462 TT
1 TT
162464 ATTTTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 3 0.10
11 28 0.90
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTGTATTAT
Found at i:162969 original size:9 final size:9
Alignment explanation
Indices: 162931--162977 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
162921 TCTTTTCGTC
*
162931 ATTTAATTT
1 ATTTATTTT
*
162940 A-TTAATTT
1 ATTTATTTT
*
162948 ATATATATTT
1 ATTTAT-TTT
162958 ATTTATTTT
1 ATTTATTTT
162967 ATTTATTTT
1 ATTTATTTT
162976 AT
1 AT
162978 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 8 0.24
9 17 0.52
10 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTATTTT
Found at i:163000 original size:28 final size:27
Alignment explanation
Indices: 162939--163001 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
162929 TCATTTAATT
* * * *
162939 TATTAATTTATATATATTTATTTATTT
1 TATTATTTTATATATATATATATATTA
162966 TATTTATTTTATATATATATATATATATA
1 TA-TTATTTTATATATATATATATAT-TA
162995 TATTATT
1 TATTATT
163002 CGTACTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.07
28 25 0.83
29 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTATTTTATATATATATATATATTA
Found at i:164257 original size:19 final size:19
Alignment explanation
Indices: 164233--164269 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
164223 ACCTTACTAA
164233 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
164252 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
164270 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:168283 original size:22 final size:22
Alignment explanation
Indices: 168209--168285 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
168199 GCTACCCCAT
*
168209 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
168231 CAAACCTATGAGCATCACATGC
1 CAAACCTTTGAGCATCAAATGC
168253 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
168275 CAAACCTTTGA
1 CAAACCTTTGA
168286 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:169323 original size:106 final size:106
Alignment explanation
Indices: 169124--170590 Score: 2125
Period size: 106 Copynumber: 13.9 Consensus size: 106
169114 CAAGATAACA
* * * *
169124 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
169188 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
169229 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAATTTCCCAAATTCAGATCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
169294 ATTTCAACTTCACAGCGAAGGATATTGGACTCCATACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
169335 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-CCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCCCAATTTCAGAGCC
*
169399 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
169441 CAAGTTCAACTTCATGACGAAGGGACAGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
169506 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
169547 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
169612 ATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
169653 CAAGTTCAACTTCACAACGAAGGGACCTCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
169718 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
169759 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
169824 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
169865 CAATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
169930 ATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
169971 CAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
170036 ATTTCAACTTCACAGCGAAGGATTTTGGACT-CAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
170076 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACCAACAACTTCTCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
170141 ATTTCAACTTCAAAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
170182 CAAGTTCAACTTCATGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
170247 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
170288 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCATAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
** * * *
170353 ATTTCAACTTCTTAGCGAAGGATCTTGAAC-CCAAGGA-AACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-A-GACAACG
* * * ** *
170394 CAAGCTCAACTTCATGACGAAGAGG-CGGCTAATTGTCAAC-AA-AATTT--C-A-TTCAGAGTC
1 CAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
* * *
170452 AATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACA
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* ** * ** * *
170494 CAAGTTCAACTTCACAACGAAGGGATGGCTAGTTGTCAACAAACAATTTCCCGGTTCCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
170559 ATTTCAACTTCACGAAG-G-AGGATATTGGACTC
66 ATTTCAACTTCAC--AGCGAAGGATATTGGACTC
170591 AGAACAATGC
Statistics
Matches: 1238, Mismatches: 106, Indels: 35
0.90 0.08 0.03
Matches are distributed among these distances:
99 4 0.00
100 70 0.06
101 4 0.00
102 6 0.00
104 5 0.00
105 136 0.11
106 1003 0.81
107 8 0.01
108 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:171371 original size:37 final size:37
Alignment explanation
Indices: 171318--171422 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
171308 CTTTTTAGTC
*
171318 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
171355 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
171392 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
171423 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:172066 original size:27 final size:25
Alignment explanation
Indices: 172036--172086 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
172026 TTATTCTACT
172036 TATTATATTATATATGTATATTTTTTA
1 TATTATATTAT-TAT-TATATTTTTTA
*
172063 TATTTTATTATTATTATATTTTTT
1 TATTATATTATTATTATATTTTTT
172087 TACTTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
26 3 0.13
27 10 0.43
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TATTATATTATTATTATATTTTTTA
Found at i:172126 original size:12 final size:11
Alignment explanation
Indices: 172104--172144 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
172094 TCTTTCTTTT
172104 TATTATTCTTG
1 TATTATTCTTG
172115 TATTATTACTTG
1 TATTATT-CTTG
* *
172127 TATTATTTTTA
1 TATTATTCTTG
172138 TATTATT
1 TATTATT
172145 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:172550 original size:2 final size:2
Alignment explanation
Indices: 172543--172579 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
172533 GTATTGTTAC
172543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
172580 ATTATCTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:172677 original size:27 final size:29
Alignment explanation
Indices: 172617--172677 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
172607 ATTATATGTG
172617 TATATGTTCTTTTTGTCATTTAATTTATA
1 TATATGTTCTTTTTGTCATTTAATTTATA
*
172646 TATAT-TTACTTTTT-T-ATTTATTTTATA
1 TATATGTT-CTTTTTGTCATTTAATTTATA
172673 TATAT
1 TATAT
172678 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 16 0.53
28 3 0.10
29 11 0.37
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (29 bp):
TATATGTTCTTTTTGTCATTTAATTTATA
Found at i:172784 original size:28 final size:29
Alignment explanation
Indices: 172703--172800 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 29
172693 ATTCGTACTT
*
172703 TATTATTATTATTTTGTTTATTTGTTT-TATT
1 TATT-TTATTA-TTTGTTTATTT-TTTATATA
* * * *
172734 TATTTTCTTTTTCTTTTTCTTTTTTATATA
1 TATTTTATTATT-TGTTTATTTTTTATATA
172764 TATTTTATTATTTGTTT-TTTTTTACT-TA
1 TATTTTATTATTTGTTTATTTTTTA-TATA
172792 CTATTTTAT
1 -TATTTTAT
172801 CTTTGCTTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.16
29 18 0.33
30 24 0.44
31 4 0.07
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.74
Consensus pattern (29 bp):
TATTTTATTATTTGTTTATTTTTTATATA
Found at i:172805 original size:28 final size:27
Alignment explanation
Indices: 172741--172805 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
172731 ATTTATTTTC
172741 TTTT-TCTTT-TTCTTTTTTATATATA
1 TTTTATCTTTGTTCTTTTTTATATATA
* *
172766 TTTTATTATTTGTTTTTTTTTACT-TACTA
1 TTTTA-TCTTTGTTCTTTTTTA-TATA-TA
172795 TTTTATCTTTG
1 TTTTATCTTTG
172806 CTTTCTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 4 0.12
27 4 0.12
28 16 0.50
29 8 0.25
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (27 bp):
TTTTATCTTTGTTCTTTTTTATATATA
Found at i:174513 original size:22 final size:22
Alignment explanation
Indices: 174488--174554 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
174478 GAGTCGAGGG
174488 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
174510 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
*
174532 ATATACAGTGGTCATTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
174554 A
1 A
174555 AATTCTACGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (22 bp):
ATATACAGTGGTCCTTCGGGAC
Found at i:178938 original size:18 final size:18
Alignment explanation
Indices: 178908--178981 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 18
178898 AGGGATATAC
178908 AGTGGT-CTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
178925 AGTGGTCATTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
178945 ACAATGGTCCTTCGGGACAT
1 --AGTGGTCCTTCGGGACAT
*
178965 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
178982 AATTCTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.13
18 23 0.49
20 4 0.09
22 14 0.30
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:178965 original size:40 final size:39
Alignment explanation
Indices: 178902--178981 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 39
178892 GAGTCGAGGG
* *
178902 ATATACAGTGGTCTTCGGGACATAGTGGTCATTCGGGAC
1 ATATACAATGGTCTTCGGGACATAGTGGTCATACGGGAC
*
178941 ATATACAATGGTCCTTCGGGACATAGTGGTCCTACGGGAC
1 ATATACAATGGT-CTTCGGGACATAGTGGTCATACGGGAC
178981 A
1 A
178982 AATTCTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 11 0.30
40 26 0.70
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (39 bp):
ATATACAATGGTCTTCGGGACATAGTGGTCATACGGGAC
Done.