Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003525.1 Hibiscus syriacus cultivar Beakdansim tig00007447_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: 193724
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
File 2 of 2
Found at i:181734 original size:21 final size:21
Alignment explanation
Indices: 181710--181768 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
181700 TGATTTATTA
**
181710 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
181731 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
181752 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
181769 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:181984 original size:43 final size:43
Alignment explanation
Indices: 181937--182185 Score: 171
Period size: 43 Copynumber: 6.0 Consensus size: 43
181927 CGTTTGTTCT
* * * * *
181937 AAAAAAAGCCGCTATATAC-C-AGATCTTTTGCGGTGTTTGTGGG
1 AAAAAAAGCCGCTAAAT-CTCAAGACCTATTACGGCGTTTGT-GG
*
181980 AAAAACA-CCGCTAAATCTCAAGACCTATTACGGCGTTTGTGG
1 AAAAAAAGCCGCTAAATCTCAAGACCTATTACGGCGTTTGTGG
* *
182022 AAAAAACGCCGCTAAATCTCAACACC---TA---CGTTTGTGG
1 AAAAAAAGCCGCTAAATCTCAAGACCTATTACGGCGTTTGTGG
* * * * *
182059 GAAAAACGCCGCTAAATCTCAACACTTATTGCGGCGTTTGTTGG
1 AAAAAAAGCCGCTAAATCTCAAGACCTATTACGGCGTTTG-TGG
* * * * *
182103 -AAAAATGCCGCTAAATATCAACACCTATTGCGGTGTTTGTTGG
1 AAAAAAAGCCGCTAAATCTCAAGACCTATTACGGCGTTTG-TGG
* * * *
182146 -ACAAACGGCGCTAAA-CATCAACACCTATTACGGCGTTTGT
1 AAAAAAAGCCGCTAAATC-TCAAGACCTATTACGGCGTTTGT
182186 TGGACAAACG
Statistics
Matches: 173, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
37 33 0.19
40 3 0.02
41 1 0.01
42 17 0.10
43 116 0.67
44 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (43 bp):
AAAAAAAGCCGCTAAATCTCAAGACCTATTACGGCGTTTGTGG
Found at i:182071 original size:80 final size:82
Alignment explanation
Indices: 181971--182206 Score: 291
Period size: 80 Copynumber: 2.9 Consensus size: 82
181961 CTTTTGCGGT
* *
181971 GTTTGTGGGAAAAACACCGCTAAATCTCAAGACCTATTACGGCGTTTG-TGGAAAAAACGCCGCT
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTTGG-AAAAACGCCGCT
*
182035 AAATCTCAACACCTA-C-
65 AAATATCAACACCTATCG
* * *
182051 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACTTATTGCGGCGTTTGTTGGAAAAATGCCGCTA
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTTGGAAAAACGCCGCTA
182116 AATATCAACACCTATTGCGG
66 AATATCAACACCTA-T-C-G
* * * *
182136 TGTTTGTTGGACAAACGGCGCTAAA-CATCAACACCTATTACGGCGTTTGTTGGACAAACGCCGC
1 -GTTTGTGGGAAAAACGCCGCTAAATC-TCAACACCTATTACGGCGTTTGTTGGAAAAACGCCGC
*
182200 TATATAT
64 TAAATAT
182207 AGTTACCTAT
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
80 69 0.51
81 3 0.02
83 1 0.01
85 1 0.01
86 60 0.45
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (82 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTTGGAAAAACGCCGCTA
AATATCAACACCTATCG
Found at i:182186 original size:43 final size:43
Alignment explanation
Indices: 181971--182201 Score: 271
Period size: 43 Copynumber: 5.5 Consensus size: 43
181961 CTTTTGCGGT
* * *
181971 GTTTGTGGGAAAAACACCGCTAAATCTCAAGACCTATTACGGC
1 GTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTATTACGGC
182014 GTTTG-TGGAAAAAACGCCGCTAAATCTCAACACC---TA---C
1 GTTTGTTGG-AAAAACGCCGCTAAATCTCAACACCTATTACGGC
* * *
182051 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACTTATTGCGGC
1 GTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTATTACGGC
* * * *
182094 GTTTGTTGGAAAAATGCCGCTAAATATCAACACCTATTGCGGT
1 GTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTATTACGGC
* *
182137 GTTTGTTGGACAAACGGCGCTAAA-CATCAACACCTATTACGGC
1 GTTTGTTGGAAAAACGCCGCTAAATC-TCAACACCTATTACGGC
*
182180 GTTTGTTGGACAAACGCCGCTA
1 GTTTGTTGGAAAAACGCCGCTA
182202 TATATAGTTA
Statistics
Matches: 161, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
37 30 0.19
38 2 0.01
40 3 0.02
42 2 0.01
43 124 0.77
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
GTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTATTACGGC
Found at i:182215 original size:43 final size:43
Alignment explanation
Indices: 181964--182226 Score: 254
Period size: 43 Copynumber: 6.3 Consensus size: 43
181954 ACCAGATCTT
* * * * * *
181964 TTGCGGTGTTTGTGGGAAAAACACCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
* * *
182007 TTACGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGG-ACAAACGCCGCTAAATATCAACACCTA
* * * *
182050 ------CGTTTGTGGGAAAAACGCCGCTAAATCTCAACACTTA
1 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
* *
182087 TTGCGGCGTTTGTTGGAAAAATGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
* * *
182130 TTGCGGTGTTTGTTGGACAAACGGCGCTAAACATCAACACCTA
1 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
* * **
182173 TTACGGCGTTTGTTGGACAAACGCCGCTATATAT-AGTTACCTA
1 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCA-ACACCTA
182216 TTGCGGCGTTT
1 TTGCGGCGTTT
182227 TTTGTTACCA
Statistics
Matches: 187, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
37 32 0.17
38 2 0.01
42 3 0.02
43 150 0.80
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
Found at i:182215 original size:86 final size:86
Alignment explanation
Indices: 181964--182226 Score: 301
Period size: 86 Copynumber: 3.1 Consensus size: 86
181954 ACCAGATCTT
* * *
181964 TTGCGGTGTTTGTGGGAAAAACACCGCTAAATCTCAAGACCTATTACGGCGTTTG-TGGAAAAAA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTTGG-AAAAA
*
182028 CGCCGCTAAATCTCAACACCTA
65 CGCCGCTAAATATCAACACCTA
* * *
182050 ------CGTTTGTGGGAAAAACGCCGCTAAATCTCAACACTTATTGCGGCGTTTGTTGGAAAAAT
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTTGGAAAAAC
182109 GCCGCTAAATATCAACACCTA
66 GCCGCTAAATATCAACACCTA
* * * * *
182130 TTGCGGTGTTTGTTGGACAAACGGCGCTAAA-CATCAACACCTATTACGGCGTTTGTTGGACAAA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATC-TCAACACCTATTACGGCGTTTGTTGGAAAAA
* **
182194 CGCCGCTATATAT-AGTTACCTA
65 CGCCGCTAAATATCA-ACACCTA
182216 TTGCGGCGTTT
1 TTGCGGCGTTT
182227 TTTGTTACCA
Statistics
Matches: 149, Mismatches: 19, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
80 69 0.46
81 3 0.02
85 2 0.01
86 75 0.50
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (86 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTTGGAAAAAC
GCCGCTAAATATCAACACCTA
Found at i:183102 original size:5 final size:5
Alignment explanation
Indices: 183092--183116 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
183082 TATAGAAAAT
183092 CCGAA CCGAA CCGAA CCGAA CCGAA
1 CCGAA CCGAA CCGAA CCGAA CCGAA
183117 TTAAGACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
CCGAA
Found at i:191235 original size:20 final size:22
Alignment explanation
Indices: 191201--191240 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
191191 CACTCAACCA
*
191201 CTTTAGGTATTGATA-TTAAGT
1 CTTTAGGTATGGATACTTAAGT
191222 CTTT-GGTATGGATACTTAA
1 CTTTAGGTATGGATACTTAA
191241 TTTTCGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (22 bp):
CTTTAGGTATGGATACTTAAGT
Found at i:191271 original size:20 final size:20
Alignment explanation
Indices: 191216--191275 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
191206 GGTATTGATA
*
191216 TTAAGTCTTTGGTATGGATAC
1 TTAA-TCTTTGGTATGGAGAC
*
191237 TTAAT-TTTCGATATGGAGAC
1 TTAATCTTT-GGTATGGAGAC
191257 -TAATCCTTTGGTATGGAGA
1 TTAAT-CTTTGGTATGGAGA
191276 ACAATGTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 7 0.21
20 19 0.58
21 7 0.21
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (20 bp):
TTAATCTTTGGTATGGAGAC
Found at i:192648 original size:28 final size:29
Alignment explanation
Indices: 192598--192671 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 29
192588 AAATTTTGGT
*
192598 AAAATTCTAAAAAAAGCCTCTAAATTCC-A
1 AAAATCCTAAAAAAA-CCTCTAAATTCCTA
192627 GAAAATCCTAAAAAAACC-CTAAATTCCTA
1 -AAAATCCTAAAAAAACCTCTAAATTCCTA
192656 AAAATCCTAAAAAAAC
1 AAAATCCTAAAAAAAC
192672 TAATCTCTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 25 0.60
29 3 0.07
30 14 0.33
ACGTcount: A:0.55, C:0.22, G:0.03, T:0.20
Consensus pattern (29 bp):
AAAATCCTAAAAAAACCTCTAAATTCCTA
Found at i:193065 original size:16 final size:16
Alignment explanation
Indices: 193046--193094 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
193036 ATTATTATTT
193046 TATTATAAATAATATA
1 TATTATAAATAATATA
*
193062 TATTATAAAACAATATA
1 TATTAT-AAATAATATA
* *
193079 AATATAAAAATAATAT
1 TAT-TATAAATAATAT
193095 GAAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 6 0.22
17 19 0.70
18 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTATAAATAATATA
Found at i:193078 original size:17 final size:17
Alignment explanation
Indices: 193046--193087 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
193036 ATTATTATTT
*
193046 TATTAT-AAATAATATA
1 TATTATAAAACAATATA
193062 TATTATAAAACAATATA
1 TATTATAAAACAATATA
*
193079 -AATATAAAA
1 TATTATAAAA
193088 ATAATATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTATAAAACAATATA
Done.