Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009304.1 Hibiscus syriacus cultivar Beakdansim tig00113037_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: 89271
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2242 original size:93 final size:93
Alignment explanation
Indices: 2083--2269 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
2073 CTACCACCCT
2083 TAACCATTCTATTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCA
1 TAACCATTCTATTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCA
*
2148 TTTGAAAAGGTACAAGTACCATACATCA
66 TTTAAAAAGGTACAAGTACCATACATCA
2176 TAACCATTCTATTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCA
1 TAACCATTCTATTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCA
*
2241 TTTAAAAAGGTACAAGTACCGTACATCA
66 TTTAAAAAGGTACAAGTACCATACATCA
2269 T
1 T
2270 CCAATGTGCC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (93 bp):
TAACCATTCTATTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCA
TTTAAAAAGGTACAAGTACCATACATCA
Found at i:6344 original size:16 final size:16
Alignment explanation
Indices: 6310--6343 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6300 TTCAACTTTC
*
6310 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
6326 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
6341 TTT
1 TTT
6344 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:6371 original size:23 final size:25
Alignment explanation
Indices: 6332--6385 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
6322 TTCTTTTCTT
6332 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
6357 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
6380 TTTCTT
1 TTTCTT
6386 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:13671 original size:18 final size:18
Alignment explanation
Indices: 13648--13705 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
13638 AATTGGAGTG
13648 CAAAAAGAAAAGAAAAGA
1 CAAAAAGAAAAGAAAAGA
**
13666 CAAAAAGAAAA-AAAATT
1 CAAAAAGAAAAGAAAAGA
13683 CAGAAAAG--AAGAAAAGA
1 CA-AAAAGAAAAGAAAAGA
13700 -AAAAAG
1 CAAAAAG
13706 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 10 0.29
18 16 0.47
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (18 bp):
CAAAAAGAAAAGAAAAGA
Found at i:13718 original size:26 final size:26
Alignment explanation
Indices: 13660--13718 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
13650 AAAAGAAAAG
*
13660 AAAAGACA-AAAAGAAAAAAAATTCAG
1 AAAAGA-AGAAAAGAAAAAAAATTCAA
*
13686 AAAAGAAGAAAAG-AAAAAAGTTCAA
1 AAAAGAAGAAAAGAAAAAAAATTCAA
13711 AAAGAGAA
1 AAA-AGAA
13719 AGCAAGCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.73, C:0.05, G:0.15, T:0.07
Consensus pattern (26 bp):
AAAAGAAGAAAAGAAAAAAAATTCAA
Found at i:34134 original size:11 final size:10
Alignment explanation
Indices: 34108--34133 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34098 AACAAAAACC
34108 AAAAAAGGCA
1 AAAAAAGGCA
34118 AAAAAAGGCA
1 AAAAAAGGCA
34128 AAAAAA
1 AAAAAA
34134 AAAACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGGCA
Found at i:34142 original size:31 final size:33
Alignment explanation
Indices: 34094--34161 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
34084 TTTTTTTTCA
* *
34094 AAAAAACAAAAACCAAAAAAGGCAAAAAAAGGC
1 AAAAAACAAAAACCAAAAAAAGCAAAAAAAGCC
*
34127 AAAAAA-AAAAA-CAAAAAAAGCCAAAAAAGCC
1 AAAAAACAAAAACCAAAAAAAGCAAAAAAAGCC
34158 AAAA
1 AAAA
34162 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 21 0.66
32 5 0.16
33 6 0.19
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (33 bp):
AAAAAACAAAAACCAAAAAAAGCAAAAAAAGCC
Found at i:35124 original size:16 final size:16
Alignment explanation
Indices: 35103--35137 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
35093 TCTTAGCCAC
35103 ACTTGCCCGACTCACG
1 ACTTGCCCGACTCACG
35119 ACTTGCCCGACTCACG
1 ACTTGCCCGACTCACG
35135 ACT
1 ACT
35138 CAAGTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.43, G:0.17, T:0.20
Consensus pattern (16 bp):
ACTTGCCCGACTCACG
Found at i:39143 original size:1 final size:1
Alignment explanation
Indices: 39139--39182 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
39129 CTTTTTTGGC
* * *
39139 TTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39183 GAAAAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:39152 original size:19 final size:18
Alignment explanation
Indices: 39139--39183 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
39129 CTTTTTTGGC
39139 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTG
*
39157 TTTTTTTTTTTTTTTTTTG
1 -TTTTTTTGTTTTTTTTTG
39176 TTTTTTTG
1 TTTTTTTG
39184 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTTTG
Found at i:39157 original size:10 final size:10
Alignment explanation
Indices: 39139--39182 Score: 81
Period size: 10 Copynumber: 4.5 Consensus size: 10
39129 CTTTTTTGGC
39139 TTTTTTTGTT
1 TTTTTTTGTT
39149 TTTTTTTGTT
1 TTTTTTTGTT
39159 TTTTTTT-TT
1 TTTTTTTGTT
39168 TTTTTTTGTT
1 TTTTTTTGTT
39178 TTTTT
1 TTTTT
39183 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:55225 original size:37 final size:35
Alignment explanation
Indices: 55179--55252 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
55169 ATGATCACAT
*
55179 CATAATCCATCTTCCATTATAACGCCTATATAATCAC
1 CATAATCCATC-ACCA-TATAACGCCTATATAATCAC
* * * *
55216 CATAGTCCATCACCATATCACGTCTATATCATCAC
1 CATAATCCATCACCATATAACGCCTATATAATCAC
55251 CA
1 CA
55253 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 19 0.59
36 3 0.09
37 10 0.31
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (35 bp):
CATAATCCATCACCATATAACGCCTATATAATCAC
Found at i:56153 original size:35 final size:37
Alignment explanation
Indices: 56102--56181 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
56092 TTTGATAATT
*
56102 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
56137 TGGTTATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
56174 TGGTGATG
1 TGGTGATG
56182 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:65252 original size:16 final size:16
Alignment explanation
Indices: 65231--65269 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
65221 AATATATGGT
65231 AATGAAACAAGAAAAA
1 AATGAAACAAGAAAAA
* * *
65247 AATGAAAGAATAAAGA
1 AATGAAACAAGAAAAA
65263 AATGAAA
1 AATGAAA
65270 TAGTAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (16 bp):
AATGAAACAAGAAAAA
Found at i:65517 original size:23 final size:20
Alignment explanation
Indices: 65474--65520 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
65464 TGTAGGAGTC
*
65474 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGTTT
65494 TTTTTCTTCTTTCTTGTTGCTTT
1 TTTTTC-T-TTTCTTGTTG-TTT
65517 TTTT
1 TTTT
65521 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 9 0.39
23 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGTTT
Found at i:65945 original size:35 final size:37
Alignment explanation
Indices: 65899--65978 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
65889 TTTGAGAATT
*
65899 TGGTGATGATATAGACGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
* *
65934 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
65971 TGGTGATG
1 TGGTGATG
65979 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
Found at i:72556 original size:243 final size:244
Alignment explanation
Indices: 72122--72588 Score: 783
Period size: 243 Copynumber: 1.9 Consensus size: 244
72112 CCATATAATC
* * *
72122 ATCCTTCATCATCAACAAGGCACTCGTCCATTTACCACCATTGGAGGCCGAATCCATTATCACTT
1 ATCCTTCATCATCAACAAGGCACTCGTCCATTCACCAACATTGGAGGCCGAATCCATCATCACTT
* * *
72187 AAAGGATCATTCTATAATACTTCCGCAACCCTTCTTTGATAACTATTCTATCCATTTTAATTCTT
66 AAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTGATAACTATTCTATCCATTTCAATTCTT
72252 TCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTACAGATTACTTTTC
131 TCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTACAGATTACTTTTC
72317 AATTCAAGGAGTAGCATTTGGTGTCTCTCATTTCTTCATCTTTGAAATT
196 AATTCAAGGAGTAGCATTTGGTGTCTCTCATTTCTTCATCTTTGAAATT
* * * *
72366 ATCCTTCATCCTTAACAAGGCATTCGTCCA-TCACCAACATTGGAGGCTGAATCCATCATCACTT
1 ATCCTTCATCATCAACAAGGCACTCGTCCATTCACCAACATTGGAGGCCGAATCCATCATCACTT
* *
72430 GAAGGATCATTCTACAACACTTCTGCAACCCTTCTTTGATAACTATTCTATCCATTTCAATTCTT
66 AAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTGATAACTATTCTATCCATTTCAATTCTT
* * *
72495 TCCATTTCCTTTCTTAATTACTCATTTACTTAAGCAATCATTCTTCTTTGTGCATATTACTTTTC
131 TCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTACAGATTACTTTTC
*
72560 AATTCAAGGTGTAGCATTTGGTGTCTCTC
196 AATTCAAGGAGTAGCATTTGGTGTCTCTC
72589 CTAGATCGGG
Statistics
Matches: 207, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
243 180 0.87
244 27 0.13
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.40
Consensus pattern (244 bp):
ATCCTTCATCATCAACAAGGCACTCGTCCATTCACCAACATTGGAGGCCGAATCCATCATCACTT
AAAGGATCATTCTACAACACTTCCGCAACCCTTCTTTGATAACTATTCTATCCATTTCAATTCTT
TCCATTTCCTTTCTTAATTACTCATTTACTTAACCAATCATTCTTCTTTGTACAGATTACTTTTC
AATTCAAGGAGTAGCATTTGGTGTCTCTCATTTCTTCATCTTTGAAATT
Found at i:74304 original size:22 final size:20
Alignment explanation
Indices: 74279--74318 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
74269 ATGTTTGTTT
74279 ATGGTAATGTTAGCTAAGTATG
1 ATGGTAATG--AGCTAAGTATG
*
74301 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
74319 CATAATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Done.