Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003208.1 Hibiscus syriacus cultivar Beakdansim tig00006753_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: 1278004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1263988 original size:81 final size:81
Alignment explanation
Indices: 1263836--1263990 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
1263826 CGCTATGTAA
* * * * ** *
1263836 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTAACTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTAACGCATTGCGATTTTCCAATATCG
1263901 CATTGCGATAGTCAGT
66 CATTGCGATAGTCAGT
* * * *
1263917 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTAACGCATTGCGATTTT-CCAATATC
*
1263981 GCGTTGCGAT
65 GCATTGCGAT
1263991 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 59 0.97
82 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTAACGCATTGCGATTTTCCAATATCG
CATTGCGATAGTCAGT
Found at i:1264080 original size:21 final size:21
Alignment explanation
Indices: 1264040--1264080 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1264030 ACTGTAGACC
**
1264040 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1264061 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1264081 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1264327 original size:29 final size:30
Alignment explanation
Indices: 1264279--1264342 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1264269 TATTTTATGC
*
1264279 ATTTTTTTTCAATTTAGTGTCTAACG-TTT
1 ATTTTGTTTCAATTTAGTGTCTAACGTTTT
* * *
1264308 ATTTTGTTTCAGTTTGGTGTTTAACGTTTT
1 ATTTTGTTTCAATTTAGTGTCTAACGTTTT
1264338 ATTTT
1 ATTTT
1264343 ATAATTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.17, C:0.08, G:0.14, T:0.61
Consensus pattern (30 bp):
ATTTTGTTTCAATTTAGTGTCTAACGTTTT
Found at i:1265695 original size:182 final size:181
Alignment explanation
Indices: 1265343--1265987 Score: 876
Period size: 182 Copynumber: 3.6 Consensus size: 181
1265333 CGATACAAAT
* * * *
1265343 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGATAAATC-GGTGTC-ATTATGA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGA-AATGA
** *
1265406 TAAAA-CGGTAAAGCGCTACCGGATATATTG-AAGTGTCGATAAATTAATAT-AGTGTCGACACT
65 TAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
* *
1265468 TTTGTAATCTAAAAGATAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTA
* *
1265521 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
*
1265586 AAAACCGGTAAAAAGCTACCAGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
*
1265651 TTGTAATTTAAAAGAGAAGAAGTTATAGTGCCTGAAAAGTGTCGATACTTTA
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * * * *
1265703 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAAGAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
* *
1265768 AAAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGGTAAATTAATATAAGTATCGACA-TT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* *
1265832 TTCGTACTTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTA
131 TT-GTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * * * *
1265885 -AGAAAATGTTTCGATCCATAACAATATAATAGGTAAAAATATGATAAAACCGGTATCGAAATGA
1 TA-AAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGA
* **
1265949 CAAAACCGGTAAAGCGCTACCGG-T-TATGTGAAAGTGTCG
65 TAAAACCGGTAAAAAGCTACCGGATATAT-TGAAAGTGTCG
1265988 GTACTTTATA
Statistics
Matches: 416, Mismatches: 42, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
178 46 0.11
179 14 0.03
180 26 0.06
181 37 0.09
182 289 0.69
183 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (181 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTA
Found at i:1267243 original size:106 final size:107
Alignment explanation
Indices: 1267127--1267319 Score: 273
Period size: 106 Copynumber: 1.8 Consensus size: 107
1267117 ATGACAAATG
* * *
1267127 ATATAATGTAATAGGTAAATTGACAATGTAACCAGTA-AACATATACC-GTTTAATTATAAAACA
1 ATATAATGTAATAGGTAAATTGACAATGTAACCAGTAGAA-ATATACCGGGTTAATGAGAAAACA
*
1267190 GGTTAACATAAAGTATCGACACTATTAGATTTTGTGTCGATAA
65 GGTCAACATAAAGTATCGACACTATTAGATTTTGTGTCGATAA
** * * * *
1267233 ATATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGGTTCATGAGAGAATAG
1 ATATAATGTAATAGGTAAATTGACAATGTAACCAGTAGAAATATACCGGGTTAATGAGAAAACAG
1267298 GTCAACATAAAGTATCGACACT
66 GTCAACATAAAGTATCGACACT
1267320 TTGTTTAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
106 41 0.55
107 34 0.45
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (107 bp):
ATATAATGTAATAGGTAAATTGACAATGTAACCAGTAGAAATATACCGGGTTAATGAGAAAACAG
GTCAACATAAAGTATCGACACTATTAGATTTTGTGTCGATAA
Found at i:1267692 original size:198 final size:197
Alignment explanation
Indices: 1267227--1267704 Score: 527
Period size: 197 Copynumber: 2.4 Consensus size: 197
1267217 GATTTTGTGT
* * *
1267227 CGATAAATATAATGTAATAGGTAAATTTCCAATGTAACCGG-TAGAAATATACCGGGTTCATGAG
1 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTA-AAATATACC--GTTAATGAG
* * * *
1267291 AGAATAGGTCAACATAAAGTATCGACACTTTGTTTAATTTGTGTCGATACATTTTTTCAAAATGA
63 AAAATAGGTCAACATAAAGTATCGACACTCTGTTAAATATGTGTCGATACATTTTTTCAAAATGA
* * *
1267356 ATGGCAAACGAGGTGTACGCATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCTCGAAACAT
128 AAGACAAACGAGGTGCACGCATAAAGTGTCGATACA-TTTTAAAAAGTATCGATCCTCGAAACAT
* *
1267421 TGAAAT
192 CGAAAC
* * * * * *
1267427 CGATAATTATTATATTACAGGTAAATTTACAATGTAACCGGTTAAAATATACCAGCTAATTAGAA
1 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAAATATACC-GTTAATGAGAA
* * *
1267492 AATAGGTCTACATTATGTATCGACACTCT-TTAAATATGTGTCGATAC-TTTTTTCCAAAAT-AA
65 AATAGGTCAACATAAAGTATCGACACTCTGTTAAATATGTGTCGATACATTTTTT-CAAAATGAA
* *
1267554 AGCACAAACGAGTTGCACGCATAAAGTGTCGATACA-TTTAAAATTGTATCGATCCT-GAAAACA
129 AG-ACAAACGAGGTGCACGCATAAAGTGTCGATACATTTTAAAA-AGTATCGATCCTCG-AAACA
1267617 TCGAAAC
191 TCGAAAC
* * * ** * * *
1267624 CGATATTTATAATGTAATAGGTCAATTTATAATGTAATTGGTTTAAATTTACCGTTTTTATGAGA
1 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAAATATACCG--TTAATGAGA
*
1267689 AAATAGGTCAATATAA
64 AAATAGGTCAACATAA
1267705 GCGCTACTTA
Statistics
Matches: 230, Mismatches: 41, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
196 9 0.04
197 72 0.31
198 71 0.31
199 32 0.14
200 44 0.19
201 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (197 bp):
CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAAATATACCGTTAATGAGAAA
ATAGGTCAACATAAAGTATCGACACTCTGTTAAATATGTGTCGATACATTTTTTCAAAATGAAAG
ACAAACGAGGTGCACGCATAAAGTGTCGATACATTTTAAAAAGTATCGATCCTCGAAACATCGAA
AC
Found at i:1267806 original size:87 final size:87
Alignment explanation
Indices: 1267699--1267860 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
1267689 AAATAGGTCA
* * * *
1267699 ATATAAGCGCTACTTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCAACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
*
1267764 TCGGTTAAATACATATTTTATT
66 TCAGTTAAATACATATTTTATT
* *
1267786 ATATAAGCGCAACCTATTACATTATCTAAGCACTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCAACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
1267851 TCAGTTAAAT
66 TCAGTTAAAT
1267861 GATATAACAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCAACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
TCAGTTAAATACATATTTTATT
Found at i:1272385 original size:228 final size:226
Alignment explanation
Indices: 1272004--1273275 Score: 1200
Period size: 228 Copynumber: 5.6 Consensus size: 226
1271994 TGCAAGAGTT
* * * *
1272004 CTCCCATCCTCCAGCTGCTTTCCAGCAAAAATCAA-CCTCTGCTGATCTGGTGGGATTCCTTCCT
1 CTCCCATCTTCAAGCTGCTTGCCAGCAAAAAT-AAGCCTCTGCTGGTCTGG-GGGATTCCTTCCT
* * * * * * *
1272068 TGTCTTGAATCTTTTCCTTAACATTGTCTATGGTGTCTGAACTTTCAACCTCCAATGTTATTGTC
64 TGTCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAAAGTGATGGTC
* * * *
1272133 TTCCCGGTTAAG-GTCTTCACAAAGATCTGCATCCCACCACGCAAGCGTAACACCAAGTGAAGGG
129 TTTCCGG-TAAGAGTCTTCACAAAGATCTGCATACCACCACG-AAGCGTAACACCAAGTGGAGAG
* * *
1272197 TTGACTCCTTTTGGATATTATAGTCTGCCAATGTC
192 TGGACTCCTTTTGGATGTTATAGTCAGCCAATGTC
* * * * * *
1272232 CTCCCATCTTCAAGCTGCTTGCCGGCAAAGATGAGCCTTTGCTGGTCTGGGGGAATACCCTCCTT
1 CTCCCATCTTCAAGCTGCTTGCCAGCAAAAATAAGCCTCTGCTGGTCTGGGGG-ATTCCTTCCTT
* * *
1272297 GTCTTGGATCTTTGCCTTCACGTTGTCAATCGTGTCTGAACTTTCGACCTCCAAAGTGATGGT-T
65 GTCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAAAGTGATGGTCT
* * * *
1272361 TTCCCGGTAAGAGTCTTTACAAAGATCTGCATACCACCACGCAGGCGCAACACCAAGTGAAGAGT
130 TT-CCGGTAAGAGTCTTCACAAAGATCTGCATACCACCACG-AAGCGTAACACCAAGTGGAGAGT
* * *
1272426 CGACTCCTTTTGGATATTATAGTCAGCCAACGTC
193 GGACTCCTTTTGGATGTTATAGTCAGCCAATGTC
* * * * * * *
1272460 CTTCCATCTTCAAGTTGCTTGCCAGCAAAAATGAGTCTTTGCTGGTCTGGGGGGATACCCTCCTT
1 CTCCCATCTTCAAGCTGCTTGCCAGCAAAAATAAGCCTCTGCTGGTCT-GGGGGATTCCTTCCTT
* * * * *
1272525 ATCTTGGATCTTTGCCTTCACGTTGTCAATTGTGTCTGAGCTTTCAACTTCCAAAGTGATGGTCT
65 GTCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAAAGTGATGGTCT
* *
1272590 TTCCAGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAAGGCGGAGA-ACC-AGATGGAGAG
130 TTCCGGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAA-GCGTA-ACACCAAG-TGGAGAG
* * * * *
1272653 TAGACTCCTTTTGGATGTTATAATC-GGCAAGAGTT
192 TGGACTCCTTTTGGATGTTATAGTCAGCCAA-TGTC
* * * * * * * * * *
1272688 CTTCCATCTTCAAGCTGTTTTCCTGCAAAAATCAA-TCTTTGTTGGTCTGATGAGATTCCTTCTT
1 CTCCCATCTTCAAGCTGCTTGCCAGCAAAAAT-AAGCCTCTGCTGGTCTG-GGGGATTCCTTCCT
* * * * * * * * * * *
1272752 TGTCCTGAAT-TTTGGCTTTCACATTATCAATGGTATCCGAACTCTCGACCTCCAAGGTAATTGT
64 TGTCTTGGATCTTT-GCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAAAGTGATGGT
* * * * * *
1272816 CTTTCCGGTGAGAGTCTTGACAAAGATTTGCATGCCACCACGAAGACG-AAGCACTAAGTGGAGG
128 CTTTCCGGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAAG-CGTAA-CACCAAGTGGAGA
* *
1272880 GTGGACTCCTTCTGGATGTTATAGTCAGCCAGTGTC
191 GTGGACTCCTTTTGGATGTTATAGTCAGCCAATGTC
** * * * *
1272916 CGACCATCTTCAAGCTGCTTTCCAGCAAAGATAAGCCTCTGTTGGTCTGGAGGGATTCCTTCTTT
1 CTCCCATCTTCAAGCTGCTTGCCAGCAAAAATAAGCCTCTGCTGGTCTGG-GGGATTCCTTCCTT
* * * * * * * *
1272981 GTCTTGGATCTTAGCCTTGACATTATCAATAGTGTCAGAGCTTTCAACCTCCAAGGTGATCGTCT
65 GTCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAAAGTGATGGTCT
* * * * * * *
1273046 TTCCAGTCAGAGTCTTGACAAAGATTTTGCATACCACCTCGAAGTC-TAAGCACCAGGTGGAGCG
130 TTCCGGTAAGAGTCTTCACAAAGA-TCTGCATACCACCACGAAG-CGTAA-CACCAAGTGGAGAG
* * **
1273110 TGGACT-CTTTCTGGATGTTGTAGTCAGCCAGTGAG
192 TGGACTCCTTT-TGGATGTTATAGTCAGCCAATGTC
** * * *
1273145 CGGCCATCTTCAAGTTGCTTGCCAGCAAAAATAAGCCTCTGTTGGTCTGGTGGTATTCCTTCCTT
1 CTCCCATCTTCAAGCTGCTTGCCAGCAAAAATAAGCCTCTGCTGGTCTGG-GGGATTCCTTCCTT
* * * *
1273210 GTCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCCGAACTCTCCACCT-CAAGGGTGATGGTC
65 GTCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAA-AGTGATGGTC
1273274 TT
129 TT
1273276 GCCAGTGAGG
Statistics
Matches: 878, Mismatches: 141, Indels: 49
0.82 0.13 0.05
Matches are distributed among these distances:
226 1 0.00
227 25 0.03
228 665 0.76
229 187 0.21
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.31
Consensus pattern (226 bp):
CTCCCATCTTCAAGCTGCTTGCCAGCAAAAATAAGCCTCTGCTGGTCTGGGGGATTCCTTCCTTG
TCTTGGATCTTTGCCTTCACATTGTCAATGGTGTCTGAACTTTCAACCTCCAAAGTGATGGTCTT
TCCGGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAAGCGTAACACCAAGTGGAGAGTGGA
CTCCTTTTGGATGTTATAGTCAGCCAATGTC
Found at i:1277218 original size:20 final size:18
Alignment explanation
Indices: 1277174--1277220 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
1277164 CAAAAAACAT
1277174 AAAAA-TACTAAAATAAA
1 AAAAATTACTAAAATAAA
1277191 AATTAAATTACTAAAAATTAAA
1 AA--AAATTACT-AAAA-TAAA
1277213 AAAAATTA
1 AAAAATTA
1277221 ACTAGGGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.08
19 3 0.12
20 10 0.40
21 4 0.16
22 6 0.24
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATTACTAAAATAAA
Done.