Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001597.1 Hibiscus syriacus cultivar Beakdansim tig00003179_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: 188117
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:184753 original size:43 final size:43
Alignment explanation
Indices: 184714--184853 Score: 208
Period size: 43 Copynumber: 3.3 Consensus size: 43
184704 TTCGTTGTGA
* * * * *
184714 AGTTGAAACCGTGAATGTATGGGCACGATATCCTCCGTTGTGG
1 AGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
* *
184757 AGTTGAAATCGTGGATCTGTTGGTACGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
*
184800 AGTTAAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
184843 AGTTGAAATCG
1 AGTTGAAATCG
184854 CAGATGACCC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (43 bp):
AGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCGTCGTGG
Found at i:184802 original size:332 final size:336
Alignment explanation
Indices: 184109--184816 Score: 962
Period size: 332 Copynumber: 2.1 Consensus size: 336
184099 GCTGGTGGAC
* *
184109 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTCGTGAAGTTGAACCTTGAA
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGACCCATTCGTCGTGAAGTTGAACC-T-AA
* *
184174 TTGGATATCCTTCGTCGAGAAGTTGAAATCCAAGTTAAGTTGCATTGTTTCGAGGCCAATATCCT
64 TTGAATATCCTTCATCGAGAAGTTGAAATCCAAGTT-AGTTG-ATTGTTTCGAGGCCAATATCCT
* * *
184239 TCATCGTGAAGTTGAAGTTGACTATGAAACTGGAAAGTTTATTGACAAACACTCCCTCTCTGAGT
127 TCACCGTGAAGTTGAAATTGACTATGAAACTGGAAAGTTTATTGACAAACACTCACTCTCTGAGT
* * *
184304 TAGATATCATTCGTCCTGAAGTTGAAATCCCAACCTAGAGATAGATGATGCTTGTGTGTACGATT
192 TAGATATCATTCGTCCTGAAGTTGAAATCCCAACCAAGAGATAGATGATGCTCGTGTATACGATT
* * *
184369 CCCTTCGTCATGAAGTTGAAACCGTGGATATGTGGGCATGATATCCTCCGTCGTGGAGTTAAAAT
257 CCCTTCGTCATGAAGTTGAAACCGTGAATATATGGGCACGATATCCTCCGTCGTGGAGTTAAAAT
184434 CATGGATTCGTGGGT
322 CATGGATTCGTGGGT
* * * *
184449 ACGATATCCTCCGTTGTGGAGTTGAAATTGTGGATGGCCCATTCGTCGTGAAGTTG-AGC-AACT
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGACCCATTCGTCGTGAAGTTGAACCTAA-T
* * *
184512 TGAATATCCTTCATCGTGAAGTTGAAATCCAAGCTT-G-TG-TTGTTTGGAGTCCAATATCCTTC
65 TGAATATCCTTCATCGAGAAGTTGAAATCCAAG-TTAGTTGATTGTTTCGAGGCCAATATCCTTC
* * * * *
184574 ACCGTGAAGTTGAAATTGGCTCTGAAACTGGAAAGTTTATTGACAAACACTCATTCTTTGAGTTG
129 ACCGTGAAGTTGAAATTGACTATGAAACTGGAAAGTTTATTGACAAACACTCACTCTCTGAGTTA
* * * * *
184639 GATATCCTTCGTCGTGAAGTTGAAAT-CCAATCAAGAGATGGATGCTGCTCGTGTATACGATTCC
194 GATATCATTCGTCCTGAAGTTGAAATCCCAACCAAGAGATAGATGATGCTCGTGTATACGATTCC
** * * * *
184703 CTTCGTTGTGAAGTTGAAACCGTGAATGTATGGGCACGATATCCTCCGTTGTGGAGTTGAAATCG
259 CTTCGTCATGAAGTTGAAACCGTGAATATATGGGCACGATATCCTCCGTCGTGGAGTTAAAATCA
*
184768 TGGA-TCTGTTGGT
324 TGGATTC-GTGGGT
*
184781 ACGATATCCTCCGTCGTGGAGTTAAAATCGTGGATG
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
184817 TGTGGGTACG
Statistics
Matches: 325, Mismatches: 40, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
331 2 0.01
332 130 0.40
333 102 0.31
335 2 0.01
336 3 0.01
337 31 0.10
338 2 0.01
339 2 0.01
340 51 0.16
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (336 bp):
ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGACCCATTCGTCGTGAAGTTGAACCTAATT
GAATATCCTTCATCGAGAAGTTGAAATCCAAGTTAGTTGATTGTTTCGAGGCCAATATCCTTCAC
CGTGAAGTTGAAATTGACTATGAAACTGGAAAGTTTATTGACAAACACTCACTCTCTGAGTTAGA
TATCATTCGTCCTGAAGTTGAAATCCCAACCAAGAGATAGATGATGCTCGTGTATACGATTCCCT
TCGTCATGAAGTTGAAACCGTGAATATATGGGCACGATATCCTCCGTCGTGGAGTTAAAATCATG
GATTCGTGGGT
Found at i:185179 original size:63 final size:64
Alignment explanation
Indices: 185025--185179 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 64
185015 GAGCAAATTG
* * * *
185025 TGAGCTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGCTTGT
1 TGAGCACAAGATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGCTTAT
* * * * * *
185089 TGAGTACAATATCCTTCGGTGTGAAGTTGAAATTGACTCTGGATGAAA-TTGAAAAGTTGTTTAT
1 TGAGCACAAGATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAA-TTGCTTAT
* * *
185153 TGA-CAGACGCTCCTTCGCTGTGAAGTT
1 TGAGCACAAGATCCTTCGCTGTGAAGTT
185180 AAGCACCCAC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
63 24 0.31
64 53 0.69
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (64 bp):
TGAGCACAAGATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGCTTAT
Found at i:185486 original size:32 final size:32
Alignment explanation
Indices: 185412--185500 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
185402 TTGTATCAGG
** * *
185412 ATGTTGAATCCCCAAATATGCCACAATATTCA
1 ATGTTGAATCTTCAAATATGCCCCAACATTCA
*
185444 ATGTTGAATCTTCAAATATGCCCCAACATTTA
1 ATGTTGAATCTTCAAATATGCCCCAACATTCA
* * *
185476 CTGTTGAATCTTTAAAGATGCCCCA
1 ATGTTGAATCTTCAAATATGCCCCA
185501 TTGTTCCTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (32 bp):
ATGTTGAATCTTCAAATATGCCCCAACATTCA
Found at i:185654 original size:23 final size:23
Alignment explanation
Indices: 185628--185695 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
185618 TCTCTTTTTT
185628 TATTTTCAAAAGTTTTGAAAATG
1 TATTTTCAAAAGTTTTGAAAATG
** *
185651 TA-TTAGAAGAGTTTTGAAAAATG
1 TATTTTCAAAAGTTTTG-AAAATG
*
185674 T-TTAATCAAAAGTTTTGAAAAT
1 TATT-TTCAAAAGTTTTGAAAAT
185696 ATTGCCCCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
22 11 0.31
23 15 0.43
24 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (23 bp):
TATTTTCAAAAGTTTTGAAAATG
Done.