Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009397.1 Hibiscus syriacus cultivar Beakdansim tig00113302_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: 510949
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:498456 original size:18 final size:19
Alignment explanation
Indices: 498435--498472 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
498425 CGATAAAGTA
* *
498435 TTATTTAAATTATT-ATTT
1 TTATTAAAAATATTAATTT
498453 TTATTAAAAATATTAATTT
1 TTATTAAAAATATTAATTT
498472 T
1 T
498473 GCAATCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTAAAAATATTAATTT
Found at i:500900 original size:15 final size:15
Alignment explanation
Indices: 500877--500919 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
500867 TTAGCTGGGT
* *
500877 GGGCGGATGTGGGGC
1 GGGCAGATGCGGGGC
500892 GGGCAGATGCGGGGC
1 GGGCAGATGCGGGGC
* *
500907 GAGAAGATGCGGG
1 GGGCAGATGCGGG
500920 ATGGGTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.60, T:0.09
Consensus pattern (15 bp):
GGGCAGATGCGGGGC
Found at i:504387 original size:12 final size:12
Alignment explanation
Indices: 504372--504406 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
504362 GAACCTGGAT
504372 TATCACCTTTTG
1 TATCACCTTTTG
*
504384 TATCACCTTTAG
1 TATCACCTTTTG
*
504396 CATCACCTTTT
1 TATCACCTTTT
504407 CCACTACTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.46
Consensus pattern (12 bp):
TATCACCTTTTG
Found at i:504755 original size:23 final size:22
Alignment explanation
Indices: 504712--504759 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
504702 ATTCAAACCA
504712 AAATCATATAAAAATCATTTAGT
1 AAATCATATAAAAATCATTTA-T
*
504735 AAATCATATAAAGAT-ATTTTAT
1 AAATCATATAAAAATCA-TTTAT
504757 AAA
1 AAA
504760 ATAATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATCATATAAAAATCATTTAT
Found at i:510197 original size:55 final size:54
Alignment explanation
Indices: 509953--510433 Score: 529
Period size: 54 Copynumber: 9.0 Consensus size: 54
509943 CTTCAAATGG
* * *
509953 CGGGTCCGCTCCCTATTCTTTCA-GGAGTATA-AGACTTGAACAATCTTCAGAAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCA-TAAA
* * * *
510007 TGCGTCTG-TCCCTATTCATTCAGGGAGTATA-AGACTCGAATAATCTTCAATAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTC-ATAAA
*
510061 CGGGTCCGCT-CCTATTCATCCAGGGAGTATAGAACTCGAACAATC-TCATAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
* * * *
510113 CGGGTACGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTC-ATAAA
* * * *
510168 CGGGTCTGCTCCCTATTTATTTAGGGAGTATAGAACTCGAACAATCTTCAACAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTC-ATAAA
*
510223 CGGGTCCACTCCCTATTCATTC-GGGAGTATAGAACTCGAACAA--TTCATAAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAT-AAA
* * * *
510275 C-GGTCCGCTCTCT-TTC-TTGAGAGAGTATAGAACTCGAAGAATCTTCATAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
* * * *
510326 CGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAT-AAA
* * * * *
510381 CGAGTCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATC-TCATAAA
1 CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
510434 ACGAGTTTGC
Statistics
Matches: 373, Mismatches: 39, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
49 2 0.01
50 22 0.06
51 15 0.04
52 37 0.10
53 52 0.14
54 124 0.33
55 121 0.32
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (54 bp):
CGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
Found at i:510349 original size:213 final size:216
Alignment explanation
Indices: 509956--510427 Score: 610
Period size: 213 Copynumber: 2.2 Consensus size: 216
509946 CAAATGGCGG
* * * **
509956 GTCCGCTCCCTATTC-TTTCAG-GAGTATA-AGACTTGAACAATCTTCAGA-AAATGCGT-CTGT
1 GTCCGCTCCCTATTCATTT-AGAGAGTATAGA-ACTCGAACAATCTTCA-ACAAACGGGTCCACT
*
510016 CCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAATAAACGGGTCCGCTCCTATTCATC
63 CCCTATTCATTCAGGGAGTATAAGACTCGAACAA-CTTCAATAAACGGGTCCGCTCCTATTCATC
* *
510081 CAGGGAGTATAGAACTCGAACAATCTCATAAACGGGTACGCTCTCTATTCCTTCAGAGAGTATAG
127 CAGAGAGTATAGAACTCGAACAATCTCATAAACGAGTACGCTCTCTATTCCTTCAGAGAGTATAG
*
510146 AACTCGAACAATCTTCA-ATAAACGG
192 AACTCGAACAATCTTCATA-AAACGA
* * *
510171 GTCTGCTCCCTATTTATTTAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCACTCCC
1 GTCCGCTCCCTATTCATTTAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCACTCCC
**
510236 TATTCATTC-GGGAGTAT-AGAACTCGAACAA-TTC-ATAAAAC-GGTCCGCTCTCT-TTC-TTG
66 TATTCATTCAGGGAGTATAAG-ACTCGAACAACTTCAAT-AAACGGGTCCGCTC-CTATTCATCC
* *
510294 AGAGAGTATAGAACTCGAAGAATCTTCATAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAG
128 AGAGAGTATAGAACTCGAACAATC-TCATAAACGAGTACGCTCTCTATTCCTTCAGAGAGTATAG
510359 AACTCGAACAATCTTCATAAAACGA
192 AACTCGAACAATCTTCATAAAACGA
* *
510384 GTCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATCT
1 GTCCGCTCCCTATTCATTTAGAGAGTATAGAACTCGAACAATCT
510428 CATAAAACGA
Statistics
Matches: 227, Mismatches: 20, Indels: 22
0.84 0.07 0.08
Matches are distributed among these distances:
212 23 0.10
213 113 0.50
214 10 0.04
215 18 0.08
216 48 0.21
217 15 0.07
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (216 bp):
GTCCGCTCCCTATTCATTTAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCACTCCC
TATTCATTCAGGGAGTATAAGACTCGAACAACTTCAATAAACGGGTCCGCTCCTATTCATCCAGA
GAGTATAGAACTCGAACAATCTCATAAACGAGTACGCTCTCTATTCCTTCAGAGAGTATAGAACT
CGAACAATCTTCATAAAACGA
Found at i:510493 original size:37 final size:36
Alignment explanation
Indices: 510438--510509 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
510428 CATAAAACGA
510438 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
*
510475 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
510510 TGACTGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Done.