Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007717.1 Hibiscus syriacus cultivar Beakdansim tig00109948_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: 900945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:884895 original size:33 final size:32
Alignment explanation
Indices: 884852--884914 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 32
884842 TATTCTGATA
884852 TTTTTTTTAGT-TCTTTACTTTATATTTTAATC
1 TTTTTTTTAGTCT-TTTACTTTATATTTTAATC
884884 TTTTATTTTAGTCTTTTACTTTATATTTTAA
1 TTTT-TTTTAGTCTTTTACTTTATATTTTAA
884915 ATTTATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 4 0.14
33 24 0.83
34 1 0.03
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (32 bp):
TTTTTTTTAGTCTTTTACTTTATATTTTAATC
Found at i:884953 original size:14 final size:13
Alignment explanation
Indices: 884930--884981 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
884920 TGCATTTACT
884930 TTTTATTTATTTAA
1 TTTTA-TTATTTAA
884944 TTTTAGTTATTTAA
1 TTTTA-TTATTTAA
*
884958 TTTCATTACTTTAA
1 TTTTATTA-TTTAA
884972 TTTT-TTATTT
1 TTTTATTATTT
884982 TTGCTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 25 0.74
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTATTATTTAA
Found at i:888376 original size:19 final size:21
Alignment explanation
Indices: 888333--888384 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
888323 TTTCCCATTA
*
888333 CATTTGCATTTTTTTAGTTTG
1 CATTTGCATTTTTATAGTTTG
888354 CATTTGCATTTTTATA-TTT-
1 CATTTGCATTTTTATAGTTTG
*
888373 CATTTACATTTT
1 CATTTGCATTTT
888385 CATTTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 15 0.52
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.62
Consensus pattern (21 bp):
CATTTGCATTTTTATAGTTTG
Found at i:890426 original size:72 final size:71
Alignment explanation
Indices: 890330--890468 Score: 210
Period size: 72 Copynumber: 1.9 Consensus size: 71
890320 ATACAATAAA
*
890330 GCTTGAGTTATCCCCTAAAGCAATTGGTTAA-TAGCCCAGGCTTTATGGATAA-TATTCAGCTAG
1 GCTTGAGTTATCCCCTAAAGCAATTGGTTAATTA-CCCAGGCTTTATGGATAAGT-TTCAACTAG
890393 CCTGTTAT
64 CCTGTTAT
* *
890401 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATTACCCCGGCTTTATGGATAAGTTTCAACTAGC
1 GCTTGAGTTAT-CCCCTAAAGCAATTGGTTAATTACCCAGGCTTTATGGATAAGTTTCAACTAGC
890466 CTG
65 CTG
890469 ATAAAGGTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
71 10 0.16
72 49 0.79
73 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (71 bp):
GCTTGAGTTATCCCCTAAAGCAATTGGTTAATTACCCAGGCTTTATGGATAAGTTTCAACTAGCC
TGTTAT
Found at i:892358 original size:24 final size:24
Alignment explanation
Indices: 892326--892372 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
892316 GGGCATTTTA
*
892326 AAGGCCACTTCAGACAGATCCATG
1 AAGGCCACTTCAGACAAATCCATG
892350 AAGGCCACTTCAGACAAATCCAT
1 AAGGCCACTTCAGACAAATCCAT
892373 ATGGGGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (24 bp):
AAGGCCACTTCAGACAAATCCATG
Found at i:898655 original size:19 final size:19
Alignment explanation
Indices: 898631--898678 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
898621 CAAAAAGCAG
898631 CTGTTCGAAAAAAGAGAGA
1 CTGTTCGAAAAAAGAGAGA
898650 CTGTTCGAAAAAAGAGAGA
1 CTGTTCGAAAAAAGAGAGA
898669 CTGTTCGAAA
1 CTGTTCGAAA
898679 GAAAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (19 bp):
CTGTTCGAAAAAAGAGAGA
Done.