Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005190.1 Hibiscus syriacus cultivar Beakdansim tig00011725_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: 43963
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:11362 original size:17 final size:17
Alignment explanation
Indices: 11340--11381 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
11330 AACTCCCTTC
11340 TGAAGTAGTTTAGTCAT
1 TGAAGTAGTTTAGTCAT
11357 TGAAGTAGTTTAGTCAT
1 TGAAGTAGTTTAGTCAT
*
11374 TGAGGTAG
1 TGAAGTAG
11382 CTATCATGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.38
Consensus pattern (17 bp):
TGAAGTAGTTTAGTCAT
Found at i:13353 original size:14 final size:14
Alignment explanation
Indices: 13334--13365 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13324 GGGTGTATCT
*
13334 ACTCATTCGAATGA
1 ACTCATTCAAATGA
13348 ACTCATTCAAATGA
1 ACTCATTCAAATGA
13362 ACTC
1 ACTC
13366 CTGCTCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (14 bp):
ACTCATTCAAATGA
Found at i:15159 original size:22 final size:23
Alignment explanation
Indices: 15134--15182 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
15124 CAATACCCTT
15134 AACTAAAG-TACCGATACTTCTG
1 AACTAAAGATACCGATACTTCTG
*
15156 AACT-ACGATACCGATACTTCTG
1 AACTAAAGATACCGATACTTCTG
15178 AACTA
1 AACTA
15183 CGGTATCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (23 bp):
AACTAAAGATACCGATACTTCTG
Found at i:15183 original size:22 final size:22
Alignment explanation
Indices: 15142--15194 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
15132 TTAACTAAAG
15142 TACCGATACTTCTGAACTACGA
1 TACCGATACTTCTGAACTACGA
*
15164 TACCGATACTTCTGAACTACGG
1 TACCGATACTTCTGAACTACGA
*
15186 TATCGATAC
1 TACCGATAC
15195 CATCATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (22 bp):
TACCGATACTTCTGAACTACGA
Found at i:22687 original size:23 final size:23
Alignment explanation
Indices: 22661--22715 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
22651 TTGCTTTATG
22661 CAGCTTGCAAACTAAACCATCAC
1 CAGCTTGCAAACTAAACCATCAC
22684 CAGCTTGCAAACTAAACCATCAC
1 CAGCTTGCAAACTAAACCATCAC
22707 CAGCTTGCA
1 CAGCTTGCA
22716 CAAAACCAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.35, G:0.11, T:0.18
Consensus pattern (23 bp):
CAGCTTGCAAACTAAACCATCAC
Found at i:32663 original size:23 final size:23
Alignment explanation
Indices: 32637--32700 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
32627 TGCTACAAGA
*
32637 TAACAAACTATTCTAGAATTAGC
1 TAACAAACTATTCTAGAATTAAC
32660 TAACAAACTATTCTAGAATTAAC
1 TAACAAACTATTCTAGAATTAAC
32683 TAACAAACTATTCTAGAA
1 TAACAAACTATTCTAGAA
32701 CTCACAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (23 bp):
TAACAAACTATTCTAGAATTAAC
Found at i:35006 original size:27 final size:27
Alignment explanation
Indices: 34962--35013 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
34952 ATCATTTGCA
34962 TATCAAACTTGTCAAATTGGTCAAATT
1 TATCAAACTTGTCAAATTGGTCAAATT
*
34989 TATCAAACTTATTC-AATTGGTCAAA
1 TATCAAACTT-GTCAAATTGGTCAAA
35014 CTTGTTAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (27 bp):
TATCAAACTTGTCAAATTGGTCAAATT
Found at i:38987 original size:9 final size:10
Alignment explanation
Indices: 38965--38989 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38955 ATTTATGATC
38965 TTTTTATTAT
1 TTTTTATTAT
38975 TTTTTATTAT
1 TTTTTATTAT
38985 TTTTT
1 TTTTT
38990 CTTTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTAT
Done.