Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005402.1 Hibiscus syriacus cultivar Beakdansim tig00012387_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: 66088
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2331 original size:16 final size:16
Alignment explanation
Indices: 2312--2343 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2302 TTTAATGATC
2312 ATTTATAAATTTTATT
1 ATTTATAAATTTTATT
2328 ATTTATAAATTTTATT
1 ATTTATAAATTTTATT
2344 CTATAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATAAATTTTATT
Found at i:2488 original size:31 final size:31
Alignment explanation
Indices: 2451--2510 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
2441 TAGTTGTATG
2451 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTCAGTATTGTAAAACTAA
2482 AATTATTTAAATTTCAGTATTGTAAAACT
1 AATTATTTAAATTTCAGTATTGTAAAACT
2511 CTTTTAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTGTAAAACTAA
Found at i:24745 original size:18 final size:18
Alignment explanation
Indices: 24722--24756 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24712 TGAAAATCAC
24722 TTTTTATGATTATGTATA
1 TTTTTATGATTATGTATA
*
24740 TTTTTATGATTGTGTAT
1 TTTTTATGATTATGTAT
24757 GTTGTCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
TTTTTATGATTATGTATA
Found at i:24972 original size:17 final size:18
Alignment explanation
Indices: 24952--24989 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
24942 ATATATTTTT
24952 AATAT-AAATACATAAAA
1 AATATAAAATACATAAAA
*
24969 AATATAAAATATATAAAA
1 AATATAAAATACATAAAA
24987 AAT
1 AAT
24990 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAAATACATAAAA
Found at i:39625 original size:6 final size:6
Alignment explanation
Indices: 39616--39651 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
39606 ATCCACCACC
* *
39616 GGCGGA GGCGGA GGCGGA GGCAGA GGCCGA GGCGGA
1 GGCGGA GGCGGA GGCGGA GGCGGA GGCGGA GGCGGA
39652 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.61, T:0.00
Consensus pattern (6 bp):
GGCGGA
Found at i:44601 original size:10 final size:11
Alignment explanation
Indices: 44579--44612 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
44569 TTAAAAATTT
44579 TATTTTTATAA
1 TATTTTTATAA
44590 TATTTTTA-AA
1 TATTTTTATAA
44600 TATTTATTATAA
1 TATTT-TTATAA
44612 T
1 T
44613 TATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 11 0.52
12 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:45009 original size:43 final size:43
Alignment explanation
Indices: 44961--45048 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
44951 CTAGTGGAGG
44961 TATTACTTATATGACGAAGGCTTCGTGCAAGGCTCTCAATGGT
1 TATTACTTATATGACGAAGGCTTCGTGCAAGGCTCTCAATGGT
45004 TATTACTTATATGACGAAGGCTTCGTGCAAGGCTCTCAATGGT
1 TATTACTTATATGACGAAGGCTTCGTGCAAGGCTCTCAATGGT
45047 TA
1 TA
45049 GTAGCAGAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (43 bp):
TATTACTTATATGACGAAGGCTTCGTGCAAGGCTCTCAATGGT
Found at i:46551 original size:26 final size:26
Alignment explanation
Indices: 46521--46572 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
46511 CAAAGTGCTA
46521 CTCCCTGTAGCTTTAAGGACATTCCC
1 CTCCCTGTAGCTTTAAGGACATTCCC
46547 CTCCCTGTAGCTTTAAGGACATTCCC
1 CTCCCTGTAGCTTTAAGGACATTCCC
46573 TCGTACGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (26 bp):
CTCCCTGTAGCTTTAAGGACATTCCC
Found at i:49210 original size:22 final size:22
Alignment explanation
Indices: 49185--49227 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49175 ATATAAGATC
49185 AATAAAT-ATACATACACACTAT
1 AATAAATCA-ACATACACACTAT
*
49207 AATAAATCAATATACACACTA
1 AATAAATCAACATACACACTA
49228 AACAATAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAATCAACATACACACTAT
Found at i:51413 original size:29 final size:29
Alignment explanation
Indices: 51375--51430 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
51365 TTCCCCCATA
51375 TTTTTATTAAACTAGGCCATTAGATTATT
1 TTTTTATTAAACTAGGCCATTAGATTATT
51404 TTTTTATTAAACTAGGCCATTAGATTA
1 TTTTTATTAAACTAGGCCATTAGATTA
51431 AATTTTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (29 bp):
TTTTTATTAAACTAGGCCATTAGATTATT
Found at i:51436 original size:29 final size:29
Alignment explanation
Indices: 51374--51436 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
51364 TTTCCCCCAT
*
51374 ATTTTTATTAAACTAGGCCATTAGATTAT
1 ATTTTTATTAAACTAGGCCATTAGATTAA
*
51403 TTTTTTATTAAACTAGGCCATTAGATTAA
1 ATTTTTATTAAACTAGGCCATTAGATTAA
51432 ATTTT
1 ATTTT
51437 AGAGTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (29 bp):
ATTTTTATTAAACTAGGCCATTAGATTAA
Found at i:52766 original size:150 final size:150
Alignment explanation
Indices: 52334--52788 Score: 581
Period size: 150 Copynumber: 3.0 Consensus size: 150
52324 CTGAAAACAG
* *
52334 AATT-CACTAGGGGATTGCATTCCCATCTCCAGTGGCATCAACACATCTGAAACTACCCCACCCT
1 AATTCCACTCGGGGATTGCATTCCCATCTCCAGTGGCATCAACAAATCTGAAACTACCCCACCCT
* * * *
52398 GCTCTACATTGGTTCTGCATCTAGAGCCTTCTCCATCAGCTATGACATTTTTTTCACTTATTGCT
66 GCTCTACATTGGTTTTGTATCTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACATATTGCT
*
52463 TTACCACGATAATGGGAACC
131 TTACCAGGATAATGGGAACC
* * * ** * * *
52483 AATTCCACTCGAGGATTGCATTCCCATCTTCACTGGCGCCATCAAACCTAAAACTACCCCACCCT
1 AATTCCACTCGGGGATTGCATTCCCATCTCCAGTGGCATCAACAAATCTGAAACTACCCCACCCT
* * * * * * *
52548 GCTCTACAAT-GCTTCGATACCTAGAGCCTTCTCTATCAGCTATGACATCTTTTTCACGTATTAC
66 GCTCTACATTGGTTTTG-TATCTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACATATTGC
52612 TTTACCAGGATAATGGGAACC
130 TTTACCAGGATAATGGGAACC
* * ** *
52633 AATTCCACTCGGGGATTGCGTTCCCATCTCCAGTGGCATCAAGAAATCTGAAACTACCTTACCAT
1 AATTCCACTCGGGGATTGCATTCCCATCTCCAGTGGCATCAACAAATCTGAAACTACCCCACCCT
* * * *
52698 GCTCTACTTTGGTTTTGTATCTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCAAACATTGGT
66 GCTCTACATTGGTTTTGTATCTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACATATTGCT
* * *
52763 TTACCAGAATAATGAGAGCC
131 TTACCAGGATAATGGGAACC
52783 AATTCC
1 AATTCC
52789 GGTCATGTAG
Statistics
Matches: 255, Mismatches: 48, Indels: 5
0.83 0.16 0.02
Matches are distributed among these distances:
149 7 0.03
150 244 0.96
151 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.31
Consensus pattern (150 bp):
AATTCCACTCGGGGATTGCATTCCCATCTCCAGTGGCATCAACAAATCTGAAACTACCCCACCCT
GCTCTACATTGGTTTTGTATCTAGAGCCTTCTCCATCAGCTATGACATCTTTTTCACATATTGCT
TTACCAGGATAATGGGAACC
Done.