Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006381.1 Hibiscus syriacus cultivar Beakdansim tig00015360_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: 58907
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:398 original size:42 final size:42
Alignment explanation
Indices: 346--598 Score: 257
Period size: 42 Copynumber: 6.1 Consensus size: 42
336 AAATTCAACC
* * * *
346 CAATTATTGTCGAGTTGAGTTTTCGAACGATCTACTCTCGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
* * * *
388 CAATCATTGTCGAGTCGAACTTTCCAACAACCTACTCCCGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
* * * * *
430 CAATCATTGTCGAGTTGAGTTTTTTCAAACGACATACTCTTGTT
1 CAATCATTGTCGAGTCGAG--CTTTCGAACGACCTACTCTCGTT
* *
474 CAATCATTGTCGAGT-----TTTC-AGACAACCTACTCTTGTT
1 CAATCATTGTCGAGTCGAGCTTTCGA-ACGACCTACTCTCGTT
* *
511 CAATCATTGTCGAGTCGAACTTTCGAACGACCTACTCTAGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
* *
553 CAATCATTGTCGAGTCGAGCTTTGGAACTACCTACTCTCAGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTC-GTT
596 CAA
1 CAA
599 GTATGATGGT
Statistics
Matches: 177, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
36 1 0.01
37 33 0.19
42 104 0.59
43 7 0.04
44 32 0.18
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (42 bp):
CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
Found at i:14798 original size:31 final size:31
Alignment explanation
Indices: 14722--14805 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
14712 GTTCAAGTTT
*
14722 TTTCGAGATCGAGTCGAGCTTCAATTTTTTA
1 TTTCGAAATCGAGTCGAGCTTCAATTTTTTA
* * *
14753 TTTCG-AGTCAAGTCGAGCTTCATTTTTTTA
1 TTTCGAAATCGAGTCGAGCTTCAATTTTTTA
*
14783 TTTCGAAATTGAGTCGAGCTTCA
1 TTTCGAAATCGAGTCGAGCTTCA
14806 CAATATTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 26 0.58
31 19 0.42
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (31 bp):
TTTCGAAATCGAGTCGAGCTTCAATTTTTTA
Found at i:18510 original size:30 final size:30
Alignment explanation
Indices: 18438--18513 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
18428 ACCTTGATTG
* * * *
18438 AATTTAAGGGTCAAATTGACATTTTATCTAA
1 AATTTAA-GGTTAAAATGACACTTCATCTAA
18469 AATTTATAGGTTAAAATGACACTTCATC-AA
1 AATTTA-AGGTTAAAATGACACTTCATCTAA
18499 AAGTTTAAGGTTAAA
1 AA-TTTAAGGTTAAA
18514 TTAGTATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 12 0.31
31 26 0.67
32 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (30 bp):
AATTTAAGGTTAAAATGACACTTCATCTAA
Found at i:23536 original size:20 final size:20
Alignment explanation
Indices: 23511--23550 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23501 TGAATAGTGC
*
23511 AATATTAAATTATGTTTTTA
1 AATATTAAATTATGATTTTA
23531 AATATTAAATTATGATTTTA
1 AATATTAAATTATGATTTTA
23551 TGTGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AATATTAAATTATGATTTTA
Found at i:25929 original size:30 final size:31
Alignment explanation
Indices: 25893--25953 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
25883 AATCATTACA
25893 ACCTTAACTGTT-GTTAAGGAGTGACTTAAT
1 ACCTTAACTGTTCGTTAAGGAGTGACTTAAT
* *
25923 ACCTTAACTGTTCTTTAAGGTGTGACTTAAT
1 ACCTTAACTGTTCGTTAAGGAGTGACTTAAT
25954 TAAATTTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (31 bp):
ACCTTAACTGTTCGTTAAGGAGTGACTTAAT
Found at i:32048 original size:103 final size:103
Alignment explanation
Indices: 31869--32074 Score: 324
Period size: 103 Copynumber: 2.0 Consensus size: 103
31859 ATTAAATATT
* *
31869 CTCAATCATTTGGCAATGAACATTCGTATTCGTAATATATTTAGTGTTTGAACCCGAAATTTTAA
1 CTCAATCATTTGGCAATGAACATTAGTATTCGCAATATATTTAGTGTTTGAACCCGAAATTTTAA
* *
31934 AGAATAACAACAAATTTCTTAACCATTAA-AGTCGATTC
66 AAAATAACAACAAATTTCTTAACCACTAAGA-TCGATTC
* * *
31972 CTCAATCTTTTGGCAATGAACGTTAGTATTCGCGATATATTTAGTGTTTGAACCCGAAATTTTAA
1 CTCAATCATTTGGCAATGAACATTAGTATTCGCAATATATTTAGTGTTTGAACCCGAAATTTTAA
*
32037 AAAATAACAACAAATTTTTTAACCACTAAGATCGATTC
66 AAAATAACAACAAATTTCTTAACCACTAAGATCGATTC
32075 GTTGATGCTT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 93 0.99
104 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (103 bp):
CTCAATCATTTGGCAATGAACATTAGTATTCGCAATATATTTAGTGTTTGAACCCGAAATTTTAA
AAAATAACAACAAATTTCTTAACCACTAAGATCGATTC
Found at i:38003 original size:37 final size:37
Alignment explanation
Indices: 37930--38004 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
37920 GTTGGAAAAT
* *
37930 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
37967 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
38004 A
1 A
38005 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:42834 original size:202 final size:202
Alignment explanation
Indices: 42478--42904 Score: 818
Period size: 202 Copynumber: 2.1 Consensus size: 202
42468 AGGCATAGGC
* *
42478 AAGCACATTGTCATTAAAGCCAAACGGATGGCTACGAACACCCATTAAGATAGTTTATAGACAAC
1 AAGCTCATTCTCATTAAAGCCAAACGGATGGCTACGAACACCCATTAAGATAGTTTATAGACAAC
42543 TTCTAGTCAGTTATTTTTCGTTGCATTAGGTAGAGAAATCTATTGCTATAAAAGATGCAGAAATC
66 TTCTAGTCAGTTATTTTTCGTTGCATTAGGTAGAGAAATCTATTGCTATAAAAGATGCAGAAATC
42608 GCCCATAGCTTGTTAGATACAATGTCTATTAGCTGTTAAGTTGGATATTTATAAGACTGAACCAG
131 GCCCATAGCTTGTTAGATACAATGTCTATTAGCTGTTAAGTTGGATATTTATAAGACTGAACCAG
42673 GCATTAT
196 GCATTAT
42680 AAGCTCATTCTCATTAAAGCCAAACGGATGGCTACGAACACCCATTAAGATAGTTTATAGACAAC
1 AAGCTCATTCTCATTAAAGCCAAACGGATGGCTACGAACACCCATTAAGATAGTTTATAGACAAC
*
42745 TTCTAGTCAGTTATTTTTGGTTGCATTAGGTAGAGAAATCTATTGCTATAAAAGATGCAGAAATC
66 TTCTAGTCAGTTATTTTTCGTTGCATTAGGTAGAGAAATCTATTGCTATAAAAGATGCAGAAATC
42810 GCCCATAGCTTGTTAGATACAATGTCTATTAGCTGTTAAGTTGGATATTTATAAGACTGAACCAG
131 GCCCATAGCTTGTTAGATACAATGTCTATTAGCTGTTAAGTTGGATATTTATAAGACTGAACCAG
42875 GCATTAT
196 GCATTAT
*
42882 AAGCTCATTCTCATTAAAACCAA
1 AAGCTCATTCTCATTAAAGCCAA
42905 CAAGAAGGAT
Statistics
Matches: 221, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
202 221 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (202 bp):
AAGCTCATTCTCATTAAAGCCAAACGGATGGCTACGAACACCCATTAAGATAGTTTATAGACAAC
TTCTAGTCAGTTATTTTTCGTTGCATTAGGTAGAGAAATCTATTGCTATAAAAGATGCAGAAATC
GCCCATAGCTTGTTAGATACAATGTCTATTAGCTGTTAAGTTGGATATTTATAAGACTGAACCAG
GCATTAT
Found at i:45613 original size:25 final size:26
Alignment explanation
Indices: 45553--45613 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
45543 TTTTAAAGAA
45553 ATTTTATTTCTATATTAGTATTTCAAC
1 ATTTTATTT-TATATTAGTATTTCAAC
* * *
45580 -TTTGATTTTAT-TTATTATTTTAAC
1 ATTTTATTTTATATTAGTATTTCAAC
45604 ATTTTATTTT
1 ATTTTATTTT
45614 TATCAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.38
25 11 0.38
26 7 0.24
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTTATTTTATATTAGTATTTCAAC
Found at i:46092 original size:27 final size:27
Alignment explanation
Indices: 46053--46105 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
46043 ACATAAAAAC
46053 AATCATAACCCACACATCTAAATCAAT
1 AATCATAACCCACACATCTAAATCAAT
* *
46080 AATCATAAGCCACACGTCTAAATCAA
1 AATCATAACCCACACATCTAAATCAA
46106 CGCATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (27 bp):
AATCATAACCCACACATCTAAATCAAT
Found at i:47463 original size:2 final size:2
Alignment explanation
Indices: 47456--47482 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47446 GTATTTATTC
47456 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
47483 AACCTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51777 original size:6 final size:6
Alignment explanation
Indices: 51758--51787 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
51748 TCTCATGGTA
51758 AAAAAT ATAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT A-AAAAT AAAAAT AAAAAT AAAAA
51788 GAATTTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Done.