Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005565.1 Hibiscus syriacus cultivar Beakdansim tig00012906_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: 39186
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:906 original size:31 final size:31
Alignment explanation
Indices: 868--927 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
858 GGATCATACA
*
868 TTTTTTTTTG-AAGGACGGATCATACACTTT
1 TTTTTTTTTGAAAGAACGGATCATACACTTT
*
898 TTTTTTTTTGAAATAACGGATCATACACTT
1 TTTTTTTTTGAAAGAACGGATCATACACTT
928 GATTGTAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (31 bp):
TTTTTTTTTGAAAGAACGGATCATACACTTT
Found at i:29575 original size:18 final size:18
Alignment explanation
Indices: 29552--29589 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29542 ACATTTTGTT
29552 TCGTACTCTTCTTTGAAA
1 TCGTACTCTTCTTTGAAA
29570 TCGTACTCTTCTTTGAAA
1 TCGTACTCTTCTTTGAAA
29588 TC
1 TC
29590 AAGTTACCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (18 bp):
TCGTACTCTTCTTTGAAA
Found at i:31681 original size:31 final size:31
Alignment explanation
Indices: 31646--31704 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
31636 GCGAGCCTAA
* *
31646 AATTTTCAAGCTCGACTCGAACTCGAAAGAT
1 AATTTTCAAACTCGACTCAAACTCGAAAGAT
*
31677 AATTTTGAAACTCGACTCAAACTCGAAA
1 AATTTTCAAACTCGACTCAAACTCGAAA
31705 AGGCTCGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (31 bp):
AATTTTCAAACTCGACTCAAACTCGAAAGAT
Found at i:31757 original size:24 final size:23
Alignment explanation
Indices: 31730--31775 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
31720 AAAAATTAGT
31730 AGCTCGATTGAAGCTCGAGACTCG
1 AGCTCGATTGAAGCTCGA-ACTCG
31754 AGCTCGATTGAAGCTCGAACTC
1 AGCTCGATTGAAGCTCGAACTC
31776 AATTCAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
AGCTCGATTGAAGCTCGAACTCG
Found at i:31784 original size:17 final size:17
Alignment explanation
Indices: 31750--31826 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
31740 AAGCTCGAGA
* *
31750 CTCGAGCTCGATTGAAG
1 CTCGAACTCGATTCAAG
*
31767 CTCGAACTCAATTCAAG
1 CTCGAACTCGATTCAAG
* *
31784 CTCGTACTCGATTTAAG
1 CTCGAACTCGATTCAAG
*
31801 CTCGTACTCGATTCAAG
1 CTCGAACTCGATTCAAG
31818 CTCGAACTC
1 CTCGAACTC
31827 AAACTCGAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (17 bp):
CTCGAACTCGATTCAAG
Found at i:35242 original size:64 final size:63
Alignment explanation
Indices: 35145--35285 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 63
35135 CATATTCAAT
* * *
35145 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAA-TTGATGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTTG-TGCATCGATGCAT-AGGTA
* * * *
35208 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTTGTGCATCGATGCATAGGTA
*
35272 GTGCATTGATGCAC
1 GTGCATCGATGCAC
35286 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
63 18 0.27
64 45 0.68
65 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTTGTGCATCGATGCATAGGTA
Found at i:36237 original size:31 final size:31
Alignment explanation
Indices: 36199--36263 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
36189 AAGAGTCGAG
* *
36199 GTTTACCTATG-TCTTTCGAGACATATGGATA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
*
36230 GTTTACCTAGGTTCTTCGAGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
36261 GTT
1 GTT
36264 GTCGAGTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:36282 original size:29 final size:29
Alignment explanation
Indices: 36240--36316 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
36230 GTTTACCTAG
* * * **
36240 GTTCTTCGAGACCTATGGACAGTTGTCGA
1 GTTCTTTGTGACCTCTGGACAGTTACCGA
* *
36269 GTTCTTTGTGACCTCTGGATAGTTACCGG
1 GTTCTTTGTGACCTCTGGACAGTTACCGA
*
36298 GGTCTTTGTGACCTCTGGA
1 GTTCTTTGTGACCTCTGGA
36317 TAAGTCCTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.35
Consensus pattern (29 bp):
GTTCTTTGTGACCTCTGGACAGTTACCGA
Found at i:37567 original size:21 final size:20
Alignment explanation
Indices: 37510--37567 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
37500 TTTATGTGAA
*
37510 TAACT-TAAACCCTAAACCC
1 TAACTCTAAACACTAAACCC
*
37529 TAACTCTTAACACATAAACCC
1 TAACTCTAAACAC-TAAACCC
* *
37550 TAAATTCTAAACTCTAAA
1 T-AACTCTAAACACTAAA
37568 TTTAAATCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 12 0.39
22 9 0.29
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (20 bp):
TAACTCTAAACACTAAACCC
Found at i:37908 original size:14 final size:14
Alignment explanation
Indices: 37891--37931 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
37881 TTTATTCATA
37891 AATAATGTATTTTT
1 AATAATGTATTTTT
37905 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
37916 AATAATGTAATTTT
1 AATAATGTATTTTT
37930 AA
1 AA
37932 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Done.