Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001932.1 Hibiscus syriacus cultivar Beakdansim tig00003910_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: 56555
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4158 original size:61 final size:61
Alignment explanation
Indices: 4061--4217 Score: 188
Period size: 61 Copynumber: 2.5 Consensus size: 61
4051 GTAGTGCTAA
* * * * * *
4061 ACCTAAACTAAGTTTACGCTCTAGTGCTAATCTGGATATGATACGTAGGGTCGTGCCCACC
1 ACCTACACTAGGTTTACACTCTAGTGCTAATCTGGATATGACACATAAGGTCGTGCCCACC
*
4122 ACCTACACTAGGTTTACACTCTAGTGCTAATTTGGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAGGTTTACACTCTAGTGCTAATCTGGATATGACACATAAGGTCGTGCCCACC
* * *
4183 ATCTGCACTTAGTGTCCTTACACACTAGTGCTAAT
1 ACCTACAC-TAG-GT--TTACACTCTAGTGCTAAT
4218 ATAAACTTGC
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
61 60 0.73
62 3 0.04
63 2 0.02
65 17 0.21
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (61 bp):
ACCTACACTAGGTTTACACTCTAGTGCTAATCTGGATATGACACATAAGGTCGTGCCCACC
Found at i:9596 original size:21 final size:21
Alignment explanation
Indices: 9555--9596 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9545 TATCAAAAGA
*
9555 TATTATATGTCTTAAATAAGT
1 TATTATATGTCTTAAACAAGT
*
9576 TATTATAGTGT-TTAGACAAGT
1 TATTATA-TGTCTTAAACAAGT
9597 GACATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (21 bp):
TATTATATGTCTTAAACAAGT
Found at i:12733 original size:2 final size:2
Alignment explanation
Indices: 12726--12778 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
12716 ATTGTAATGT
12726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12768 TA TA TA CA TA T
1 TA TA TA TA TA T
12779 TATGGTTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:33526 original size:17 final size:17
Alignment explanation
Indices: 33497--33529 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33487 AATTTGGCTC
33497 CTTAACTTTGTATTTTA
1 CTTAACTTTGTATTTTA
33514 CTTAA-TTTAGTATTTT
1 CTTAACTTT-GTATTTT
33530 GAATGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTAACTTTGTATTTTA
Found at i:34103 original size:26 final size:26
Alignment explanation
Indices: 34065--34120 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
34055 GCCAAATATA
* * *
34065 TAATTTTATCATTTAGTTAAA-AAGTT
1 TAATTTGACCATTTAATTAAACAA-TT
34091 TAATTTGACCATTTAATTAAACAATT
1 TAATTTGACCATTTAATTAAACAATT
34117 TAAT
1 TAAT
34121 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (26 bp):
TAATTTGACCATTTAATTAAACAATT
Found at i:36272 original size:81 final size:80
Alignment explanation
Indices: 36171--36332 Score: 263
Period size: 81 Copynumber: 2.0 Consensus size: 80
36161 GGTTGCCTAT
*
36171 TTGTTATATGTATGCGTGAGTTTTTGAACATAAATGATCATTTGTTATTTTTT-TCAATCTCATG
1 TTGTTATATGCATGCGTGAGTTTTTGAACATAAATGATCATTTGTTATTTTTTAT--ATCTCATG
36235 TATGTTAAAATGTGTTA
64 TATGTTAAAATGTGTTA
* * *
36252 TTGTTTTATGCATGCGTGAGTTTTTGAACATAAATGATCATTTGTTATTTTTTATATGTTATGTA
1 TTGTTATATGCATGCGTGAGTTTTTGAACATAAATGATCATTTGTTATTTTTTATATCTCATGTA
36317 TGTTAAAATGTGTTA
66 TGTTAAAATGTGTTA
36332 T
1 T
36333 GGTGAACATT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
80 24 0.32
81 51 0.67
82 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.51
Consensus pattern (80 bp):
TTGTTATATGCATGCGTGAGTTTTTGAACATAAATGATCATTTGTTATTTTTTATATCTCATGTA
TGTTAAAATGTGTTA
Found at i:37349 original size:15 final size:16
Alignment explanation
Indices: 37329--37358 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37319 AAAGGGGAGC
37329 TTAAA-TATTTTTTTA
1 TTAAATTATTTTTTTA
37344 TTAAATTATTTTTTT
1 TTAAATTATTTTTTT
37359 TCAAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAAATTATTTTTTTA
Found at i:37370 original size:17 final size:17
Alignment explanation
Indices: 37333--37373 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
37323 GGGAGCTTAA
*
37333 ATATTTTTTTATTAAAT
1 ATATTTTTTTATAAAAT
37350 -TATTTTTTT-TCAAAAT
1 ATATTTTTTTAT-AAAAT
37366 ATATTTTT
1 ATATTTTT
37374 CTAAAGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTTTTTATAAAAT
Found at i:37372 original size:15 final size:16
Alignment explanation
Indices: 37331--37373 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
37321 AGGGGAGCTT
*
37331 AAATATTTTTTTATTA
1 AAATATTTTTTTATCA
*
37347 AATTATTTTTTT-TCA
1 AAATATTTTTTTATCA
*
37362 AAATATATTTTT
1 AAATATTTTTTT
37374 CTAAAGGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
AAATATTTTTTTATCA
Found at i:37673 original size:12 final size:12
Alignment explanation
Indices: 37656--37680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37646 AGTCACTATT
37656 TGACACTGTTCA
1 TGACACTGTTCA
37668 TGACACTGTTCA
1 TGACACTGTTCA
37680 T
1 T
37681 ACATGAGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TGACACTGTTCA
Found at i:40735 original size:14 final size:14
Alignment explanation
Indices: 40716--40742 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40706 AGTCAATCCA
40716 TTGACTTTGACCCG
1 TTGACTTTGACCCG
40730 TTGACTTTGACCC
1 TTGACTTTGACCC
40743 AAAAAGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.37
Consensus pattern (14 bp):
TTGACTTTGACCCG
Found at i:48231 original size:29 final size:28
Alignment explanation
Indices: 48189--48243 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
48179 ATTTTTTTTC
48189 AAAAAAAAAAAAAAAAAAACAAAAAGGA
1 AAAAAAAAAAAAAAAAAAACAAAAAGGA
48217 AAAAAAACAAAAAAAAAAAACAAAAAG
1 AAAAAAA-AAAAAAAAAAAACAAAAAG
48244 CCACAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAAAAAAAAAAACAAAAAGGA
Found at i:48261 original size:1 final size:1
Alignment explanation
Indices: 48189--48242 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
48179 ATTTTTTTTC
* ** * *
48189 AAAAAAAAAAAAAAAAAAACAAAAAGGAAAAAAAACAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
48243 GCCACAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.91, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Done.