Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004906.1 Hibiscus syriacus cultivar Beakdansim tig00011035_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: 47159
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2039 original size:255 final size:243
Alignment explanation
Indices: 1577--2064 Score: 664
Period size: 255 Copynumber: 2.0 Consensus size: 243
1567 CTTTATTTTA
*
1577 GTCGGGCGATTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGTGTTTAGGGTGAAAAATACT
1 GTCGGGCGATTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGTGTTTAGGGTGAAAAATACC
1642 CGACCCGAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATATACCCTCTATATAT
66 CGACCCGAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATATACCCTCTATATAT
* *
1707 AATTTTTTTTCAATTAGTCATTTTTATTGAATAAAAATAATTTTTTATTATTTCGGTCGGGTAGG
131 AATTTTTTTCCAATTAGTCATTTTTATTGAATAAAAATAATTTTTTATTATTTCGGTCGGGTA-C
* *
1772 GTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGGTTTTATTTTTCGG
195 G-CAGATTTCTAATTCATATATTAGGGTCGCGTCGGGTTTTATTTTTCGG
* *
1822 GTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTC-TGTTTAGGGTGAAAAATAC
1 GTCGGG-CGATTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGTGTTTAGGGTGAAAAAT--
1886 CCGACCCGACCCGACCCAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATA
63 ---ACCCGACCCG-----AAAATATATAATTTTACCTTATATATTTAGGAATAATTACAAT-ATA
* *
1951 CCCCTCTCTATAT-ATTTTTTTCCAATTAAGTCACTTTTTTATTGAAT-AAAATATTTTTTTTAT
119 -CCCTCTATATATAATTTTTTTCCAATT-AGTCA--TTTTTATTGAATAAAAATA-ATTTTTTAT
*
2014 TATTTCGGGTCGGGT-CG-AG-TTTCTAATTCATGTATTAGGGTCGCGTCGGGT
179 TATTTC-GGTCGGGTACGCAGATTTCTAATTCATATATTAGGGTCGCGTCGGGT
2065 GAACTTTATT
Statistics
Matches: 215, Mismatches: 10, Indels: 26
0.86 0.04 0.10
Matches are distributed among these distances:
245 23 0.11
246 36 0.17
250 9 0.04
255 72 0.33
256 18 0.08
257 16 0.07
258 7 0.03
259 26 0.12
260 8 0.04
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (243 bp):
GTCGGGCGATTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGTGTTTAGGGTGAAAAATACC
CGACCCGAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATATACCCTCTATATAT
AATTTTTTTCCAATTAGTCATTTTTATTGAATAAAAATAATTTTTTATTATTTCGGTCGGGTACG
CAGATTTCTAATTCATATATTAGGGTCGCGTCGGGTTTTATTTTTCGG
Found at i:13240 original size:19 final size:19
Alignment explanation
Indices: 13212--13250 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13202 CCGAGTACAC
* *
13212 TTGACTCGACCCATTAACT
1 TTGACCCGACACATTAACT
*
13231 TTGACCCGACACATTGACT
1 TTGACCCGACACATTAACT
13250 T
1 T
13251 GAGTTGACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (19 bp):
TTGACCCGACACATTAACT
Found at i:15157 original size:13 final size:13
Alignment explanation
Indices: 15139--15164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15129 GATCTTCCCC
15139 TACCCTTGGTATA
1 TACCCTTGGTATA
15152 TACCCTTGGTATA
1 TACCCTTGGTATA
15165 GGTTTGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TACCCTTGGTATA
Found at i:17463 original size:21 final size:21
Alignment explanation
Indices: 17439--17501 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
17429 GTCGAGGGAT
17439 TATATGAGGTTCTTCGGGACA
1 TATATGAGGTTCTTCGGGACA
* *
17460 TATACGAGGTCCTTCGGGACA
1 TATATGAGGTTCTTCGGGACA
*
17481 TACATGAGG-TCATTCGGGACA
1 TATATGAGGTTC-TTCGGGACA
17502 AATTTCATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (21 bp):
TATATGAGGTTCTTCGGGACA
Found at i:23280 original size:21 final size:21
Alignment explanation
Indices: 23256--23318 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
23246 GTCGAGGGAT
*
23256 TATATGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTTGGGACA
23277 TATATGAGGTCCTTTGGGACA
1 TATATGAGGTCCTTTGGGACA
* *
23298 TACATGAGGTCATTTGGGACA
1 TATATGAGGTCCTTTGGGACA
23319 AATTTCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (21 bp):
TATATGAGGTCCTTTGGGACA
Found at i:26896 original size:35 final size:35
Alignment explanation
Indices: 26857--26926 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
26847 GACCTTATGA
26857 ACCCAATGTGCTCCCTTAGGTTATGTAGTTATGGG
1 ACCCAATGTGCTCCCTTAGGTTATGTAGTTATGGG
26892 ACCCAATGTGCTCCCTTAGGTTATGTAGTTATGGG
1 ACCCAATGTGCTCCCTTAGGTTATGTAGTTATGGG
26927 GAACTGCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (35 bp):
ACCCAATGTGCTCCCTTAGGTTATGTAGTTATGGG
Found at i:41839 original size:62 final size:63
Alignment explanation
Indices: 41748--41872 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 63
41738 TATATTTTCT
*
41748 TTAAAAAATCCAAATCAAAATAAGATAAACTTTGAAATATTACCTGAGTTTAGTTAAATAAAA
1 TTAAAAAATCAAAATCAAAATAAGATAAACTTTGAAATATTACCTGAGTTTAGTTAAATAAAA
41811 TTAAAAAATCAAAATC-AAATAAGATAAACTTTGAAATATTACCTGAGTTTAGTTAAATAAAA
1 TTAAAAAATCAAAATCAAAATAAGATAAACTTTGAAATATTACCTGAGTTTAGTTAAATAAAA
41873 CGGAAACAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 46 0.75
63 15 0.25
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (63 bp):
TTAAAAAATCAAAATCAAAATAAGATAAACTTTGAAATATTACCTGAGTTTAGTTAAATAAAA
Found at i:46553 original size:41 final size:41
Alignment explanation
Indices: 46424--46645 Score: 207
Period size: 41 Copynumber: 5.4 Consensus size: 41
46414 TAGTGGTATT
* *
46424 TTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTAC
* * * * *
46465 TTTAATGAC-TCCTTTAGTAGCATACGCCT-CTATAGACTCATAC
1 TTTAGTGGCGT-TTTTA-TA-CAAACG-CTGCTATAGACTCGTAC
* *
46508 TTTAGTGGTGTTTTTATACAAACGCTGCTATAGACTCGTAA
1 TTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTAC
* * * *
46549 TTTAGTGGCGTTTCTATATAAACGGTGCTAAAGACTCGTA-
1 TTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTAC
* * * * *
46589 TGTTAGTGGCGTTTCTATACAAATGCCGCTAAAGACTCATAC
1 T-TTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTAC
*
46631 TTTAGTGGCATTTTT
1 TTTAGTGGCGTTTTT
46646 TGTAAACGCC
Statistics
Matches: 147, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
40 4 0.03
41 108 0.73
42 5 0.03
43 28 0.19
44 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTAC
Done.