Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007002.1 Hibiscus syriacus cultivar Beakdansim tig00018070_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: 55095
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4668 original size:4 final size:4
Alignment explanation
Indices: 4651--4702 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
4641 AATAAAAACA
* * *
4651 ATGT ATGT ACGT ATGT A--T ATAT ATAT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4697 ATGT AT
1 ATGT AT
4703 CAGGTCGGCT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
4 41 0.95
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:8941 original size:2 final size:2
Alignment explanation
Indices: 8866--8921 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
8856 CATTAAAATG
*
8866 TA TA TA T- TA AA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
8905 TA TT TA -A TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA
8922 AAATTTCCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15290 original size:18 final size:19
Alignment explanation
Indices: 15253--15290 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
15243 TCATAACTTT
*
15253 AAATTATAATATATAGATA
1 AAATTATAATAAATAGATA
*
15272 AAATTAT-ATAAATATATA
1 AAATTATAATAAATAGATA
15290 A
1 A
15291 CGTGAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
AAATTATAATAAATAGATA
Found at i:16095 original size:2 final size:2
Alignment explanation
Indices: 16083--16133 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
16073 CTATTATAAG
*
16083 TA TA TA CA 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
16125 TA TA TA TA T
1 TA TA TA TA T
16134 TAAAATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16148 original size:13 final size:14
Alignment explanation
Indices: 16092--16149 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 14
16082 GTATATACAT
*
16092 ATATATATATATATAT
1 ATATATATAT-TA-AA
*
16108 ATATATATATATATAT
1 ATATATATAT-TA-AA
16124 ATATATATATTAAA
1 ATATATATATTAAA
16138 ATATA-ATATTAA
1 ATATATATATTAA
16150 GCAAAAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 7 0.17
14 6 0.15
15 2 0.05
16 26 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATATATTAAA
Found at i:17508 original size:16 final size:15
Alignment explanation
Indices: 17483--17512 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17473 GCCTGACACA
17483 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
17498 AAAAATAAAAATAAA
1 AAAAAT-AAAATAAA
17513 ATGTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:18367 original size:105 final size:105
Alignment explanation
Indices: 18028--18716 Score: 1096
Period size: 105 Copynumber: 6.7 Consensus size: 105
18018 TGGATATCCA
* * * *
18028 TCGTCGTGAAGTTGGACTTGCGTTGTCTAGAGTCCAATATTCTTCGTTGTGAAG-T----TTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
* * * *
18088 TCTGAGATTGGGAAGTTGTT-GTTGACAAGCAGCGGTCCCT
66 TCTGAAATTGAGAA-ATGTTCGTTGACAACCAGCGGTCCCT
* * *
18128 TCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATTCTTCGTTGTGAAG-T----TTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
* * * *
18188 TCTGAGATTGGGAAGTTGTT-GTTGACAAGCAGCGGTCCCT
66 TCTGAAATTGAGAA-ATGTTCGTTGACAACCAGCGGTCCCT
* *
18228 TCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
18293 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
66 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
18333 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
18398 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
66 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
*
18438 TCGTCGTGAAGTTGAACTTACGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
18503 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
66 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
18543 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
* *
18608 CCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCT
66 TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
18648 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
18713 TCTG
66 TCTG
18717 GGTAAAACCT
Statistics
Matches: 568, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
100 150 0.26
101 1 0.00
104 4 0.01
105 413 0.73
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
TCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCT
Found at i:28991 original size:10 final size:10
Alignment explanation
Indices: 28966--28999 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
28956 AACGTTAGTA
*
28966 AAATAGAAAT
1 AAATAAAAAT
*
28976 AGATAAAAAT
1 AAATAAAAAT
28986 AAATAAAAAT
1 AAATAAAAAT
28996 AAAT
1 AAAT
29000 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:30171 original size:2 final size:2
Alignment explanation
Indices: 30159--30191 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30149 CTATTATAAG
*
30159 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30192 TAAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31563 original size:16 final size:15
Alignment explanation
Indices: 31538--31567 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31528 GCCTGACACA
31538 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
31553 AAAAATAAAAATAAA
1 AAAAAT-AAAATAAA
31568 ATGTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:33235 original size:6 final size:6
Alignment explanation
Indices: 33224--33260 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
33214 ACGATGATAT
*
33224 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGATAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
33261 TCTGCTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:33247 original size:18 final size:18
Alignment explanation
Indices: 33217--33260 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
33207 TTAATTAACG
*
33217 ATGATATTGGTAATGGTA
1 ATGATAATGGTAATGGTA
*
33235 ATGGTAATGGTAATGGTA
1 ATGATAATGGTAATGGTA
33253 ATGATAAT
1 ATGATAAT
33261 TCTGCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (18 bp):
ATGATAATGGTAATGGTA
Found at i:37936 original size:2 final size:2
Alignment explanation
Indices: 37931--37976 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
37921 CTTTCAGTGA
37931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37973 AT AT
1 AT AT
37977 TTTAAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44680 original size:29 final size:30
Alignment explanation
Indices: 44618--44683 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
44608 AGGGTGAATT
* ** **
44618 TAAATTTATAAAATTTTAAAGGGATTAACT
1 TAAATTTATAAAATTATAAAGGGACGAAAA
44648 TAAATTTATAAAATTAT-AAGGGACGAAAA
1 TAAATTTATAAAATTATAAAGGGACGAAAA
44677 TAAATTT
1 TAAATTT
44684 TTAATAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (30 bp):
TAAATTTATAAAATTATAAAGGGACGAAAA
Found at i:54268 original size:14 final size:14
Alignment explanation
Indices: 54236--54269 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54226 ACATTTCTGA
*
54236 AAAACGTTTTCCGG
1 AAAATGTTTTCCGG
*
54250 AAAATGTTTTCCGT
1 AAAATGTTTTCCGG
54264 AAAATG
1 AAAATG
54270 AATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (14 bp):
AAAATGTTTTCCGG
Found at i:54578 original size:22 final size:23
Alignment explanation
Indices: 54530--54579 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
54520 TAGTGTTATT
**
54530 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
54553 ATATTTT-AATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
54575 ATATT
1 ATATT
54580 AGATTATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:54664 original size:21 final size:21
Alignment explanation
Indices: 54638--54696 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 21
54628 ATTTCTATGA
54638 AATAATAAATAATATAATATT
1 AATAATAAATAATATAATATT
* *
54659 AATAAT--CT-ATATATTATT
1 AATAATAAATAATATAATATT
* *
54677 AAAAATAAAAAATATAATAT
1 AATAATAAATAATATAATAT
54697 ATTATTATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
21 14 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATAATAAATAATATAATATT
Found at i:55007 original size:13 final size:13
Alignment explanation
Indices: 54989--55013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54979 ACCAAACATT
54989 GAAAAATATTTTC
1 GAAAAATATTTTC
55002 GAAAAATATTTT
1 GAAAAATATTTT
55014 ACGTGAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
GAAAAATATTTTC
Done.