Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002958.1 Hibiscus syriacus cultivar Beakdansim tig00006114_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: 63926
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4580 original size:23 final size:23
Alignment explanation
Indices: 4553--4599 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4543 ATGACAAAAG
4553 AAACGTCTCACAAAGG-AATATAA
1 AAACGTCTCACAAAGGCAA-ATAA
* *
4576 AAACGTGTCATAAAGGCAAATAA
1 AAACGTCTCACAAAGGCAAATAA
4599 A
1 A
4600 GGCAGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (23 bp):
AAACGTCTCACAAAGGCAAATAA
Found at i:8031 original size:10 final size:10
Alignment explanation
Indices: 8010--8053 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
8000 TAATGTTTCT
*
8010 TTAATTTTAA
1 TTAATATTAA
*
8020 TTGATATTAA
1 TTAATATTAA
*
8030 TTAAATTTTAA
1 TT-AATATTAA
8041 TTAATATTAA
1 TTAATATTAA
8051 TTA
1 TTA
8054 GACTTAATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
TTAATATTAA
Found at i:8036 original size:21 final size:21
Alignment explanation
Indices: 8012--8053 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8002 ATGTTTCTTT
*
8012 AATTTTAATTGATATTAATTA
1 AATTTTAATTAATATTAATTA
8033 AATTTTAATTAATATTAATTA
1 AATTTTAATTAATATTAATTA
8054 GACTTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTTTAATTAATATTAATTA
Found at i:10186 original size:21 final size:21
Alignment explanation
Indices: 10162--10225 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
10152 TAATAAATTT
10162 TATTTTTATATTATTAAAATA
1 TATTTTTATATTATTAAAATA
*
10183 TATTATTTA-ATTATTAGAATA
1 TATT-TTTATATTATTAAAATA
**
10204 TA-AATT-TATTA-TAAAATA
1 TATTTTTATATTATTAAAATA
10222 TATT
1 TATT
10226 AATTTAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
21 17 0.49
22 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTTTATATTATTAAAATA
Found at i:10231 original size:40 final size:41
Alignment explanation
Indices: 10170--10247 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 41
10160 TTTATTTTTA
* *
10170 TATTATTAAAATATATTATTTAATTA-TTAGAATATAAATT
1 TATTATTAAAATATATTATTTAATCATTTAAAATATAAATT
10210 TATTA-TAAAATATATTAATTTAATCATTTAAAATATAA
1 TATTATTAAAATATATT-ATTTAATCATTTAAAATATAA
10248 TAAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 11 0.32
40 13 0.38
41 10 0.29
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
TATTATTAAAATATATTATTTAATCATTTAAAATATAAATT
Found at i:11238 original size:2 final size:2
Alignment explanation
Indices: 11231--11282 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11221 ATTTGAACCA
11231 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
11273 AT AT AT AT AT
1 AT AT AT AT AT
11283 CTGATCGCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18520 original size:101 final size:102
Alignment explanation
Indices: 18293--18527 Score: 323
Period size: 102 Copynumber: 2.3 Consensus size: 102
18283 ACATCCCTAT
* * * *
18293 AGTTCAAGGGGAAAACATTCATCTACCATCTTCTTTGATCTCAACATGGAAATGTCATCGACACA
1 AGTTCAAGGGGAAGACATTCATCTGCCAACTTCTTGGATCTCAACATGGAAATGTCATCGACACA
* * * *
18358 ACAGTCTGTTCAATACCCATATGACACTATGCCTTCA
66 ACAATCTATTCAATAACCATATGACACAATGCCTTCA
* * * *
18395 AGTT-ATAGGGGAAGACATTCATCTGTCAACTTCTTGGATCTCAATATGGAGATGT-ATTTGACA
1 AGTTCA-AGGGGAAGACATTCATCTGCCAACTTCTTGGATCTCAACATGGAAATGTCA-TCGACA
18458 CAACAATCTATTCAA-AACCATATGACACAATGCCTTCA
64 CAACAATCTATTCAATAACCATATGACACAATGCCTTCA
18496 AGTTCAAGGGGAAGACATTCATCTGCCAACTT
1 AGTTCAAGGGGAAGACATTCATCTGCCAACTT
18528 GTTCAACCTG
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
101 52 0.44
102 65 0.56
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (102 bp):
AGTTCAAGGGGAAGACATTCATCTGCCAACTTCTTGGATCTCAACATGGAAATGTCATCGACACA
ACAATCTATTCAATAACCATATGACACAATGCCTTCA
Found at i:20727 original size:24 final size:23
Alignment explanation
Indices: 20692--20740 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
20682 TAATTGCATT
20692 TTCTAATATTTCAATTTATATGA
1 TTCTAATATTTCAATTTATATGA
* *
20715 TTCTTATACTTTCAATTTATGTGA
1 TTCTAATA-TTTCAATTTATATGA
20739 TT
1 TT
20741 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (23 bp):
TTCTAATATTTCAATTTATATGA
Found at i:27760 original size:20 final size:21
Alignment explanation
Indices: 27737--27777 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
27727 GACTTAGAAA
27737 TATAAAACATCTATA-AAAAT
1 TATAAAACATCTATACAAAAT
*
27757 TATAAAATATCTATACAAAAT
1 TATAAAACATCTATACAAAAT
27778 AAAATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (21 bp):
TATAAAACATCTATACAAAAT
Found at i:27781 original size:18 final size:19
Alignment explanation
Indices: 27734--27782 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
27724 CATGACTTAG
*
27734 AAATATAAAACATCTATAA
1 AAATATAAAATATCTATAA
*
27753 AAATTATAAAATATCTATAC
1 AAA-TATAAAATATCTATAA
27773 AAA-ATAAAAT
1 AAATATAAAAT
27783 TATGTGACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 17 0.63
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATATAAAATATCTATAA
Found at i:41754 original size:134 final size:134
Alignment explanation
Indices: 41512--41771 Score: 362
Period size: 134 Copynumber: 1.9 Consensus size: 134
41502 GCATCCTAAT
* * * *
41512 ATTCAAATGTCTGATTCAAAATTTAGAGTCTAACTGATAAAATATATTCTAATCTAATGAAATTC
1 ATTCAAATGTCTGATTCAAAATTTAGAGACTAACTGATAAAACATAGTCCAATCTAATGAAATTC
* * * * * *
41577 GATCAATAACATTATCAATTGGACTTTAATTTTTATATTAGAGAAGTTGAGGGACTAAATTTTAA
66 AATCAATAACATTATCAACTGGACTTTAATTTATAAATCAGAGAAGTTGAAGGACTAAATTTTAA
41642 TGAA
131 TGAA
*
41646 ATTCAAA-GATCTGATTCAAAATTTAGAGACTAATTGATAAAACATAGTCCAA-CTTAATGAAAT
1 ATTCAAATG-TCTGATTCAAAATTTAGAGACTAACTGATAAAACATAGTCCAATC-TAATGAAAT
** *
41709 TCAATCAATAATGTTATCAACTGGTCTTTAATTTATAAATCAGAGAAGTTGAAGGACTAAATT
64 TCAATCAATAACATTATCAACTGGACTTTAATTTATAAATCAGAGAAGTTGAAGGACTAAATT
41772 CCTGGAACTA
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
133 2 0.02
134 108 0.98
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (134 bp):
ATTCAAATGTCTGATTCAAAATTTAGAGACTAACTGATAAAACATAGTCCAATCTAATGAAATTC
AATCAATAACATTATCAACTGGACTTTAATTTATAAATCAGAGAAGTTGAAGGACTAAATTTTAA
TGAA
Found at i:42936 original size:27 final size:27
Alignment explanation
Indices: 42852--42936 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 27
42842 GTGTAAATAA
* * * *
42852 TTAACTTAAATTCATAATATTTTATAT
1 TTAACTTAATTTAAAAATATTTTTTAT
* *
42879 AT-A-TTAATTTTAAAAA-ATATTTTTACA
1 TTAACTTAA-TTTAAAAATAT-TTTTTA-T
42906 TTAACTTAATTTAAAAATATTTTTTAT
1 TTAACTTAATTTAAAAATATTTTTTAT
42933 TTAA
1 TTAA
42937 ATATATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
25 6 0.14
26 11 0.25
27 6 0.14
28 15 0.34
29 6 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAACTTAATTTAAAAATATTTTTTAT
Found at i:42976 original size:33 final size:32
Alignment explanation
Indices: 42932--43012 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
42922 ATATTTTTTA
* * *
42932 TTTAAATATATATATATTATTTTTATCT-AATCT
1 TTTAAAAATATATAT-TTATTATTAT-TAAAACT
42965 TTTAAAAATATAT-TTTATTATTATTAAAACT
1 TTTAAAAATATATATTTATTATTATTAAAACT
* *
42996 TTTCAAAGTATATATTT
1 TTTAAAAATATATATTT
43013 TATGTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 24 0.59
32 4 0.10
33 12 0.29
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (32 bp):
TTTAAAAATATATATTTATTATTATTAAAACT
Found at i:43151 original size:24 final size:25
Alignment explanation
Indices: 43114--43160 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
43104 AAATCAAAAT
*
43114 TAATTTAATAATAAAATATATTTAA
1 TAATTTAATAATAAAAAATATTTAA
43139 TAATTTAAT-ATAAAAAATATTT
1 TAATTTAATAATAAAAAATATTT
43161 GTTAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATTTAATAATAAAAAATATTTAA
Found at i:44831 original size:180 final size:178
Alignment explanation
Indices: 44596--44960 Score: 562
Period size: 180 Copynumber: 2.0 Consensus size: 178
44586 ATAAAAAATA
* *
44596 AATATTTTTTAATTCAAAAAAAGTTTATTAATTTAATAATATATAAATAAAAAT-AAAATTTTAG
1 AATATTTTTTAATTCAAAAAAAGTTTAATAATTTAATAATATATAAATAAAAATAAAAAATTTAG
44660 ATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATT
66 AT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATT
*
44725 GGATTTTAAATGGTTTGGGCTT-AGCCCATATG-T-TATATAATATATTT
130 GGATTTTAAATGATTTGGG-TTGAGCCCATATGTTATATATAATATATTT
44772 AATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATAT-AATATAAAATAAAAA
1 AATATTTTTTAATTCAAAAAA-AGTTT---AATAATTT-AATAATATATAAATA-AAAATAAAAA
*
44835 ATTTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
60 ATTTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
*
44900 TAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTT
125 TAATTGGATTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTT
*
44954 AAAATTT
1 AATATTT
44961 AAAATTTAAT
Statistics
Matches: 173, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
175 6 0.03
176 19 0.11
179 13 0.08
180 104 0.60
181 11 0.06
182 20 0.12
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (178 bp):
AATATTTTTTAATTCAAAAAAAGTTTAATAATTTAATAATATATAAATAAAAATAAAAAATTTAG
ATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATTG
GATTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTT
Found at i:54383 original size:13 final size:13
Alignment explanation
Indices: 54365--54392 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54355 GTCAAAATTT
54365 AAAAAATCAATAA
1 AAAAAATCAATAA
54378 AAAAAATCAATAA
1 AAAAAATCAATAA
54391 AA
1 AA
54393 TATATTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATCAATAA
Found at i:56127 original size:22 final size:19
Alignment explanation
Indices: 56102--56146 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 19
56092 CACCTATCTA
56102 TTAATTAATTTTATTGTATTAT
1 TTAATT-ATTTTA-T-TATTAT
56124 TTAATTATTTTATTATTAT
1 TTAATTATTTTATTATTAT
56143 TTAA
1 TTAA
56147 ATCATAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 1 0.04
21 6 0.26
22 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTAATTATTTTATTATTAT
Found at i:59481 original size:15 final size:16
Alignment explanation
Indices: 59453--59486 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
59443 TCAGTTTATC
59453 AACATATTGAGCTATA
1 AACATATTGAGCTATA
*
59469 AACA-ATTGGGCTATA
1 AACATATTGAGCTATA
59484 AAC
1 AAC
59487 CTAAGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (16 bp):
AACATATTGAGCTATA
Done.