Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007402.1 Hibiscus syriacus cultivar Beakdansim tig00019977_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: 49166
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5807 original size:20 final size:22
Alignment explanation
Indices: 5782--5823 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5772 GGCACTGAAT
5782 TCGGTG-CCCCCC-TTTTGCAG
1 TCGGTGCCCCCCCTTTTTGCAG
5802 TCGGTGCCCCCCCTTTTTGCAG
1 TCGGTGCCCCCCCTTTTTGCAG
5824 CTATTGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.05, C:0.40, G:0.24, T:0.31
Consensus pattern (22 bp):
TCGGTGCCCCCCCTTTTTGCAG
Found at i:11062 original size:39 final size:39
Alignment explanation
Indices: 11008--11104 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
10998 TTGATCTAAC
11008 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
1 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
*
11047 GACACGAAATGTTCAAAATTTAAGAATTCATAAATTTAA
1 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
* *
11086 GA-ATGGAA-GTTCAAAATTT
1 GACACGAAATGTTCAAAATTT
11105 TAATATTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 11 0.20
38 4 0.07
39 40 0.73
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (39 bp):
GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
Found at i:11083 original size:16 final size:15
Alignment explanation
Indices: 11058--11089 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
11048 ACACGAAATG
11058 TTCAAAATTTAAGAA
1 TTCAAAATTTAAGAA
11073 TTCATAAATTTAAGAA
1 TTCA-AAATTTAAGAA
11089 T
1 T
11090 GGAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCAAAATTTAAGAA
Found at i:11787 original size:5 final size:5
Alignment explanation
Indices: 11777--11808 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
11767 ATAAATGTAT
11777 TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
11809 TATACTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:14474 original size:2 final size:2
Alignment explanation
Indices: 14467--14495 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14457 CTAAAAGTTT
14467 TA TA 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 T
14496 GGACAGGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15704 original size:25 final size:22
Alignment explanation
Indices: 15673--15724 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
15663 ATTTTTTTGT
*
15673 TATTTTTATAGAACGATTGTCTTTA
1 TATTTTTATACAAC-ATT-T-TTTA
*
15698 TATTTTTTTACAACATTTTTTA
1 TATTTTTATACAACATTTTTTA
15720 TATTT
1 TATTT
15725 AGTCTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 1 0.04
24 3 0.12
25 12 0.48
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.60
Consensus pattern (22 bp):
TATTTTTATACAACATTTTTTA
Found at i:17365 original size:22 final size:22
Alignment explanation
Indices: 17342--17414 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
17332 ATGAGTTACG
*
17342 GGAGTTACATGATATAATTTCG
1 GGAGTTACATGATATAATTTCA
17364 GGAGTTACATGATATAATTTCA
1 GGAGTTACATGATATAATTTCA
17386 GGAGTTACATGATATAATTTCA
1 GGAGTTACATGATATAATTTCA
17408 GGAGTTA
1 GGAGTTA
17415 TAATAGCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (22 bp):
GGAGTTACATGATATAATTTCA
Found at i:27502 original size:2 final size:2
Alignment explanation
Indices: 27495--27519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27485 TGATACCCCA
27495 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
27520 GTGGTTTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:29152 original size:25 final size:25
Alignment explanation
Indices: 29119--29172 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29109 TAGGTAATTT
*
29119 ATTTTTTTTCTATAAAATTCTT-TAA
1 ATTTATTTTCTATAAAATT-TTATAA
*
29144 ATTTATTTTCTCTAAAATTTTATAA
1 ATTTATTTTCTATAAAATTTTATAA
29169 ATTT
1 ATTT
29173 TAAATTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTATTTTCTATAAAATTTTATAA
Found at i:30225 original size:16 final size:16
Alignment explanation
Indices: 30204--30235 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30194 ACCGCCCAGG
30204 GCAGCATGTAGGGGCA
1 GCAGCATGTAGGGGCA
30220 GCAGCATGTAGGGGCA
1 GCAGCATGTAGGGGCA
30236 TCATTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.44, T:0.12
Consensus pattern (16 bp):
GCAGCATGTAGGGGCA
Found at i:33529 original size:17 final size:16
Alignment explanation
Indices: 33507--33545 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
33497 AAATTATCAA
* *
33507 TTTTATTTAAATTAAT
1 TTTTATTGAAAATAAT
33523 TTATTATTGAAAATAAT
1 TT-TTATTGAAAATAAT
33540 TTTTAT
1 TTTTAT
33546 CAATTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTATTGAAAATAAT
Found at i:35001 original size:25 final size:25
Alignment explanation
Indices: 34941--34990 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
34931 TATTTGTAGT
*
34941 AGAAAAATAATATTTATTATAATGA
1 AGAAAAATAATATTAATTATAATGA
34966 AGAAAAATAATATTAATTATAATGA
1 AGAAAAATAATATTAATTATAATGA
34991 CTAAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (25 bp):
AGAAAAATAATATTAATTATAATGA
Found at i:38947 original size:17 final size:17
Alignment explanation
Indices: 38897--38947 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
38887 GTAAATTAAT
*
38897 ATTAAAATAA-ATAAATA
1 ATTAAAATAACA-CAATA
* *
38914 AATAAAATATTCACAATA
1 ATTAAAATA-ACACAATA
38932 ATTAAAATAACACAAT
1 ATTAAAATAACACAAT
38948 TTAAATTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.52
18 12 0.44
19 1 0.04
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (17 bp):
ATTAAAATAACACAATA
Found at i:45182 original size:127 final size:128
Alignment explanation
Indices: 45017--45619 Score: 1033
Period size: 127 Copynumber: 4.8 Consensus size: 128
45007 ACTATTCACA
45017 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
45082 TTATGTCACTCATGTCCATCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGTGGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
** * *
45145 TGAAGGCGATTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
45210 TATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTA-T-TTTCTCAGGGGACT
66 TATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
45270 TGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
45335 TTATGTCACTCATGTCCCTTGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
45398 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATA--TTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
45461 TATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
45523 TGAAGGAGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
45588 TATGTCACTCATGTCCCTCGGGGACACTAGAT
66 TATGTCACTCATGTCCCTCGGGGACACTAGAT
45620 GGATTGTGAA
Statistics
Matches: 447, Mismatches: 19, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
124 1 0.00
125 151 0.34
126 85 0.19
127 157 0.35
128 53 0.12
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:45515 original size:253 final size:253
Alignment explanation
Indices: 45017--45619 Score: 1095
Period size: 253 Copynumber: 2.4 Consensus size: 253
45007 ACTATTCACA
45017 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
45082 TTATGTCACTCATGTCCATCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGTGGACTTG
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
*
45147 AAGGCGATTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
131 AAGGCGAGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
45212 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTTTCTCAGGGGACT
196 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTTTCTCAGGGGACT
*
45270 TGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
45335 TTATGTCACTCATGTCCCTTGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
45400 AAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAG-A-ATATTATCATTGCCCTATTA
131 AAGGCGAGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
45463 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
196 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTA-T-TTTCTCAGGGGACT
*
45523 TGAAGGAGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
45587 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
45620 GGATTGTGAA
Statistics
Matches: 338, Mismatches: 10, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
251 63 0.19
252 77 0.23
253 198 0.59
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (253 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
AAGGCGAGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTTTCTCAGGGGACT
Found at i:46016 original size:34 final size:33
Alignment explanation
Indices: 45977--46048 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
45967 TAAGTTGAAA
*
45977 TTTAATGTTAAATTTTGAATACA-ATAATTTATAT
1 TTTAATGTTAAATTTCGAATA-ATA-AATTTATAT
* *
46011 TTTAATTTTAAATTTCGAATAATAAATTTGTAT
1 TTTAATGTTAAATTTCGAATAATAAATTTATAT
46044 TTTAA
1 TTTAA
46049 AAACATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 14 0.41
34 20 0.59
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (33 bp):
TTTAATGTTAAATTTCGAATAATAAATTTATAT
Found at i:46582 original size:21 final size:21
Alignment explanation
Indices: 46556--46622 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
46546 AAAACCCTGC
*
46556 GGCTAGGCATGTAACCTGGCG
1 GGCTAGGAATGTAACCTGGCG
46577 GGCTAGGAATGTAACCCT-GCG
1 GGCTAGGAATGTAA-CCTGGCG
* * * *
46598 GGCTCGTAATGTAAACTGGTG
1 GGCTAGGAATGTAACCTGGCG
46619 GGCT
1 GGCT
46623 TGGCATATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.87
22 3 0.08
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (21 bp):
GGCTAGGAATGTAACCTGGCG
Found at i:47220 original size:22 final size:21
Alignment explanation
Indices: 47182--47224 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
47172 CTGAAACTGA
47182 AATATAAATATACAATTCAAAT
1 AATATAAATATACAATT-AAAT
*
47204 AATA-AAATATTCTAATTAAAT
1 AATATAAATATAC-AATTAAAT
47225 CTAGCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATAAATATACAATTAAAT
Found at i:48408 original size:32 final size:33
Alignment explanation
Indices: 48340--48423 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
48330 TTAATAATTC
* * **
48340 TAAATAAATAATAATTATATAAATATTTTTTAA
1 TAAATAAATAATATTTACATAAATATTTAATAA
48373 TAAA-AAATAATATTTACATAAATATATTAAT-A
1 TAAATAAATAATATTTACATAAATAT-TTAATAA
48405 TAAAATAAATAACTATTTA
1 T-AAATAAATAA-TATTTA
48424 AAAAAATACT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
32 21 0.49
33 10 0.23
34 6 0.14
35 6 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (33 bp):
TAAATAAATAATATTTACATAAATATTTAATAA
Done.