Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000311.1 Hibiscus syriacus cultivar Beakdansim tig00000585_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: 47523
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:20983 original size:2 final size:2
Alignment explanation
Indices: 20923--20964 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20913 TTTAAGTGTT
20923 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
20965 AGTATCGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21468 original size:185 final size:185
Alignment explanation
Indices: 21125--21496 Score: 451
Period size: 185 Copynumber: 2.0 Consensus size: 185
21115 GGGTGCAATA
* * * *** * * * *
21125 TATTTTATTAATACAAATATTAACATTATAGATCGCTACTTGTTTCTTAGTGAGCCGTGGCATTA
1 TATTTTATTAATAAAAATATTAAAATTACAGATCAAAACATGTTTCTTAGTGAACCATGACATTA
*** * * *
21190 TTGGACTCAATTGTATTTCTTAGATATATTCAAAACATTTTCGACTTTAAACTTATTTTTTTATC
66 TTGGAAGAAATCGTATTTCTTAGATATATTCAAAACATTTTAGACTTTAAACTTATTTTCTTATC
* * * *
21255 GTGAGAAAATCAAGGCTCCATCAACTTAAACTGTGATAATATTTTAGGCGCAACC
131 ATGAGAAAATCAAGGCTACATCAACTTAAACTCTGATAACATTTTAGGCGCAACC
*
21310 TATTTTATTAATAAAAATATTAAAATTACATATCAAAACATGTTTCTTAGTGAACCATGACATTA
1 TATTTTATTAATAAAAATATTAAAATTACAGATCAAAACATGTTTCTTAGTGAACCATGACATTA
* * * *
21375 TTGGAAGAAATCGTATTTCTTATATATATTCATAACATTTTTAG-CTTTTAACTTATTTTCTTGT
66 TTGGAAGAAATCGTATTTCTTAGATATATTCAAAACA-TTTTAGACTTTAAACTTATTTTCTTAT
* * * *
21439 CATG-GAAAATCCAATGCTATATTAACTTAAATTCTGATAACATTTTAGGCGCAACC
130 CATGAGAAAAT-CAAGGCTACATCAACTTAAACTCTGATAACATTTTAGGCGCAACC
21495 TA
1 TA
21497 AAATATTAAT
Statistics
Matches: 156, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
184 6 0.04
185 145 0.93
186 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (185 bp):
TATTTTATTAATAAAAATATTAAAATTACAGATCAAAACATGTTTCTTAGTGAACCATGACATTA
TTGGAAGAAATCGTATTTCTTAGATATATTCAAAACATTTTAGACTTTAAACTTATTTTCTTATC
ATGAGAAAATCAAGGCTACATCAACTTAAACTCTGATAACATTTTAGGCGCAACC
Found at i:21852 original size:31 final size:31
Alignment explanation
Indices: 21813--21880 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
21803 TATGTTGCAC
21813 GACGAACTTAAACTTATAAAATTCTAGGGAA
1 GACGAACTTAAACTTATAAAATTCTAGGGAA
* *
21844 TACGAACTTAAACTTATAAAATTCTAGGTAA
1 GACGAACTTAAACTTATAAAATTCTAGGGAA
21875 GACGAA
1 GACGAA
21881 AATAGATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (31 bp):
GACGAACTTAAACTTATAAAATTCTAGGGAA
Found at i:26311 original size:3 final size:3
Alignment explanation
Indices: 26297--26329 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
26287 ATCTACAAAC
26297 TCT TCT TCCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TC
26330 CTCCTCCCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:33377 original size:39 final size:39
Alignment explanation
Indices: 33334--33431 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 39
33324 TTTCTTATTG
* * *
33334 GTCTGAAGACGTCGTGCATTCCTGGGATTTTCTCCATTT
1 GTCTGAAGACATCATGCAGTCCTGGGATTTTCTCCATTT
* * *
33373 GTCTGAAGACATCATGCAGTCGTGGGGTTTTCTTCATTT
1 GTCTGAAGACATCATGCAGTCCTGGGATTTTCTCCATTT
*
33412 GT-TGAAGACACCATGCAGTC
1 GTCTGAAGACATCATGCAGTC
33432 GTGAAATCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
38 17 0.33
39 35 0.67
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (39 bp):
GTCTGAAGACATCATGCAGTCCTGGGATTTTCTCCATTT
Found at i:33427 original size:38 final size:39
Alignment explanation
Indices: 33356--33434 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 39
33346 CGTGCATTCC
*
33356 TGGGATTTTCTCCATTTGTCTGAAGACATCATGCAGTCG
1 TGGGATTTTCTCCATTTGTCTGAAGACACCATGCAGTCG
* *
33395 TGGGGTTTTCTTCATTTGT-TGAAGACACCATGCAGTCG
1 TGGGATTTTCTCCATTTGTCTGAAGACACCATGCAGTCG
33433 TG
1 TG
33435 AAATCTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 20 0.54
39 17 0.46
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (39 bp):
TGGGATTTTCTCCATTTGTCTGAAGACACCATGCAGTCG
Found at i:39463 original size:2 final size:2
Alignment explanation
Indices: 39456--39481 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39446 GTACAATTAA
39456 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
39482 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:47263 original size:15 final size:15
Alignment explanation
Indices: 47219--47268 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
47209 TCAAACTACA
*
47219 TTATTTTTTCTTTATT
1 TTATTTTTTATTT-TT
47235 TTATTGCTTATTATTTTT
1 TTATT--TT-TTATTTTT
47253 TTATTTTTTATTTTT
1 TTATTTTTTATTTTT
47268 T
1 T
47269 CTGTAACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.30
16 7 0.23
18 9 0.30
19 5 0.17
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (15 bp):
TTATTTTTTATTTTT
Done.