Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001015.1 Hibiscus syriacus cultivar Beakdansim tig00002025_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: 48201
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1367 original size:24 final size:23
Alignment explanation
Indices: 1340--1398 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1330 GGTATGGAAA
1340 TGATCTATGTGTAAGTAAATTATG
1 TGATCTATGTGTAAGT-AATTATG
* *
1364 TGAT-TATGTGATTATGTGATTATG
1 TGATCTATGTG--TAAGTAATTATG
1388 TGA-CTATGTGT
1 TGATCTATGTGT
1399 GAAATAGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
22 1 0.03
23 6 0.20
24 19 0.63
25 4 0.13
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (23 bp):
TGATCTATGTGTAAGTAATTATG
Found at i:1371 original size:8 final size:8
Alignment explanation
Indices: 1358--1397 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
1348 GTGTAAGTAA
1358 ATTATGTG
1 ATTATGTG
1366 ATTATGTG
1 ATTATGTG
1374 ATTATGTG
1 ATTATGTG
1382 ATTATGTG
1 ATTATGTG
*
1390 ACTATGTG
1 ATTATGTG
1398 TGAAATAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (8 bp):
ATTATGTG
Found at i:2090 original size:23 final size:23
Alignment explanation
Indices: 2057--2124 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
2047 AACCTTATTT
2057 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
2080 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
2103 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2125 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:4186 original size:21 final size:20
Alignment explanation
Indices: 4140--4187 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4130 AAATTACTTT
4140 TTTTTAT-TAATTTTAATAA
1 TTTTTATATAATTTTAATAA
*
4159 TTCTTATATATATTTTAA-ATA
1 TTTTTATATA-ATTTTAATA-A
4180 TTTTTATA
1 TTTTTATA
4188 ACTTCTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 15 0.62
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTATATAATTTTAATAA
Found at i:4242 original size:17 final size:19
Alignment explanation
Indices: 4208--4244 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
4198 TTTTAACGAC
*
4208 ATATATTTATACATTTTTA
1 ATATATTTATACAATTTTA
4227 ATAT-TTTAT-CAATTTTA
1 ATATATTTATACAATTTTA
4244 A
1 A
4245 ATGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTTATACAATTTTA
Found at i:5318 original size:18 final size:16
Alignment explanation
Indices: 5286--5316 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5276 AATATTGAAA
5286 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
5302 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
5317 AATTTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:9635 original size:28 final size:28
Alignment explanation
Indices: 9603--9657 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
9593 ATTTATTTAC
*
9603 ATTATGTCGTCGAATCAGTGTTTAAAAT
1 ATTATGTCATCGAATCAGTGTTTAAAAT
* **
9631 ATTATGTTATCGGCTCAGTGTTTAAAA
1 ATTATGTCATCGAATCAGTGTTTAAAA
9658 GTAACGACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (28 bp):
ATTATGTCATCGAATCAGTGTTTAAAAT
Found at i:13898 original size:3 final size:3
Alignment explanation
Indices: 13890--13952 Score: 69
Period size: 3 Copynumber: 21.0 Consensus size: 3
13880 TTGTAGCAGT
*
13890 GAA GAA GAA GAA GAA -AA GAAA GGA GATA G-A GAA TGAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA G-AA GAA GA-A GAA GAA -GAA GAA GAA GAA
13936 GAA GAA -AA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA
13953 AGATTGCCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 6 0.12
3 38 0.73
4 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:19345 original size:6 final size:6
Alignment explanation
Indices: 19334--19358 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19324 AAACAAGGGG
19334 GGCATA GGCATA GGCATA GGCATA G
1 GGCATA GGCATA GGCATA GGCATA G
19359 ACATGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCATA
Found at i:22112 original size:36 final size:36
Alignment explanation
Indices: 22064--22134 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
22054 TAAATCAAGA
*
22064 AATAAGTCTATTCATC-AAGTGAGATAACTTATTATT
1 AATAAGTATATTCA-CAAAGTGAGATAACTTATTATT
* *
22100 AATAAGTATATTCACAAAGTGATATGACTTATTAT
1 AATAAGTATATTCACAAAGTGAGATAACTTATTAT
22135 AAATCACATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (36 bp):
AATAAGTATATTCACAAAGTGAGATAACTTATTATT
Found at i:25065 original size:20 final size:20
Alignment explanation
Indices: 25040--25100 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
25030 TCAAGAGGAA
*
25040 AGGACAAGCTCAAATTGGAC
1 AGGACAAGTTCAAATTGGAC
25060 AGGACAAGTTCAAATTGGAC
1 AGGACAAGTTCAAATTGGAC
25080 AGGACAAGTTCAAATTGGAC
1 AGGACAAGTTCAAATTGGAC
25100 A
1 A
25101 AGTTGCTGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (20 bp):
AGGACAAGTTCAAATTGGAC
Done.