Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009335.1 Hibiscus syriacus cultivar Beakdansim tig00113102_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: 51253
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1242 original size:18 final size:19
Alignment explanation
Indices: 1209--1248 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1199 GTCAAAGAAA
1209 GTCAACGGTCAACGGTCCG
1 GTCAACGGTCAACGGTCCG
*
1228 GTCAACGGT-AACGGTCGG
1 GTCAACGGTCAACGGTCCG
1246 GTC
1 GTC
1249 GGGTCAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (19 bp):
GTCAACGGTCAACGGTCCG
Found at i:1263 original size:17 final size:17
Alignment explanation
Indices: 1241--1273 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1231 AACGGTAACG
1241 GTCGGGTCGGGTCAACA
1 GTCGGGTCGGGTCAACA
1258 GTCGGGTCGGGTCAAC
1 GTCGGGTCGGGTCAAC
1274 CCGGTTCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.42, T:0.18
Consensus pattern (17 bp):
GTCGGGTCGGGTCAACA
Found at i:1308 original size:18 final size:19
Alignment explanation
Indices: 1267--1318 Score: 88
Period size: 18 Copynumber: 2.8 Consensus size: 19
1257 AGTCGGGTCG
*
1267 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1286 GGTCAAACCGGTTCAGA-C
1 GGTCAAACCGGTTCAGACC
1304 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
1319 AATTGGTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1333 original size:18 final size:18
Alignment explanation
Indices: 1267--1334 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1257 AGTCGGGTCG
* *
1267 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCA-AAC
*
1286 GGTCAAACCGGTTCAGAC
1 GGTCAAACCGGTTCAAAC
*
1304 GGTCAAACCGGTTCAAATT
1 GGTCAAACCGGTTCAAA-C
1323 GGTCAAA-CGGTT
1 GGTCAAACCGGTT
1335 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.51
19 21 0.49
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (18 bp):
GGTCAAACCGGTTCAAAC
Found at i:8500 original size:6 final size:7
Alignment explanation
Indices: 8478--8524 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
8468 GTCAAAGAAA
8478 GTCAACG
1 GTCAACG
8485 GTCAACG
1 GTCAACG
8492 GTC-ACG
1 GTCAACG
8498 GTCAACG
1 GTCAACG
8505 GTC-ACG
1 GTCAACG
8511 G-CAAACG
1 GTC-AACG
8518 GTCAACG
1 GTCAACG
8525 CTCGGGTCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 1 0.03
6 10 0.28
7 24 0.67
8 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:8500 original size:13 final size:13
Alignment explanation
Indices: 8482--8521 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
8472 AAGAAAGTCA
8482 ACGGTCAACGGTC
1 ACGGTCAACGGTC
8495 ACGGTCAACGGTC
1 ACGGTCAACGGTC
8508 ACGG-CAAACGGTC
1 ACGGTC-AACGGTC
8521 A
1 A
8522 ACGCTCGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 1 0.04
13 25 0.96
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:8539 original size:17 final size:16
Alignment explanation
Indices: 8517--8573 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
8507 CACGGCAAAC
8517 GGTCAACGCTCGGGTCG
1 GGTCAACG-TCGGGTCG
8534 GGTCAACGATCGGGTCG
1 GGTCAACG-TCGGGTCG
*
8551 AGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
8568 GGTCAA
1 GGTCAA
8574 ACCGGTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 35 0.97
18 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.18
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:9285 original size:17 final size:17
Alignment explanation
Indices: 9263--9296 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9253 TCAATTTTCA
*
9263 CAATTAACGTCCAATTT
1 CAATTAAAGTCCAATTT
*
9280 CAATTAAATTCCAATTT
1 CAATTAAAGTCCAATTT
9297 TGTAAACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (17 bp):
CAATTAAAGTCCAATTT
Found at i:20409 original size:33 final size:33
Alignment explanation
Indices: 20367--20435 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20357 GTTGATGAAT
*
20367 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
20400 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
20433 GAA
1 GAA
20436 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:20858 original size:19 final size:20
Alignment explanation
Indices: 20811--20861 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
20801 GAAATCCCTT
**
20811 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
20831 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
20850 TGAAGATACATG
1 TGAAAATACATG
20862 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:24449 original size:33 final size:33
Alignment explanation
Indices: 24407--24475 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
24397 GTTGATGAAT
*
24407 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
24440 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
24473 GAA
1 GAA
24476 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:24898 original size:19 final size:20
Alignment explanation
Indices: 24851--24901 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
24841 GAAATCCCTT
**
24851 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
24871 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
24890 TGAAGATACATG
1 TGAAAATACATG
24902 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.