Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005186.1 Hibiscus syriacus cultivar Beakdansim tig00011711_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: 43577
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:14349 original size:17 final size:17
Alignment explanation
Indices: 14327--14360 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
14317 TGTACCAATG
14327 CCCATCACATGTTAGGT
1 CCCATCACATGTTAGGT
14344 CCCATCACATGTTAGGT
1 CCCATCACATGTTAGGT
14361 GGATATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (17 bp):
CCCATCACATGTTAGGT
Found at i:15464 original size:31 final size:31
Alignment explanation
Indices: 15394--15464 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
15384 TTAACGAAAC
*
15394 TAATA-TAGAGACTTAAATTAAACAAATCAA
1 TAATATTAGAGACTTAAATCAAACAAATCAA
** *
15424 TAACGTTAGAGACTTAAATCGAACAAAAT-AA
1 TAATATTAGAGACTTAAATCAAAC-AAATCAA
15455 TAATATTAGA
1 TAATATTAGA
15465 TATCATTTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (31 bp):
TAATATTAGAGACTTAAATCAAACAAATCAA
Found at i:22384 original size:7 final size:7
Alignment explanation
Indices: 22372--22423 Score: 97
Period size: 7 Copynumber: 7.6 Consensus size: 7
22362 TTGGTGAAAT
22372 TGAGGCA
1 TGAGGCA
22379 TGAGGCA
1 TGAGGCA
22386 TGAGGCA
1 TGAGGCA
22393 TGAGGCA
1 TGAGGCA
22400 TGAGGCA
1 TGAGGCA
22407 TGAGGCA
1 TGAGGCA
22414 TGAGGC-
1 TGAGGCA
22420 TGAG
1 TGAG
22424 TCTTTGTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 4 0.09
7 41 0.91
ACGTcount: A:0.27, C:0.13, G:0.44, T:0.15
Consensus pattern (7 bp):
TGAGGCA
Found at i:29475 original size:18 final size:18
Alignment explanation
Indices: 29452--29487 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29442 TATTTTATTG
29452 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
29470 AATAAATATATTATTTTT
1 AATAAAAATAATATTTTT
29488 GGCCGGATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:34310 original size:17 final size:17
Alignment explanation
Indices: 34288--34321 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34278 TGTACCAATG
34288 CCCATCACATGTTAGGT
1 CCCATCACATGTTAGGT
34305 CCCATCACATGTTAGGT
1 CCCATCACATGTTAGGT
34322 GGATATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (17 bp):
CCCATCACATGTTAGGT
Found at i:35427 original size:31 final size:31
Alignment explanation
Indices: 35357--35427 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
35347 TTAACGAAAC
*
35357 TAATA-TAGAGACTTAAATTAAACAAATCAA
1 TAATATTAGAGACTTAAATCAAACAAATCAA
** *
35387 TAACGTTAGAGACTTAAATCGAACAAAAT-AA
1 TAATATTAGAGACTTAAATCAAAC-AAATCAA
35418 TAATATTAGA
1 TAATATTAGA
35428 TATCATTTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (31 bp):
TAATATTAGAGACTTAAATCAAACAAATCAA
Found at i:42342 original size:7 final size:7
Alignment explanation
Indices: 42330--42383 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
42320 TTGGTGAAAT
42330 TGAGGCA
1 TGAGGCA
42337 TGAGGCA
1 TGAGGCA
42344 TGAGGCA
1 TGAGGCA
42351 TGAGGCA
1 TGAGGCA
42358 TGAGGCA
1 TGAGGCA
42365 TGAGGCA
1 TGAGGCA
42372 TGAGGCA
1 TGAGGCA
42379 TGAGG
1 TGAGG
42384 AGAGTCTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.28, C:0.13, G:0.44, T:0.15
Consensus pattern (7 bp):
TGAGGCA
Done.