Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009103.1 Hibiscus syriacus cultivar Beakdansim tig00112568_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: 40790
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:4650 original size:29 final size:29
Alignment explanation
Indices: 4583--4651 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
4573 CCTTGGCTTG
*
4583 CTTTCTCTTTTTCTTTTCTTTTATTCTTTT
1 CTTTCT-TTTTTCTCTTCTTTTATTCTTTT
* *
4613 CTGAT-TTTTTTCTCTTCTTTT-GTCTTTTT
1 CT-TTCTTTTTTCTCTTCTTTTATTC-TTTT
4642 CTTTCTTTTT
1 CTTTCTTTTT
4652 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
28 3 0.09
29 25 0.78
30 3 0.09
31 1 0.03
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (29 bp):
CTTTCTTTTTTCTCTTCTTTTATTCTTTT
Found at i:12530 original size:22 final size:20
Alignment explanation
Indices: 12505--12544 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12495 ATGTTTGTTT
12505 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
12527 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
12545 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:16806 original size:22 final size:20
Alignment explanation
Indices: 16781--16820 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16771 ATGTTTGTTT
16781 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
16803 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
16821 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:17055 original size:15 final size:15
Alignment explanation
Indices: 17032--17067 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17022 ACTAATATTC
* *
17032 TTATCATAATATATA
1 TTATAATAACATATA
17047 TTATAATAACATATA
1 TTATAATAACATATA
17062 TTATAA
1 TTATAA
17068 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:21079 original size:22 final size:20
Alignment explanation
Indices: 21054--21093 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21044 ATGTTTGTTT
21054 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
21076 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
21094 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:21328 original size:15 final size:15
Alignment explanation
Indices: 21305--21340 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21295 ACTAATATTC
* *
21305 TTATCATAATATATA
1 TTATAATAACATATA
21320 TTATAATAACATATA
1 TTATAATAACATATA
21335 TTATAA
1 TTATAA
21341 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:25351 original size:22 final size:20
Alignment explanation
Indices: 25326--25365 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25316 ATGTTTGTTT
25326 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
25348 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
25366 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:29616 original size:22 final size:20
Alignment explanation
Indices: 29591--29630 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29581 ATGTTTGTTT
29591 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
29613 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
29631 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:33864 original size:22 final size:20
Alignment explanation
Indices: 33839--33878 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33829 ATGTTTGTTT
33839 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
33861 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
33879 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:35306 original size:15 final size:15
Alignment explanation
Indices: 35276--35308 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35266 TGTAGCCATC
35276 TCTATCATTTCTTTA
1 TCTATCATTTCTTTA
35291 TCTATTCATTTC-TTA
1 TCTA-TCATTTCTTTA
35306 TCT
1 TCT
35309 TTATTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (15 bp):
TCTATCATTTCTTTA
Done.