Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004429.1 Hibiscus syriacus cultivar Beakdansim tig00009710_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: 132253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:125460 original size:20 final size:21
Alignment explanation
Indices: 125415--125460 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
125405 CCAGTAAAAA
*
125415 ATTTTACCTAAAAACATTATT
1 ATTTTACCTAAAAACATTAAT
*
125436 ATTTTACCT-TAAACATTAAT
1 ATTTTACCTAAAAACATTAAT
*
125456 GTTTT
1 ATTTT
125461 TAACATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTACCTAAAAACATTAAT
Found at i:125462 original size:21 final size:21
Alignment explanation
Indices: 125415--125453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
125405 CCAGTAAAAA
125415 ATTTTACCTAAAAACATTATT
1 ATTTTACCTAAAAACATTATT
*
125436 ATTTTACCT-TAAACATTA
1 ATTTTACCTAAAAACATTA
125454 ATGTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTTACCTAAAAACATTATT
Found at i:127928 original size:13 final size:13
Alignment explanation
Indices: 127912--127941 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
127902 CTTAATTGCG
127912 AAAATTAAAAATT
1 AAAATTAAAAATT
*
127925 AAAATTAAAATTT
1 AAAATTAAAAATT
127938 AAAA
1 AAAA
127942 GTATTCGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:128579 original size:14 final size:13
Alignment explanation
Indices: 128551--128585 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
128541 GGGCCTATAC
128551 AAAT-AATAAAAT
1 AAATAAATAAAAT
128563 AAATAAATAATAAT
1 AAATAAATAA-AAT
128577 AAATAAATA
1 AAATAAATA
128586 TTTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 5 0.24
14 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:129194 original size:36 final size:36
Alignment explanation
Indices: 129147--129228 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
129137 CATTCAATAT
* *
129147 TTTGTTTCAAGGGAAACTGTCTCAAGATAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCCCAAGAGAGATAAAA
*
129183 TTTGTTTCAAGGGAAACTGTCCCAAGAGAGATAAGA
1 TTTGTTTCAAGGGAAACTGTCCCAAGAGAGATAAAA
129219 -TTGTTTCAAG
1 TTTGTTTCAAG
129229 AGAGATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
35 10 0.23
36 33 0.77
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCCCAAGAGAGATAAAA
Found at i:131099 original size:18 final size:18
Alignment explanation
Indices: 131047--131105 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
131037 GCGTCTTGTC
* *
131047 TTCT-TTTTCTTTATTTT
1 TTCTCTTTTGTTTTTTTT
*
131064 TTC-C-TTTG-TTTTTGT
1 TTCTCTTTTGTTTTTTTT
131079 TTCTCTTTTGTTTTTTTT
1 TTCTCTTTTGTTTTTTTT
131097 TTCTCTTTT
1 TTCTCTTTT
131106 TTCCTTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 7 0.21
18 15 0.44
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (18 bp):
TTCTCTTTTGTTTTTTTT
Found at i:131113 original size:18 final size:18
Alignment explanation
Indices: 131053--131118 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
131043 TGTCTTCTTT
* *
131053 TTCTTTATTTTTTCCTTTG
1 TTCTTT-TTTTCTCTTTTG
*
131072 TT-TTTGTTTCTCTTTTG
1 TTCTTTTTTTCTCTTTTG
*
131089 TTTTTTTTTTCTCTTTT-
1 TTCTTTTTTTCTCTTTTG
*
131106 TTCCTTTTGTTCT
1 TT-CTTTTTTTCT
131119 GATTGAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 13 0.33
18 24 0.62
19 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (18 bp):
TTCTTTTTTTCTCTTTTG
Done.