Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005737.1 Hibiscus syriacus cultivar Beakdansim tig00013412_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: 68368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5200 original size:31 final size:31
Alignment explanation
Indices: 5165--5223 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5155 TAAGTTGTTT
*
5165 GGACCAACTT-GTAATTTTGTGAAAGTTAGGG
1 GGACCAACTTGGTAATTTTG-AAAAGTTAGGG
* *
5196 GGACCTATTTGGTAATTTTGAAAAGTTA
1 GGACCAACTTGGTAATTTTGAAAAGTTA
5224 TGAGGTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 15 0.62
32 9 0.38
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (31 bp):
GGACCAACTTGGTAATTTTGAAAAGTTAGGG
Found at i:13076 original size:16 final size:16
Alignment explanation
Indices: 13055--13094 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
13045 TATAAGTTAT
13055 CTTCATTTTCTCTTTA
1 CTTCATTTTCTCTTTA
13071 CTTCATTTTCTCTTTA
1 CTTCATTTTCTCTTTA
13087 CTTCATTT
1 CTTCATTT
13095 CCTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTCATTTTCTCTTTA
Found at i:17982 original size:12 final size:12
Alignment explanation
Indices: 17952--17986 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17942 TATCTTTTAT
17952 TTATCTTGTTT-
1 TTATCTTGTTTC
*
17963 TAATCTTGTTTC
1 TTATCTTGTTTC
17975 TTATCTTGTTTC
1 TTATCTTGTTTC
17987 CAGCACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:23006 original size:15 final size:15
Alignment explanation
Indices: 22986--23029 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
22976 CATCTCTATC
22986 CATTTCATTTCTTAT
1 CATTTCATTTCTTAT
23001 CATTTCATTTCTT-T
1 CATTTCATTTCTTAT
*
23015 TATTTCATTTCTTAT
1 CATTTCATTTCTTAT
23030 TTCCATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (15 bp):
CATTTCATTTCTTAT
Found at i:23058 original size:21 final size:20
Alignment explanation
Indices: 22997--23058 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
22987 ATTTCATTTC
22997 TTATCATTTCATTTCTTTTA-
1 TTATCATTTC-TTTCTTTTAT
**
23017 TT-TCATTTCTTAT-TTCCAT
1 TTATCATTTCTT-TCTTTTAT
23036 TTAATCATTTCTTTCTTTTAT
1 TT-ATCATTTCTTTCTTTTAT
23057 TT
1 TT
23059 GTGCAGATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
18 5 0.15
19 10 0.30
20 3 0.09
21 15 0.45
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATCATTTCTTTCTTTTAT
Found at i:34822 original size:6 final size:6
Alignment explanation
Indices: 34811--34839 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34801 AAGACCCATA
34811 GGTCAT GGTCAT GGTCAT GGTCAT GGTCA
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCA
34840 CGATTATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (6 bp):
GGTCAT
Found at i:35967 original size:16 final size:16
Alignment explanation
Indices: 35946--35976 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35936 ATATATTATA
35946 AGAAGAAGAAAAAAAC
1 AGAAGAAGAAAAAAAC
35962 AGAAGAAGAAAAAAA
1 AGAAGAAGAAAAAAA
35977 ATAGAAAAAA
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:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAGAAGAAAAAAAC
Found at i:45288 original size:15 final size:15
Alignment explanation
Indices: 45268--45298 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45258 GATAACATTC
*
45268 CTTTCCATTTCTATT
1 CTTTCCAATTCTATT
45283 CTTTCCAATTCTATT
1 CTTTCCAATTCTATT
45298 C
1 C
45299 ACTTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTCCAATTCTATT
Found at i:45513 original size:17 final size:17
Alignment explanation
Indices: 45493--45525 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45483 CAAAAAGAGA
45493 AAAAGA-AAGAAGAAAAT
1 AAAAGAGAA-AAGAAAAT
45510 AAAAGAGAAAAGAAAA
1 AAAAGAGAAAAGAAAA
45526 AGACTCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAAT
Found at i:45526 original size:13 final size:12
Alignment explanation
Indices: 45484--45528 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
45474 CAAAAGCAAC
45484 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
45496 AGAAAGAAGAAAA
1 AAAAAG-AGAAAA
*
45509 TAAAAGAGAAAA
1 AAAAAGAGAAAA
45521 GAAAAAGA
1 -AAAAAGA
45529 CTCCTACATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:50862 original size:19 final size:20
Alignment explanation
Indices: 50838--50890 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
50828 TTCGGCCAAG
* *
50838 ATCATGTGTCTTCAT-TAAA
1 ATCATGTATCTTCATCAAAA
*
50857 ATCATGTATTTTCATCAAAA
1 ATCATGTATCTTCATCAAAA
*
50877 ATCATGTATTTTCA
1 ATCATGTATCTTCA
50891 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (20 bp):
ATCATGTATCTTCATCAAAA
Found at i:51344 original size:19 final size:19
Alignment explanation
Indices: 51302--51341 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51292 TATCCTTTCT
**
51302 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATAATTA
51321 TTATTTCATTTCAATAATTA
1 TTATTTCATTTC-ATAATTA
51341 T
1 T
51342 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTTCATTTCATAATTA
Found at i:60623 original size:32 final size:32
Alignment explanation
Indices: 60578--60639 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
60568 TTTTCTTTTC
60578 TTTTTTTTAATTTTCAGAATT-TTGTTTTTGT
1 TTTTTTTTAATTTTCAGAATTCTTGTTTTTGT
* *
60609 TTTTGTTTTAATTTTCGGAATTCTTTTTTTT
1 TTTT-TTTTAATTTTCAGAATTCTTGTTTTT
60640 CAAGATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 16 0.59
33 7 0.26
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (32 bp):
TTTTTTTTAATTTTCAGAATTCTTGTTTTTGT
Found at i:65006 original size:31 final size:31
Alignment explanation
Indices: 64948--65007 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
64938 TTTTCTTTTC
**
64948 TTTTTTTAATTTTCAGAATTTTGTTTTTGTT
1 TTTTTTTAATTTTCAGAATCGTGTTTTTGTT
* *
64979 TTTTTTTAATTTTCGGAAATCGTTTTTTT
1 TTTTTTTAATTTTCAG-AATCGTGTTTTT
65008 TCAAGTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 15 0.62
32 9 0.38
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (31 bp):
TTTTTTTAATTTTCAGAATCGTGTTTTTGTT
Done.