Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005672.1 Hibiscus syriacus cultivar Beakdansim tig00013261_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: 82289
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:773 original size:24 final size:24
Alignment explanation
Indices: 740--798 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
730 AAGAAAAATT
* *
740 AGAAAAAAAAGTGAAGCACTCAAA
1 AGAAAGAAAAGTCAAGCACTCAAA
* *
764 AGAAAGAAAACTCCAGCACTCAAA
1 AGAAAGAAAAGTCAAGCACTCAAA
788 A-AGAAGAAAAG
1 AGA-AAGAAAAG
799 CAAATAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (24 bp):
AGAAAGAAAAGTCAAGCACTCAAA
Found at i:11750 original size:19 final size:20
Alignment explanation
Indices: 11703--11753 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11693 GAAACCCCTT
**
11703 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
11723 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11742 TGAAGATACATG
1 TGAAAATACATG
11754 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:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:14909 original size:13 final size:13
Alignment explanation
Indices: 14888--14929 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
14878 TGTAGGAGTC
14888 TTTTCTTTTGCTT
1 TTTTCTTTTGCTT
* *
14901 TTTTGTTTTTCTT
1 TTTTCTTTTGCTT
*
14914 ATTTCTTTTGCTT
1 TTTTCTTTTGCTT
14927 TTT
1 TTT
14930 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTGCTT
Found at i:15259 original size:20 final size:21
Alignment explanation
Indices: 15222--15260 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15212 GATGGTCTTG
*
15222 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
15243 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
15261 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:15640 original size:19 final size:20
Alignment explanation
Indices: 15599--15649 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
15589 GAAACCCCTT
*
15599 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
15619 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
15638 TGAAGATACATG
1 TGAAAATACATG
15650 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:17607 original size:19 final size:20
Alignment explanation
Indices: 17560--17609 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
17550 GAAACCCTTT
**
17560 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
17580 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
17599 TGAAGATACAT
1 TGAAAATACAT
17610 ACTCTTGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:20643 original size:19 final size:20
Alignment explanation
Indices: 20615--20654 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
20605 GAATAATAAT
20615 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
20635 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
20654 A
1 A
20655 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:27423 original size:11 final size:11
Alignment explanation
Indices: 27402--27438 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
27392 GTTGTTGCAT
27402 GCTCC-ATTTA
1 GCTCCAATTTA
27412 GCTCCAATTTA
1 GCTCCAATTTA
*
27423 GCTCCAATGTA
1 GCTCCAATTTA
27434 GCTCC
1 GCTCC
27439 CAAGTGTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (11 bp):
GCTCCAATTTA
Found at i:30539 original size:35 final size:40
Alignment explanation
Indices: 30494--30572 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 40
30484 CTTTCCTTGG
*
30494 CTTTCTTTCTTTT-TGAATTTT-T-TTCTTTT-TC-TTTT
1 CTTTCCTTCTTTTCTGAATTTTCTCTTCTTTTATCTTTTT
*
30529 CTTTCCTTCTTTTCTGATTTTTCTCTTCTTTTATCTTTTT
1 CTTTCCTTCTTTTCTGAATTTTCTCTTCTTTTATCTTTTT
30569 CTTT
1 CTTT
30573 ATTTTTGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 12 0.32
36 7 0.19
37 1 0.03
38 7 0.19
39 2 0.05
40 8 0.22
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.73
Consensus pattern (40 bp):
CTTTCCTTCTTTTCTGAATTTTCTCTTCTTTTATCTTTTT
Found at i:30540 original size:19 final size:20
Alignment explanation
Indices: 30516--30572 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
30506 TTGAATTTTT
30516 TTCTTTTTCTTTTCTTTC-C
1 TTCTTTTTCTTTTCTTTCTC
*
30535 TTC-TTTTCTGATT-TTTCTC
1 TTCTTTTTCT-TTTCTTTCTC
30554 TTCTTTTATCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
30573 ATTTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 10 0.33
19 9 0.30
20 3 0.10
21 4 0.13
22 4 0.13
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTTTCTTTTCTTTCTC
Found at i:30879 original size:19 final size:20
Alignment explanation
Indices: 30843--30882 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
30833 GAATAATAAT
30843 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
30863 ATAAG-AATTAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
30882 A
1 A
30883 AGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:38367 original size:23 final size:23
Alignment explanation
Indices: 38337--38382 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
38327 TTTCTTTTCT
38337 TTGCTTTTTC-TTCTTTTGAGTG
1 TTGCTTTTTCTTTCTTTTGAGTG
38359 TTGCATTTTTCTTTCTTTTGAGTG
1 TTGC-TTTTTCTTTCTTTTGAGTG
38383 CTTCACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.18
23 6 0.27
24 12 0.55
ACGTcount: A:0.07, C:0.13, G:0.17, T:0.63
Consensus pattern (23 bp):
TTGCTTTTTCTTTCTTTTGAGTG
Found at i:38392 original size:23 final size:24
Alignment explanation
Indices: 38343--38395 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
38333 TTCTTTGCTT
*
38343 TTTC-TTCTTTTGAGTGTTGCATT
1 TTTCTTTCTTTTGAGTGTTGCATC
38366 TTTCTTTCTTTTGAGTGCTT-CA-C
1 TTTCTTTCTTTTGAGTG-TTGCATC
38389 TTTCTTT
1 TTTCTTT
38396 TTTGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 11 0.41
24 14 0.52
25 2 0.07
ACGTcount: A:0.08, C:0.17, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGTTGCATC
Found at i:42837 original size:19 final size:19
Alignment explanation
Indices: 42809--42867 Score: 109
Period size: 19 Copynumber: 3.1 Consensus size: 19
42799 GGATAATAAT
42809 ATAAGTAATGAAAAGAAATA
1 ATAAG-AATGAAAAGAAATA
42829 ATAAGAATGAAAAGAAATA
1 ATAAGAATGAAAAGAAATA
42848 ATAAGAATGAAAAGAAATA
1 ATAAGAATGAAAAGAAATA
42867 A
1 A
42868 GGATGGGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
19 34 0.87
20 5 0.13
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (19 bp):
ATAAGAATGAAAAGAAATA
Found at i:43320 original size:19 final size:20
Alignment explanation
Indices: 43282--43324 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
43272 GAAACCCCTT
*
43282 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
43302 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
43321 TGAA
1 TGAA
43325 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:46571 original size:14 final size:13
Alignment explanation
Indices: 46541--46589 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
46531 TTGAACTTCT
46541 TTTTCTTTTAT-TC
1 TTTTCTTTT-TGTC
46554 TTTTCTTAATTTGT-
1 TTTTCTT--TTTGTC
46568 TTTTCTTTTTGTC
1 TTTTCTTTTTGTC
46581 TTTTCTTTT
1 TTTTCTTTT
46590 CGCACTCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.16
13 16 0.50
14 8 0.25
15 3 0.09
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTGTC
Found at i:46885 original size:19 final size:20
Alignment explanation
Indices: 46857--46896 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
46847 GGATAATAAT
46857 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
46877 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
46896 A
1 A
46897 GGGATAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:47345 original size:19 final size:20
Alignment explanation
Indices: 47307--47349 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
47297 GAAACCCCTT
*
47307 TGAAAAGACATGATTTTTAA
1 TGAAAAGACATGAATTTTAA
*
47327 TGAAAATACAT-AATTTTAA
1 TGAAAAGACATGAATTTTAA
47346 TGAA
1 TGAA
47350 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAAGACATGAATTTTAA
Found at i:59008 original size:18 final size:18
Alignment explanation
Indices: 58973--59006 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58963 CTATCCCTTT
*
58973 CTTTTTTCTTATCATTTC
1 CTTTCTTCTTATCATTTC
58991 CTTTCTTCTT-TCATTT
1 CTTTCTTCTTATCATTT
59007 TCTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTCTTCTTATCATTTC
Found at i:65535 original size:24 final size:25
Alignment explanation
Indices: 65489--65536 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
65479 CAACATGATC
* * *
65489 TGCATTTTCTTCAGTTTCTTCGTCT
1 TGCATTGTCTTCAGGTTCCTCGTCT
65514 TGCATTGT-TTCAGGTTCCTCGTC
1 TGCATTGTCTTCAGGTTCCTCGTC
65537 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.08, C:0.25, G:0.17, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCGTCT
Found at i:68707 original size:12 final size:12
Alignment explanation
Indices: 68690--68732 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
68680 TTTTTTTCAA
68690 AAAAAAAAAAGC
1 AAAAAAAAAAGC
*
68702 AAAAAAAAAGGC
1 AAAAAAAAAAGC
*
68714 ACAAAAAAAAGC
1 AAAAAAAAAAGC
68726 AAAAAAA
1 AAAAAAA
68733 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:68961 original size:15 final size:15
Alignment explanation
Indices: 68941--68972 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
68931 AATTTTGTAG
*
68941 TGAAACTTTATATAT
1 TGAAACTTCATATAT
68956 TGAAACTTCATATAT
1 TGAAACTTCATATAT
68971 TG
1 TG
68973 GAGATCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (15 bp):
TGAAACTTCATATAT
Done.