Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008998.1 Hibiscus syriacus cultivar Beakdansim tig00112374_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: 69212
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:9487 original size:20 final size:19
Alignment explanation
Indices: 9458--9499 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9448 AAACTCCTTC
*
9458 GAAAACACATGATTTTTAAT
1 GAAAACACAT-AATTTTAAT
*
9478 GAAAATACATAATTTTAAT
1 GAAAACACATAATTTTAAT
9497 GAA
1 GAA
9500 GATAAATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (19 bp):
GAAAACACATAATTTTAAT
Found at i:13670 original size:11 final size:12
Alignment explanation
Indices: 13654--13682 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13644 CATACTAAAC
13654 ACCTTTC-ACAT
1 ACCTTTCAACAT
13665 ACCTTTCAACAT
1 ACCTTTCAACAT
13677 ACCTTT
1 ACCTTT
13683 TCATCTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (12 bp):
ACCTTTCAACAT
Found at i:16827 original size:36 final size:35
Alignment explanation
Indices: 16782--16900 Score: 148
Period size: 35 Copynumber: 3.4 Consensus size: 35
16772 ATCACCATTT
*
16782 TTTCACGCCTACAACATCACCATCTTCCATCACCA
1 TTTCACGCCTATAACATCACCATCTTCCATCACCA
* *
16817 TATTCACGCCTATAACATCACCATATTCCATCATCA
1 T-TTCACGCCTATAACATCACCATCTTCCATCACCA
* * * *
16853 TTGCACGCCTATATCATCACCAACTTCTATCACCA
1 TTTCACGCCTATAACATCACCATCTTCCATCACCA
* *
16888 TTTTATGCCTATA
1 TTTCACGCCTATA
16901 TAACCAACAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 39 0.55
36 32 0.45
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.31
Consensus pattern (35 bp):
TTTCACGCCTATAACATCACCATCTTCCATCACCA
Found at i:21352 original size:38 final size:38
Alignment explanation
Indices: 21301--21440 Score: 182
Period size: 36 Copynumber: 3.8 Consensus size: 38
21291 TAAGATACTA
**
21301 CCTATAACATCACCATCTTCCATCACCATTTTTTCATT
1 CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
21339 CCTATAACATCACCATCTTCCATCACCA--TTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
* *
21375 CCTATAACATCACCATATTCCATCACCA---TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
* * *
21410 CCTATATCATCACCAACTTCTATCACCATTT
1 CCTATAACATCACCATCTTCCATCACCATTT
21441 AACGCCTATA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
35 30 0.33
36 33 0.36
38 28 0.31
ACGTcount: A:0.29, C:0.36, G:0.02, T:0.33
Consensus pattern (38 bp):
CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
Found at i:21400 original size:13 final size:13
Alignment explanation
Indices: 21346--21403 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
21336 ATTCCTATAA
*
21346 CATCACCATCTTC
1 CATCACCATATTC
*
21359 CATCACCAT-TTT
1 CATCACCATATTC
* **
21371 CA-CGCC-TATAA
1 CATCACCATATTC
21382 CATCACCATATTC
1 CATCACCATATTC
21395 CATCACCAT
1 CATCACCAT
21404 TGCACGCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.17
12 7 0.20
13 21 0.60
ACGTcount: A:0.29, C:0.40, G:0.02, T:0.29
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:21421 original size:35 final size:36
Alignment explanation
Indices: 21301--21450 Score: 180
Period size: 35 Copynumber: 4.2 Consensus size: 36
21291 TAAGATACTA
* **
21301 CCTATAACATCACCATCTTCCATCACCATTTTTTCATT
1 CCTATAACATCACCATATTCCATCACCA--TTTTCACG
*
21339 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATATTCCATCACCATTTTCACG
*
21375 CCTATAACATCACCATATTCCATCACCA-TTGCACG
1 CCTATAACATCACCATATTCCATCACCATTTTCACG
* * *
21410 CCTATATCATCACCA-ACTTCTATCACCA-TTTAACG
1 CCTATAACATCACCATA-TTCCATCACCATTTTCACG
21445 CCTATA
1 CCTATA
21451 TAACCAGTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
34 1 0.01
35 41 0.40
36 33 0.32
38 28 0.27
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.32
Consensus pattern (36 bp):
CCTATAACATCACCATATTCCATCACCATTTTCACG
Found at i:25506 original size:11 final size:13
Alignment explanation
Indices: 25474--25503 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25464 TGGCCAAAGA
25474 TGAAAAGGTATGT
1 TGAAAAGGTATGT
25487 TGAAAAGGTATG-
1 TGAAAAGGTATGT
25499 TGAAA
1 TGAAA
25504 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:31015 original size:22 final size:25
Alignment explanation
Indices: 30966--31019 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
30956 CTTTTCTTTT
*
30966 TTTCTTCCTCTTTGGGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
30991 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
31014 TTTCTT
1 TTTCTT
31020 TGCTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 18 0.69
24 2 0.08
25 6 0.23
ACGTcount: A:0.07, C:0.19, G:0.15, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:33779 original size:19 final size:19
Alignment explanation
Indices: 33741--33780 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33731 GTGCTTTAAC
*
33741 TTTCTTTATTTTCTTTTCT
1 TTTCTTTATTTTCTTCTCT
33760 TTTCTTT-TTTTCTTCCTCT
1 TTTCTTTATTTTCTT-CTCT
33779 TT
1 TT
33781 GGGTGCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTATTTTCTTCTCT
Found at i:33817 original size:22 final size:25
Alignment explanation
Indices: 33768--33821 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
33758 CTTTTCTTTT
*
33768 TTTCTTCCTCTTTGGGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
33793 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
33816 TTTCTT
1 TTTCTT
33822 TGCTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 18 0.69
24 2 0.08
25 6 0.23
ACGTcount: A:0.07, C:0.19, G:0.15, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:37271 original size:11 final size:13
Alignment explanation
Indices: 37239--37268 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
37229 TGGCCAAAGA
37239 TGAAAAGGTATGT
1 TGAAAAGGTATGT
37252 TGAAAAGGTATG-
1 TGAAAAGGTATGT
37264 TGAAA
1 TGAAA
37269 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:40028 original size:18 final size:19
Alignment explanation
Indices: 39990--40028 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
39980 AAGGAAAAAG
*
39990 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
40009 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
40027 AA
1 AA
40029 AAAAGCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:42820 original size:11 final size:13
Alignment explanation
Indices: 42788--42817 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42778 TGGCCAAAGA
42788 TGAAAAGGTATGT
1 TGAAAAGGTATGT
42801 TGAAAAGGTATG-
1 TGAAAAGGTATGT
42813 TGAAA
1 TGAAA
42818 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:46786 original size:5 final size:5
Alignment explanation
Indices: 46772--46805 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
46762 GTGCTTTAAC
46772 TTTC- TTTCT TTTCT TTTCT TTTCT TTT-T TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
46806 CCTCTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:46811 original size:15 final size:15
Alignment explanation
Indices: 46772--46812 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
46762 GTGCTTTAAC
46772 TTTCTT-TCTTTTCT
1 TTTCTTCTCTTTTCT
*
46786 TTTCTTTTCTTTT-T
1 TTTCTTCTCTTTTCT
46800 TTTCTTCCTCTTT
1 TTTCTT-CTCTTT
46813 GGGTGCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTCTCTTTTCT
Found at i:46849 original size:22 final size:25
Alignment explanation
Indices: 46800--46853 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
46790 TTTTCTTTTT
*
46800 TTTCTTCCTCTTTGGGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
46825 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
46848 TTTCTT
1 TTTCTT
46854 TGCTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 18 0.69
24 2 0.08
25 6 0.23
ACGTcount: A:0.07, C:0.19, G:0.15, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:60766 original size:19 final size:21
Alignment explanation
Indices: 60738--60779 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
60728 TGTAGGAGTC
60738 TTTTTCTTTTCTT-TTT-TTG
1 TTTTTCTTTTCTTCTTTCTTG
*
60757 TTTTTTTTTTCTTCTTTCTTG
1 TTTTTCTTTTCTTCTTTCTTG
60778 TT
1 TT
60780 ACTTTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 3 0.15
21 5 0.25
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (21 bp):
TTTTTCTTTTCTTCTTTCTTG
Found at i:61221 original size:14 final size:14
Alignment explanation
Indices: 61193--61229 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
61183 TGGCGTGAAA
*
61193 GTGATGG-ATGATG
1 GTGATGGAAAGATG
61206 GTGATGGAAAGATG
1 GTGATGGAAAGATG
61220 GTGATGGAAA
1 GTGATGGAAA
61230 TAGTATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.43, T:0.24
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:61596 original size:20 final size:19
Alignment explanation
Indices: 61568--61608 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
61558 AACCCTTTGA
*
61568 AAAACACATGATTTTTAATG
1 AAAACACAT-AATTTTAATG
*
61588 AAAATACATAATTTTAATG
1 AAAACACATAATTTTAATG
61607 AA
1 AA
61609 GATAAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAACACATAATTTTAATG
Found at i:62959 original size:21 final size:21
Alignment explanation
Indices: 62913--62952 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
62903 CTATTTTTTT
62913 AAAAAAAAAGGCAAAAAAACA
1 AAAAAAAAAGGCAAAAAAACA
*
62934 AAAAAAAAAGTCAAAAAAA
1 AAAAAAAAAGGCAAAAAAA
62953 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAGGCAAAAAAACA
Done.