Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005956.1 Hibiscus syriacus cultivar Beakdansim tig00013995_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: 67681
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1649 original size:24 final size:24
Alignment explanation
Indices: 1622--1693 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
1612 AGTCTTCCTG
*
1622 ATGATATATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1646 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
1670 ATGACGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1694 TATGTCATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:2942 original size:29 final size:30
Alignment explanation
Indices: 2897--2954 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2887 TTTAGTCCCT
*
2897 AAACTTTTCAAAGTTTAT-ACTTGGTCACC
1 AAACTTTCCAAAGTTTATAACTTGGTCACC
*
2926 AAACTTTACCAAA-TTTATAATTTGGTCAC
1 AAACTTT-CCAAAGTTTATAACTTGGTCAC
2955 TAAATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (30 bp):
AAACTTTCCAAAGTTTATAACTTGGTCACC
Found at i:8894 original size:23 final size:23
Alignment explanation
Indices: 8866--8986 Score: 83
Period size: 23 Copynumber: 5.1 Consensus size: 23
8856 ACAATCTGTC
*
8866 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
8889 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
8912 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
8937 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
8961 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCACCATAT
8985 CA
1 CA
8987 CGCCTATATT
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
22 9 0.11
23 29 0.37
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:8903 original size:36 final size:36
Alignment explanation
Indices: 8863--9003 Score: 257
Period size: 36 Copynumber: 3.9 Consensus size: 36
8853 GATACAATCT
8863 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
8899 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
8935 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
8971 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
9004 ACTTATAAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
35 21 0.20
36 82 0.80
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:8907 original size:13 final size:11
Alignment explanation
Indices: 8866--8986 Score: 86
Period size: 11 Copynumber: 10.2 Consensus size: 11
8856 ACAATCTGTC
8866 CATCACCATTAT
1 CATCACCA-TAT
*
8878 CA-CGCCTATAT
1 CATCACC-ATAT
8889 CATCACCATAGT
1 CATCACCATA-T
8901 CCATCACCATTAT
1 -CATCACCA-TAT
*
8914 CA-CGCCTATAT
1 CATCACC-ATAT
8925 CATCACCATAGT
1 CATCACCATA-T
8937 CCATCACCATTAT
1 -CATCACCA-TAT
*
8950 CA-CGCCTATAT
1 CATCACC-ATAT
8961 CATCACCATATT
1 CATCACCATA-T
8973 CCATCACCATAT
1 -CATCACCATAT
8985 CA
1 CA
8987 CGCCTATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 35 0.39
12 22 0.25
13 28 0.31
14 4 0.04
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:12965 original size:36 final size:36
Alignment explanation
Indices: 12918--13023 Score: 189
Period size: 34 Copynumber: 3.0 Consensus size: 36
12908 GATACAATCT
*
12918 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
12954 GTCCATCACCATTATCACGCCTATATCAT--CCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
12988 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13024 TCACGCCTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
34 34 0.51
36 33 0.49
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:21470 original size:22 final size:22
Alignment explanation
Indices: 21416--21470 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
21406 AAAAATACTG
* *
21416 TGAACTGTAAGGCATAGTACCA
1 TGAACAGTAATGCATAGTACCA
21438 TGAACAGTAATGCATAGTACCA
1 TGAACAGTAATGCATAGTACCA
21460 TGAACAGTAAT
1 TGAACAGTAAT
21471 TAACATTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (22 bp):
TGAACAGTAATGCATAGTACCA
Found at i:21480 original size:22 final size:22
Alignment explanation
Indices: 21431--21485 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
21421 TGTAAGGCAT
* *
21431 AGTACCATGAACAGTAATGCAT
1 AGTACCATGAACAGTAATGAAC
*
21453 AGTACCATGAACAGTAATTAAC
1 AGTACCATGAACAGTAATGAAC
* *
21475 ATTACCGTGAA
1 AGTACCATGAA
21486 TAGTGAACAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (22 bp):
AGTACCATGAACAGTAATGAAC
Found at i:33499 original size:31 final size:30
Alignment explanation
Indices: 33453--33519 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 30
33443 GTGCATAATT
33453 AAGAGTACGCTAGCATAGTAGATAACATGA
1 AAGAGTACGCTAGCATAGTAGATAACATGA
*
33483 AAGAGTATGACTAGCATAGTAGATAACATGA
1 AAGAGTACG-CTAGCATAGTAGATAACATGA
33514 AAGAGT
1 AAGAGT
33520 TTGCTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (30 bp):
AAGAGTACGCTAGCATAGTAGATAACATGA
Found at i:39666 original size:19 final size:20
Alignment explanation
Indices: 39627--39677 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
39617 GAAATCCATT
*
39627 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
39647 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
39666 TGAAAATACATG
1 TGAAAATACATG
39678 CTCTGGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:44587 original size:18 final size:20
Alignment explanation
Indices: 44564--44600 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
44554 TTGGAGTGCA
44564 AAAAAGAA-AAGAA-AAGAC
1 AAAAAGAAGAAGAATAAGAC
44582 AAAAAGAAGAAGAATAAGA
1 AAAAAGAAGAAGAATAAGA
44601 AATTCAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAAAGAAGAAGAATAAGAC
Found at i:46865 original size:21 final size:22
Alignment explanation
Indices: 46826--46866 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
46816 GACTATTAAG
* *
46826 CAAAGGATGGTAATTCTTCATC
1 CAAAGGATCGTAATCCTTCATC
46848 CAAAGGA-CGTAATCCTTCA
1 CAAAGGATCGTAATCCTTCA
46867 AGAATCAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (22 bp):
CAAAGGATCGTAATCCTTCATC
Found at i:48723 original size:26 final size:23
Alignment explanation
Indices: 48687--48738 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 23
48677 TATCCCTTAT
*
48687 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTT-A-TTCTT-CCTTTA
*
48713 TTATTTTATTTATTCTTCCTTTA
1 TTATTTCATTTATTCTTCCTTTA
48736 TTA
1 TTA
48739 ATCATTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 5 0.21
25 1 0.04
26 10 0.42
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTTCATTTATTCTTCCTTTA
Found at i:65803 original size:24 final size:24
Alignment explanation
Indices: 65776--65826 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
65766 TGTGGATCAC
* *
65776 CAAAAGTCACGTTTATTGATTCTT
1 CAAAAGACACGTTTATTGAATCTT
* *
65800 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACACGTTTATTGAATCTT
65824 CAA
1 CAA
65827 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACACGTTTATTGAATCTT
Done.