Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006337.1 Hibiscus syriacus cultivar Beakdansim tig00015148_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: 58150
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2377 original size:21 final size:21
Alignment explanation
Indices: 2351--2390 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2341 ATAAACTACA
**
2351 ATTTTTTAATTAAATTATTAC
1 ATTTTTTAAAAAAATTATTAC
2372 ATTTTTTAAAAAAATTATT
1 ATTTTTTAAAAAAATTATT
2391 GTTTGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTTAAAAAAATTATTAC
Found at i:11685 original size:11 final size:11
Alignment explanation
Indices: 11671--11695 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11661 TGAGTAATAT
11671 TTTATTTATTA
1 TTTATTTATTA
11682 TTTATTTATTA
1 TTTATTTATTA
11693 TTT
1 TTT
11696 TACTTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:30156 original size:15 final size:15
Alignment explanation
Indices: 30124--30166 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
30114 AGTTAAACAC
*
30124 TTATATA-TTATAAA
1 TTATATATTTAAAAA
30138 -TATATATTTAAAAA
1 TTATATATTTAAAAA
30152 TTATATATATTAAAA
1 TTATATAT-TTAAAA
30167 GTTAATTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 7 0.28
16 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATATATTTAAAAA
Found at i:32073 original size:41 final size:41
Alignment explanation
Indices: 32028--32113 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
32018 CATGCTTATA
* *
32028 AGGCTTTTTAATAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
1 AGGCTTTTAAAAAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
**
32069 AGGCTTTTAAAAAGGCCTGGGCCTGGCCTGTTTAGTTAAAT
1 AGGCTTTTAAAAAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
32110 AGGC
1 AGGC
32114 CAGGCCCAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (41 bp):
AGGCTTTTAAAAAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
Found at i:32343 original size:23 final size:23
Alignment explanation
Indices: 32297--32448 Score: 128
Period size: 23 Copynumber: 6.7 Consensus size: 23
32287 TTCTGAATCA
** *
32297 TTCTTCTTCTTCCATTGACTCAT
1 TTCTTCTTCTTCCATAAACCCAT
*
32320 TGCTTCTTCTTCCATAAACCCAT
1 TTCTTCTTCTTCCATAAACCCAT
* * * *
32343 TTTTTCTT-ATACATAAACACAT
1 TTCTTCTTCTTCCATAAACCCAT
* * * *
32365 TTATT-TGTCTTTCATAAACTCGT
1 TTCTTCT-TCTTCCATAAACCCAT
* *
32388 TTCTTCTTCTTCCACAATCCCAT
1 TTCTTCTTCTTCCATAAACCCAT
* *
32411 TTCTTTTTCTTCCAAAAACCCAT
1 TTCTTCTTCTTCCATAAACCCAT
*
32434 TTTTTCTTCTTCCAT
1 TTCTTCTTCTTCCAT
32449 TAGTTTGAGA
Statistics
Matches: 100, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
21 1 0.01
22 16 0.16
23 82 0.82
24 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.03, T:0.48
Consensus pattern (23 bp):
TTCTTCTTCTTCCATAAACCCAT
Found at i:33414 original size:3 final size:3
Alignment explanation
Indices: 33406--33437 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
33396 GGATTAAATC
*
33406 ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
33438 ATACACATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:35842 original size:29 final size:29
Alignment explanation
Indices: 35799--35881 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
35789 CTCACCTAAC
35799 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
35829 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
35858 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
35882 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:40613 original size:29 final size:29
Alignment explanation
Indices: 40570--40652 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
40560 CTCACCTAAC
40570 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
40600 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
40629 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
40653 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:41701 original size:24 final size:25
Alignment explanation
Indices: 41656--41708 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
41646 ATTTGAATAA
*
41656 TATAATCAACACTCATAATAAA-AT
1 TATAATCAACACTAATAATAAACAT
* * *
41680 TATAATCAATATTAATATTAAACAT
1 TATAATCAACACTAATAATAAACAT
41705 TATA
1 TATA
41709 TATGTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (25 bp):
TATAATCAACACTAATAATAAACAT
Found at i:41893 original size:19 final size:19
Alignment explanation
Indices: 41852--41904 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
41842 TAATTAATTT
41852 AAATTAAA-TTAATAAAAG
1 AAATTAAATTTAATAAAAG
*
41870 TAATTAAATTTAATAAATA-
1 AAATTAAATTTAATAAA-AG
*
41889 AAATTAGATTCTAATA
1 AAATTAAATT-TAATA
41905 CATATTCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
AAATTAAATTTAATAAAAG
Found at i:42622 original size:18 final size:19
Alignment explanation
Indices: 42587--42624 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
42577 CACGGAATGT
42587 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
42607 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
42625 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:42638 original size:15 final size:16
Alignment explanation
Indices: 42586--42630 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
42576 TCACGGAATG
42586 TAAGATTACCAGTGGGAA
1 TAAGATTACCA--GGGAA
42604 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
42622 TAAGATTAC
1 TAAGATTAC
42631 TGGGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 7 0.28
20 10 0.40
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Done.