Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007268.1 Hibiscus syriacus cultivar Beakdansim tig00019271_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: 47916
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5988 original size:11 final size:11
Alignment explanation
Indices: 5972--6002 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5962 TTCTTTTCAT
*
5972 TTTATTTGCTG
1 TTTATTTACTG
5983 TTTATTTACTG
1 TTTATTTACTG
5994 TTTATTTAC
1 TTTATTTAC
6003 CATTTCCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (11 bp):
TTTATTTACTG
Found at i:10386 original size:16 final size:16
Alignment explanation
Indices: 10361--10393 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10351 TAGTTAGCTC
*
10361 ATTTGTATTCTAACAT
1 ATTTGCATTCTAACAT
10377 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
10393 A
1 A
10394 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:13914 original size:16 final size:16
Alignment explanation
Indices: 13893--13925 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13883 TAGTTAGCTC
13893 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
13909 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
13925 A
1 A
13926 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:16334 original size:13 final size:13
Alignment explanation
Indices: 16316--16341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16306 CTATCTGTTC
16316 ATCACCATTTTCA
1 ATCACCATTTTCA
16329 ATCACCATTTTCA
1 ATCACCATTTTCA
16342 CGCCTATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ATCACCATTTTCA
Found at i:17221 original size:19 final size:20
Alignment explanation
Indices: 17197--17249 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
17187 TTCGGCCAAG
* *
17197 ATCATGTATCTTCAT-TAAA
1 ATCATGTATTTTCATAAAAA
17216 ATCATGTATTTTCATAAAAA
1 ATCATGTATTTTCATAAAAA
17236 ATCATGTATTTTCA
1 ATCATGTATTTTCA
17250 AAGGGGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (20 bp):
ATCATGTATTTTCATAAAAA
Found at i:18013 original size:13 final size:12
Alignment explanation
Indices: 17997--18038 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
17987 GTGCAAAAAG
17997 AAAGAAAATCAGA
1 AAAGAAAATCA-A
*
18010 AAAGAAAA-GAA
1 AAAGAAAATCAA
18021 AAAGAAAATTCAA
1 AAAGAAAA-TCAA
18034 AAAGA
1 AAAGA
18039 GAAAGTAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAGAAAATCAA
Found at i:18028 original size:24 final size:25
Alignment explanation
Indices: 17997--18043 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
17987 GTGCAAAAAG
17997 AAAGAAAA-TCAGAAAAGA-AAAGAA
1 AAAGAAAATTCA-AAAAGAGAAAGAA
18021 AAAGAAAATTCAAAAAGAGAAAG
1 AAAGAAAATTCAAAAAGAGAAAG
18044 TAAGCCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAGAAAATTCAAAAAGAGAAAGAA
Found at i:29640 original size:35 final size:35
Alignment explanation
Indices: 29528--29639 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
29518 TAAGCTACTA
*
29528 CCTATAACATCACCATCTTCCATCACCATTTTCATG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
29564 CCTATAACTTCACCATCTTCCATCACCATTGCACA
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* *
29599 CCTATATCATCACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
29634 CCTATA
1 CCTATA
29640 TAACCACCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 40 0.60
36 27 0.40
ACGTcount: A:0.28, C:0.38, G:0.03, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:29816 original size:6 final size:6
Alignment explanation
Indices: 29805--29832 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29795 ATTTAAATTC
29805 TTTCCA TTTCCA TTTCCA TTTCCA TTTC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTC
29833 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCCA
Found at i:34437 original size:20 final size:22
Alignment explanation
Indices: 34412--34454 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
34402 GTGATTCAGC
*
34412 AAGTACATAGTT-TTTAA-TGA
1 AAGTACATAATTATTTAAGTGA
34432 AAGTACATAATTATTTAAGTGA
1 AAGTACATAATTATTTAAGTGA
34454 A
1 A
34455 TGAATATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
AAGTACATAATTATTTAAGTGA
Found at i:35317 original size:2 final size:2
Alignment explanation
Indices: 35310--35359 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
35300 ATAAATGTAG
35310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35352 TA TA TA TA
1 TA TA TA TA
35360 CTATGTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42414 original size:15 final size:16
Alignment explanation
Indices: 42394--42465 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 16
42384 CATTTATTTC
42394 CATTTCCTTTCTT-AT
1 CATTTCCTTTCTTAAT
**
42409 CATTTCCTTTCTTCTT
1 CATTTCCTTTCTTAAT
*
42425 CTATTT-CTTT-TTTAT
1 C-ATTTCCTTTCTTAAT
*
42440 -ATTTCC-ATCTTAAT
1 CATTTCCTTTCTTAAT
42454 CATTT-CTTTCTT
1 CATTTCCTTTCTT
42466 TTAATTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
15 24 0.53
16 6 0.13
17 4 0.09
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCCTTTCTTAAT
Found at i:47593 original size:21 final size:21
Alignment explanation
Indices: 47541--47586 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
47531 ACTATCATTC
*
47541 CATCACCATTCACGTCTATAT
1 CATCACCATTCACGCCTATAT
47562 CATCACCATTCACGCCTATAT
1 CATCACCATTCACGCCTATAT
47583 CATC
1 CATC
47587 GTCATTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.37, G:0.04, T:0.30
Consensus pattern (21 bp):
CATCACCATTCACGCCTATAT
Done.