Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000862.1 Hibiscus syriacus cultivar Beakdansim tig00001668_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: 55389
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1438 original size:13 final size:13
Alignment explanation
Indices: 1420--1446 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1410 ACCATGATAG
1420 AACTAACCTAATT
1 AACTAACCTAATT
1433 AACTAACCTAATT
1 AACTAACCTAATT
1446 A
1 A
1447 TCTCCTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AACTAACCTAATT
Found at i:8284 original size:15 final size:15
Alignment explanation
Indices: 8264--8300 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
8254 TGAGACATTA
*
8264 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
8279 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
8294 CCCGCCC
1 CCCGCCC
8301 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:10014 original size:14 final size:14
Alignment explanation
Indices: 9995--10030 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
9985 CATAACCCCA
9995 ATCAGCTCTTCGGT
1 ATCAGCTCTTCGGT
10009 ATCAGCTCTTCGGT
1 ATCAGCTCTTCGGT
10023 ATCAGCTC
1 ATCAGCTC
10031 CTAACATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (14 bp):
ATCAGCTCTTCGGT
Found at i:13943 original size:31 final size:30
Alignment explanation
Indices: 13867--13944 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
13857 TATAAAAATA
13867 TAAGATATAGTCACTTTCTTTTTTATTTAAT
1 TAAGATAT-GTCACTTTCTTTTTTATTTAAT
*
13898 TAGGATATGATCACTTT-TGTTTTTATTTAAT
1 TAAGATATG-TCACTTTCT-TTTTTATTTAAT
*
13929 TAAGATGTCGTCACTT
1 TAAGATAT-GTCACTT
13945 CGAATTAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.05
31 38 0.93
32 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (30 bp):
TAAGATATGTCACTTTCTTTTTTATTTAAT
Found at i:23615 original size:3 final size:3
Alignment explanation
Indices: 23607--23637 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
23597 TCCTTGCATT
*
23607 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23638 AGGATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:31321 original size:21 final size:21
Alignment explanation
Indices: 31279--31330 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
31269 TTATATTTTT
*
31279 TTATTTTTTAATAATAAAATA
1 TTATTTTTAAATAATAAAATA
*
31300 TTATTTTTAAAT-ATATATATA
1 TTATTTTTAAATAATA-AAATA
31321 TT-TTTTTAAA
1 TTATTTTTAAA
31331 AATCAACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTTTTAAATAATAAAATA
Found at i:34811 original size:80 final size:80
Alignment explanation
Indices: 34678--34841 Score: 328
Period size: 80 Copynumber: 2.0 Consensus size: 80
34668 TCATGTGCAT
34678 TTCTTCATTATACTCATTGTGCATACATGACTAAATAATGACATGATTTGTATTTTTCATTAGTA
1 TTCTTCATTATACTCATTGTGCATACATGACTAAATAATGACATGATTTGTATTTTTCATTAGTA
34743 TGTGAACTGAACATG
66 TGTGAACTGAACATG
34758 TTCTTCATTATACTCATTGTGCATACATGACTAAATAATGACATGATTTGTATTTTTCATTAGTA
1 TTCTTCATTATACTCATTGTGCATACATGACTAAATAATGACATGATTTGTATTTTTCATTAGTA
34823 TGTGAACTGAACATG
66 TGTGAACTGAACATG
34838 TTCT
1 TTCT
34842 GACCGTATGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (80 bp):
TTCTTCATTATACTCATTGTGCATACATGACTAAATAATGACATGATTTGTATTTTTCATTAGTA
TGTGAACTGAACATG
Found at i:38877 original size:30 final size:30
Alignment explanation
Indices: 38841--38903 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
38831 TAATATCAAT
*
38841 TAAGGTTTCGGATTCGAGTATTTATGTATG
1 TAAGGTTTCGGATTCGAGTATCTATGTATG
* *
38871 TAAGGTTTCGGGTTCGAGTCTCTATGTATG
1 TAAGGTTTCGGATTCGAGTATCTATGTATG
38901 TAA
1 TAA
38904 AAAATCTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (30 bp):
TAAGGTTTCGGATTCGAGTATCTATGTATG
Found at i:39151 original size:33 final size:33
Alignment explanation
Indices: 39114--39183 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
39104 TAGGAGCCAG
39114 TTGCACCTTCGTGCTTTCTTCTTCCCTTCTTCT
1 TTGCACCTTCGTGCTTTCTTCTTCCCTTCTTCT
39147 TTGCACCTTCGTGCTTTCTTCTTCCCTTCTTCT
1 TTGCACCTTCGTGCTTTCTTCTTCCCTTCTTCT
39180 TTGC
1 TTGC
39184 TTCATCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.03, C:0.36, G:0.10, T:0.51
Consensus pattern (33 bp):
TTGCACCTTCGTGCTTTCTTCTTCCCTTCTTCT
Found at i:39174 original size:19 final size:19
Alignment explanation
Indices: 39119--39175 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
39109 GCCAGTTGCA
39119 CCTTCGTGCTTTCTTCTTC
1 CCTTCGTGCTTTCTTCTTC
*
39138 CC-T--T-C-TTCTT-TGC
1 CCTTCGTGCTTTCTTCTTC
39151 ACCTTCGTGCTTTCTTCTTC
1 -CCTTCGTGCTTTCTTCTTC
39171 CCTTC
1 CCTTC
39176 TTCTTTGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
13 2 0.07
14 7 0.24
15 2 0.07
16 1 0.03
17 1 0.03
18 2 0.07
19 12 0.41
20 2 0.07
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.51
Consensus pattern (19 bp):
CCTTCGTGCTTTCTTCTTC
Found at i:51320 original size:37 final size:36
Alignment explanation
Indices: 51245--51320 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
51235 TTTTTATATT
*
51245 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
51281 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
51318 TTT
1 TTT
51321 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Done.