Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003545.1 Hibiscus syriacus cultivar Beakdansim tig00007477_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: 173267
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:141700 original size:6 final size:6
Alignment explanation
Indices: 141689--141763 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
141679 TCTCGTCTCG
141689 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
141737 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
141764 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:141866 original size:20 final size:20
Alignment explanation
Indices: 141841--141884 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
141831 TTTTTAACTA
*
141841 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
141861 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
141881 TTCT
1 TTCT
141885 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:141894 original size:20 final size:20
Alignment explanation
Indices: 141871--142145 Score: 153
Period size: 20 Copynumber: 13.6 Consensus size: 20
141861 TTCTTTTTAA
141871 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
141891 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
141911 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
141931 CATTGCGATTCTC-ACAGTCG
1 CGTTGCGATTTTCTA-AATCG
* * * *
141951 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * *
141971 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
141991 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
142011 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
142034 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
142055 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
142073 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
142095 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
142115 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
142134 CGTTGCGATTTT
1 CGTTGCGATTTT
142146 ATTGGTCATT
Statistics
Matches: 209, Mismatches: 36, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 18 0.09
20 158 0.76
21 13 0.06
22 4 0.02
23 14 0.07
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:141917 original size:40 final size:40
Alignment explanation
Indices: 141873--142020 Score: 197
Period size: 40 Copynumber: 3.7 Consensus size: 40
141863 CTTTTTAACG
* * *
141873 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
* *
141913 TTGCGATTCTATAAATCGCATTGCGATTCTCACAGTCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
* * * * *
141953 TTGCGATTCTCTCAGTCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
*
141993 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTATAAATCGCATTGCGATT
142021 TTCTTCTAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:141938 original size:60 final size:60
Alignment explanation
Indices: 141873--142020 Score: 226
Period size: 60 Copynumber: 2.5 Consensus size: 60
141863 CTTTTTAACG
* *
141873 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* *
141933 TTGCGATTCTC-ACAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTA-AATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* *
141993 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTCTAAATCGCATTGCGATT
142021 TTCTTCTAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 78 0.99
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (60 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
Found at i:142135 original size:19 final size:20
Alignment explanation
Indices: 142095--142145 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
142085 TTCTTTTTAA
*
142095 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
142115 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
142134 CGTTGCGATTTT
1 CGTTGCGATTTT
142146 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:150918 original size:22 final size:19
Alignment explanation
Indices: 150889--150928 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
150879 TACAAGAGAG
150889 TTTACACTCACTGTTTTTTTA
1 TTTACACT--CTGTTTTTTTA
150910 TTTATCACTCTGTTTTTTT
1 TTTA-CACTCTGTTTTTTT
150929 CCCGGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTACACTCTGTTTTTTTA
Found at i:151406 original size:3 final size:3
Alignment explanation
Indices: 151400--151443 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
151390 AAATTATTAG
151400 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
151444 TATATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:157193 original size:17 final size:17
Alignment explanation
Indices: 157173--157216 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
157163 ATAATTTTAA
157173 TATTATTCTTAGG-ATTT
1 TATT-TTCTTAGGTATTT
*
157190 TATTTTGTTTAGGTATTT
1 TATTTT-CTTAGGTATTT
157208 TATTTTCTT
1 TATTTTCTT
157217 CATGTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 11 0.48
18 10 0.43
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTTTCTTAGGTATTT
Found at i:160847 original size:16 final size:16
Alignment explanation
Indices: 160806--160844 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
160796 GTTATTTTTG
160806 TTTATTTAATTTATTT
1 TTTATTTAATTTATTT
*
160822 TCTATTTAATTTATTT
1 TTTATTTAATTTATTT
160838 ATTTATT
1 -TTTATT
160845 AATGTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTTAATTTATTT
Found at i:171133 original size:40 final size:39
Alignment explanation
Indices: 171074--171158 Score: 143
Period size: 40 Copynumber: 2.2 Consensus size: 39
171064 GTCTTTTGAT
* *
171074 TCGATATTGAACCCCGAGTATTGATACCCAATGAAAAATA
1 TCGATATCGAACCCAGAGTATTGATACCCAATG-AAAATA
171114 TCGATATCGAACCCAGAGTATTGATACCCAATGAAAATA
1 TCGATATCGAACCCAGAGTATTGATACCCAATGAAAATA
171153 TCGATA
1 TCGATA
171159 CCCCAAGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (39 bp):
TCGATATCGAACCCAGAGTATTGATACCCAATGAAAATA
Done.