Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000294.1 Hibiscus syriacus cultivar Beakdansim tig00000540_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: 38882
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:7027 original size:23 final size:23
Alignment explanation
Indices: 6994--7066 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
6984 CAACTCGTAT
6994 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* *
7017 AATTGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCATGTAG
* *
7040 AAATGCACTGAAGTGCCATATA-
1 AAATGCACCGAAGTGCCATGTAG
7062 AAATG
1 AAATG
7067 TCCATAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 5 0.11
23 39 0.89
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:8067 original size:64 final size:63
Alignment explanation
Indices: 7942--8077 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 63
7932 AATTTCAAGG
* *** *
7942 GGGTGCATCGATGCACTAACTGTACATCAGTACACTCCTTGCATTCGATGTTTTTATTTTAAA
1 GGGTGCATCCATGCACTAACTGTACATCAGTACACTCAAGGCATTCGATGTTTTTACTTTAAA
* * *
8005 TGGGTGCATCCATGCACTAACTGTGCATCCGTACACTCAAGGCATTTGATGTTTCTT-CTTTAAA
1 -GGGTGCATCCATGCACTAACTGTACATCAGTACACTCAAGGCATTCGATGTTT-TTACTTTAAA
*
8069 GAGTGCATC
1 GGGTGCATC
8078 AGTACACTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 8 0.13
64 52 0.84
65 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (63 bp):
GGGTGCATCCATGCACTAACTGTACATCAGTACACTCAAGGCATTCGATGTTTTTACTTTAAA
Found at i:17523 original size:309 final size:309
Alignment explanation
Indices: 16964--17600 Score: 1258
Period size: 309 Copynumber: 2.1 Consensus size: 309
16954 TGTGATATGG
*
16964 TTATATATATATATATATAAAAAATTTTATTATTATAATAAATTTTACCTTATGCTGATGGTCTT
1 TTATATATATATATATATATAAAATTTTATTATTATAATAAATTTTACCTTATGCTGATGGTCTT
17029 AGTTTTTCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGG
66 AGTTTTTCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGG
17094 GAGAAGAATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATC
131 GAGAAGAATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATC
17159 GCATGGATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCCTAGTACTGTAA
196 GCATGGATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCCTAGTACTGTAA
17224 CAATCACCCTATTTCAATAAATAATCACAACCTACATTTGTATTTCGGA
261 CAATCACCCTATTTCAATAAATAATCACAACCTACATTTGTATTTCGGA
17273 TTATATATATATATATATATAAAATTTTATTATTATAATAAATTTTACCTTATGCTGATGGTCTT
1 TTATATATATATATATATATAAAATTTTATTATTATAATAAATTTTACCTTATGCTGATGGTCTT
17338 AGTTTTTCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGG
66 AGTTTTTCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGG
17403 GAGAAGAATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATC
131 GAGAAGAATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATC
17468 GCATGGATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCCTAGTACTGTAA
196 GCATGGATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCCTAGTACTGTAA
17533 CAATCACCCTATTTCAATAAATAATCACAACCTACATTTGTATTTCGGA
261 CAATCACCCTATTTCAATAAATAATCACAACCTACATTTGTATTTCGGA
17582 TTATATATATATATA-ATAT
1 TTATATATATATATATATAT
17601 TATGCTCATA
Statistics
Matches: 327, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
308 4 0.01
309 323 0.99
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (309 bp):
TTATATATATATATATATATAAAATTTTATTATTATAATAAATTTTACCTTATGCTGATGGTCTT
AGTTTTTCCTGTCGTTTCATGGCATTGTCATGAAAGAACCGCCAGGGTAATTAACGTGAAAGAGG
GAGAAGAATTGAAGAAAAAAATTGAAAAGGTGAGAGACACTACAAACATGGTGTCTTCCTTGATC
GCATGGATTGTTGTTCGACTTCCCTTGGTCGCATGAACCATAGAGCGTCTCCCCTAGTACTGTAA
CAATCACCCTATTTCAATAAATAATCACAACCTACATTTGTATTTCGGA
Found at i:27691 original size:11 final size:10
Alignment explanation
Indices: 27667--27697 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
27657 GATACTTTAA
27667 AAGAAGAAAG
1 AAGAAGAAAG
27677 AAGAAGAAGAG
1 AAGAAGAA-AG
27688 AAGAAGAAAG
1 AAGAAGAAAG
27698 TTGGGATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAG
Found at i:29880 original size:18 final size:18
Alignment explanation
Indices: 29846--29880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29836 ACTGAATATT
*
29846 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
29864 TGTCCCGAAGGATCACT
1 TGTCCCGAAGGACCACT
29881 CCTTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:35102 original size:22 final size:22
Alignment explanation
Indices: 35074--35130 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
35064 AGTCGAGAGT
*
35074 TACATAGGTTCTCCAGGACATA
1 TACATAGGTCCTCCAGGACATA
***
35096 TACATAGGTCCTTGGGGACATA
1 TACATAGGTCCTCCAGGACATA
35118 TACATGAGGTCCT
1 TACAT-AGGTCCT
35131 TCGAGACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTCCAGGACATA
Found at i:35131 original size:23 final size:22
Alignment explanation
Indices: 35089--35131 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
35079 AGGTTCTCCA
35089 GGACATATACATAGGTCCTTGG
1 GGACATATACATAGGTCCTTGG
35111 GGACATATACATGAGGTCCTT
1 GGACATATACAT-AGGTCCTT
35132 CGAGACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (22 bp):
GGACATATACATAGGTCCTTGG
Found at i:35138 original size:23 final size:22
Alignment explanation
Indices: 35090--35138 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
35080 GGTTCTCCAG
* *
35090 GACATATACATAGGTCCTTGGG
1 GACATATACATAGGTCCTTCGA
35112 GACATATACATGAGGTCCTTCGA
1 GACATATACAT-AGGTCCTTCGA
35135 GACA
1 GACA
35139 AATTTCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (22 bp):
GACATATACATAGGTCCTTCGA
Done.