Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004041.1 Hibiscus syriacus cultivar Beakdansim tig00008826_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: 68443
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:8014 original size:29 final size:29
Alignment explanation
Indices: 7970--8044 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 29
7960 ACTAAATCCG
7970 TCCCGTCCCCGTTTAACATAAACGATTTTT
1 TCCCGT-CCCGTTTAACATAAACGATTTTT
8000 TCCCGTCCCGTTTAACATAAACGATTTTT
1 TCCCGTCCCGTTTAACATAAACGATTTTT
* *
8029 CCCCGTTTCCGTTTAA
1 TCCCG-TCCCGTTTAA
8045 TTCAGTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.21, C:0.31, G:0.11, T:0.37
Consensus pattern (29 bp):
TCCCGTCCCGTTTAACATAAACGATTTTT
Found at i:16366 original size:21 final size:21
Alignment explanation
Indices: 16342--16395 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
16332 CTGTCGGTTT
16342 AGATGACATCGCCTCACTTTC
1 AGATGACATCGCCTCACTTTC
* *
16363 AGATGCCACCGCCTCACTTTC
1 AGATGACATCGCCTCACTTTC
*
16384 AGATGTCATCGC
1 AGATGACATCGC
16396 AGCTAGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (21 bp):
AGATGACATCGCCTCACTTTC
Found at i:26204 original size:232 final size:232
Alignment explanation
Indices: 25798--26245 Score: 725
Period size: 232 Copynumber: 1.9 Consensus size: 232
25788 AAGCAACGTC
*
25798 TGAATTGATTTTAATCCATTGAGGAGGGGGGAACCCAGCGGGTCCAACCACGAGGAATTCCCAAC
1 TGAATTGATTTCAATCCATTGAGGAGGGGGGAACCCAGCGGGTCCAACCACGAGGAATTCCCAAC
* *
25863 ACCTGAACTGAGGTTGTCGTGACCTTCAATTGATTTCGATTCATCATCTCAACAAGACGAGCACT
66 ACCTGAACTGAGGTCGTCGTGACCTTCAATTGATTTCGATTCATCATCTCAACAAGACAAGCACT
* * * *
25928 CCGAGTAACAATCGAGTCCTCACCGTCTATTGTGGAATTGAAGACCTTTGCATTCCGAGAGATCC
131 CCGAGTAACAACCGAGCCCTCACCATCTATTGGGGAATTGAAGACCTTTGCATTCCGAGAGATCC
*
25993 ATAAGTTCCAAAAGACTGCCGCAAACATTAAAATCAT
196 ATAACTTCCAAAAGACTGCCGCAAACATTAAAATCAT
* * **
26030 TGAATTGATTTCAATCCATTGAGGAGGGGGGAGCTCAGCGGGTCGGACCACGAGGAATTCCCAAC
1 TGAATTGATTTCAATCCATTGAGGAGGGGGGAACCCAGCGGGTCCAACCACGAGGAATTCCCAAC
** * * *
26095 GGCTGAACTGAGGTCGTCGTGACCTTCAATTGATTTTGGTTCATCATCTCATCAAGACAAGCACT
66 ACCTGAACTGAGGTCGTCGTGACCTTCAATTGATTTCGATTCATCATCTCAACAAGACAAGCACT
*
26160 CCGAGTAACAACCGAGCCCTCACCATCTATTGGGGAATTGAAGACCTTTTCATTCCGAGAGATCC
131 CCGAGTAACAACCGAGCCCTCACCATCTATTGGGGAATTGAAGACCTTTGCATTCCGAGAGATCC
*
26225 ATAACTTCCAAAGGACTGCCG
196 ATAACTTCCAAAAGACTGCCG
26246 GACTGCCGCA
Statistics
Matches: 197, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
232 197 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (232 bp):
TGAATTGATTTCAATCCATTGAGGAGGGGGGAACCCAGCGGGTCCAACCACGAGGAATTCCCAAC
ACCTGAACTGAGGTCGTCGTGACCTTCAATTGATTTCGATTCATCATCTCAACAAGACAAGCACT
CCGAGTAACAACCGAGCCCTCACCATCTATTGGGGAATTGAAGACCTTTGCATTCCGAGAGATCC
ATAACTTCCAAAAGACTGCCGCAAACATTAAAATCAT
Found at i:36198 original size:81 final size:81
Alignment explanation
Indices: 36061--36229 Score: 230
Period size: 81 Copynumber: 2.1 Consensus size: 81
36051 GTAAGTCATG
* * * * *
36061 TAGAAACTTGACTCCTTTTTTGGTTGCAACCTGATTTATCAATGTAAAAACCTATTTTTAGTTGC
1 TAGAAACTTGACTCATTTTTAGGTTGCAACCTAATTTATCAATGAAAAAACCTATTTTTAATTGC
*
36126 AACCTAAATTATTGTA
66 AACCTAAACTATTGTA
* * ** *
36142 TAGAAATTTGATTCATTTTTAGGTTGCAACCTAATTTATCAATGAAAAAATTTATTTTTAATTTC
1 TAGAAACTTGACTCATTTTTAGGTTGCAACCTAATTTATCAATGAAAAAACCTATTTTTAATTGC
*
36207 AACTTAAACTATTGTA
66 AACCTAAACTATTGTA
36223 TAGAAAC
1 TAGAAAC
36230 CTGTTTTCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (81 bp):
TAGAAACTTGACTCATTTTTAGGTTGCAACCTAATTTATCAATGAAAAAACCTATTTTTAATTGC
AACCTAAACTATTGTA
Found at i:48688 original size:18 final size:18
Alignment explanation
Indices: 48660--48709 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
48650 GGAAAGAAAA
*
48660 AAAATCTCAAACTCGATT
1 AAAACCTCAAACTCGATT
*
48678 AAAGCCTCAAACTCGATT
1 AAAACCTCAAACTCGATT
48696 AAAACCTCAAACTC
1 AAAACCTCAAACTC
48710 AAACTCGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAACCTCAAACTCGATT
Found at i:55457 original size:73 final size:72
Alignment explanation
Indices: 55377--55520 Score: 261
Period size: 73 Copynumber: 2.0 Consensus size: 72
55367 ATAATATATC
*
55377 AAAATTAATGAATATAATATATTATAAAACTTCAGAAAAGAGATCGATTTTAATCTTAATAATAT
1 AAAATTAATGAATATAATATATTATAAAACTTCAG-AAAGAGATCAATTTTAATCTTAATAATAT
55442 GAGAGGGA
65 GAGAGGGA
*
55450 AAAATTAATGAATATAATATATTATAAAACTTCAGAAAGAGATCAATTTTAATCTTAATATTATG
1 AAAATTAATGAATATAATATATTATAAAACTTCAGAAAGAGATCAATTTTAATCTTAATAATATG
55515 AGAGGG
66 AGAGGG
55521 GAGGAGAGAC
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 34 0.49
73 35 0.51
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.33
Consensus pattern (72 bp):
AAAATTAATGAATATAATATATTATAAAACTTCAGAAAGAGATCAATTTTAATCTTAATAATATG
AGAGGGA
Found at i:62245 original size:30 final size:31
Alignment explanation
Indices: 62209--62267 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
62199 GATTTTGAAA
62209 AAATTGAAAGTTAAGATACTAAA-ACATACG
1 AAATTGAAAGTTAAGATACTAAACACATACG
* * *
62239 AAATTGATAGTTTAGGTACTAAACACATA
1 AAATTGAAAGTTAAGATACTAAACACATA
62268 ATTTATCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (31 bp):
AAATTGAAAGTTAAGATACTAAACACATACG
Found at i:65164 original size:12 final size:12
Alignment explanation
Indices: 65147--65173 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
65137 AGAACCGGAC
65147 AAAAAGAAAAGG
1 AAAAAGAAAAGG
65159 AAAAAGAAAAGG
1 AAAAAGAAAAGG
65171 AAA
1 AAA
65174 GAACTAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Done.