Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003228.1 Hibiscus syriacus cultivar Beakdansim tig00006798_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: 35971
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:873 original size:23 final size:23
Alignment explanation
Indices: 847--914 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
837 ATTATTATAT
*
847 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
870 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
**
893 GGCACTTTGGTGCAATTCTACG
1 GGCACTACGGTGCAATTCTACG
915 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:7699 original size:18 final size:18
Alignment explanation
Indices: 7647--7697 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
7637 TTGATATTTT
*
7647 TATTATGTTTAAATTTT-A
1 TATTATATTT-AATTTTAA
7665 TATTTATATTT-ATTTTAA
1 TA-TTATATTTAATTTTAA
7683 TATTAT-TTTAATTTT
1 TATTATATTTAATTTT
7698 TATAACATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.10
17 14 0.48
18 5 0.17
19 7 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTATATTTAATTTTAA
Found at i:9561 original size:18 final size:18
Alignment explanation
Indices: 9538--9610 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
9528 ACTGAATATT
9538 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
9556 TGTCCCGAAAGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
9575 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
9594 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
9611 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:9585 original size:38 final size:38
Alignment explanation
Indices: 9537--9613 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
9527 CACTGAATAT
*
9537 TTGTCCCGAAGGACCACTATGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAAGACCACTGA
* *
9575 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAAGACCACTGA
9613 T
1 T
9614 AATCCCTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAAGACCACTGA
Found at i:27964 original size:19 final size:20
Alignment explanation
Indices: 27923--27968 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
27913 AGTCGGATCT
*
27923 TGGGCTTTGGGTCGTTCAAC
1 TGGGCTCTGGGTCGTTCAAC
* *
27943 TGGGCTCTGGGT-TTTCAGC
1 TGGGCTCTGGGTCGTTCAAC
27962 TGGGCTC
1 TGGGCTC
27969 CAGTTGGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.07, C:0.22, G:0.37, T:0.35
Consensus pattern (20 bp):
TGGGCTCTGGGTCGTTCAAC
Found at i:28088 original size:3 final size:3
Alignment explanation
Indices: 28080--28146 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
28070 GTAGCCTGTA
*
28080 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT -AT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28126 AAT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
28147 TTATTATTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 6 0.10
3 53 0.90
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28130 original size:31 final size:32
Alignment explanation
Indices: 28080--28146 Score: 118
Period size: 31 Copynumber: 2.1 Consensus size: 32
28070 GTAGCCTGTA
*
28080 AATAATAATAATAATAATAATAATAATATAAT
1 AATAATAATAATAACAATAATAATAATATAAT
28112 AATAAT-ATAATAACAATAATAATAATATAAT
1 AATAATAATAATAACAATAATAATAATATAAT
28143 AATA
1 AATA
28147 TTATTATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (32 bp):
AATAATAATAATAACAATAATAATAATATAAT
Found at i:28157 original size:17 final size:17
Alignment explanation
Indices: 28080--28146 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
28070 GTAGCCTGTA
28080 AATAATAATAATAATAAT
1 AATAATAAT-ATAATAAT
28098 AATAATAATATAATAAT
1 AATAATAATATAATAAT
*
28115 AAT-AT-A-ATAACAAT
1 AATAATAATATAATAAT
28129 AATAATAATATAATAAT
1 AATAATAATATAATAAT
28146 A
1 A
28147 TTATTATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.23
15 3 0.07
16 3 0.07
17 19 0.43
18 9 0.20
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATATAATAAT
Found at i:28588 original size:18 final size:17
Alignment explanation
Indices: 28561--28606 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
28551 GTTTATGAGT
28561 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
* *
28579 GAATTTGAATCTGTCAG
1 GAATTGGAATCTGTAAG
28596 GAATTGGAATC
1 GAATTGGAATC
28607 CAATTCCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:29236 original size:37 final size:38
Alignment explanation
Indices: 29158--29236 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
29148 ACCCGACCCG
* * * *
29158 AATATCACACTTAAAAAAACCCGACTCGACTCGACCCA
1 AATATCACACTTAAAAAAACCCGACACGACCCGAACAA
*
29196 AATATCACACTT-AAAAAACCTGACACGACCCGAACAA
1 AATATCACACTTAAAAAAACCCGACACGACCCGAACAA
29233 AATA
1 AATA
29237 AAATTTCACC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 24 0.67
38 12 0.33
ACGTcount: A:0.47, C:0.30, G:0.08, T:0.15
Consensus pattern (38 bp):
AATATCACACTTAAAAAAACCCGACACGACCCGAACAA
Done.