Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007532.1 Hibiscus syriacus cultivar Beakdansim tig00021039_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: 23739
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Found at i:10726 original size:15 final size:15
Alignment explanation
Indices: 10706--10734 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10696 GTTCTTGCTG
10706 AAACTGCTCACTGCA
1 AAACTGCTCACTGCA
10721 AAACTGCTCACTGC
1 AAACTGCTCACTGC
10735 GTCTGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (15 bp):
AAACTGCTCACTGCA
Found at i:11724 original size:14 final size:14
Alignment explanation
Indices: 11705--11733 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11695 CAAATATATA
11705 ATAATTTATAGTTT
1 ATAATTTATAGTTT
11719 ATAATTTATAGTTT
1 ATAATTTATAGTTT
11733 A
1 A
11734 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:11931 original size:21 final size:23
Alignment explanation
Indices: 11907--11950 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
11897 AATAATCTAA
*
11907 ATTAATTTAA-TTTA-AGAATAT
1 ATTAATATAATTTTATAGAATAT
11928 ATTAATATAATTTTATAGAATAT
1 ATTAATATAATTTTATAGAATAT
11951 GATTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTAATATAATTTTATAGAATAT
Found at i:14488 original size:13 final size:13
Alignment explanation
Indices: 14470--14494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14460 AACATATTAA
14470 TATAATTTAAATC
1 TATAATTTAAATC
14483 TATAATTTAAAT
1 TATAATTTAAAT
14495 ATTAATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:14774 original size:21 final size:21
Alignment explanation
Indices: 14748--14809 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
14738 TTATAAATTA
14748 ATTAATTTAAATTAAGAATAT
1 ATTAATTTAAATTAAGAATAT
* **
14769 ATTAATTTAATTTTTG-ATAT
1 ATTAATTTAAATTAAGAATAT
* * *
14789 TTTAATTTAAATAAATAATAT
1 ATTAATTTAAATTAAGAATAT
14810 TATAGTAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
ATTAATTTAAATTAAGAATAT
Found at i:17017 original size:18 final size:18
Alignment explanation
Indices: 16994--17029 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16984 GATGCACGAT
16994 AATGCTTAACACACTTCA
1 AATGCTTAACACACTTCA
*
17012 AATGCTTAACACATTTCA
1 AATGCTTAACACACTTCA
17030 TTTGTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (18 bp):
AATGCTTAACACACTTCA
Found at i:18839 original size:15 final size:17
Alignment explanation
Indices: 18815--18851 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
18805 TAATCTGATC
*
18815 CAAATGTAAAAA-AATT
1 CAAATATAAAAATAATT
18831 -AAATATAAAAATAATT
1 CAAATATAAAAATAATT
18847 CAAAT
1 CAAAT
18852 GCATCGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
CAAATATAAAAATAATT
Found at i:18982 original size:17 final size:18
Alignment explanation
Indices: 18948--18987 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
18938 ATATTCATGC
*
18948 AATAAATAAAAATTAATT
1 AATAAATAAAAATAAATT
18966 AATAAATAAAAA-AAATT
1 AATAAATAAAAATAAATT
18983 AATAA
1 AATAA
18988 TCAGATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAATAAAAATAAATT
Found at i:20998 original size:26 final size:25
Alignment explanation
Indices: 20978--21030 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
20968 CACAATTCAC
*
20978 ATCATAATTCAAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAAT-ATA
*
21004 ATCATTATCCAAATCAAACAA-ATA
1 ATCATAATCCAAATCAAACAATATA
21028 ATC
1 ATC
21031 CGAGTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
26 19 0.76
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.26
Consensus pattern (25 bp):
ATCATAATCCAAATCAAACAATATA
Found at i:21182 original size:38 final size:36
Alignment explanation
Indices: 21139--21217 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 36
21129 AAGAATATAA
* * *
21139 TATAATTTAAATTAATGTATTCTTA-TATATTTATAATT
1 TATAATTTAAA-T-AT-TATTATTATTATATTAATAAAT
21177 TATAATTTAAATATTATTATTATTATATTAATAAAT
1 TATAATTTAAATATTATTATTATTATATTAATAAAT
21213 TATAA
1 TATAA
21218 ATAATTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 7 0.19
36 18 0.49
37 1 0.03
38 11 0.30
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
TATAATTTAAATATTATTATTATTATATTAATAAAT
Found at i:22125 original size:16 final size:16
Alignment explanation
Indices: 22099--22141 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
22089 ATGATATTTT
22099 ATAATTATAA-TTTATAA
1 ATAATT-TAATTTTA-AA
22116 ATAATTTAATTTTAAA
1 ATAATTTAATTTTAAA
*
22132 ATAAATTAAT
1 ATAATTTAAT
22142 AAAACTATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTAATTTTAAA
Done.