Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001450.1 Hibiscus syriacus cultivar Beakdansim tig00002802_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: 55920
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3663 original size:37 final size:39
Alignment explanation
Indices: 3617--3692 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
3607 TTAAGATTTT
* *
3617 TAATATTATTAATTAGGA-TTTTGGTTTGTTAGAATTAA
1 TAATATTATTAATTAGGATTTTTAGTTTATTAGAATTAA
3655 TAAT-TTATTAATTAGGATTTTTAGTTTATTAGAATTAA
1 TAATATTATTAATTAGGATTTTTAGTTTATTAGAATTAA
3693 GAGTTTGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 13 0.37
38 22 0.63
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (39 bp):
TAATATTATTAATTAGGATTTTTAGTTTATTAGAATTAA
Found at i:4920 original size:27 final size:27
Alignment explanation
Indices: 4863--4922 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
4853 GTTTTAGTAT
* *
4863 CTAAATTTAATTTTTTCAAAATCATAT
1 CTAAATTTAATTTTTTCAAAACCATAC
*
4890 CTAACTTTCAATTTTTTCAAAACCAT-C
1 CTAAATTT-AATTTTTTCAAAACCATAC
4917 CTAAAT
1 CTAAAT
4923 CCCCCTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.43
Consensus pattern (27 bp):
CTAAATTTAATTTTTTCAAAACCATAC
Found at i:11494 original size:21 final size:21
Alignment explanation
Indices: 11465--11521 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
11455 CATATGGAAC
*
11465 CAACCGGTTTAGATGCTATCG
1 CAACTGGTTTAGATGCTATCG
11486 CAACTGGTTTAGATGCTATCG
1 CAACTGGTTTAGATGCTATCG
*
11507 CAACTGGTTCAGATG
1 CAACTGGTTTAGATG
11522 TCACCACCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
CAACTGGTTTAGATGCTATCG
Found at i:12061 original size:13 final size:14
Alignment explanation
Indices: 12043--12071 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12033 GTAACATTTG
12043 TATTTAA-TGTTTT
1 TATTTAATTGTTTT
12056 TATTTAATTGTTTT
1 TATTTAATTGTTTT
12070 TA
1 TA
12072 CTATTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
TATTTAATTGTTTT
Found at i:14086 original size:2 final size:2
Alignment explanation
Indices: 14079--14111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14069 ATTATTATGT
14079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14112 TTATTATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15051 original size:2 final size:2
Alignment explanation
Indices: 15044--15069 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15034 GTGATTAGGT
15044 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
15070 GTGGCGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15249 original size:2 final size:2
Alignment explanation
Indices: 15242--15303 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
15232 GATCCGCCAC
15242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15284 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
15304 ATCACGTTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17821 original size:23 final size:22
Alignment explanation
Indices: 17786--17828 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
17776 ATAATTATTT
17786 AAAAAATTAAATAAAAAATATC
1 AAAAAATTAAATAAAAAATATC
*
17808 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
17829 AGTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATATC
Found at i:20326 original size:32 final size:32
Alignment explanation
Indices: 20290--20355 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
20280 TGAAGATGAT
* * ** *
20290 GATTGTAGCATCAATGGAGTGAGGAGGAAGAC
1 GATTGCAGCATCAATGAAACGAGGACGAAGAC
20322 GATTGCAGCATCAATGAAACGAGGACGAAGAC
1 GATTGCAGCATCAATGAAACGAGGACGAAGAC
20354 GA
1 GA
20356 CAATTAATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.33, T:0.15
Consensus pattern (32 bp):
GATTGCAGCATCAATGAAACGAGGACGAAGAC
Found at i:40589 original size:32 final size:32
Alignment explanation
Indices: 40553--40629 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
40543 ACAAAGTTTA
*
40553 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
40585 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
40618 CGATAATTGAAA
1 CGATAATTGAAA
40630 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:40643 original size:21 final size:21
Alignment explanation
Indices: 40618--40659 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40608 CTTCCAAGTT
40618 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
40639 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
40660 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Done.