Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018781.1 Corchorus olitorius cultivar O-4 contig18814, 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: 53966
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:7473 original size:2 final size:2
Alignment explanation
Indices: 7466--7491 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7456 TCCATTGTAA
7466 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
7492 GTACTGAATC
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):
AT
Found at i:7912 original size:27 final size:28
Alignment explanation
Indices: 7872--8007 Score: 100
Period size: 27 Copynumber: 4.9 Consensus size: 28
7862 AATGGAGTGG
* * *
7872 AAATGACCACAATGCCCCCT-GAAGCAC
1 AAATGACCAAAATGCCCCCTAGATGTAC
* * *
7899 AAATGACTAAAATGCCCCCTAGGTGTAA
1 AAATGACCAAAATGCCCCCTAGATGTAC
* *
7927 AAATGACCAAAATG-CCCCTGGATGTGC
1 AAATGACCAAAATGCCCCCTAGATGTAC
* * * *
7954 AAATGACTAAAACG-CCCCTGGATTTTGA-
1 AAATGACCAAAATGCCCCCTAGA-TGT-AC
*
7982 AAATGACCCAAAATGCCCCATAGATG
1 AAATGA-CCAAAATGCCCCCTAGATG
8008 ACCCTGATGC
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 47 0.56
28 24 0.29
29 7 0.08
30 6 0.07
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCCTAGATGTAC
Found at i:15895 original size:38 final size:38
Alignment explanation
Indices: 15853--16071 Score: 217
Period size: 38 Copynumber: 5.9 Consensus size: 38
15843 TCTAAAGAGG
* *
15853 GACCTAAGCAGGTTTGA-TTAAACGAAGCTCTAAGCATA
1 GACCTAAGCAGGTTT-ACTTAAACGAAACTCTAAGCAGA
* * *
15891 GACCTAAGAAGGTTTACTTGAATG-AACTCTAAGCAGA
1 GACCTAAGCAGGTTTACTTAAACGAAACTCTAAGCAGA
15928 GATCCTAAGCAGGTTTACTTAAACG--A----AA-CAGA
1 GA-CCTAAGCAGGTTTACTTAAACGAAACTCTAAGCAGA
* * * *
15960 GACCTAAGAAGGTTTACTTAAATGGAAATTCTAAAC-GA
1 GACCTAAGCAGGTTTACTTAAA-CGAAACTCTAAGCAGA
*
15998 GGACCTAAGCAGG-TTAGATTAAACGAAACTCTAAGCAGA
1 -GACCTAAGCAGGTTTA-CTTAAACGAAACTCTAAGCAGA
*
16037 GACCTAAGCAGGTTTACTTAAATGAAACTCTAAGC
1 GACCTAAGCAGGTTTACTTAAACGAAACTCTAAGC
16072 GATGGTCTTA
Statistics
Matches: 150, Mismatches: 17, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
31 19 0.13
32 7 0.05
33 2 0.01
34 1 0.01
37 15 0.10
38 84 0.56
39 22 0.15
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (38 bp):
GACCTAAGCAGGTTTACTTAAACGAAACTCTAAGCAGA
Found at i:16023 original size:70 final size:69
Alignment explanation
Indices: 15890--16069 Score: 186
Period size: 69 Copynumber: 2.5 Consensus size: 69
15880 CTCTAAGCAT
* * *
15890 AGACCTAAGAAGGTTTACTTGAATGAACTCTAAGCAGAGATCCTAAGCAGGTTTACTTAAACGAA
1 AGACCTAAGAAGGTTTACTTAAATGAACTCTAAACAGAGATCCTAAGCAGGTTTAATTAAACGAA
15955 ACAG
66 ACAG
*
15959 AGACCTAAGAAGGTTTACTTAAATGGAAATTCTAAAC-GAGGA-CCTAAGCAGG-TTAGATTAAA
1 AGACCTAAGAAGGTTTACTTAAAT-G-AACTCTAAACAGA-GATCCTAAGCAGGTTTA-ATTAAA
16021 CGAAACTCTAAGCAG
62 CG--A----AA-CAG
*
16036 AGACCTAAGCAGGTTTACTTAAATGAAACTCTAA
1 AGACCTAAGAAGGTTTACTTAAATG-AACTCTAA
16070 GCGATGGTCT
Statistics
Matches: 94, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
69 26 0.28
70 20 0.21
71 10 0.11
72 1 0.01
76 11 0.12
77 26 0.28
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (69 bp):
AGACCTAAGAAGGTTTACTTAAATGAACTCTAAACAGAGATCCTAAGCAGGTTTAATTAAACGAA
ACAG
Found at i:16184 original size:16 final size:16
Alignment explanation
Indices: 16160--16204 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
16150 AATGGAATGC
*
16160 TGTTGTTGTTGTTG-TT
1 TGTTTTTGTT-TTGTTT
16176 TGTTTTTGTTTTGTTT
1 TGTTTTTGTTTTGTTT
16192 TGTTTTGTGTTTT
1 TGTTTT-TGTTTT
16205 TATTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 17 0.65
17 6 0.23
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (16 bp):
TGTTTTTGTTTTGTTT
Found at i:24908 original size:21 final size:21
Alignment explanation
Indices: 24884--24945 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
24874 TTAGGCAACC
24884 CCAATGAGCTTGAAACCTTCT
1 CCAATGAGCTTGAAACCTTCT
*
24905 CCAATGAGCTTGAAACTTTCT
1 CCAATGAGCTTGAAACCTTCT
24926 CCAATGAGCTTGAAA-CTTCT
1 CCAATGAGCTTGAAACCTTCT
24946 TTGTGAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (21 bp):
CCAATGAGCTTGAAACCTTCT
Found at i:35079 original size:20 final size:20
Alignment explanation
Indices: 35041--35079 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35031 ATAGTCATTA
*
35041 GAAACTTTGATAAGCCTATG
1 GAAACTTTGAAAAGCCTATG
*
35061 GAAACTTTGAAAAGGCTAT
1 GAAACTTTGAAAAGCCTAT
35080 TACATTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (20 bp):
GAAACTTTGAAAAGCCTATG
Found at i:46107 original size:12 final size:13
Alignment explanation
Indices: 46085--46114 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
46075 ACTAACAATT
46085 AAAATCAATCAAG
1 AAAATCAATCAAG
46098 AAAA-CAATCAAG
1 AAAATCAATCAAG
46110 AAAAT
1 AAAAT
46115 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Done.