Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009754.1 Corchorus olitorius cultivar O-4 contig09786, 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: 8562
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Found at i:620 original size:36 final size:35
Alignment explanation
Indices: 524--658 Score: 141
Period size: 36 Copynumber: 3.8 Consensus size: 35
514 CGAAAATCCA
* *
524 AAAATTGGGAAAGTTCCCACCAGGTTTT-GGTTTT
1 AAAATTGGGAAAGTTCCCATCAGGTTTTAAGTTTT
* * * *
558 TAAATTGGGAAAGTTCCTAACAAGTTTTTAAGTTTT
1 AAAATTGGGAAAGTTCCCATC-AGGTTTTAAGTTTT
* *
594 AAAATCGGGAAAGTTCCCATTCA-GTTTCCAAAGTTTT
1 AAAATTGGGAAAGTTCCCA-TCAGGTTT--TAAGTTTT
631 -AAATTGGGAAAGTTCCCATCAGGTTTTA
1 AAAATTGGGAAAGTTCCCATCAGGTTTTA
659 GCTTTCGATT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
34 19 0.23
35 12 0.15
36 43 0.52
37 8 0.10
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (35 bp):
AAAATTGGGAAAGTTCCCATCAGGTTTTAAGTTTT
Found at i:2154 original size:78 final size:78
Alignment explanation
Indices: 2023--2268 Score: 220
Period size: 75 Copynumber: 3.2 Consensus size: 78
2013 AACTTTAATG
* * *
2023 GGATCTTTCCCTTAATTGAAAACTTCGAAAAAGACTAGATGGGATCTTTCCCTAAATT-AAAACT
1 GGATCTTTCCCTAAATTAAAAACTTCG--AAAGACTAGATGAGATCTTTCCCTAAATTAAAAACT
2087 TGAAAAAAAACTTGAT-
64 T--AAAAAAACTTGATA
* *
2103 GAGATCTTTCCCTAAATTAAAAACTTTG-AAGACTGGATGAGATCTTTCCCTAAATTAAAAACTT
1 G-GATCTTTCCCTAAATTAAAAACTTCGAAAGACTAGATGAGATCTTTCCCTAAATTAAAAACTT
*
2167 AAACAAACTTGATA
65 AAAAAAACTTGATA
* * * * * ** *
2181 GGATCTTTCCC--AATTAGAAATCTT-GAAAG-TTTGAGGGGATCTTTTTCTAAATTGAAAACTT
1 GGATCTTTCCCTAAATTA-AAAACTTCGAAAGACTAGATGAGATCTTTCCCTAAATTAAAAACTT
* * *
2242 GAAAAATAC-TGGTG
65 -AAAAAAACTTGATA
2256 GGATCTTTCCCTA
1 GGATCTTTCCCTA
2269 TTTTGAAATC
Statistics
Matches: 140, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
75 45 0.32
76 15 0.11
77 22 0.16
78 27 0.19
79 7 0.05
80 1 0.01
81 23 0.16
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (78 bp):
GGATCTTTCCCTAAATTAAAAACTTCGAAAGACTAGATGAGATCTTTCCCTAAATTAAAAACTTA
AAAAAACTTGATA
Found at i:2276 original size:39 final size:39
Alignment explanation
Indices: 2020--2268 Score: 212
Period size: 38 Copynumber: 6.4 Consensus size: 39
2010 TAAAACTTTA
*
2020 ATGGGATCTTTCCCTTAATTGAAAACTTCGAAAAAGACTAG
1 ATGGGATCTTTCCCTAAATTGAAAACTT-GAAAAAGACT-G
*
2061 ATGGGATCTTTCCCTAAATT-AAAACTTGAAAAAAAACTTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTG-AAAAAGAC-TG
* *
2101 ATGAGATCTTTCCCTAAATTAAAAACTTTG---AAGACTGG
1 ATGGGATCTTTCCCTAAATTGAAAAC-TTGAAAAAGACT-G
* *
2139 ATGAGATCTTTCCCTAAATTAAAAACTT-AAACAA-ACTTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTGAAA-AAGAC-TG
* * **
2178 ATAGGATCTTTCCC--AATTAGAAATCTTG--AAAGTTTG
1 ATGGGATCTTTCCCTAAATT-GAAAACTTGAAAAAGACTG
* ** *
2214 AGGGGATCTTTTTCTAAATTGAAAACTTGAAAAATACTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTGAAAAAGACTG
*
2253 GTGGGATCTTTCCCTA
1 ATGGGATCTTTCCCTA
2269 TTTTGAAATC
Statistics
Matches: 169, Mismatches: 22, Indels: 36
0.74 0.10 0.16
Matches are distributed among these distances:
36 14 0.08
37 16 0.09
38 41 0.24
39 33 0.20
40 37 0.22
41 25 0.15
42 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (39 bp):
ATGGGATCTTTCCCTAAATTGAAAACTTGAAAAAGACTG
Found at i:3689 original size:21 final size:21
Alignment explanation
Indices: 3663--3720 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
3653 ATTGAATTTT
3663 CCTTTATTCGGTACCCGCTCC
1 CCTTTATTCGGTACCCGCTCC
*
3684 CCTTTATTCGATACCCGCTCC
1 CCTTTATTCGGTACCCGCTCC
*
3705 TCTTTATTCGGTACCC
1 CCTTTATTCGGTACCC
3721 ACTTTCCCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.12, C:0.40, G:0.12, T:0.36
Consensus pattern (21 bp):
CCTTTATTCGGTACCCGCTCC
Found at i:3800 original size:45 final size:45
Alignment explanation
Indices: 3751--3840 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
3741 AATTTCCTCA
* * * *
3751 ACCCTAGACCCAATATGGCGGCTCCACTTGATTTTCTCATTGATT
1 ACCCTAAACCCAATATAGCGCCTCCACTTGATTTCCTCATTGATT
*
3796 ACCCTAAACCCAATATAGCGCCTCCTCTTGATTTCCTCATTGATT
1 ACCCTAAACCCAATATAGCGCCTCCACTTGATTTCCTCATTGATT
3841 TGGTTCTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33
Consensus pattern (45 bp):
ACCCTAAACCCAATATAGCGCCTCCACTTGATTTCCTCATTGATT
Done.