Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010775.1 Corchorus olitorius cultivar O-4 contig10807, 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: 3529
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Found at i:198 original size:28 final size:28
Alignment explanation
Indices: 159--406 Score: 185
Period size: 28 Copynumber: 8.6 Consensus size: 28
149 GAACATGAAA
159 AAAAATGACCAAAATGCCCCTGGACACG
1 AAAAATGACCAAAATGCCCCTGGACACG
* *
187 AAAAATGACCAAAATGCCCCCGGACATG
1 AAAAATGACCAAAATGCCCCTGGACACG
* * * *
215 AATAATGATCACAATTCCCCTCTGGAC-CTAG
1 AAAAATGACCA-AAATGCCC-CTGGACAC--G
* * * *
246 AAGAATGACCAGAATGCCCCTGAACATG
1 AAAAATGACCAAAATGCCCCTGGACACG
274 TAAAAAATGACCAAAATGCCCCTGGACACG
1 --AAAAATGACCAAAATGCCCCTGGACACG
** *
304 AAAAATGACCAAAATGCCCCCAGACATG
1 AAAAATGACCAAAATGCCCCTGGACACG
* * * *
332 AATAATGATCACAATTCCCCTCTGGAC-CTAG
1 AAAAATGACCA-AAATGCCC-CTGGACAC--G
* * ** *
363 AAGAATGACCAGAATGCCCCTAAACATG
1 AAAAATGACCAAAATGCCCCTGGACACG
*
391 TAAAATGACCAAAATG
1 AAAAATGACCAAAATG
407 AGAAGCAAAG
Statistics
Matches: 168, Mismatches: 40, Indels: 24
0.72 0.17 0.10
Matches are distributed among these distances:
28 84 0.50
29 21 0.12
30 43 0.26
31 20 0.12
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTGGACACG
Found at i:256 original size:59 final size:59
Alignment explanation
Indices: 190--382 Score: 241
Period size: 59 Copynumber: 3.3 Consensus size: 59
180 GGACACGAAA
190 AATGACCAAAATGCCCCCGGACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAG
1 AATGACCAAAATGCCCCCGGACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAG
* * * * * * * *
249 AATGACCAGAATGCCCCTGAACATGTAAAAAATGACCA-AAATGCCC-CTGGA-C-ACGAAA
1 AATGACCAAAATGCCCCCGGACATG--AATAATGATCACAATTCCCCTCTGGACCTA-GAAG
*
307 AATGACCAAAATGCCCCCAGACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAG
1 AATGACCAAAATGCCCCCGGACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAG
*
366 AATGACCAGAATGCCCC
1 AATGACCAAAATGCCCC
383 TAAACATGTA
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
56 9 0.08
57 7 0.06
58 30 0.28
59 47 0.43
60 7 0.06
61 9 0.08
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (59 bp):
AATGACCAAAATGCCCCCGGACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAG
Found at i:338 original size:117 final size:117
Alignment explanation
Indices: 144--406 Score: 476
Period size: 117 Copynumber: 2.3 Consensus size: 117
134 CTAAAATGCC
* *
144 CCCCTGAACATGAAAAAAAATGACCAAAATGCCCCTGGACACGAAAAATGACCAAAATGCCCCCG
1 CCCCTGAACATG-TAAAAAATGACCAAAATGCCCCTGGACACGAAAAATGACCAAAATGCCCCCA
209 GACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAGAATGACCAGAATG
65 GACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAGAATGACCAGAATG
262 CCCCTGAACATGTAAAAAATGACCAAAATGCCCCTGGACACGAAAAATGACCAAAATGCCCCCAG
1 CCCCTGAACATGTAAAAAATGACCAAAATGCCCCTGGACACGAAAAATGACCAAAATGCCCCCAG
327 ACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAGAATGACCAGAATG
66 ACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAGAATGACCAGAATG
*
379 CCCCTAAACATGT--AAAATGACCAAAATG
1 CCCCTGAACATGTAAAAAATGACCAAAATG
407 AGAAGCAAAG
Statistics
Matches: 142, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
115 15 0.11
117 115 0.81
118 12 0.08
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (117 bp):
CCCCTGAACATGTAAAAAATGACCAAAATGCCCCTGGACACGAAAAATGACCAAAATGCCCCCAG
ACATGAATAATGATCACAATTCCCCTCTGGACCTAGAAGAATGACCAGAATG
Found at i:690 original size:50 final size:50
Alignment explanation
Indices: 628--854 Score: 328
Period size: 50 Copynumber: 4.5 Consensus size: 50
618 CGATCAACTT
* * * * * *
628 CTTTGAATTGTCTCCCAATTTAATATTTAAGGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
678 CTTTGAACTGTCTACCAATCCAACCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
728 CTTTGAACTATCTACCAATTTAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
778 GTTTGAACTGTCTACCAACTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
828 GTTTGAACTGTCTACCAACTCAATCTT
1 CTTTGAACTGTCTACCAATTCAATCTT
855 GATATCTGGT
Statistics
Matches: 161, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 161 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Done.