Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011795.1 Corchorus capsularis cultivar CVL-1 contig11816, 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: 59003
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:11227 original size:30 final size:29
Alignment explanation
Indices: 11160--11231 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
11150 ACACCGAACC
****
11160 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
11189 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
11219 GTCAAATAAGCCC
1 GTCAAATAAGCCC
11232 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:11875 original size:25 final size:25
Alignment explanation
Indices: 11841--11890 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
11831 AAGAAAAGGA
11841 TAGTAAGATTAGACTAGACAATTCT
1 TAGTAAGATTAGACTAGACAATTCT
11866 TAGTAAGATTAGACTAGACAATTCT
1 TAGTAAGATTAGACTAGACAATTCT
11891 GATTTCCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (25 bp):
TAGTAAGATTAGACTAGACAATTCT
Found at i:17104 original size:51 final size:51
Alignment explanation
Indices: 17028--17129 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
17018 ATTAAGATGT
* *
17028 TTATGATAGAATTAAATTCTGGTTATATATGCTTTTGATATGTTGGAAGGA
1 TTATGATAGAATTAAATTCTGGTTATATATGCTTTTGAGATATTGGAAGGA
*
17079 TTATGATAGAATTAAATTTTGGTTATATATGCTTTTGAGATATTGGAAGGA
1 TTATGATAGAATTAAATTCTGGTTATATATGCTTTTGAGATATTGGAAGGA
17130 ATTAAAGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (51 bp):
TTATGATAGAATTAAATTCTGGTTATATATGCTTTTGAGATATTGGAAGGA
Found at i:25129 original size:3 final size:3
Alignment explanation
Indices: 25123--25165 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
25113 CCTTTTGTTG
25123 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
25166 TTCGTATACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36293 original size:2 final size:2
Alignment explanation
Indices: 36288--36323 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36278 ATAAATTTTT
36288 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
36324 GTAGTTGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36976 original size:95 final size:95
Alignment explanation
Indices: 36813--37002 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
36803 GTCGCGTTTA
36813 TTTAAGGGAAATTTTATGTAAAAATTTTGATTAGGATAAAGTCAAGTAGCTAGATATACCAACGA
1 TTTAAGGGAAATTTTATGTAAAAATTTTGATTAGGATAAAGTCAAGTAGCTAGATATACCAACGA
36878 TCATCCATTATGTATAGTATATTAAGTATT
66 TCATCCATTATGTATAGTATATTAAGTATT
36908 TTTAAGGGAAATTTTATGTAAAAATTTTGATTAGGATAAAGTCAAGTAGCTAGATATACCAACGA
1 TTTAAGGGAAATTTTATGTAAAAATTTTGATTAGGATAAAGTCAAGTAGCTAGATATACCAACGA
36973 TCATCCATTATGTATAGTATATTAAGTATT
66 TCATCCATTATGTATAGTATATTAAGTATT
37003 ACACCATTAT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (95 bp):
TTTAAGGGAAATTTTATGTAAAAATTTTGATTAGGATAAAGTCAAGTAGCTAGATATACCAACGA
TCATCCATTATGTATAGTATATTAAGTATT
Found at i:40957 original size:31 final size:28
Alignment explanation
Indices: 40900--40972 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 28
40890 TGTCTATATT
40900 AAGTTATAGCTA--TTTTTTTTCGAATA
1 AAGTTATAGCTATTTTTTTTTTCGAATA
*
40926 AAGTTATAGCTATTTTTTTTTTGGATAAATA
1 AAGTTATAGCTATTTTTTTTTTCG---AATA
40957 AAGTTATAGCTATTTT
1 AAGTTATAGCTATTTT
40973 AATTGAACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 12 0.29
28 9 0.22
31 20 0.49
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (28 bp):
AAGTTATAGCTATTTTTTTTTTCGAATA
Found at i:56806 original size:3 final size:3
Alignment explanation
Indices: 56798--56835 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
56788 GTGTAATGAT
*
56798 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56836 GCATCTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.