Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006431.1 Corchorus capsularis cultivar CVL-1 contig06452, 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: 2994
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34


Found at i:1386 original size:33 final size:33

Alignment explanation


    Indices: 1338--1434  Score: 140
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       1328 GTCTTTTAGA

                                  *   *      
       1338 TGTTGTTTGTGATGATACTAAACCTAATTTGAG
          1 TGTTGTTTGTGATGATACTAAATCTATTTTGAG

                     **              *    *  
       1371 TGTTGTTTGCAATGATACTAAATCTGTTTTAAG
          1 TGTTGTTTGTGATGATACTAAATCTATTTTGAG

                                           
       1404 TGTTGTTTGTGATGATACTAAATCTATTTTG
          1 TGTTGTTTGTGATGATACTAAATCTATTTTG

       1435 GATGCTAATT


Statistics
Matches: 54,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   54  1.00

ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46


Consensus pattern (33 bp):   
TGTTGTTTGTGATGATACTAAATCTATTTTGAG

Found at i:1465 original size:66 final size:66

Alignment explanation


    Indices: 1338--1466  Score: 145
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       1328 GTCTTTTAGA

                                               * **         *       *        
       1338 TGTTGTTTGTGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGATACTAAATCTGTTTTAA
          1 TGTTGTTTGTGATGATACTAAACCTAATTTGAGTGCTAATTGCAATGAAACTAAATATGTTTTAA

             
       1403 G
         66 G

                                  *   *                **                    
       1404 TGTTGTTTGTGATGATACTAAATCTATTTTG-GATGCTAATTGTGATGAAAAC-AAATATGTTTT
          1 TGTTGTTTGTGATGATACTAAACCTAATTTGAG-TGCTAATTGCAATG-AAACTAAATATGTTTT

       1467 GATTGATCAT


Statistics
Matches: 52,  Mismatches: 9, Indels: 4
        0.80            0.14        0.06

Matches are distributed among these distances:
  65    1  0.02
  66   48  0.92
  67    3  0.06

ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44


Consensus pattern (66 bp):   
TGTTGTTTGTGATGATACTAAACCTAATTTGAGTGCTAATTGCAATGAAACTAAATATGTTTTAA
G

Found at i:1507 original size:33 final size:33

Alignment explanation


    Indices: 1464--1534  Score: 115
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       1454 ACAAATATGT

                *                            
       1464 TTTGATTGATCATAGCATTGCAAATAATTCTGA
          1 TTTGGTTGATCATAGCATTGCAAATAATTCTGA

                                *           *
       1497 TTTGGTTGATCATAGCATTGTAAATAATTCTGT
          1 TTTGGTTGATCATAGCATTGCAAATAATTCTGA

                 
       1530 TTTGG
          1 TTTGG

       1535 GAGAAAAGAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44


Consensus pattern (33 bp):   
TTTGGTTGATCATAGCATTGCAAATAATTCTGA
Done.