Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003810.1 Corchorus capsularis cultivar CVL-1 contig03818, 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: 2010
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:760 original size:28 final size:28

Alignment explanation


    Indices: 720--776  Score: 114
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        710 TGATATCGAT

                                        
        720 AATTTGCATACTTAATCATGGATGCTAC
          1 AATTTGCATACTTAATCATGGATGCTAC

                                        
        748 AATTTGCATACTTAATCATGGATGCTAC
          1 AATTTGCATACTTAATCATGGATGCTAC

             
        776 A
          1 A

        777 CACTCTAAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   29  1.00

ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35


Consensus pattern (28 bp):   
AATTTGCATACTTAATCATGGATGCTAC

Found at i:1291 original size:23 final size:23

Alignment explanation


    Indices: 1262--1305  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1252 TGATTAAAAA

                      *            
       1262 ATAATTTTTTGAAAAAAAAATAT
          1 ATAATTTTTTAAAAAAAAAATAT

                                 
       1285 ATAATTTTTTAAAAAAAAAAT
          1 ATAATTTTTTAAAAAAAAAAT

       1306 TGGTGAGGGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39


Consensus pattern (23 bp):   
ATAATTTTTTAAAAAAAAAATAT

Found at i:1373 original size:30 final size:31

Alignment explanation


    Indices: 1311--1385  Score: 91
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       1301 AAAATTGGTG

                              *            
       1311 AGGGACCCAATTGCTCAATTAACTCAACTTC
          1 AGGGACCCAATTGCTCAACTAACTCAACTTC

                  *                *        
       1342 AGGGACTCAATTGCTC-ACTAAGTTC-ACTTC
          1 AGGGACCCAATTGCTCAACTAA-CTCAACTTC

                     *    
       1372 AGGGACCCATTTGC
          1 AGGGACCCAATTGC

       1386 ACATTTGCCC


Statistics
Matches: 38,  Mismatches: 5, Indels: 3
        0.83            0.11        0.07

Matches are distributed among these distances:
  30   21  0.55
  31   17  0.45

ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27


Consensus pattern (31 bp):   
AGGGACCCAATTGCTCAACTAACTCAACTTC
Done.