Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005084.1 Corchorus capsularis cultivar CVL-1 contig05102, 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: 8487
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32


Found at i:5319 original size:2 final size:2

Alignment explanation


    Indices: 5312--5348  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       5302 AGCAAGTGCT

                                                                   
       5312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5349 GGAAGATAGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:5730 original size:89 final size:89

Alignment explanation


    Indices: 5578--5758  Score: 326
    Period size: 89  Copynumber: 2.0  Consensus size: 89

       5568 ATTTTTGGAG

                                                                *            
       5578 AGTAGACTTGAGAAAATTTCAGTTTAATTAATGCAAATTGAAACTCCTTTGGTTGTTTAGGAATT
          1 AGTAGACTTGAGAAAATTTCAGTTTAATTAATGCAAATTGAAACTCCTTTGGCTGTTTAGGAATT

                                    
       5643 AATGTTGAAGGCTATCTACAAAAT
         66 AATGTTGAAGGCTATCTACAAAAT

                               *                                      *      
       5667 AGTAGACTTGAGAAAATTTTAGTTTAATTAATGCAAATTGAAACTCCTTTGGCTGTTTGGGAATT
          1 AGTAGACTTGAGAAAATTTCAGTTTAATTAATGCAAATTGAAACTCCTTTGGCTGTTTAGGAATT

             *                      
       5732 ATTGTTGAAGGCTATCTACAAAAT
         66 AATGTTGAAGGCTATCTACAAAAT

               
       5756 AGT
          1 AGT

       5759 CATAAACCTT


Statistics
Matches: 88,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  89   88  1.00

ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36


Consensus pattern (89 bp):   
AGTAGACTTGAGAAAATTTCAGTTTAATTAATGCAAATTGAAACTCCTTTGGCTGTTTAGGAATT
AATGTTGAAGGCTATCTACAAAAT

Found at i:6870 original size:30 final size:29

Alignment explanation


    Indices: 6808--6877  Score: 86
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       6798 ACCGAACCGT

                                  ****   
       6808 CAAATAAGCCCCTGAACTATTATTTCGGC
          1 CAAATAAGCCCCTGAACTATTAAAAAGGC

                              *           
       6837 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
          1 CAAATAAGCCCCTGAACTATT-AAAAAGGC

                       
       6867 CAAATAAGCCC
          1 CAAATAAGCCC

       6878 TGATGCCAAG


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   20  0.57
  30   15  0.43

ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20


Consensus pattern (29 bp):   
CAAATAAGCCCCTGAACTATTAAAAAGGC
Done.