Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009028.1 Corchorus capsularis cultivar CVL-1 contig09049, 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: 5648
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1840 original size:27 final size:27

Alignment explanation


    Indices: 1810--1877  Score: 84
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       1800 GTCAGACTCT

                 *           *          
       1810 CATTCCAAGTTAGTCAAGACAG-TTCTC
          1 CATTCAAAGTTAGTCAAAACAGTTTC-C

                    **                 
       1837 CATTCAAAACTAGTCAAAACAGTTTCC
          1 CATTCAAAGTTAGTCAAAACAGTTTCC

                          
       1864 CATTCAAAGTTAGT
          1 CATTCAAAGTTAGT

       1878 TCCCTAGGAT


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  27   31  0.91
  28    3  0.09

ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29


Consensus pattern (27 bp):   
CATTCAAAGTTAGTCAAAACAGTTTCC

Found at i:3018 original size:27 final size:27

Alignment explanation


    Indices: 2988--3066  Score: 86
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       2978 GCATTGGGGT

                      *                
       2988 CGCCCAAGGGTATTTTGGTCATTTTCG
          1 CGCCCAAGGGCATTTTGGTCATTTTCG

                  *                  **
       3015 CGCCCAGGGGCATTTTGGTCATTTTTA
          1 CGCCCAAGGGCATTTTGGTCATTTTCG

             * * *          *        
       3042 CACTCGAGGGCATTTTAGTCATTTT
          1 CGCCCAAGGGCATTTTGGTCATTTT

       3067 TAAGTTCACC


Statistics
Matches: 43,  Mismatches: 9, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  27   43  1.00

ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38


Consensus pattern (27 bp):   
CGCCCAAGGGCATTTTGGTCATTTTCG

Found at i:3713 original size:21 final size:21

Alignment explanation


    Indices: 3689--3732  Score: 54
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       3679 GGCTTTTATT

                                  
       3689 TACAAA-ACAGTACCAAATAAA
          1 TACAAATACA-TACCAAATAAA

                        *         
       3710 TACAAATTACATGCCAAATAAA
          1 TACAAA-TACATACCAAATAAA

             
       3732 T
          1 T

       3733 GTAAAGTAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  21    6  0.30
  22   11  0.55
  23    3  0.15

ACGTcount: A:0.57, C:0.18, G:0.05, T:0.20


Consensus pattern (21 bp):   
TACAAATACATACCAAATAAA
Done.