Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011870.1 Corchorus capsularis cultivar CVL-1 contig11891, 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: 3091
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37


Found at i:336 original size:14 final size:14

Alignment explanation


    Indices: 317--359  Score: 61
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        307 CAATTTTGAC

                          
        317 CTTCTTACTGATTA
          1 CTTCTTACTGATTA

                  *       
        331 CTTCTTCCTGATTA
          1 CTTCTTACTGATTA

                           
        345 CTT-TTACCTGATTA
          1 CTTCTTA-CTGATTA

             
        359 C
          1 C

        360 CTTTTACTAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  13    2  0.08
  14   24  0.92

ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49


Consensus pattern (14 bp):   
CTTCTTACTGATTA

Found at i:399 original size:14 final size:14

Alignment explanation


    Indices: 382--415  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        372 TTTGCCATTT

                          
        382 TTACTTTTTACCGA
          1 TTACTTTTTACCGA

                 *     *  
        396 TTACTCTTTACTGA
          1 TTACTTTTTACCGA

                  
        410 TTACTT
          1 TTACTT

        416 CCTTTAATTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53


Consensus pattern (14 bp):   
TTACTTTTTACCGA

Found at i:895 original size:22 final size:23

Alignment explanation


    Indices: 870--913  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        860 TTTTCACTTA

                                   
        870 ATTACTA-TTACTTTGACTCTTG
          1 ATTACTATTTACTTTGACTCTTG

                       *          
        892 ATTACTATTTATTTTGACTCTT
          1 ATTACTATTTACTTTGACTCTT

        914 AATTTTTATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22    7  0.35
  23   13  0.65

ACGTcount: A:0.23, C:0.16, G:0.07, T:0.55


Consensus pattern (23 bp):   
ATTACTATTTACTTTGACTCTTG

Found at i:2653 original size:2 final size:2

Alignment explanation


    Indices: 2646--2674  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2636 CTACTGTTGG

                                                       
       2646 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 T

       2675 GCCTGAGTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.