Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007927.1 Corchorus capsularis cultivar CVL-1 contig07948, 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: 24246
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34


Found at i:1803 original size:10 final size:10

Alignment explanation


    Indices: 1790--1814  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       1780 TATATTCAGC

                      
       1790 CCATATAAGT
          1 CCATATAAGT

                      
       1800 CCATATAAGT
          1 CCATATAAGT

                 
       1810 CCATA
          1 CCATA

       1815 ATTGGAGTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28


Consensus pattern (10 bp):   
CCATATAAGT

Found at i:9262 original size:2 final size:2

Alignment explanation


    Indices: 9257--9283  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       9247 TGTGTGTGTC

                                                    
       9257 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 T

       9284 TAATAATGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:12792 original size:24 final size:24

Alignment explanation


    Indices: 12765--12819  Score: 74
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      12755 AATATATATT

                *                   
      12765 ATATTTATAAAATATAAAAGCATA
          1 ATATATATAAAATATAAAAGCATA

                    ***             
      12789 ATATATATTTTATATAAAAGCATA
          1 ATATATATAAAATATAAAAGCATA

                   
      12813 ATATATA
          1 ATATATA

      12820 CTTTCCCCGA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38


Consensus pattern (24 bp):   
ATATATATAAAATATAAAAGCATA

Found at i:14561 original size:13 final size:13

Alignment explanation


    Indices: 14543--14567  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      14533 TTTATAACCT

                         
      14543 CATAAATCATATC
          1 CATAAATCATATC

                        
      14556 CATAAATCATAT
          1 CATAAATCATAT

      14568 TTAATATATA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32


Consensus pattern (13 bp):   
CATAAATCATATC

Found at i:23636 original size:23 final size:23

Alignment explanation


    Indices: 23610--23655  Score: 74
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      23600 TTCGAAAGTT

                         *   *     
      23610 GTCATGCCTCTACTATTGTTGAG
          1 GTCATGCCTCTACCATTATTGAG

                                   
      23633 GTCATGCCTCTACCATTATTGAG
          1 GTCATGCCTCTACCATTATTGAG

      23656 ATTAAGCAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37


Consensus pattern (23 bp):   
GTCATGCCTCTACCATTATTGAG
Done.