Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000553.1 Corchorus capsularis cultivar CVL-1 contig00553, 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: 11809
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:9276 original size:10 final size:10

Alignment explanation


    Indices: 9261--9300  Score: 55
    Period size: 10  Copynumber: 4.1  Consensus size: 10

       9251 GCTATGCTCA

                      
       9261 TCTTTTTTTT
          1 TCTTTTTTTT

                  *   
       9271 TCTTTTCTTT
          1 TCTTTTTTTT

                    * 
       9281 TC-TTTTTGT
          1 TCTTTTTTTT

                      
       9290 TCTTTTTTTT
          1 TCTTTTTTTT

             
       9300 T
          1 T

       9301 AGATTTTCCT


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
   9    7  0.28
  10   18  0.72

ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85


Consensus pattern (10 bp):   
TCTTTTTTTT

Found at i:9300 original size:19 final size:19

Alignment explanation


    Indices: 9264--9299  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       9254 ATGCTCATCT

                 *             
       9264 TTTTTTTTCTTTTCTTTTC
          1 TTTTTGTTCTTTTCTTTTC

                              
       9283 TTTTTGTTCTTTT-TTTT
          1 TTTTTGTTCTTTTCTTTT

       9300 TAGATTTTCC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    4  0.25
  19   12  0.75

ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86


Consensus pattern (19 bp):   
TTTTTGTTCTTTTCTTTTC

Found at i:11458 original size:73 final size:74

Alignment explanation


    Indices: 11378--11528  Score: 225
    Period size: 73  Copynumber: 2.1  Consensus size: 74

      11368 TGGTCTTTTC

                      **                            *                *       
      11378 ACACTTTTCGGGTGACTAAAAAGCCCCTCCATGAGTTTC-CCCTATTCCTTTTCCTTCTACCC-T
          1 ACACTTTTCGAATGACTAAAAAGCCCCTCCATGAGTTTCAACC-ATTCCTTTTCCTTATACCCTT

                      
      11441 TTTCGTAATT
         65 TTTCGTAATT

                    *                    *                                   
      11451 ACACTTTTTGAATGACTAAAAAGCCCCTCTATGAGTTTCAACCATTCCTTTTCCTTATACCCTTT
          1 ACACTTTTCGAATGACTAAAAAGCCCCTCCATGAGTTTCAACCATTCCTTTTCCTTATACCCTTT

                     
      11516 TTCGTAATT
         66 TTCGTAATT

                
      11525 ACAC
          1 ACAC

      11529 ATTCACTTCC


Statistics
Matches: 70,  Mismatches: 6, Indels: 3
        0.89            0.08        0.04

Matches are distributed among these distances:
  73   53  0.76
  74   17  0.24

ACGTcount: A:0.23, C:0.29, G:0.09, T:0.38


Consensus pattern (74 bp):   
ACACTTTTCGAATGACTAAAAAGCCCCTCCATGAGTTTCAACCATTCCTTTTCCTTATACCCTTT
TTCGTAATT
Done.