Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015745.1 Corchorus capsularis cultivar CVL-1 contig15766, 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: 17014
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:8476 original size:30 final size:32

Alignment explanation


    Indices: 8409--8481  Score: 98
    Period size: 33  Copynumber: 2.3  Consensus size: 32

       8399 TCGCATGGAG

                                             
       8409 CAACCGGCCATCGCATGAGGCATCAACCAGCCA
          1 CAACCGGCCATCGCATGAGGCATC-ACCAGCCA

                             *               
       8442 CAACCGGCCATCGCATGGGGCAT--CC-GCGCA
          1 CAACCGGCCATCGCATGAGGCATCACCAGC-CA

                      
       8472 CAACCGGCCA
          1 CAACCGGCCA

       8482 ATGGATCCTT


Statistics
Matches: 38,  Mismatches: 1, Indels: 5
        0.86            0.02        0.11

Matches are distributed among these distances:
  29    2  0.05
  30   14  0.37
  33   22  0.58

ACGTcount: A:0.26, C:0.41, G:0.25, T:0.08


Consensus pattern (32 bp):   
CAACCGGCCATCGCATGAGGCATCACCAGCCA

Found at i:11533 original size:23 final size:23

Alignment explanation


    Indices: 11475--11533  Score: 66
    Period size: 23  Copynumber: 2.6  Consensus size: 23

      11465 TTAACGAATT

                        *          
      11475 AAGAAAACTAAAGCAAATTATAA
          1 AAGAAAACTAAATCAAATTATAA

             *    *                 
      11498 AGGAAACCTAAATC-AATATATAA
          1 AAGAAAACTAAATCAAAT-TATAA

                  *      
      11521 AAGAAATCTAAAT
          1 AAGAAAACTAAAT

      11534 ATATGAAAGA


Statistics
Matches: 30,  Mismatches: 5, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  22    3  0.10
  23   27  0.90

ACGTcount: A:0.61, C:0.10, G:0.08, T:0.20


Consensus pattern (23 bp):   
AAGAAAACTAAATCAAATTATAA

Found at i:16578 original size:29 final size:30

Alignment explanation


    Indices: 16543--16602  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

      16533 TATATAAATA

                    *                 *   
      16543 ATATAATATAATTAAATAA-TTATATTTAT
          1 ATATAATAAAATTAAATAATTTATATGTAT

                         *                
      16572 ATATAATAAAATTGAATAATTTATATGTAT
          1 ATATAATAAAATTAAATAATTTATATGTAT

             
      16602 A
          1 A

      16603 CATTAATTAG


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  29   17  0.63
  30   10  0.37

ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45


Consensus pattern (30 bp):   
ATATAATAAAATTAAATAATTTATATGTAT
Done.