Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012653.1 Corchorus capsularis cultivar CVL-1 contig12674, 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: 11199
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:654 original size:26 final size:28

Alignment explanation


    Indices: 611--663  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 28

        601 TTTTCCTGGC

                  * *                   
        611 AGGCTTGTTCAAATCCTTT-TTCTTTGT
          1 AGGCTTCTCCAAATCCTTTCTTCTTTGT

                                       
        638 AGGCTTCTCCAAA-CCTTTCTTCTTTG
          1 AGGCTTCTCCAAATCCTTTCTTCTTTG

        664 AAGACTTTTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  26    5  0.22
  27   18  0.78

ACGTcount: A:0.15, C:0.25, G:0.13, T:0.47


Consensus pattern (28 bp):   
AGGCTTCTCCAAATCCTTTCTTCTTTGT

Found at i:5599 original size:28 final size:28

Alignment explanation


    Indices: 5559--5616  Score: 89
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       5549 GTGATTCATG

                                        
       5559 AAAGTCGTAAATCATGAAATAACCTTTT
          1 AAAGTCGTAAATCATGAAATAACCTTTT

                 *              * *     
       5587 AAAGTTGTAAATCATGAAATTATCTTTT
          1 AAAGTCGTAAATCATGAAATAACCTTTT

              
       5615 AA
          1 AA

       5617 TAGAGACTTG


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36


Consensus pattern (28 bp):   
AAAGTCGTAAATCATGAAATAACCTTTT

Found at i:7945 original size:2 final size:2

Alignment explanation


    Indices: 7932--7966  Score: 61
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7922 GTTAAAAATA

                                                               
       7932 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT

       7967 TTTTTGTCTG


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   30  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Done.