Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010568.1 Corchorus capsularis cultivar CVL-1 contig10589, 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: 30702
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1558 original size:2 final size:2

Alignment explanation


    Indices: 1551--1581  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1541 CAAAAGTCAG

                                                          
       1551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1582 GTCATGTTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:7225 original size:10 final size:10

Alignment explanation


    Indices: 7210--7245  Score: 63
    Period size: 10  Copynumber: 3.6  Consensus size: 10

       7200 AATTTAATAT

                      
       7210 GGATATTTAC
          1 GGATATTTAC

                     *
       7220 GGATATTTAT
          1 GGATATTTAC

                      
       7230 GGATATTTAC
          1 GGATATTTAC

                  
       7240 GGATAT
          1 GGATAT

       7246 ATCGAGATTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  10   24  1.00

ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42


Consensus pattern (10 bp):   
GGATATTTAC

Found at i:7232 original size:20 final size:20

Alignment explanation


    Indices: 7207--7245  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       7197 TTTAATTTAA

                                
       7207 TATGGATATTTACGGATATT
          1 TATGGATATTTACGGATATT

                               
       7227 TATGGATATTTACGGATAT
          1 TATGGATATTTACGGATAT

       7246 ATCGAGATTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44


Consensus pattern (20 bp):   
TATGGATATTTACGGATATT

Found at i:14464 original size:45 final size:45

Alignment explanation


    Indices: 14413--14550  Score: 276
    Period size: 45  Copynumber: 3.1  Consensus size: 45

      14403 ACCCAGATGC

                                                         
      14413 ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG
          1 ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG

                                                         
      14458 ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG
          1 ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG

                                                         
      14503 ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG
          1 ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG

               
      14548 ATC
          1 ATC

      14551 CTCATTTGTT


Statistics
Matches: 93,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   93  1.00

ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31


Consensus pattern (45 bp):   
ATCTTTTTCTTCACTACAGGCAGGTAATATATGCACAGCACTAAG
Done.