Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012929.1 Corchorus capsularis cultivar CVL-1 contig12950, 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: 6104
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1851 original size:42 final size:42

Alignment explanation


    Indices: 1782--1872  Score: 157
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       1772 AGTGCATTAC

                                   *                  
       1782 CTAA-ATTCTACTCCATCTCAAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCATCTCAAGATAATTCATCAAAATAAAG

                                *                     
       1823 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCATCTCAAGATAATTCATCAAAATAAAG

                    
       1865 CTAATATT
          1 CTAATATT

       1873 AATTGTTGCT


Statistics
Matches: 47,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  41    4  0.09
  42   43  0.91

ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33


Consensus pattern (42 bp):   
CTAATATTCTACTCCATCTCAAGATAATTCATCAAAATAAAG

Found at i:5600 original size:27 final size:27

Alignment explanation


    Indices: 5563--5665  Score: 118
    Period size: 27  Copynumber: 3.8  Consensus size: 27

       5553 GTATCAGGGT

                  *                    
       5563 CATCCATGGGCATTTTGGTCATTTGCA
          1 CATCCAAGGGCATTTTGGTCATTTGCA

            **  * *                    
       5590 TGTCTAGGGGCATTTTGGTCATTTGCA
          1 CATCCAAGGGCATTTTGGTCATTTGCA

                      *                
       5617 CATCCAAGGGTATTTTGGTCATTTGCA
          1 CATCCAAGGGCATTTTGGTCATTTGCA

               *  *                
       5644 CATTCAGGGGCATTCTT-GTCAT
          1 CATCCAAGGGCATT-TTGGTCAT

       5666 CTCAGGTCCA


Statistics
Matches: 63,  Mismatches: 12, Indels: 2
        0.82            0.16        0.03

Matches are distributed among these distances:
  27   61  0.97
  28    2  0.03

ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38


Consensus pattern (27 bp):   
CATCCAAGGGCATTTTGGTCATTTGCA

Found at i:5653 original size:54 final size:54

Alignment explanation


    Indices: 5563--5665  Score: 140
    Period size: 54  Copynumber: 1.9  Consensus size: 54

       5553 GTATCAGGGT

                  *                                                
       5563 CATCCATGGGCATTTTGGTCATTTGCATGTCTAGGGGCATT-TTGGTCATTTGCA
          1 CATCCAAGGGCATTTTGGTCATTTGCATGTCTAGGGGCATTCTT-GTCATTTGCA

                      *                                        
       5617 CATCCAAGGGTATTTTGGTCATTTGCACAT-TC-AGGGGCATTCTTGTCAT
          1 CATCCAAGGGCATTTTGGTCATTTG--CATGTCTAGGGGCATTCTTGTCAT

       5666 CTCAGGTCCA


Statistics
Matches: 44,  Mismatches: 2, Indels: 6
        0.85            0.04        0.12

Matches are distributed among these distances:
  54   37  0.84
  55    4  0.09
  56    3  0.07

ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38


Consensus pattern (54 bp):   
CATCCAAGGGCATTTTGGTCATTTGCATGTCTAGGGGCATTCTTGTCATTTGCA

Found at i:5756 original size:22 final size:20

Alignment explanation


    Indices: 5724--5763  Score: 62
    Period size: 22  Copynumber: 1.9  Consensus size: 20

       5714 ATTGCATTTG

                                
       5724 AAAAAAGAAGAAGAAAAACA
          1 AAAAAAGAAGAAGAAAAACA

                                
       5744 AAAAAAGAAAAGAAGAAAAA
          1 AAAAAAG--AAGAAGAAAAA

       5764 ATATCTTAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    7  0.39
  22   11  0.61

ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00


Consensus pattern (20 bp):   
AAAAAAGAAGAAGAAAAACA
Done.