Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001243.1 Corchorus olitorius cultivar O-4 contig01243, 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, 704

Length: 1174
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23


Found at i:353 original size:28 final size:28

Alignment explanation


    Indices: 331--408  Score: 138
    Period size: 28  Copynumber: 2.8  Consensus size: 28

        321 CCCCTAGATG

                  *      *              
        331 TGTAAATTGACCAAAATGCCCCTGGACA
          1 TGTAAAATGACCAGAATGCCCCTGGACA

                                        
        359 TGTAAAATGACCAGAATGCCCCTGGACA
          1 TGTAAAATGACCAGAATGCCCCTGGACA

                                  
        387 TGTAAAATGACCAGAATGCCCC
          1 TGTAAAATGACCAGAATGCCCC

        409 CTTAAGTGAC


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   48  1.00

ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19


Consensus pattern (28 bp):   
TGTAAAATGACCAGAATGCCCCTGGACA

Found at i:994 original size:41 final size:42

Alignment explanation


    Indices: 893--1149  Score: 367
    Period size: 41  Copynumber: 6.1  Consensus size: 42

        883 CCAATAACCA

                     *                  *            * 
        893 AAAGTCCCCGAACACATATATAACACAGGGGCATCTCTATTCC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTCTATTAC

                    *                   *              
        936 AAAAGTCCTCAAACACATATATAACACAAAGGCA-TCTATTAC
          1 -AAAGTCCCCAAACACATATATAACACAGAGGCACTCTATTAC

                                        *              
        978 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTCTATTAC

                   *                                  
       1021 AAAGTCCTCAAACACATATATAACACAGAGGCA-TCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACTCTATTAC

                                        *              
       1062 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTCTATTAC

                   *                           *      
       1105 AAAGTCCTCAAACACATATATAACACAGAGGCA-TTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACTCTATTAC

                
       1146 AAAG
          1 AAAG

       1150 GGCAAAGGCT


Statistics
Matches: 194,  Mismatches: 15, Indels: 11
        0.88            0.07        0.05

Matches are distributed among these distances:
  41   80  0.41
  42    7  0.04
  43   78  0.40
  44   29  0.15

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (42 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCACTCTATTAC

Found at i:1060 original size:84 final size:84

Alignment explanation


    Indices: 893--1149  Score: 460
    Period size: 84  Copynumber: 3.0  Consensus size: 84

        883 CCAATAACCA

                     *                       *       *                       
        893 AAAGTCCCCGAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC-AAAGTCCTCAAACACATATAT

                  *             
        958 AACACAAAGGCATCTATTAC
         65 AACACAGAGGCATCTATTAC

                                                                             
        978 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA

                               
       1043 ACACAGAGGCATCTATTAC
         66 ACACAGAGGCATCTATTAC

                                                                             
       1062 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA

                        *      
       1127 ACACAGAGGCATTTATTAC
         66 ACACAGAGGCATCTATTAC

                
       1146 AAAG
          1 AAAG

       1150 GGCAAAGGCT


Statistics
Matches: 167,  Mismatches: 5, Indels: 1
        0.97            0.03        0.01

Matches are distributed among these distances:
  84  127  0.76
  85   40  0.24

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATTAC
Done.