Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003704.1 Corchorus capsularis cultivar CVL-1 contig03712, 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, 902

Length: 1504
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27


Found at i:151 original size:21 final size:21

Alignment explanation


    Indices: 127--195  Score: 86
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        117 AATAATAATC

                                 
        127 AGTAAAAAGGTAATCAGTAAG
          1 AGTAAAAAGGTAATCAGTAAG

                                  
        148 AGTAAAATA-GTAATCAGTAAG
          1 AGTAAAA-AGGTAATCAGTAAG

              *    *      *       
        169 AGCAAAATGGTAATTAGTAAAG
          1 AGTAAAAAGGTAATCAGT-AAG

                 
        191 AGTAA
          1 AGTAA

        196 TCAGTAAAGA


Statistics
Matches: 41,  Mismatches: 4, Indels: 5
        0.82            0.08        0.10

Matches are distributed among these distances:
  21   33  0.80
  22    8  0.20

ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22


Consensus pattern (21 bp):   
AGTAAAAAGGTAATCAGTAAG

Found at i:202 original size:42 final size:42

Alignment explanation


    Indices: 54--202  Score: 97
    Period size: 42  Copynumber: 3.4  Consensus size: 42

         44 AGTAAAACTA

                                                   *   *    
         54 AAAGAAGTAATCAGTAAATCAGTAAAAGCAAAAATGGCAAAGAATAGT
          1 AAAG-AGTAATCAGT-AATCAGTAAAAGC-AAAATGG--TA-ATTAGT

               *        *       *    *  *    *      *   
        102 AAAAAGTAATCGGGTAAT-AATAATCAGTAAAAAGGTAATCAGT
          1 AAAGAGTAATC-AGTAATCAGTAA-AAGCAAAATGGTAATTAGT

                                     *                  
        145 -AAGAGTAAAAT-AGTAATCAGTAAGAGCAAAATGGTAATTAGT
          1 AAAGAGT--AATCAGTAATCAGTAAAAGCAAAATGGTAATTAGT

                            
        187 AAAGAGTAATCAGTAA
          1 AAAGAGTAATCAGTAA

        203 AGAGAAAAGG


Statistics
Matches: 78,  Mismatches: 16, Indels: 20
        0.68            0.14        0.18

Matches are distributed among these distances:
  41    3  0.04
  42   30  0.38
  43   14  0.18
  44    4  0.05
  46   10  0.13
  47   12  0.15
  48    5  0.06

ACGTcount: A:0.53, C:0.07, G:0.19, T:0.21


Consensus pattern (42 bp):   
AAAGAGTAATCAGTAATCAGTAAAAGCAAAATGGTAATTAGT

Found at i:1151 original size:13 final size:13

Alignment explanation


    Indices: 1128--1165  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       1118 AATTCCGAAA

                      *  
       1128 AAAATCAAAAATC
          1 AAAATCAAAATTC

                          
       1141 AAAATTCAAAATTC
          1 AAAA-TCAAAATTC

                        
       1155 AAAA-CAAAATT
          1 AAAATCAAAATT

       1166 TCATTCCAAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  12    7  0.30
  13    4  0.17
  14   12  0.52

ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21


Consensus pattern (13 bp):   
AAAATCAAAATTC
Done.