Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003314.1 Corchorus capsularis cultivar CVL-1 contig03322, 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, 745

Length: 1242
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38


Found at i:389 original size:39 final size:40

Alignment explanation


    Indices: 330--407  Score: 104
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        320 CTTTAAGATC

                          *            *            
        330 ATTGCTTTATCAGTTAATTTCAGAATCGTATTC-AGGATT
          1 ATTGCTTTATCAGTGAATTTCAGAATCCTATTCGAGGATT

                *          *       *               
        369 ATTGTTTTATCAGTGGATTTCAGGATCCTATTCGAGGAT
          1 ATTGCTTTATCAGTGAATTTCAGAATCCTATTCGAGGAT

        408 CTCTTTGCTT


Statistics
Matches: 33,  Mismatches: 5, Indels: 1
        0.85            0.13        0.03

Matches are distributed among these distances:
  39   28  0.85
  40    5  0.15

ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42


Consensus pattern (40 bp):   
ATTGCTTTATCAGTGAATTTCAGAATCCTATTCGAGGATT

Found at i:722 original size:28 final size:27

Alignment explanation


    Indices: 661--790  Score: 172
    Period size: 27  Copynumber: 4.8  Consensus size: 27

        651 TAGGGTCACC

                           *     *     
        661 CAGGGGCATTTTGGTGATTTTCACATT
          1 CAGGGGCATTTTGGTCATTTTTACATT

                  *               *    
        688 CAGGGGTATTTTGGTCATTTTTGCATT
          1 CAGGGGCATTTTGGTCATTTTTACATT

                   *                    
        715 CAGGGGGTATTTTGGTCATTTTTACATT
          1 CA-GGGGCATTTTGGTCATTTTTACATT

                                   *    
        743 CAGGGGCATTCTT-GTCATTTTTGCATT
          1 CAGGGGCATT-TTGGTCATTTTTACATT

                         *       
        770 CAGGGGCATTTTGATCATTTT
          1 CAGGGGCATTTTGGTCATTTT

        791 GAATCCATTT


Statistics
Matches: 92,  Mismatches: 8, Indels: 6
        0.87            0.08        0.06

Matches are distributed among these distances:
  26    2  0.02
  27   62  0.67
  28   28  0.30

ACGTcount: A:0.17, C:0.14, G:0.25, T:0.45


Consensus pattern (27 bp):   
CAGGGGCATTTTGGTCATTTTTACATT

Found at i:728 original size:55 final size:55

Alignment explanation


    Indices: 663--790  Score: 188
    Period size: 55  Copynumber: 2.3  Consensus size: 55

        653 GGGTCACCCA

                         *                 *                        
        663 GGGGCATTTTGGTGATTTTCACATTCAGGGGTATT-TTGGTCATTTTTGCATTCAG
          1 GGGGCATTTTGGTCATTTTCACATTCAGGGGCATTCTT-GTCATTTTTGCATTCAG

                *              *                                   
        718 GGGGTATTTTGGTCATTTTTACATTCAGGGGCATTCTTGTCATTTTTGCATTCA-
          1 GGGGCATTTTGGTCATTTTCACATTCAGGGGCATTCTTGTCATTTTTGCATTCAG

                       *       
        772 GGGGCATTTTGATCATTTT
          1 GGGGCATTTTGGTCATTTT

        791 GAATCCATTT


Statistics
Matches: 66,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  54   17  0.26
  55   47  0.71
  56    2  0.03

ACGTcount: A:0.16, C:0.13, G:0.25, T:0.45


Consensus pattern (55 bp):   
GGGGCATTTTGGTCATTTTCACATTCAGGGGCATTCTTGTCATTTTTGCATTCAG
Done.