Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005905.1 Corchorus olitorius cultivar O-4 contig05930, 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, 952

Length: 1587
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36


Found at i:896 original size:21 final size:22

Alignment explanation


    Indices: 870--950  Score: 110
    Period size: 22  Copynumber: 3.7  Consensus size: 22

        860 CATATGGAGT

                  *               
        870 TTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTTATAGGGTAA

                            *   **
        891 TTATCAAAATTTTATATGGTGG
          1 TTATCAAAATTTTATAGGGTAA

                        *         
        913 TTATCAAAATTTAATAGGGTAA
          1 TTATCAAAATTTTATAGGGTAA

                            
        935 TTATCAAAATTTTATA
          1 TTATCAAAATTTTATA

        951 AAAATATTCA


Statistics
Matches: 51,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  21   15  0.29
  22   36  0.71

ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43


Consensus pattern (22 bp):   
TTATCAAAATTTTATAGGGTAA

Found at i:900 original size:65 final size:64

Alignment explanation


    Indices: 826--950  Score: 146
    Period size: 65  Copynumber: 1.9  Consensus size: 64

        816 ATAGGAAAAT

                *             *            *   *                *            
        826 TTATTAAAATTTCATA-GTTAGGTTATCAAAGTTTCATATGGAGT-TTATCACAATTTTATAGGT
          1 TTATCAAAATTTCATATGGT-GGTTATCAAAATTTAATA-GG-GTATTATCAAAATTTTATAGGT

              
        889 AA
         63 AA

                        *                                               
        891 TTATCAAAATTTTATATGGTGGTTATCAAAATTTAATAGGGTAATTATCAAAATTTTATA
          1 TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAGGGT-ATTATCAAAATTTTATA

        951 AAAATATTCA


Statistics
Matches: 51,  Mismatches: 6, Indels: 6
        0.81            0.10        0.10

Matches are distributed among these distances:
  63    2  0.04
  64    2  0.04
  65   45  0.88
  66    2  0.04

ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43


Consensus pattern (64 bp):   
TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAGGGTATTATCAAAATTTTATAGGTAA

Found at i:908 original size:43 final size:44

Alignment explanation


    Indices: 848--950  Score: 145
    Period size: 43  Copynumber: 2.4  Consensus size: 44

        838 CATAGTTAGG

                    *   *        *      *     *         
        848 TTATCAAAGTTTCATATGGAGTTTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTTATATGGAGGTTATCAAAATTTAATAGGGTAA

                               *                        
        891 TTATCAAAATTTTATATGGTGGTTATCAAAATTTAATAGGGTAA
          1 TTATCAAAATTTTATATGGAGGTTATCAAAATTTAATAGGGTAA

                            
        935 TTATCAAAATTTTATA
          1 TTATCAAAATTTTATA

        951 AAAATATTCA


Statistics
Matches: 53,  Mismatches: 6, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  43   32  0.60
  44   21  0.40

ACGTcount: A:0.38, C:0.07, G:0.13, T:0.43


Consensus pattern (44 bp):   
TTATCAAAATTTTATATGGAGGTTATCAAAATTTAATAGGGTAA

Found at i:919 original size:22 final size:22

Alignment explanation


    Indices: 848--950  Score: 109
    Period size: 22  Copynumber: 4.7  Consensus size: 22

        838 CATAGTTAGG

                    *   *      * *
        848 TTATCAAAGTTTCATATGGAGT
          1 TTATCAAAATTTTATATGGTGA

                  *             * 
        870 TTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTTATATGGTGA

                                 *
        891 TTATCAAAATTTTATATGGTGG
          1 TTATCAAAATTTTATATGGTGA

                        *   *   * 
        913 TTATCAAAATTTAATAGGGTAA
          1 TTATCAAAATTTTATATGGTGA

                            
        935 TTATCAAAATTTTATA
          1 TTATCAAAATTTTATA

        951 AAAATATTCA


Statistics
Matches: 66,  Mismatches: 14, Indels: 2
        0.80            0.17        0.02

Matches are distributed among these distances:
  21   17  0.26
  22   49  0.74

ACGTcount: A:0.38, C:0.07, G:0.13, T:0.43


Consensus pattern (22 bp):   
TTATCAAAATTTTATATGGTGA
Done.