Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017802.1 Corchorus olitorius cultivar O-4 contig17835, 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: 5034
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Found at i:3222 original size:21 final size:22

Alignment explanation


    Indices: 3196--3272  Score: 102
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       3186 CTTATGGAAT

                  *     *        *
       3196 TTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTAATAGGGTAG

                        *   *     
       3217 TTATCAAAATTTCATATGGTAG
          1 TTATCAAAATTTAATAGGGTAG

                                  
       3239 TTATCAAAATTTAATAGGGTAG
          1 TTATCAAAATTTAATAGGGTAG

                        
       3261 TTATCAAAATTT
          1 TTATCAAAATTT

       3273 CATAAAAATA


Statistics
Matches: 50,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  21   14  0.28
  22   36  0.72

ACGTcount: A:0.39, C:0.08, G:0.12, T:0.42


Consensus pattern (22 bp):   
TTATCAAAATTTAATAGGGTAG

Found at i:3235 original size:43 final size:44

Alignment explanation


    Indices: 3174--3276  Score: 136
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       3164 CATTGTTAGG

                    *    *       *      *     *         
       3174 TTATCAAAGTTTCTTATGGAATTTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGGGTAA

                               *                       *
       3217 TTATCAAAATTTCATATGGTAGTTATCAAAATTTAATAGGGTAG
          1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGGGTAA

                            
       3261 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

       3277 AAAATATTCA


Statistics
Matches: 52,  Mismatches: 7, Indels: 1
        0.87            0.12        0.02

Matches are distributed among these distances:
  43   32  0.62
  44   20  0.38

ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42


Consensus pattern (44 bp):   
TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGGGTAA
Done.