Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000817.1 Corchorus olitorius cultivar O-4 contig00817, 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, 609

Length: 1015
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26


Found at i:402 original size:44 final size:43

Alignment explanation


    Indices: 344--471  Score: 148
    Period size: 44  Copynumber: 2.9  Consensus size: 43

        334 TTCATAGGAA

                   *       *    *            *    *     
        344 AGTTTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCTTATGG
          1 AGTTTATCAAAATTTAATAGGTA-GTTATCAAAATTTCATATGG

                     *     *       *                   
        388 AGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGG
          1 AGTTTATCAAAATTTAATAGGTAGTTATCAAAATTTCATATGG

            * *                                      
        431 TGGTTATCAAAATTTAATAGGGTAGTTATCAAAATTTCATA
          1 AGTTTATCAAAATTTAATA-GGTAGTTATCAAAATTTCATA

        472 AAAATATTCA


Statistics
Matches: 71,  Mismatches: 12, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  43   32  0.45
  44   39  0.55

ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42


Consensus pattern (43 bp):   
AGTTTATCAAAATTTAATAGGTAGTTATCAAAATTTCATATGG

Found at i:430 original size:43 final size:44

Alignment explanation


    Indices: 369--471  Score: 136
    Period size: 43  Copynumber: 2.4  Consensus size: 44

        359 CATAGTTAGG

                    *    *       *      *     *         
        369 TTATCAAAGTTTCTTATGGAGTTTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA

                               *                       *
        412 TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAGGGTAG
          1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA

                            
        456 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

        472 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:0.36, C:0.09, G:0.14, T:0.42


Consensus pattern (44 bp):   
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA

Found at i:438 original size:22 final size:21

Alignment explanation


    Indices: 347--471  Score: 106
    Period size: 22  Copynumber: 5.8  Consensus size: 21

        337 ATAGGAAAGT

                *            *    
        347 TTATTAAAATTTCATAGTTAGG
          1 TTATCAAAATTTCATAGGT-GG

                    *    *     * *
        369 TTATCAAAGTTTCTTATGGAGT
          1 TTATCAAAATTTCATA-GGTGG

                  *     *      **
        391 TTATCACAATTTTATAGGTAA
          1 TTATCAAAATTTCATAGGTGG

                                  
        412 TTATCAAAATTTCATATGGTGG
          1 TTATCAAAATTTCATA-GGTGG

                        *       * 
        434 TTATCAAAATTTAATAGGGTAG
          1 TTATCAAAATTTCATA-GGTGG

                            
        456 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

        472 AAAATATTCA


Statistics
Matches: 80,  Mismatches: 21, Indels: 4
        0.76            0.20        0.04

Matches are distributed among these distances:
  21   16  0.20
  22   63  0.79
  23    1  0.01

ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42


Consensus pattern (21 bp):   
TTATCAAAATTTCATAGGTGG
Done.