Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002432.1 Corchorus olitorius cultivar O-4 contig02432, 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, 624

Length: 1040
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40


Found at i:125 original size:36 final size:36

Alignment explanation


    Indices: 78--146  Score: 138
    Period size: 36  Copynumber: 1.9  Consensus size: 36

         68 CGTCTCTATC

                                                
         78 GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT
          1 GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT

                                             
        114 GTTTTCTGTATTATTAGAAATTTGTGATTCTTT
          1 GTTTTCTGTATTATTAGAAATTTGTGATTCTTT

        147 CTTTTTACTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.20, C:0.06, G:0.14, T:0.59


Consensus pattern (36 bp):   
GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT

Found at i:437 original size:21 final size:21

Alignment explanation


    Indices: 411--459  Score: 80
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        401 TGTCATCATC

                  *        *     
        411 ATTATCTTTAGGATTCTTGGT
          1 ATTATCATTAGGATTATTGGT

                                 
        432 ATTATCATTAGGATTATTGGT
          1 ATTATCATTAGGATTATTGGT

                   
        453 ATTATCA
          1 ATTATCA

        460 GTATCATCGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49


Consensus pattern (21 bp):   
ATTATCATTAGGATTATTGGT

Found at i:438 original size:27 final size:27

Alignment explanation


    Indices: 379--441  Score: 92
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        369 TTCCTCTAGT

                                       
        379 TTATCATTATCATTAGGATTCTTGTCA
          1 TTATCATTATCATTAGGATTCTTGTCA

             *         *                
        406 TCATCATTATCTTTAGGATTCTTGGT-A
          1 TTATCATTATCATTAGGATTCTT-GTCA

                     
        433 TTATCATTA
          1 TTATCATTA

        442 GGATTATTGG


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  27   30  0.94
  28    2  0.06

ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49


Consensus pattern (27 bp):   
TTATCATTATCATTAGGATTCTTGTCA

Found at i:726 original size:27 final size:27

Alignment explanation


    Indices: 460--711  Score: 423
    Period size: 27  Copynumber: 9.3  Consensus size: 27

        450 GGTATTATCA

                           *           
        460 GTATCATCGGTATTAATAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                              **       
        487 GTATCATCGGTATTAGTAGGAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                                       
        514 GTATCATCGGTATTAGTAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                                       
        541 GTATCATCGGTATTAGTAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                                       
        568 GTATCATCGGTATTAGTAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                              *      * 
        595 GTATCATCGGTATTAGTATAAGTATCG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                              *      * 
        622 GTATCATCGGTATTAGTATAAGTATCG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                           *           
        649 GTATCATCGGTATTAATAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                               *       
        676 GTATCATCGGTATTAGTAAGAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                     
        703 GTATCATCG
          1 GTATCATCG

        712 CTTTTTTTAA


Statistics
Matches: 213,  Mismatches: 12, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27  213  1.00

ACGTcount: A:0.32, C:0.09, G:0.23, T:0.37


Consensus pattern (27 bp):   
GTATCATCGGTATTAGTAAAAGTATTG

Done.