Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000554.1 Corchorus olitorius cultivar O-4 contig00554, 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, 604

Length: 1007
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30


Found at i:375 original size:27 final size:27

Alignment explanation


    Indices: 345--438  Score: 81
    Period size: 27  Copynumber: 3.6  Consensus size: 27

        335 GATTTTCTCG

                                       
        345 AGATTGAATTGGAAGACGGTCCTTTTA
          1 AGATTGAATTGGAAGACGGTCCTTTTA

                        *    *      ** 
        372 AGATTGAATTGGTAGACAG---TTCAA
          1 AGATTGAATTGGAAGACGGTCCTTTTA

                     **                 
        396 AGGA-T-AAGCGGAAGACGGTCCTTTTA
          1 A-GATTGAATTGGAAGACGGTCCTTTTA

                        *    
        422 AGATTGAATTGGTAGAC
          1 AGATTGAATTGGAAGAC

        439 AGTTCAAAGG


Statistics
Matches: 48,  Mismatches: 13, Indels: 12
        0.66            0.18        0.16

Matches are distributed among these distances:
  23    9  0.19
  24    5  0.10
  25    4  0.08
  26    5  0.10
  27   25  0.52

ACGTcount: A:0.33, C:0.11, G:0.28, T:0.29


Consensus pattern (27 bp):   
AGATTGAATTGGAAGACGGTCCTTTTA

Found at i:414 original size:50 final size:50

Alignment explanation


    Indices: 355--662  Score: 548
    Period size: 50  Copynumber: 6.2  Consensus size: 50

        345 AGATTGAATT

                                                              
        355 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC
          1 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

                                                              
        405 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC
          1 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

                    *                          *              
        455 GGAAGACGATCCTTTTAAGATTGAATTGGTAGACAATTCAAAGGATAAGC
          1 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

                                                              
        505 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC
          1 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

                                                              
        555 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC
          1 GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

                                          *           *        
        605 -GAGAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAGGGATAAGC
          1 GGA-AGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

                     
        655 AGG-AGACG
          1 -GGAAGACG

        663 ATCCATTCCG


Statistics
Matches: 249,  Mismatches: 6, Indels: 6
        0.95            0.02        0.02

Matches are distributed among these distances:
  49    2  0.01
  50  246  0.99
  52    1  0.00

ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25


Consensus pattern (50 bp):   
GGAAGACGGTCCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGC

Found at i:958 original size:28 final size:29

Alignment explanation


    Indices: 888--961  Score: 89
    Period size: 28  Copynumber: 2.6  Consensus size: 29

        878 GGATCACCTA

                             *           
        888 GGGCATTTTGGTCATTTTCAAAAATCTAG
          1 GGGCATTTTGGTCATTTGCAAAAATCTAG

                     *           * *     
        917 GGGCATTTTAGTCATTTGC-ATATTC-AG
          1 GGGCATTTTGGTCATTTGCAAAAATCTAG

                              
        944 GGGTCATTTTGGTCATTT
          1 GGG-CATTTTGGTCATTT

        962 TAAGGCCACG


Statistics
Matches: 39,  Mismatches: 5, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  27    5  0.13
  28   17  0.44
  29   17  0.44

ACGTcount: A:0.22, C:0.14, G:0.23, T:0.42


Consensus pattern (29 bp):   
GGGCATTTTGGTCATTTGCAAAAATCTAG
Done.