Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000763.1 Corchorus olitorius cultivar O-4 contig00763, 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, 700

Length: 1167
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38


Found at i:746 original size:2 final size:2

Alignment explanation


    Indices: 739--842  Score: 71
    Period size: 2  Copynumber: 54.5  Consensus size: 2

        729 TTTGACATTA

                                       *    *                              
        739 AT AT AT AT AT AT AT AT -T TT GAC AT -T A- AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT

                              *    *                                     * 
        779 AT AT AT AT AT AT TT GAC AT -T A- AT AT AT AT AT AT AT AT -T TT
          1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              *                                   
        819 GAC AT -T A- AT AT AT AT AT AT AT AT A
          1 -AT AT AT AT AT AT AT AT AT AT AT AT A

        843 GACACAAAAA


Statistics
Matches: 81,  Mismatches: 10, Indels: 22
        0.72            0.09        0.19

Matches are distributed among these distances:
   1    8  0.10
   2   73  0.90

ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:756 original size:26 final size:26

Alignment explanation


    Indices: 727--841  Score: 124
    Period size: 26  Copynumber: 4.1  Consensus size: 26

        717 AGAAAAAATG

                                      
        727 ATTTTGACATTAATATATATATATAT
          1 ATTTTGACATTAATATATATATATAT

                                      
        753 ATTTTGACATTAATATATATATATAT
          1 ATTTTGACATTAATATATATATATAT

                      *                         
        779 ATATATAT-ATATTTGACATTAATATATATATATAT
          1 AT-T-T-TGACA-TT-A-A-T-ATA--TATATATAT

                                      
        814 ATTTTGACATTAATATATATATATAT
          1 ATTTTGACATTAATATATATATATAT

              
        840 AT
          1 AT

        842 AGACACAAAA


Statistics
Matches: 76,  Mismatches: 2, Indels: 22
        0.76            0.02        0.22

Matches are distributed among these distances:
  26   39  0.51
  27    1  0.01
  28    6  0.08
  29    4  0.05
  30    2  0.03
  31    2  0.03
  32    4  0.05
  33    6  0.08
  34    1  0.01
  35   11  0.14

ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50


Consensus pattern (26 bp):   
ATTTTGACATTAATATATATATATAT

Found at i:857 original size:61 final size:61

Alignment explanation


    Indices: 731--858  Score: 202
    Period size: 61  Copynumber: 2.1  Consensus size: 61

        721 AAAATGATTT

                                                               * * * * **
        731 TGACATTAATATATATATATATATTTTGACATTAATATATATATATATATATATATATATT
          1 TGACATTAATATATATATATATATTTTGACATTAATATATATATATATATAGACACAAAAA

                                                                         
        792 TGACATTAATATATATATATATATTTTGACATTAATATATATATATATATAGACACAAAAA
          1 TGACATTAATATATATATATATATTTTGACATTAATATATATATATATATAGACACAAAAA

                  
        853 TGACAT
          1 TGACAT

        859 GTCATAATCA


Statistics
Matches: 61,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  61   61  1.00

ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44


Consensus pattern (61 bp):   
TGACATTAATATATATATATATATTTTGACATTAATATATATATATATATAGACACAAAAA
Done.