Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010755.1 Corchorus olitorius cultivar O-4 contig10787, 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: 8055
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:6504 original size:25 final size:25

Alignment explanation


    Indices: 6476--6541  Score: 75
    Period size: 23  Copynumber: 2.6  Consensus size: 25

       6466 TATATTAACT

                                      
       6476 TAAATATAATTATATATTAT-TTATA
          1 TAAATATAATTATATATT-TCTTATA

                        *            
       6501 TAAATAT-A-TAAATATTTCTTATA
          1 TAAATATAATTATATATTTCTTATA

                              
       6524 TATAATATAATATATATA
          1 TA-AATATAAT-TATATA

       6542 ATATAAAAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 8
        0.77            0.05        0.18

Matches are distributed among these distances:
  22    1  0.03
  23   14  0.41
  24    6  0.18
  25    8  0.24
  27    5  0.15

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (25 bp):   
TAAATATAATTATATATTTCTTATA

Found at i:6509 original size:27 final size:29

Alignment explanation


    Indices: 6464--6546  Score: 77
    Period size: 27  Copynumber: 3.0  Consensus size: 29

       6454 CTGAATTAAA

                                    *     
       6464 ATTATAT-TAACT-TAA-ATATAATTATAT
          1 ATTATATATAA-TATAATATATAAATATAT

                 *                     * 
       6491 ATTATTTAT-ATA-AATATATAAATATTT
          1 ATTATATATAATATAATATATAAATATAT

            *                            
       6518 CTTATATATAATATAATATATATAATATA
          1 ATTATATATAATATAATATATA-AATATA

       6547 AAAAATTAAT


Statistics
Matches: 44,  Mismatches: 6, Indels: 9
        0.75            0.10        0.15

Matches are distributed among these distances:
  26    3  0.07
  27   24  0.55
  28    4  0.09
  29    8  0.18
  30    5  0.11

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48


Consensus pattern (29 bp):   
ATTATATATAATATAATATATAAATATAT

Found at i:6539 original size:14 final size:14

Alignment explanation


    Indices: 6520--6571  Score: 61
    Period size: 14  Copynumber: 3.7  Consensus size: 14

       6510 AAATATTTCT

                          
       6520 TATATATAATATAA
          1 TATATATAATATAA

                          
       6534 TATATATAATATAA
          1 TATATATAATATAA

            * *          * 
       6548 AAAAT-TAATTATTA
          1 TATATATAA-TATAA

                      
       6562 TATATATAAT
          1 TATATATAAT

       6572 CGGTTTGTCG


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  13    3  0.10
  14   25  0.81
  15    3  0.10

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (14 bp):   
TATATATAATATAA
Done.