Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009695.1 Corchorus olitorius cultivar O-4 contig09727, 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: 8956
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:3888 original size:17 final size:16

Alignment explanation


    Indices: 3838--3884  Score: 58
    Period size: 17  Copynumber: 2.8  Consensus size: 16

       3828 TTAGGATCAC

                             
       3838 CACTAGTGATCTAAGAT
          1 CACTAGTGATC-AAGAT

               *             
       3855 CACCAGTGATGCAAGAT
          1 CACTAGTGAT-CAAGAT

                *        
       3872 CACTGGTGATCAA
          1 CACTAGTGATCAA

       3885 AGATTACATG


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  16    3  0.12
  17   22  0.85
  18    1  0.04

ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23


Consensus pattern (16 bp):   
CACTAGTGATCAAGAT

Found at i:7813 original size:9 final size:9

Alignment explanation


    Indices: 7799--7823  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       7789 GCAAATCCAA

                     
       7799 GCCCCAATG
          1 GCCCCAATG

                     
       7808 GCCCCAATG
          1 GCCCCAATG

                   
       7817 GCCCCAA
          1 GCCCCAA

       7824 AGCCTTTTAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.24, C:0.48, G:0.20, T:0.08


Consensus pattern (9 bp):   
GCCCCAATG

Found at i:8659 original size:24 final size:24

Alignment explanation


    Indices: 8632--8681  Score: 73
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       8622 TTCTGAGTAC

                    *          *    
       8632 TTTGCAACGGAATCAAAAAGGGAA
          1 TTTGCAACAGAATCAAAAACGGAA

                   *                
       8656 TTTGCAATAGAATCAAAAACGGAA
          1 TTTGCAACAGAATCAAAAACGGAA

              
       8680 TT
          1 TT

       8682 CTATCTATTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22


Consensus pattern (24 bp):   
TTTGCAACAGAATCAAAAACGGAA
Done.