Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017286.1 Corchorus olitorius cultivar O-4 contig17319, 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: 20736
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


Found at i:709 original size:24 final size:24

Alignment explanation


    Indices: 681--736  Score: 103
    Period size: 24  Copynumber: 2.3  Consensus size: 24

        671 CAGAAACGGT

                   *                
        681 GTTTGAGGTGATTCAAGCCAGTTG
          1 GTTTGAGATGATTCAAGCCAGTTG

                                    
        705 GTTTGAGATGATTCAAGCCAGTTG
          1 GTTTGAGATGATTCAAGCCAGTTG

                    
        729 GTTTGAGA
          1 GTTTGAGA

        737 AATGATAACA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.23, C:0.11, G:0.32, T:0.34


Consensus pattern (24 bp):   
GTTTGAGATGATTCAAGCCAGTTG

Found at i:1603 original size:28 final size:29

Alignment explanation


    Indices: 1529--1609  Score: 82
    Period size: 28  Copynumber: 2.9  Consensus size: 29

       1519 CAGTAAACTT

                           *           * 
       1529 AAAATGACCAAAA-CGCCCCT-GAATGTA
          1 AAAATGACCAAAATCCCCCCTAGAATGCA

                            *        *    
       1556 AAAATGACCCAAAAT-TCCCCTAG-GTGCA
          1 AAAATGA-CCAAAATCCCCCCTAGAATGCA

                                       
       1584 AAAATGACCAAAATCCCCCCTA-AATG
          1 AAAATGACCAAAATCCCCCCTAGAATG

       1610 ACCTAAGTGC


Statistics
Matches: 44,  Mismatches: 5, Indels: 9
        0.76            0.09        0.16

Matches are distributed among these distances:
  27   14  0.32
  28   29  0.66
  29    1  0.02

ACGTcount: A:0.43, C:0.28, G:0.12, T:0.16


Consensus pattern (29 bp):   
AAAATGACCAAAATCCCCCCTAGAATGCA

Found at i:9581 original size:35 final size:36

Alignment explanation


    Indices: 9542--9609  Score: 95
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       9532 TGCGTTTTTC

                                   *             
       9542 TTTTTCTCTGCGT-TTT-ATTCTGAAAAAAAAAATAT
          1 TTTTTCTCTGCGTCTTTAATT-TAAAAAAAAAAATAT

                   *                         
       9577 TTTTTCTTTGCGTCTTTAATTTAAAAAAAAAAA
          1 TTTTTCTCTGCGTCTTTAATTTAAAAAAAAAAA

       9610 AACTTTTGTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  35   12  0.41
  36   14  0.48
  37    3  0.10

ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46


Consensus pattern (36 bp):   
TTTTTCTCTGCGTCTTTAATTTAAAAAAAAAAATAT

Found at i:12246 original size:15 final size:16

Alignment explanation


    Indices: 12218--12260  Score: 63
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      12208 TTTACTTTTT

                             
      12218 CTTTGCATTG-TTA-TG
          1 CTTTG-ATTGATTATTG

                            
      12233 CTTTGATTGATTATTG
          1 CTTTGATTGATTATTG

                        
      12249 CTTTGATTGATT
          1 CTTTGATTGATT

      12261 GCCTATTTCT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    4  0.15
  15    8  0.31
  16   14  0.54

ACGTcount: A:0.16, C:0.09, G:0.19, T:0.56


Consensus pattern (16 bp):   
CTTTGATTGATTATTG

Done.