Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009799.1 Corchorus olitorius cultivar O-4 contig09831, 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: 5395
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:672 original size:23 final size:23

Alignment explanation


    Indices: 645--720  Score: 68
    Period size: 22  Copynumber: 3.3  Consensus size: 23

        635 TAGTAATATT

                                   
        645 TATAATTAAATATATATTTTATA
          1 TATAATTAAATATATATTTTATA

                  *             *    
        668 TATAA-AAAATA-ATATTAGATATA
          1 TATAATTAAATATATATT--TTATA

                    *        * *   
        691 TATAATTACATATATA-ATAATA
          1 TATAATTAAATATATATTTTATA

                    
        713 TATAATTA
          1 TATAATTA

        721 TTAAACGGTT


Statistics
Matches: 42,  Mismatches: 7, Indels: 9
        0.72            0.12        0.16

Matches are distributed among these distances:
  21    5  0.12
  22   16  0.38
  23   14  0.33
  24    4  0.10
  25    3  0.07

ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43


Consensus pattern (23 bp):   
TATAATTAAATATATATTTTATA

Found at i:682 original size:21 final size:22

Alignment explanation


    Indices: 652--692  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

        642 ATTTATAATT

                       **         
        652 AAATATATATTTTATATATAAA
          1 AAATATATATTAGATATATAAA

                                
        674 AAATA-ATATTAGATATATA
          1 AAATATATATTAGATATATA

        693 TAATTACATA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   12  0.71
  22    5  0.29

ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41


Consensus pattern (22 bp):   
AAATATATATTAGATATATAAA

Found at i:705 original size:12 final size:11

Alignment explanation


    Indices: 688--720  Score: 50
    Period size: 10  Copynumber: 3.0  Consensus size: 11

        678 AATATTAGAT

                       
        688 ATATATAATTA
          1 ATATATAATTA

                        
        699 CATATATAA-TA
          1 -ATATATAATTA

                       
        710 ATATATAATTA
          1 ATATATAATTA

        721 TTAAACGGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  10    8  0.40
  11    4  0.20
  12    8  0.40

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (11 bp):   
ATATATAATTA
Done.