Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022962.1 Corchorus olitorius cultivar O-4 contig22995, 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: 1859
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35


Found at i:344 original size:33 final size:33

Alignment explanation


    Indices: 307--468  Score: 105
    Period size: 33  Copynumber: 4.9  Consensus size: 33

        297 CTAATTTGAG

                      *                      
        307 TGTTGTTTGTAATGACACGAAATCTGTTTTAGA
          1 TGTTGTTTGTGATGACACGAAATCTGTTTTAGA

                   *       *  *   *  **      
        340 TGTTGTTAGTGATGATACTAAACCTAATTT-GA
          1 TGTTGTTTGTGATGACACGAAATCTGTTTTAGA

              *   *   *        *             *
        372 GTATTGCTTGCGATGACACTAAATCTGTTTTAGG
          1 -TGTTGTTTGTGATGACACGAAATCTGTTTTAGA

             *               *             *  
        406 TATTGTTTGTGATGA-AAGAAATTCTGTTTTGGA
          1 TGTTGTTTGTGATGACACGAAA-TCTGTTTTAGA

              * **          *              
        439 TGCTAATTGTGATGAAAAC-AAATCTGTTTT
          1 TGTTGTTTGTGATG-ACACGAAATCTGTTTT

        469 GGTTGATCAT


Statistics
Matches: 97,  Mismatches: 27, Indels: 10
        0.72            0.20        0.07

Matches are distributed among these distances:
  32    6  0.06
  33   85  0.88
  34    5  0.05
  35    1  0.01

ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACGAAATCTGTTTTAGA

Found at i:371 original size:66 final size:66

Alignment explanation


    Indices: 294--420  Score: 182
    Period size: 66  Copynumber: 1.9  Consensus size: 66

        284 AGTAATTCTG

                          *   *   *                        *                 
        294 AACCTAATTTGAGTGTTGTTTGTAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTATTGCTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT

             
        359 A
         66 A

                                   *       *             *       *       
        360 AACCTAATTTGAGTATTGCTTGCGATGACACTAAATCTGTTTTAGGTATTGTTTGTGATGA
          1 AACCTAATTTGAGTATTGCTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGA

        421 AAGAAATTCT


Statistics
Matches: 53,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  66   53  1.00

ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41


Consensus pattern (66 bp):   
AACCTAATTTGAGTATTGCTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT
A

Found at i:863 original size:21 final size:21

Alignment explanation


    Indices: 837--878  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        827 TAAGGAAGAA

                                 
        837 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
        858 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

        879 CCTAAGATGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG
Done.