Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004396.1 Corchorus olitorius cultivar O-4 contig04411, 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, 610

Length: 1017
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35


Found at i:402 original size:33 final size:33

Alignment explanation


    Indices: 360--561  Score: 212
    Period size: 33  Copynumber: 6.1  Consensus size: 33

        350 CTGAACCTAA

                           **       *        
        360 TTTGAGTGTTGTTTGCAATGACACGAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                         *       *      *  **
        393 TTTGAGTGTTGTTAGTGATGATACTAAACCTAA
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                           *                 
        426 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

             *            *       *      *  **
        459 TCT-AGATGTTGTTAGTGATGATACTAAAACTAA
          1 TTTGAG-TGTTGTTTGTGATGACACTAAATCTGT

                                             
        492 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                                  *            
        525 TTT-AGGTGTTGTTTGTGATGAAAC-AAATTCTGT
          1 TTTGA-GTGTTGTTTGTGATGACACTAAA-TCTGT

                
        558 TTTG
          1 TTTG

        562 GATGCTAATT


Statistics
Matches: 136,  Mismatches: 28, Indels: 9
        0.79            0.16        0.05

Matches are distributed among these distances:
  32    6  0.04
  33  128  0.94
  34    2  0.01

ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42


Consensus pattern (33 bp):   
TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

Found at i:430 original size:66 final size:65

Alignment explanation


    Indices: 353--545  Score: 305
    Period size: 66  Copynumber: 2.9  Consensus size: 65

        343 AGTAATTCTG

                                   *       *                                 
        353 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTGAGTGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTT-AGTGTTGTTAGTGATGATACT

             
        418 A
         65 A

                                                     *                       
        419 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAG-TGTTGTTAGTGATGATACT

             
        484 A
         65 A

              *                   *                              *       
        485 AAACTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTA-GTGTTGTTAGTGATGA

        546 AACAAATTCT


Statistics
Matches: 118,  Mismatches: 7, Indels: 4
        0.91            0.05        0.03

Matches are distributed among these distances:
  65    2  0.02
  66  115  0.97
  67    1  0.01

ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41


Consensus pattern (65 bp):   
AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGTGTTGTTAGTGATGATACTA

Done.