Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000221.1 Corchorus olitorius cultivar O-4 contig00221, 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, 988

Length: 1648
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36


Found at i:525 original size:33 final size:33

Alignment explanation


    Indices: 483--684  Score: 203
    Period size: 33  Copynumber: 6.1  Consensus size: 33

        473 CTGAACCTAA

                           **       *        
        483 TTTGAGTGTTGTTTGCAATGACACGAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                         *       *      *  **
        516 TTTGAGTGTTGTTAGTGATGATACTAAACCTAA
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                           *             *   
        549 TTTGAGTGTTGTTTGCGATGACACTAAATTTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

             *            *       *      *  **
        582 TCT-AGATGTTGTTAGTGATGATACTAAAACTAA
          1 TTTGAG-TGTTGTTTGTGATGACACTAAATCTGT

                                             
        615 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

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

                
        681 TTTG
          1 TTTG

        685 GATGCTAATT


Statistics
Matches: 134,  Mismatches: 30, Indels: 9
        0.77            0.17        0.05

Matches are distributed among these distances:
  32    6  0.04
  33  126  0.94
  34    2  0.01

ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43


Consensus pattern (33 bp):   
TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

Found at i:553 original size:66 final size:65

Alignment explanation


    Indices: 476--668  Score: 296
    Period size: 66  Copynumber: 2.9  Consensus size: 65

        466 AGTAATTCTG

                                   *       *                                 
        476 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTGAGTGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTT-AGTGTTGTTAGTGATGATACT

             
        541 A
         65 A

                                                *    *                       
        542 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATTTGTTCTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAG-TGTTGTTAGTGATGATACT

             
        607 A
         65 A

              *                   *                              *       
        608 AAACTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTA-GTGTTGTTAGTGATGA

        669 AACAAATTCT


Statistics
Matches: 116,  Mismatches: 9, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
  65    2  0.02
  66  113  0.97
  67    1  0.01

ACGTcount: A:0.26, C:0.09, G:0.23, T:0.41


Consensus pattern (65 bp):   
AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGTGTTGTTAGTGATGATACTA

Found at i:699 original size:99 final size:99

Alignment explanation


    Indices: 516--701  Score: 225
    Period size: 99  Copynumber: 1.9  Consensus size: 99

        506 CGAAATCTGT

                                 *                                *          
        516 TTTGAGTGTTGTTAGTGATGATACTAAACCTAATTTGAGTGTTGTTTGCGATGACACTAAATTTG
          1 TTTGAGTGTTGTTAGTGATGACACTAAACCTAATTTGAGTGTTGTTTGCGATGAAACTAAATTTG

                      **                      
        581 TTCTAGATGTTGTTAGTGATGATACTAAAACTAA
         66 TTCTAGATGTAATTAGTGATGATACTAAAACTAA

                         *              *   *   *            *               
        615 TTTGAGTGTTGTTTGTGATGACACTAAATCT-GTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
          1 TTTGAGTGTTGTTAGTGATGACACTAAACCTAATTTGA-GTGTTGTTTGCGATGAAACTAAATT-

                * *                  
        678 TGTTTTGGATGCTAATT-GTGATGA
         64 TGTTCTAGATG-TAATTAGTGATGA

        702 AAACAAATCT


Statistics
Matches: 73,  Mismatches: 11, Indels: 6
        0.81            0.12        0.07

Matches are distributed among these distances:
  98    9  0.12
  99   61  0.84
 100    3  0.04

ACGTcount: A:0.26, C:0.08, G:0.23, T:0.42


Consensus pattern (99 bp):   
TTTGAGTGTTGTTAGTGATGACACTAAACCTAATTTGAGTGTTGTTTGCGATGAAACTAAATTTG
TTCTAGATGTAATTAGTGATGATACTAAAACTAA
Done.