Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009078.1 Corchorus olitorius cultivar O-4 contig09106, 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, 675

Length: 1126
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33


Found at i:396 original size:26 final size:26

Alignment explanation


    Indices: 367--416  Score: 100
    Period size: 26  Copynumber: 1.9  Consensus size: 26

        357 TGAGGGGATG

                                      
        367 TTTGAGTGCCTATGTAAAAGGGGAAC
          1 TTTGAGTGCCTATGTAAAAGGGGAAC

                                    
        393 TTTGAGTGCCTATGTAAAAGGGGA
          1 TTTGAGTGCCTATGTAAAAGGGGA

        417 TGTTCTAAGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28


Consensus pattern (26 bp):   
TTTGAGTGCCTATGTAAAAGGGGAAC

Found at i:1001 original size:33 final size:33

Alignment explanation


    Indices: 959--1126  Score: 185
    Period size: 33  Copynumber: 5.1  Consensus size: 33

        949 CTGAACCTAA

                           **       *        
        959 TTTGAGTGTTGTTTGCAATGACACGAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                         *       *      *  **
        992 TTTGAGTGTTGTTAGTGATGATACTAAACCTAA
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                           *                 
       1025 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

             *            *       *      *  **
       1058 TCT-AGATGTTGTTAGTGATGATACTAAAACTAA
          1 TTTGAG-TGTTGTTTGTGATGACACTAAATCTGT

                                             
       1091 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

               
       1124 TTT
          1 TTT


Statistics
Matches: 106,  Mismatches: 27, Indels: 4
        0.77            0.20        0.03

Matches are distributed among these distances:
  32    2  0.02
  33  102  0.96
  34    2  0.02

ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42


Consensus pattern (33 bp):   
TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

Found at i:1029 original size:66 final size:66

Alignment explanation


    Indices: 952--1126  Score: 289
    Period size: 66  Copynumber: 2.7  Consensus size: 66

        942 AGTAATTCTG

                                   *       *                                 
        952 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTT-GAGTGTTGTTAGTGATGATAC
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGA-TGTTGTTAGTGATGATAC

              
       1016 TA
         65 TA

                                                     *                       
       1018 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACT

             
       1083 A
         66 A

              *                   *                    
       1084 AAACTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTT


Statistics
Matches: 102,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  66  100  0.98
  67    2  0.02

ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41


Consensus pattern (66 bp):   
AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A
Done.