Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004971.1 Corchorus capsularis cultivar CVL-1 contig04989, 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: 4294
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32


Found at i:3781 original size:54 final size:54

Alignment explanation


    Indices: 3699--3807  Score: 209
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       3689 ATAACTAAAT

                 *                                                
       3699 AGCTTCTTTTGTAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATG
          1 AGCTTATTTTGTAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATG

                                                                  
       3753 AGCTTATTTTGTAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATG
          1 AGCTTATTTTGTAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATG

             
       3807 A
          1 A

       3808 AATTGTTATC


Statistics
Matches: 54,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   54  1.00

ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48


Consensus pattern (54 bp):   
AGCTTATTTTGTAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATG

Found at i:3822 original size:54 final size:54

Alignment explanation


    Indices: 3710--3822  Score: 181
    Period size: 54  Copynumber: 2.1  Consensus size: 54

       3700 GCTTCTTTTG

                                                        **     * *
       3710 TAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATGAGCTTATTTTG
          1 TAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATGAAATTATTATC

                                                            *     
       3764 TAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATGAAATTGTTATC
          1 TAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATGAAATTATTATC

                 
       3818 TAATT
          1 TAATT

       3823 AATTCCTAAT


Statistics
Matches: 54,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  54   54  1.00

ACGTcount: A:0.32, C:0.09, G:0.12, T:0.48


Consensus pattern (54 bp):   
TAATTGTATATTATAAATTTAATAGCCTCCATTATTGTTGATGAAATTATTATC

Found at i:3963 original size:61 final size:61

Alignment explanation


    Indices: 3868--3991  Score: 248
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       3858 ATGTATATTG

                                                                         
       3868 TTTTTGAAAAAATATATAACTTTTTAGTAACTAGTAACCACCTACTATCTAATAACTTCTA
          1 TTTTTGAAAAAATATATAACTTTTTAGTAACTAGTAACCACCTACTATCTAATAACTTCTA

                                                                         
       3929 TTTTTGAAAAAATATATAACTTTTTAGTAACTAGTAACCACCTACTATCTAATAACTTCTA
          1 TTTTTGAAAAAATATATAACTTTTTAGTAACTAGTAACCACCTACTATCTAATAACTTCTA

              
       3990 TT
          1 TT

       3992 ATCGATAAAA


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   63  1.00

ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40


Consensus pattern (61 bp):   
TTTTTGAAAAAATATATAACTTTTTAGTAACTAGTAACCACCTACTATCTAATAACTTCTA

Done.