Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013480.1 Corchorus olitorius cultivar O-4 contig13513, 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: 6607
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:174 original size:30 final size:27

Alignment explanation


    Indices: 141--223  Score: 112
    Period size: 30  Copynumber: 3.0  Consensus size: 27

        131 ATACCACTAA

                *        *             
        141 TAATTATTATTATTATAATAATAAGTT
          1 TAATAATTATTATAATAATAATAAGTT

                      *                   
        168 TAATAATTATAATACCACTAATAATAAGTT
          1 TAATAATTATTATA--A-TAATAATAAGTT

                                      
        198 TAATAATTATTATAATAATAATAAGT
          1 TAATAATTATTATAATAATAATAAGT

        224 CTAAATTAAC


Statistics
Matches: 49,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
  27   22  0.45
  28    1  0.02
  29    1  0.02
  30   25  0.51

ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43


Consensus pattern (27 bp):   
TAATAATTATTATAATAATAATAAGTT

Found at i:3376 original size:22 final size:22

Alignment explanation


    Indices: 3348--3390  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3338 TTTACCGTAA

                             *     
       3348 CAAGTCCTAGG-CAGGAGTTGTC
          1 CAAGTCCT-GGACAGGACTTGTC

                                 
       3370 CAAGTCCTGGACAGGACTTGT
          1 CAAGTCCTGGACAGGACTTGT

       3391 TCTGAATTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21    2  0.11
  22   17  0.89

ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23


Consensus pattern (22 bp):   
CAAGTCCTGGACAGGACTTGTC

Found at i:3446 original size:21 final size:21

Alignment explanation


    Indices: 3420--3461  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3410 TTCAACAGAC

                                 
       3420 CAAGTCCTGGGCAGGAGTTGT
          1 CAAGTCCTGGGCAGGAGTTGT

                                 
       3441 CAAGTCCTGGGCAGGAGTTGT
          1 CAAGTCCTGGGCAGGAGTTGT

       3462 TCTGATTTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24


Consensus pattern (21 bp):   
CAAGTCCTGGGCAGGAGTTGT

Found at i:3462 original size:71 final size:71

Alignment explanation


    Indices: 3348--3532  Score: 280
    Period size: 71  Copynumber: 2.6  Consensus size: 71

       3338 TTTACCGTAA

                    *                       *                           *    
       3348 CAAGTCCTAGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCATTTTTC
          1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCATCTTTC

                   
       3413 AACAGAC
         65 AACAGAC

                                                 *         *       * *       
       3420 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTTCGTCTTTCA
          1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCATCTTTCA

                  
       3485 ACAGAC
         66 ACAGAC

              * *                                     
       3491 CAGGCCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
          1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT

       3533 CCTGTTTTTA


Statistics
Matches: 103,  Mismatches: 10, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  71   83  0.81
  72   20  0.19

ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30


Consensus pattern (71 bp):   
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCATCTTTCA
ACAGAC
Done.