Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017233.1 Corchorus olitorius cultivar O-4 contig17266, 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: 11586
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32


Found at i:2135 original size:14 final size:15

Alignment explanation


    Indices: 2107--2135  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       2097 GTATAATTAT

                           
       2107 CCAAAATACAAATAA
          1 CCAAAATACAAATAA

                           
       2122 CCAAAATA-AAATAA
          1 CCAAAATACAAATAA

       2136 TTTACAAAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    6  0.43
  15    8  0.57

ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14


Consensus pattern (15 bp):   
CCAAAATACAAATAA

Found at i:6978 original size:13 final size:13

Alignment explanation


    Indices: 6960--6984  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       6950 TTGGAATTCA

                         
       6960 AAATAATATTTAT
          1 AAATAATATTTAT

                        
       6973 AAATAATATTTA
          1 AAATAATATTTA

       6985 GAATATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT

Found at i:9478 original size:20 final size:21

Alignment explanation


    Indices: 9443--9481  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       9433 TTTCCTTACT

                     *           
       9443 TTTCTTTTCTCTTTTCTTTTA
          1 TTTCTTTTCACTTTTCTTTTA

                               
       9464 TTTCTTTT-ACTTTTCTTT
          1 TTTCTTTTCACTTTTCTTT

       9482 AAAATTGGGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    9  0.53
  21    8  0.47

ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77


Consensus pattern (21 bp):   
TTTCTTTTCACTTTTCTTTTA

Found at i:9594 original size:14 final size:14

Alignment explanation


    Indices: 9569--9625  Score: 55
    Period size: 14  Copynumber: 4.1  Consensus size: 14

       9559 CCAGCTGGAC

                           
       9569 CGCGCGCTGGCCCAG
          1 CGCGC-CTGGCCCAG

                       ** 
       9584 CGCGCCTGGCCTGG
          1 CGCGCCTGGCCCAG

             *       *    
       9598 CCCGCCTGGGCC-G
          1 CGCGCCTGGCCCAG

                          
       9611 CGCG-CTGGCCCAG
          1 CGCGCCTGGCCCAG

              
       9624 CG
          1 CG

       9626 TGCTTGGCCT


Statistics
Matches: 34,  Mismatches: 7, Indels: 4
        0.76            0.16        0.09

Matches are distributed among these distances:
  12    6  0.18
  13    7  0.21
  14   16  0.47
  15    5  0.15

ACGTcount: A:0.04, C:0.47, G:0.40, T:0.09


Consensus pattern (14 bp):   
CGCGCCTGGCCCAG

Found at i:9620 original size:40 final size:40

Alignment explanation


    Indices: 9563--9649  Score: 129
    Period size: 40  Copynumber: 2.2  Consensus size: 40

       9553 GCCAAGCCAG

                *                               *   
       9563 CTGGACCGCGCGCTGGCCCAGCGCGCCTGGCCTGGCCCGC
          1 CTGGGCCGCGCGCTGGCCCAGCGCGCCTGGCCTGGCACGC

                                   *  *             
       9603 CTGGGCCGCGCGCTGGCCCAGCGTGCTTGGCCTGGCACGC
          1 CTGGGCCGCGCGCTGGCCCAGCGCGCCTGGCCTGGCACGC

            *      
       9643 TTGGGCC
          1 CTGGGCC

       9650 ACGCCAGGCA


Statistics
Matches: 42,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  40   42  1.00

ACGTcount: A:0.05, C:0.43, G:0.39, T:0.14


Consensus pattern (40 bp):   
CTGGGCCGCGCGCTGGCCCAGCGCGCCTGGCCTGGCACGC
Done.