Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021125.1 Corchorus olitorius cultivar O-4 contig21158, 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: 36611
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:635 original size:16 final size:16

Alignment explanation


    Indices: 613--649  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 16

        603 TTTTAAAATC

                            
        613 ATTTTCTTCTTTTTTT
          1 ATTTTCTTCTTTTTTT

            *       *       
        629 CTTTTCTTTTTTTTTT
          1 ATTTTCTTCTTTTTTT

                 
        645 ATTTT
          1 ATTTT

        650 TTCAAAAAAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84


Consensus pattern (16 bp):   
ATTTTCTTCTTTTTTT

Found at i:8771 original size:31 final size:31

Alignment explanation


    Indices: 8694--8771  Score: 81
    Period size: 29  Copynumber: 2.6  Consensus size: 31

       8684 TTGACCAAAA

                 *           *             
       8694 CTTGTAAGTAGAGGGACTAAATTGATCATAT
          1 CTTGTGAGTAGAGGGACCAAATTGATCATAT

                        *                 * 
       8725 -TT-TGAGTAGATGGACCAAATTGA-CATTTT
          1 CTTGTGAGTAGAGGGACCAAATTGATCA-TAT

                      *       
       8754 CTTGTGAGTACAGGGACC
          1 CTTGTGAGTAGAGGGACC

       8772 TGCTGAGTAT


Statistics
Matches: 38,  Mismatches: 6, Indels: 6
        0.76            0.12        0.12

Matches are distributed among these distances:
  28    2  0.05
  29   20  0.53
  30    4  0.11
  31   12  0.32

ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32


Consensus pattern (31 bp):   
CTTGTGAGTAGAGGGACCAAATTGATCATAT

Found at i:17196 original size:51 final size:51

Alignment explanation


    Indices: 17120--17217  Score: 144
    Period size: 51  Copynumber: 1.9  Consensus size: 51

      17110 AGAAATGAGG

                                              *                
      17120 AGCAAAGCAGAGTTACAAGCTAAGTTCAAGAACTGCATGTCAAAGCCTATC
          1 AGCAAAGCAGAGTTACAAGCTAAGTTCAAGAACTACATGTCAAAGCCTATC

                          *            *   *                
      17171 AGCAAAGCAGAGTTGCAAG-TCAAGTTGAAGCACTACATGTCAAAGCC
          1 AGCAAAGCAGAGTTACAAGCT-AAGTTCAAGAACTACATGTCAAAGCC

      17218 CAAGAAAGCT


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  50    1  0.02
  51   41  0.98

ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18


Consensus pattern (51 bp):   
AGCAAAGCAGAGTTACAAGCTAAGTTCAAGAACTACATGTCAAAGCCTATC

Found at i:23017 original size:12 final size:11

Alignment explanation


    Indices: 23000--23032  Score: 50
    Period size: 12  Copynumber: 3.0  Consensus size: 11

      22990 GTTGGTGACA

                        
      23000 TTCTTTTTTCTT
          1 TTCTTTTTT-TT

                       
      23012 TTCTTTTTTTT
          1 TTCTTTTTTTT

                       
      23023 TT-TTTTTTTT
          1 TTCTTTTTTTT

      23033 GTAAAATTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  10    8  0.38
  11    4  0.19
  12    9  0.43

ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91


Consensus pattern (11 bp):   
TTCTTTTTTTT
Done.