Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022194.1 Corchorus olitorius cultivar O-4 contig22227, 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: 10836
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29


Found at i:2541 original size:28 final size:28

Alignment explanation


    Indices: 2504--2561  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       2494 TTTAGGTTTA

                                        
       2504 TTGCTTGAATAATTGAGTCATATGCTAT
          1 TTGCTTGAATAATTGAGTCATATGCTAT

                                        
       2532 TTGCTTGAATAATTGAGTCATATGCTAT
          1 TTGCTTGAATAATTGAGTCATATGCTAT

              
       2560 TT
          1 TT

       2562 ATTTGCATGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45


Consensus pattern (28 bp):   
TTGCTTGAATAATTGAGTCATATGCTAT

Found at i:6263 original size:16 final size:17

Alignment explanation


    Indices: 6231--6270  Score: 64
    Period size: 16  Copynumber: 2.4  Consensus size: 17

       6221 AAGATACTAA

                   *         
       6231 CTTCTTTTTTGTGTTTT
          1 CTTCTTTCTTGTGTTTT

                             
       6248 CTTCTTTCTT-TGTTTT
          1 CTTCTTTCTTGTGTTTT

                   
       6264 CTTCTTT
          1 CTTCTTT

       6271 TTGCATTTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  16   13  0.59
  17    9  0.41

ACGTcount: A:0.00, C:0.17, G:0.07, T:0.75


Consensus pattern (17 bp):   
CTTCTTTCTTGTGTTTT

Found at i:9070 original size:21 final size:21

Alignment explanation


    Indices: 9046--9090  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       9036 ATTAAGAGAG

                   *             
       9046 GAAATCAGGCGCAAAGATGAA
          1 GAAATCAAGCGCAAAGATGAA

                       * *       
       9067 GAAATCAAGCGTAGAGATGAA
          1 GAAATCAAGCGCAAAGATGAA

               
       9088 GAA
          1 GAA

       9091 GCAAGGCGCC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.49, C:0.11, G:0.29, T:0.11


Consensus pattern (21 bp):   
GAAATCAAGCGCAAAGATGAA
Done.