Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021203.1 Corchorus olitorius cultivar O-4 contig21236, 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: 38902
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:15345 original size:21 final size:22

Alignment explanation


    Indices: 15319--15370  Score: 77
    Period size: 22  Copynumber: 2.4  Consensus size: 22

      15309 TTTTTTCTAT

                    *        * *  
      15319 AAAAAAAATTTGCGTTTTTGAA
          1 AAAAAAAAATTGCGTTTCTAAA

                                  
      15341 AAAAAAAAATTGCGTTTCTAAA
          1 AAAAAAAAATTGCGTTTCTAAA

                    
      15363 AAAAAAAA
          1 AAAAAAAA

      15371 TTGTTTTTAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.58, C:0.06, G:0.10, T:0.27


Consensus pattern (22 bp):   
AAAAAAAAATTGCGTTTCTAAA

Found at i:15371 original size:21 final size:21

Alignment explanation


    Indices: 15312--15373  Score: 88
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      15302 TTTTGCGTTT

                  *        *     
      15312 TTTCTATAAAAAAAATTTGCG
          1 TTTCTAAAAAAAAAAATTGCG

               *                  
      15333 TTTTTGAAAAAAAAAAATTGCG
          1 TTTCT-AAAAAAAAAAATTGCG

                               
      15355 TTTCTAAAAAAAAAAATTG
          1 TTTCTAAAAAAAAAAATTG

      15374 TTTTTACGTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   18  0.50
  22   18  0.50

ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34


Consensus pattern (21 bp):   
TTTCTAAAAAAAAAAATTGCG

Found at i:23542 original size:20 final size:20

Alignment explanation


    Indices: 23517--23554  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      23507 CCGACATCGG

                                
      23517 TCATAACTTTTACATTTTGT
          1 TCATAACTTTTACATTTTGT

                              
      23537 TCATAACTTTTACATTTT
          1 TCATAACTTTTACATTTT

      23555 CCTATAGTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.26, C:0.16, G:0.03, T:0.55


Consensus pattern (20 bp):   
TCATAACTTTTACATTTTGT

Found at i:24314 original size:21 final size:21

Alignment explanation


    Indices: 24285--24339  Score: 103
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      24275 CCGGGTCAAA

                                 
      24285 ATGG-ATTGCGTCAGAAAGGG
          1 ATGGAATTGCGTCAGAAAGGG

                                 
      24305 ATGGAATTGCGTCAGAAAGGG
          1 ATGGAATTGCGTCAGAAAGGG

                          
      24326 ATGGAATTGCGTCA
          1 ATGGAATTGCGTCA

      24340 AGGCCATGTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  20    4  0.12
  21   30  0.88

ACGTcount: A:0.31, C:0.11, G:0.36, T:0.22


Consensus pattern (21 bp):   
ATGGAATTGCGTCAGAAAGGG

Found at i:33055 original size:24 final size:24

Alignment explanation


    Indices: 33025--33073  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      33015 TGGTTCCAAC

                          *         
      33025 GATGATGAATAAGCGGTGGAACAT
          1 GATGATGAATAAGCAGTGGAACAT

                                    
      33049 GATGATGAATAAGCAGTGGAACAT
          1 GATGATGAATAAGCAGTGGAACAT

             
      33073 G
          1 G

      33074 GAGATCTCGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20


Consensus pattern (24 bp):   
GATGATGAATAAGCAGTGGAACAT

Found at i:38549 original size:15 final size:15

Alignment explanation


    Indices: 38529--38590  Score: 72
    Period size: 15  Copynumber: 4.2  Consensus size: 15

      38519 GCTGATGACT

                           
      38529 GTTGGGCAGTGGGGA
          1 GTTGGGCAGTGGGGA

                          *
      38544 GTTGGGCAGTGGGGT
          1 GTTGGGCAGTGGGGA

             *         *  *
      38559 GCTGGGCAGTGTGGT
          1 GTTGGGCAGTGGGGA

             *             
      38574 GCTGGGCAGT-GGGA
          1 GTTGGGCAGTGGGGA

               
      38588 GTT
          1 GTT

      38591 TCTTCCACTT


Statistics
Matches: 41,  Mismatches: 6, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  14    4  0.10
  15   37  0.90

ACGTcount: A:0.10, C:0.10, G:0.56, T:0.24


Consensus pattern (15 bp):   
GTTGGGCAGTGGGGA
Done.