Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022445.1 Corchorus olitorius cultivar O-4 contig22478, 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: 31067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:9527 original size:31 final size:31

Alignment explanation


    Indices: 9489--9581  Score: 186
    Period size: 31  Copynumber: 3.0  Consensus size: 31

       9479 ACAGCTGATC

                                           
       9489 TTGTGCTCAGTCGCCACATCCGAAATTGAAA
          1 TTGTGCTCAGTCGCCACATCCGAAATTGAAA

                                           
       9520 TTGTGCTCAGTCGCCACATCCGAAATTGAAA
          1 TTGTGCTCAGTCGCCACATCCGAAATTGAAA

                                           
       9551 TTGTGCTCAGTCGCCACATCCGAAATTGAAA
          1 TTGTGCTCAGTCGCCACATCCGAAATTGAAA

       9582 GTGGCTTGCT


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   62  1.00

ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26


Consensus pattern (31 bp):   
TTGTGCTCAGTCGCCACATCCGAAATTGAAA

Found at i:17649 original size:19 final size:20

Alignment explanation


    Indices: 17619--17682  Score: 76
    Period size: 21  Copynumber: 3.1  Consensus size: 20

      17609 TTAACACTAT

                                 
      17619 TTAGCAACTGTACAGATGAGA
          1 TTAGC-ACTGTACAGATGAGA

                            *   
      17640 TTA-CACTGTACAGATTAGA
          1 TTAGCACTGTACAGATGAGA

                 *        *      
      17659 TTAGGTACTGTACATATGAGA
          1 TTA-GCACTGTACAGATGAGA

               
      17680 TTA
          1 TTA

      17683 TTAGAGCAGC


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  19   17  0.46
  20    1  0.03
  21   19  0.51

ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31


Consensus pattern (20 bp):   
TTAGCACTGTACAGATGAGA

Found at i:17670 original size:21 final size:19

Alignment explanation


    Indices: 17625--17682  Score: 71
    Period size: 19  Copynumber: 2.9  Consensus size: 19

      17615 CTATTTAGCA

                               
      17625 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

                       *        *
      17644 ACTGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA--C

                    *         
      17665 ACTGTACATATGAGATTA
          1 ACTGTACAGATGAGATTA

      17683 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   17  0.52
  21   16  0.48

ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC

Found at i:20031 original size:62 final size:60

Alignment explanation


    Indices: 19927--20058  Score: 140
    Period size: 62  Copynumber: 2.2  Consensus size: 60

      19917 ACGGTGTCCG

                      *   *                      *                        
      19927 ACGTGGCACGTCACGTGTACTAAAAAGCGACATGTGATATGCTACGTAAATTAAAAATCGAC
          1 ACGTGGCACGCCACATGTACTAAAAAGCGACATGTGACATGCTACGTAAA-TAAAAAT-GAC

                                        *     *  *      *   **           
      19989 ACGTGGCACGCCACATGTA-TCAAAAAGTGACATTTGGCATGCTTCGTGCATAAAAATGAC
          1 ACGTGGCACGCCACATGTACT-AAAAAGCGACATGTGACATGCTACGTAAATAAAAATGAC

                 *    
      20049 ACGTGTCACG
          1 ACGTGGCACG

      20059 TGTCATTTTT


Statistics
Matches: 59,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  60   12  0.20
  61    8  0.14
  62   39  0.66

ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23


Consensus pattern (60 bp):   
ACGTGGCACGCCACATGTACTAAAAAGCGACATGTGACATGCTACGTAAATAAAAATGAC
Done.