Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015447.1 Corchorus capsularis cultivar CVL-1 contig15468, 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: 11639
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:328 original size:92 final size:92

Alignment explanation


    Indices: 171--353  Score: 330
    Period size: 92  Copynumber: 2.0  Consensus size: 92

        161 CTTCACACAT

                                                                             
        171 ACTCACTTTAGAAATGAGTGTCAAAAATCTAGTACTCCATATATAATGTCAGCCCCTGAATTTGT
          1 ACTCACTTTAGAAATGAGTGTCAAAAATCTAGTACTCCATATATAATGTCAGCCCCTGAATTTGT

                          *            
        236 TTTACGAGTCCATTGGAAGACAAACTG
         66 TTTACGAGTCCATTCGAAGACAAACTG

                            *                                    *     *     
        263 ACTCACTTTAGAAATGTGTGTCAAAAATCTAGTACTCCATATATAATGTCAGCTCCTGAGTTTGT
          1 ACTCACTTTAGAAATGAGTGTCAAAAATCTAGTACTCCATATATAATGTCAGCCCCTGAATTTGT

                                      
        328 TTTACGAGTCCATTCGAAGACAAACT
         66 TTTACGAGTCCATTCGAAGACAAACT

        354 CAGTTGGCAA


Statistics
Matches: 87,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  92   87  1.00

ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32


Consensus pattern (92 bp):   
ACTCACTTTAGAAATGAGTGTCAAAAATCTAGTACTCCATATATAATGTCAGCCCCTGAATTTGT
TTTACGAGTCCATTCGAAGACAAACTG

Found at i:2007 original size:9 final size:9

Alignment explanation


    Indices: 1993--2031  Score: 51
    Period size: 9  Copynumber: 4.1  Consensus size: 9

       1983 AGCTTCTTTT

                     
       1993 TATATATTA
          1 TATATATTA

                      
       2002 TATATATATA
          1 TATATAT-TA

                   *  
       2012 CTATATACTA
          1 -TATATATTA

                     
       2022 TATATATTA
          1 TATATATTA

             
       2031 T
          1 T

       2032 TTTTAGTGGC


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
   9   16  0.62
  10    4  0.15
  11    6  0.23

ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51


Consensus pattern (9 bp):   
TATATATTA

Found at i:7826 original size:18 final size:18

Alignment explanation


    Indices: 7800--7837  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       7790 ATCAAGGAGT

                         *    
       7800 GCAAGGAAGCATGGACAA
          1 GCAAGGAAGCATGCACAA

                *             
       7818 GCAATGAAGCATGCACAA
          1 GCAAGGAAGCATGCACAA

              
       7836 GC
          1 GC

       7838 TTAAAGGAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.42, C:0.21, G:0.29, T:0.08


Consensus pattern (18 bp):   
GCAAGGAAGCATGCACAA

Found at i:10001 original size:17 final size:17

Alignment explanation


    Indices: 9963--9995  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       9953 CTCATAGTAC

                             
       9963 CTAGGTAGTATGAGGTA
          1 CTAGGTAGTATGAGGTA

                            
       9980 CTAGGTAGTATGAGGT
          1 CTAGGTAGTATGAGGT

       9996 GATAGGCTGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30


Consensus pattern (17 bp):   
CTAGGTAGTATGAGGTA
Done.