Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003332.1 Corchorus capsularis cultivar CVL-1 contig03340, 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, 736

Length: 1227
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35


Found at i:150 original size:35 final size:35

Alignment explanation


    Indices: 86--165  Score: 97
    Period size: 35  Copynumber: 2.3  Consensus size: 35

         76 CTATTCTTCG

                     *        **    *          
         86 AAAATCAAAGTTCAAAATTTGCATTTCATAATTCA
          1 AAAATCAAAATTCAAAATCAGCATCTCATAATTCA

                                          *   *
        121 AAAATCAAAATTCAAAATCAGCATCTCATAGTTCG
          1 AAAATCAAAATTCAAAATCAGCATCTCATAATTCA

               *      
        156 AAATTCAAAA
          1 AAAATCAAAA

        166 CCTGCATTTC


Statistics
Matches: 38,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  35   38  1.00

ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29


Consensus pattern (35 bp):   
AAAATCAAAATTCAAAATCAGCATCTCATAATTCA

Found at i:182 original size:28 final size:28

Alignment explanation


    Indices: 128--182  Score: 65
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        118 TCAAAAATCA

                      *          *      
        128 AAATTCAAAATCAGCATCTCATAGTTCG
          1 AAATTCAAAACCAGCATCTCACAGTTCG

                        *    *    *    
        156 AAATTCAAAACCTGCATTTCACGGTTC
          1 AAATTCAAAACCAGCATCTCACAGTTC

        183 ATTCTTCAAA


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  28   22  1.00

ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29


Consensus pattern (28 bp):   
AAATTCAAAACCAGCATCTCACAGTTCG

Found at i:202 original size:42 final size:42

Alignment explanation


    Indices: 156--300  Score: 263
    Period size: 42  Copynumber: 3.5  Consensus size: 42

        146 TCATAGTTCG

                                                      
        156 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
          1 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA

                       *                          *   
        198 AAATTCAAAACTTGCATTTCACGGTTCATTCTTCAAAACTCA
          1 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA

                                                      
        240 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
          1 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA

                       *       
        282 AAATTCAAAACTTGCATTT
          1 AAATTCAAAACCTGCATTT

        301 TAGCATTCCG


Statistics
Matches: 98,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   98  1.00

ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32


Consensus pattern (42 bp):   
AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA

Found at i:206 original size:84 final size:84

Alignment explanation


    Indices: 115--291  Score: 205
    Period size: 84  Copynumber: 2.1  Consensus size: 84

        105 TGCATTTCAT

                                                * **  *                      
        115 AATTCAAAAATCAAAATTCA-AAATCAGCATC-TCATAGTTCGAAATTCAAAACCTGCATTTCAC
          1 AATTCAAAAATCAAAATTCACAAATCA--ATCTTCAAAACTCAAAATTCAAAACCTGCATTTCAC

                                 
        178 GGTTCATTCTTCAAAAGTCAA
         64 GGTTCATTCTTCAAAAGTCAA

                     * *** *     ***   *                                     
        199 AATTCAAAACTTGCATTTCACGGTTCATTCTTCAAAACTCAAAATTCAAAACCTGCATTTCACGG
          1 AATTCAAAAATCAAAATTCACAAATCAATCTTCAAAACTCAAAATTCAAAACCTGCATTTCACGG

                               
        264 TTCATTCTTCAAAAGTCAA
         66 TTCATTCTTCAAAAGTCAA

                     
        283 AATTCAAAA
          1 AATTCAAAA

        292 CTTGCATTTT


Statistics
Matches: 78,  Mismatches: 13, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  83    2  0.03
  84   73  0.94
  85    3  0.04

ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30


Consensus pattern (84 bp):   
AATTCAAAAATCAAAATTCACAAATCAATCTTCAAAACTCAAAATTCAAAACCTGCATTTCACGG
TTCATTCTTCAAAAGTCAA
Done.