Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011610.1 Corchorus capsularis cultivar CVL-1 contig11631, 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: 8811
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:7429 original size:50 final size:48

Alignment explanation


    Indices: 7365--7463  Score: 162
    Period size: 50  Copynumber: 2.0  Consensus size: 48

       7355 ATCTCTTTGA

                                                              
       7365 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
          1 TTGTAATCAGTGCGGGGAGCACTTGTT-TAAGCTTGGGGAAAGCTT-GGT

                *                       *                   
       7415 TTGTGATCAGTGCGGGGAGCACTTGTTTGAGCTTGGGGAAAGCTTGGT
          1 TTGTAATCAGTGCGGGGAGCACTTGTTTAAGCTTGGGGAAAGCTTGGT

             
       7463 T
          1 T

       7464 GCTGTAACCG


Statistics
Matches: 47,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  48    4  0.09
  49   17  0.36
  50   26  0.55

ACGTcount: A:0.19, C:0.13, G:0.36, T:0.31


Consensus pattern (48 bp):   
TTGTAATCAGTGCGGGGAGCACTTGTTTAAGCTTGGGGAAAGCTTGGT

Found at i:8111 original size:49 final size:50

Alignment explanation


    Indices: 7989--8287  Score: 301
    Period size: 49  Copynumber: 6.1  Consensus size: 50

       7979 ATTTTAAGGA

                     *                     *    *          *  *
       7989 AAAAGC-AACGCCTTCCGTCCGGGAAGGGGCGTTTTAGGAAA-A-CAAATA
          1 AAAAGCAAATGCCTTCCGTCCGGGAA-GGGCATTTTGGGAAATAGCAGATG

                *  **                     *                   
       8037 AAAATC-GGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAGATG
          1 AAAAGCAAATGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATG

                    *                                         
       8086 AAAA-CAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATG
          1 AAAAGCAAATGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATG

                *            * **                *         *  
       8135 -AAATCAAATGCCTTCCATTTGGGAAGGGCATTTTGGAAAATAGCAGGT-
          1 AAAAGCAAATGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATG

                 *                                *   *     *  
       8183 AAAAGTAAATGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAACAGCAGGT-
          1 AAAAGCAAATGCCTTCCGTCCGGGAAGGGCA-TTTTGGGAAATAGCAGATG

                 *                             *                
       8233 AAAAGTAAATGCCTTCCGTCCGGGAAGGGCATTTTTGGAACATAGCA-AGTG
          1 AAAAGCAAATGCCTTCCGTCCGGGAAGGGCATTTTGGGAA-ATAGCAGA-TG

                
       8284 AAAA
          1 AAAA

       8288 CTGAAAAATG


Statistics
Matches: 217,  Mismatches: 25, Indels: 15
        0.84            0.10        0.06

Matches are distributed among these distances:
  47   14  0.06
  48   26  0.12
  49  119  0.55
  50   54  0.25
  51    4  0.02

ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22


Consensus pattern (50 bp):   
AAAAGCAAATGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATG

Done.