Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015257.1 Corchorus capsularis cultivar CVL-1 contig15278, 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: 8122
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:5453 original size:23 final size:23

Alignment explanation


    Indices: 5415--5467  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       5405 TGGCCGGTTG

                       *    *      
       5415 TGGCCGGACATGTCCATGTCGCA
          1 TGGCCGGACATCTCCAAGTCGCA

                   *              *
       5438 TGGCCGGGCATCTCCAAGTCGCG
          1 TGGCCGGACATCTCCAAGTCGCA

                   
       5461 TGGCCGG
          1 TGGCCGG

       5468 TGTTGGCCAG


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  23   26  1.00

ACGTcount: A:0.13, C:0.32, G:0.36, T:0.19


Consensus pattern (23 bp):   
TGGCCGGACATCTCCAAGTCGCA

Found at i:5475 original size:33 final size:33

Alignment explanation


    Indices: 5438--5501  Score: 101
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       5428 CCATGTCGCA

                 *                *          
       5438 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGT
          1 TGGCCAGGCATCTCCAAGTCGCATGGCCGGTGT

                     *                     
       5471 TGGCCAGGCTTCTCCAAGTCGCATGGCCGGT
          1 TGGCCAGGCATCTCCAAGTCGCATGGCCGGT

       5502 CACTCGCGCC


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   28  1.00

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


Consensus pattern (33 bp):   
TGGCCAGGCATCTCCAAGTCGCATGGCCGGTGT

Found at i:7394 original size:33 final size:33

Alignment explanation


    Indices: 7357--7447  Score: 94
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       7347 CATCCAAAAA

                           *            *     
       7357 AGATTTAGTATCATCACAAACAACACTTGAAA-C
          1 AGATTTAGTATCATCGCAAACAACAC-TCAAATC

                     *    *     *           *
       7390 AGATTTAGTTTCATTGCAAAGAACACTCAAATT
          1 AGATTTAGTATCATCGCAAACAACACTCAAATC

              *        *             
       7423 AGGTTTAGTATTATCGCAAACAACA
          1 AGATTTAGTATCATCGCAAACAACA

       7448 TCTAAAACAT


Statistics
Matches: 46,  Mismatches: 11, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  32    4  0.09
  33   42  0.91

ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29


Consensus pattern (33 bp):   
AGATTTAGTATCATCGCAAACAACACTCAAATC
Done.