Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010597.1 Corchorus capsularis cultivar CVL-1 contig10618, 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: 14152
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:85 original size:33 final size:33

Alignment explanation


    Indices: 43--121  Score: 124
    Period size: 33  Copynumber: 2.4  Consensus size: 33

         33 AGGCCGCCCC

                                 *            
         43 AGTGGGGAGGCTCCGCCGTGGTTGAGCC-TCCCT
          1 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGT-CCT

                        *                    
         76 AGTGGGGAGGCTTCGCCGTGGCTGAGCCGTCCT
          1 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT

                         
        109 AGTGGGGAGGCTC
          1 AGTGGGGAGGCTC

        122 AGTGTAAAAG


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  33   41  0.98
  34    1  0.02

ACGTcount: A:0.10, C:0.27, G:0.43, T:0.20


Consensus pattern (33 bp):   
AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT

Found at i:3325 original size:24 final size:24

Alignment explanation


    Indices: 3298--3348  Score: 84
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       3288 TCCTATATTC

                *              *    
       3298 CATGTCTAGGAAGTGTCTCTTAGT
          1 CATGCCTAGGAAGTGTCTCGTAGT

                                    
       3322 CATGCCTAGGAAGTGTCTCGTAGT
          1 CATGCCTAGGAAGTGTCTCGTAGT

               
       3346 CAT
          1 CAT

       3349 TATATTCCAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33


Consensus pattern (24 bp):   
CATGCCTAGGAAGTGTCTCGTAGT

Found at i:4400 original size:33 final size:33

Alignment explanation


    Indices: 4319--4480  Score: 193
    Period size: 33  Copynumber: 4.9  Consensus size: 33

       4309 TTTGCCCTTA

                                            *
       4319 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCA
          1 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT

                  *                          
       4352 GCCAC-ACGGAGCCTCCCCACTAGGGCGGCTCT
          1 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT

                                             
       4384 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT
          1 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT

                  *  *    *     *    *   * * 
       4417 GCCACGACGTAGCCGCCCCATTAGGAC-GATTT
          1 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT

                            * *             
       4449 AGCCCACGGCGGAGCCGCTCCACTAGGGCGGC
          1 -G-CCACGGCGGAGCCTCCCCACTAGGGCGGC

       4481 AAGGCTATTT


Statistics
Matches: 109,  Mismatches: 16, Indels: 6
        0.83            0.12        0.05

Matches are distributed among these distances:
  32   33  0.30
  33   54  0.50
  34   21  0.19
  35    1  0.01

ACGTcount: A:0.16, C:0.41, G:0.31, T:0.12


Consensus pattern (33 bp):   
GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT

Found at i:7290 original size:27 final size:26

Alignment explanation


    Indices: 7251--7302  Score: 77
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       7241 GGTACTGTAC

                 *  *                  
       7251 AAATTGAATTTTTCTAAAATAAAATAA
          1 AAATTAAAATTTTCT-AAATAAAATAA

                                     
       7278 AAATTAAAATTTTCTAAATAAAATA
          1 AAATTAAAATTTTCTAAATAAAATA

       7303 TTTTGATAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  26   10  0.43
  27   13  0.57

ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37


Consensus pattern (26 bp):   
AAATTAAAATTTTCTAAATAAAATAA

Found at i:7543 original size:2 final size:2

Alignment explanation


    Indices: 7536--7571  Score: 54
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       7526 TTCATACTTT

                            *                                    
       7536 TA TA TA TA GTA GA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T

       7572 TCTAAATTGA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   2   29  0.94
   3    2  0.06

ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47


Consensus pattern (2 bp):   
TA

Done.