Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005017.1 Corchorus capsularis cultivar CVL-1 contig05035, 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: 6731
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35


Found at i:110 original size:2 final size:2

Alignment explanation


    Indices: 103--129  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

         93 GTACTGTGTC

                                                    
        103 TA TA 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 T

        130 TAATATTCAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3270 original size:2 final size:2

Alignment explanation


    Indices: 3265--3289  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3255 TGTAAAATCC

                                                 
       3265 TA 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 T

       3290 GTATGTATGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:4877 original size:26 final size:26

Alignment explanation


    Indices: 4841--4891  Score: 102
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       4831 TGGTACTGTA

                                      
       4841 AAAATTGAATTTTTCTAAATAAAATG
          1 AAAATTGAATTTTTCTAAATAAAATG

                                     
       4867 AAAATTGAATTTTTCTAAATAAAAT
          1 AAAATTGAATTTTTCTAAATAAAAT

       4892 ATTTTAATAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39


Consensus pattern (26 bp):   
AAAATTGAATTTTTCTAAATAAAATG

Found at i:6042 original size:351 final size:351

Alignment explanation


    Indices: 5388--6074  Score: 891
    Period size: 351  Copynumber: 2.0  Consensus size: 351

       5378 GTCAAGTCAA

                       *                           *   ** *                  
       5388 ATGTCTTGAAGTCTAAATCGGATATTCTTAGACCCAATTTGTTTTTGTGGAAGCCCAAAGAAGGA
          1 ATGTCTTGAAGGCTAAATCGGATATTCTTAGACCCAATTCGTTAATATGGAAGCCCAAAGAAGGA

                                                     **  *     *             
       5453 GTCCAAGTCCAATCAGTAATTATGATGCAGTAATAATCCAGGTCTGATGCAGCATTGTAAAATCT
         66 GTCCAAGTCCAATCAGTAATTATGATGCAGTAATAATCCAGCCCTCATGCAACATTGTAAAATCT

                 *  *   *    *                             **       *        
       5518 TATTCGAAGGAGGACTTCACAAGAGCAATTTTGGAAGAAAATTCATATTTTTTCATCTGAAGCTT
        131 TATTCAAAAGAGAACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTCATATGAAGCTT

                                 **                           **             
       5583 AGAAAAATGCAAATGAGATACTGTTGGAAAGAGAATTCCAAGATCTACAACTTTTATGTTTACCT
        196 AGAAAAATGCAAATGAGATACCATTGGAAAGAGAATTCCAAGATCTACAAAATTTATGTTTACCT

                           *      *             *                            
       5648 CGAGACCTAATTCTGTAGTTCCGGTGGACGATTTTATCCTTGAAATTTCAGGACAAAATTGATCT
        261 CGAGACCTAATTCTGCAGTTCCAGTGGACGATTTTACCCTTGAAATTTCAGGACAAAATTGATCT

                                      
       5713 TCTACTAAACCGGCTTGGAGAGCCAT
        326 TCTACTAAACCGGCTTGGAGAGCCAT

                               *      *     *                                
       5739 ATGTCTTGAAGGCTAAATCTGATATTTTTAGATCCAATTCGTTAATATGGAAGCCCAAAG-AGAG
          1 ATGTCTTGAAGGCTAAATCGGATATTCTTAGACCCAATTCGTTAATATGGAAGCCCAAAGAAG-G

                     *                           * *                    *    
       5803 AGTCCAAGTTCAATCAGTAATTATGATGCAGTAATGATTTCAGCCCTCATGCAACATTGTTAAAT
         65 AGTCCAAGTCCAATCAGTAATTATGATGCAGTAAT-AATCCAGCCCTCATGCAACATTGTAAAAT

                                      *    *                         *       
       5868 -TCTATTCAAAAGAGAACTTTAACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTGATAT-AG
        129 CT-TATTCAAAAGAGAAC-TTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTCATATGA-

                             *  *  *               *       *                 
       5931 AG-TTCAGAAAAATG-ACATTAGGTACCATTGGAAAGAGGATTCCAATATCTA-AAAATTTATGT
        191 AGCTT-AGAAAAATGCAAATGAGATACCATTGGAAAGAGAATTCCAAGATCTACAAAATTTATGT

                                              *      *             *     *   
       5993 TTACCTCGAGACCTAATTCTGCAGTTCCAGTGGATGATTTTGCCCTTGAAATTTCTGGACAGAAT
        255 TTACCTCGAGACCTAATTCTGCAGTTCCAGTGGACGATTTTACCCTTGAAATTTCAGGACAAAAT

                     *       
       6058 TGATCTTCTCCTAAACC
        320 TGATCTTCTACTAAACC

       6075 AACTTGGATA


Statistics
Matches: 287,  Mismatches: 43, Indels: 12
        0.84            0.13        0.04

Matches are distributed among these distances:
 350    2  0.01
 351  171  0.60
 352   67  0.23
 353   47  0.16

ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Consensus pattern (351 bp):   
ATGTCTTGAAGGCTAAATCGGATATTCTTAGACCCAATTCGTTAATATGGAAGCCCAAAGAAGGA
GTCCAAGTCCAATCAGTAATTATGATGCAGTAATAATCCAGCCCTCATGCAACATTGTAAAATCT
TATTCAAAAGAGAACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTCATATGAAGCTT
AGAAAAATGCAAATGAGATACCATTGGAAAGAGAATTCCAAGATCTACAAAATTTATGTTTACCT
CGAGACCTAATTCTGCAGTTCCAGTGGACGATTTTACCCTTGAAATTTCAGGACAAAATTGATCT
TCTACTAAACCGGCTTGGAGAGCCAT
Done.