Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014234.1 Corchorus capsularis cultivar CVL-1 contig14255, 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: 11606
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:1558 original size:19 final size:19

Alignment explanation


    Indices: 1534--1570  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       1524 TGTTTAGTAC

                               
       1534 ACCGTTTCACCACCGTTTG
          1 ACCGTTTCACCACCGTTTG

                        *     
       1553 ACCGTTTCACCATCGTTT
          1 ACCGTTTCACCACCGTTT

       1571 TGGATCCAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35


Consensus pattern (19 bp):   
ACCGTTTCACCACCGTTTG

Found at i:3925 original size:30 final size:30

Alignment explanation


    Indices: 3822--3916  Score: 106
    Period size: 30  Copynumber: 3.2  Consensus size: 30

       3812 TTCAGATTCT

                 *                         
       3822 AAGGATGATTTTGACCCGGATGAGGATCCCG
          1 AAGGAGGA-TTTGACCCGGATGAGGATCCCG

                           *  * *          
       3853 -AGGAGGATTTCGACTCGAACGAGGATCCCG
          1 AAGGAGGATTT-GACCCGGATGAGGATCCCG

                                           
       3883 AA-GAGGATTTTGACCCGGATGAGGAT-CCG
          1 AAGGAGGA-TTTGACCCGGATGAGGATCCCG

                 
       3912 AAGGA
          1 AAGGA

       3917 ACAGTTTGAG


Statistics
Matches: 53,  Mismatches: 7, Indels: 9
        0.77            0.10        0.13

Matches are distributed among these distances:
  29    8  0.15
  30   41  0.77
  31    4  0.08

ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19


Consensus pattern (30 bp):   
AAGGAGGATTTGACCCGGATGAGGATCCCG

Found at i:5317 original size:22 final size:22

Alignment explanation


    Indices: 5243--5324  Score: 69
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       5233 TCAATATTCA

                  *  *           *
       5243 TATGAAGTTTTGATAATCACAT
          1 TATGAAATTATGATAATCACAC

               *     *             
       5265 TATAAAATTGTGATAAT-ATC-C
          1 TATGAAATTATGATAATCA-CAC

                                   
       5286 TAATGAAATTATGATAATCACAC
          1 T-ATGAAATTATGATAATCACAC

                *    *      
       5309 TATGGAATTTTGATAA
          1 TATGAAATTATGATAA

       5325 CCTCCCTATT


Statistics
Matches: 48,  Mismatches: 8, Indels: 8
        0.75            0.12        0.12

Matches are distributed among these distances:
  21    2  0.04
  22   43  0.90
  23    3  0.06

ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38


Consensus pattern (22 bp):   
TATGAAATTATGATAATCACAC

Found at i:5333 original size:22 final size:22

Alignment explanation


    Indices: 5288--5537  Score: 114
    Period size: 22  Copynumber: 11.4  Consensus size: 22

       5278 TAATATCCTA

                    *      * * *  
       5288 ATGAAATTATGATAATCACACT
          1 ATGAAATTTTGATAACCTCCCT

               *                  
       5310 ATGGAATTTTGATAACCTCCCT
          1 ATGAAATTTTGATAACCTCCCT

              *              * *   
       5332 ATTAAATTTT-ATTAACTTTCCT
          1 ATGAAATTTTGA-TAACCTCCCT

                            ** *  
       5354 ATGAAATTTTGATAACGACACT
          1 ATGAAATTTTGATAACCTCCCT

                     *  *  *   *   
       5376 ATGAAATTTCGAGAATCTATCC-
          1 ATGAAATTTTGATAACCT-CCCT

               *     *  *     ** *
       5398 ATGGAATTTCGAGAACCTTTCA
          1 ATGAAATTTTGATAACCTCCCT

                  *    *        * 
       5420 ATGAAAATTTGTTAACCT-CTT
          1 ATGAAATTTTGATAACCTCCCT

             * *  *     *  *   *  
       5441 AAGGAACTTTGAAAAGCTCACT
          1 ATGAAATTTTGATAACCTCCCT

                        *        *
       5463 ATGAAATTTTGACAACCTCCCC
          1 ATGAAATTTTGATAACCTCCCT

                                   
       5485 ATGAAATTTTGATAACCAT--CT
          1 ATGAAATTTTGATAACC-TCCCT

              *        * *         
       5506 AAAGAAATTTTAAGAACCTCCCT
          1 -ATGAAATTTTGATAACCTCCCT

                     
       5529 ATGAAATTT
          1 ATGAAATTT

       5538 GTGTTGGAGA


Statistics
Matches: 166,  Mismatches: 53, Indels: 18
        0.70            0.22        0.08

Matches are distributed among these distances:
  21   17  0.10
  22  144  0.87
  23    5  0.03

ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34


Consensus pattern (22 bp):   
ATGAAATTTTGATAACCTCCCT

Found at i:6969 original size:17 final size:17

Alignment explanation


    Indices: 6947--6979  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       6937 TAGGAACTCA

                             
       6947 GAAGCTTCCATCCCATG
          1 GAAGCTTCCATCCCATG

                            
       6964 GAAGCTTCCATCCCAT
          1 GAAGCTTCCATCCCAT

       6980 ATAAACCTAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24


Consensus pattern (17 bp):   
GAAGCTTCCATCCCATG
Done.