Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011199.1 Corchorus capsularis cultivar CVL-1 contig11220, 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: 7880
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:345 original size:2 final size:2

Alignment explanation


    Indices: 338--379  Score: 57
    Period size: 2  Copynumber: 21.0  Consensus size: 2

        328 TTTCTAAGGA

                                     *     *     *                        
        338 AT AT AT AT AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        380 GGTTTTGAAG


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43


Consensus pattern (2 bp):   
AT

Found at i:1384 original size:31 final size:31

Alignment explanation


    Indices: 1346--1439  Score: 107
    Period size: 34  Copynumber: 2.9  Consensus size: 31

       1336 TTATCGGCCC

                               *           
       1346 TGCCCAGTGGGTTATAATAGCTGGAAGACCA
          1 TGCCCAGTGGGTTATAATAACTGGAAGACCA

                           *             *   *
       1377 TGCCCAGTGGCTTGTGATAATAACTGGAATACCC
          1 TGCCCAGTGG---GTTATAATAACTGGAAGACCA

                         *        *      
       1411 TGCCCAGTGGGTTTTAATAACTAGAAGAC
          1 TGCCCAGTGGGTTATAATAACTGGAAGAC

       1440 AGCCCTGCTA


Statistics
Matches: 52,  Mismatches: 8, Indels: 6
        0.79            0.12        0.09

Matches are distributed among these distances:
  31   25  0.48
  34   27  0.52

ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26


Consensus pattern (31 bp):   
TGCCCAGTGGGTTATAATAACTGGAAGACCA

Found at i:1446 original size:34 final size:31

Alignment explanation


    Indices: 1343--1447  Score: 79
    Period size: 34  Copynumber: 3.2  Consensus size: 31

       1333 GTTTTATCGG

                            *     *         
       1343 CCCTGCCCAGTGGGTTATAATAGCTGGAAG-A
          1 CCCTGCCCAGTGGGTTTTAATAACT-GAAGAA

              *          *                   * 
       1374 CCATGCCCAGTGGCTTGTGATAATAACTGGAA-TA
          1 CCCTGCCCAGTGGGTT-T--TAATAACT-GAAGAA

                                             
       1408 CCCTGCCCAGTGGGTTTTAATAACTAGAAGACA
          1 CCCTGCCCAGTGGGTTTTAATAACT-GAAGA-A

                   
       1441 GCCCTGC
          1 -CCCTGC

       1448 TAACGGGTTG


Statistics
Matches: 59,  Mismatches: 8, Indels: 11
        0.76            0.10        0.14

Matches are distributed among these distances:
  31   25  0.42
  33    2  0.03
  34   32  0.54

ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24


Consensus pattern (31 bp):   
CCCTGCCCAGTGGGTTTTAATAACTGAAGAA

Found at i:6478 original size:30 final size:30

Alignment explanation


    Indices: 6444--6505  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       6434 ATGCTCCAAA

                                          
       6444 ATCACTTCAAAACACACAGACACACAAATT
          1 ATCACTTCAAAACACACAGACACACAAATT

                              *           
       6474 ATCACTTCAAAACACACATACACACAAATT
          1 ATCACTTCAAAACACACAGACACACAAATT

              
       6504 AT
          1 AT

       6506 TATGTCAGTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.50, C:0.29, G:0.02, T:0.19


Consensus pattern (30 bp):   
ATCACTTCAAAACACACAGACACACAAATT

Found at i:7178 original size:37 final size:38

Alignment explanation


    Indices: 7123--7201  Score: 124
    Period size: 37  Copynumber: 2.1  Consensus size: 38

       7113 CTTATATACT

                                *  *               
       7123 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
          1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTTTA

                                                  
       7162 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
          1 TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA

               
       7199 TGA
          1 TGA

       7202 ATAATTATAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  37   30  0.79
  39    8  0.21

ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35


Consensus pattern (38 bp):   
TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA

Found at i:7266 original size:31 final size:31

Alignment explanation


    Indices: 7230--7289  Score: 111
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       7220 TACCTTTTAT

                                           
       7230 AGACAAATAAGTCTCTTCATAATTGTTCATA
          1 AGACAAATAAGTCTCTTCATAATTGTTCATA

                                 *       
       7261 AGACAAATAAGTCTCTTCATAGTTGTTCA
          1 AGACAAATAAGTCTCTTCATAATTGTTCA

       7290 CTTATGAACA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35


Consensus pattern (31 bp):   
AGACAAATAAGTCTCTTCATAATTGTTCATA
Done.