Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016009.1 Corchorus capsularis cultivar CVL-1 contig16030, 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: 15706
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35


Found at i:277 original size:28 final size:28

Alignment explanation


    Indices: 208--467  Score: 242
    Period size: 28  Copynumber: 9.2  Consensus size: 28

        198 TATTAGCGTC

                         *     * *       
        208 TTTTTCCTAGGCTTTATGCTTTTGGAAAA
          1 TTTTTCCTAGGCTGTATGCCTATGG-AAA

                  *       *        * *    
        237 TTTTT-GTACAGGCCGTATGCCTTTAGAAA
          1 TTTTTCCT--AGGCTGTATGCCTATGGAAA

                                        
        266 TTTTTCCTAGGCTGTATGCCTATGGAAA
          1 TTTTTCCTAGGCTGTATGCCTATGGAAA

                                        
        294 TTTTTCCTAGGCTGTATGCCTATGGAAA
          1 TTTTTCCTAGGCTGTATGCCTATGGAAA

                *             *         
        322 TTTTACCTAGGCTGTATGGCTATGGAAA
          1 TTTTTCCTAGGCTGTATGCCTATGGAAA

                  *                * *    
        350 TTTTGTGC-AGG-TCGTATGCCTTTAGAAA
          1 TTTT-TCCTAGGCT-GTATGCCTATGGAAA

              * *                       
        378 TTCTACCTAGGCTGTATGCCTATGGAAA
          1 TTTTTCCTAGGCTGTATGCCTATGGAAA

                  *                 * *    
        406 TTTTT-GTACAGG-TCGTATGCCTTTAGAAA
          1 TTTTTCCT--AGGCT-GTATGCCTATGGAAA

              * *                       
        435 TTCTACCTAGGCTGTATGCCTATGGAAA
          1 TTTTTCCTAGGCTGTATGCCTATGGAAA

                 
        463 TTTTT
          1 TTTTT

        468 GTACAGGCCG


Statistics
Matches: 186,  Mismatches: 33, Indels: 25
        0.76            0.14        0.10

Matches are distributed among these distances:
  27    3  0.02
  28  133  0.72
  29   35  0.19
  30   15  0.08

ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40


Consensus pattern (28 bp):   
TTTTTCCTAGGCTGTATGCCTATGGAAA

Found at i:486 original size:57 final size:57

Alignment explanation


    Indices: 213--487  Score: 367
    Period size: 56  Copynumber: 4.8  Consensus size: 57

        203 GCGTCTTTTT

                    *     * *                                      * *
        213 CCTAGGCTTTATGCTTTTGGAAAATTTTTGTACAGGCCGTATGCCTTTAGAAATTTTT
          1 CCTAGGCTGTATGCCTATGG-AAATTTTTGTACAGGCCGTATGCCTTTAGAAATTCTA

                                          *      *        * *      *  
        271 CCTAGGCTGTATGCCTATGGAAA-TTTT-TCCTAGGCTGTATGCCTATGGAAATTTTA
          1 CCTAGGCTGTATGCCTATGGAAATTTTTGTAC-AGGCCGTATGCCTTTAGAAATTCTA

                         *                *    *                     
        327 CCTAGGCTGTATGGCTATGGAAA-TTTTGTGCAGGTCGTATGCCTTTAGAAATTCTA
          1 CCTAGGCTGTATGCCTATGGAAATTTTTGTACAGGCCGTATGCCTTTAGAAATTCTA

                                               *                     
        383 CCTAGGCTGTATGCCTATGGAAATTTTTGTACAGGTCGTATGCCTTTAGAAATTCTA
          1 CCTAGGCTGTATGCCTATGGAAATTTTTGTACAGGCCGTATGCCTTTAGAAATTCTA

                                                   * *      
        440 CCTAGGCTGTATGCCTATGGAAATTTTTGTACAGGCCGTTTTCCTTTA
          1 CCTAGGCTGTATGCCTATGGAAATTTTTGTACAGGCCGTATGCCTTTA

        488 TGTTTTCGGA


Statistics
Matches: 194,  Mismatches: 20, Indels: 7
        0.88            0.09        0.03

Matches are distributed among these distances:
  55    2  0.01
  56   93  0.48
  57   82  0.42
  58   17  0.09

ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39


Consensus pattern (57 bp):   
CCTAGGCTGTATGCCTATGGAAATTTTTGTACAGGCCGTATGCCTTTAGAAATTCTA

Found at i:8566 original size:9 final size:9

Alignment explanation


    Indices: 8552--8578  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

       8542 GTCATCAAGG

                     
       8552 CCCAAGTGC
          1 CCCAAGTGC

                     
       8561 CCCAAGTGC
          1 CCCAAGTGC

                     
       8570 CCCAAGTGC
          1 CCCAAGTGC

       8579 AATCATCATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.22, C:0.44, G:0.22, T:0.11


Consensus pattern (9 bp):   
CCCAAGTGC

Found at i:15476 original size:2 final size:2

Alignment explanation


    Indices: 15464--15493  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      15454 ATTAAGAAGA

                                                          
      15464 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      15494 CTAATTATAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.