Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012039.1 Corchorus capsularis cultivar CVL-1 contig12060, 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: 11640
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:306 original size:16 final size:16

Alignment explanation


    Indices: 285--315  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        275 AATTTTAAGT

                            
        285 TGATGTTTCGTTGATA
          1 TGATGTTTCGTTGATA

                    *      
        301 TGATGTTTTGTTGAT
          1 TGATGTTTCGTTGAT

        316 TCTGAAAATT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.16, C:0.03, G:0.26, T:0.55


Consensus pattern (16 bp):   
TGATGTTTCGTTGATA

Found at i:3510 original size:49 final size:49

Alignment explanation


    Indices: 3447--3830  Score: 373
    Period size: 49  Copynumber: 7.9  Consensus size: 49

       3437 TAAAACTAAC

                 *   *          *    **                      
       3447 GCCTTTCGTTCGGGAAGGGCGTTTTAAGAAAAAGCAAGTAAAAATTAGT
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGT

                                 *            * *   *    *  *
       3496 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAGGTATAAATAAGC
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGT

             *                                *           *   
       3545 GTCTTCCGTCCGGGAAGGGCATTTT-GGAAAACAACAAGT-AAAATGAGT
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-AGCAAGTAAAAATTAGT

                              * *    *          *    **      
       3593 GCCTTCCGTCCGGGAAGGACGTTTTAGGAAAAAGCAGGTAAGGATTAGT
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGT

                   *         *  *    *          *        * * 
       3642 GCCTTCCATCCGGGAAGTGCGTTTTAGGAAAAA-CAGGTAAAAATCAAT
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGT

                   *    *                                     
       3690 GCCTTCCTTCCGAGAAGGGCATTTTGGGAAAAA-CAAGTAAAGAA-TAGT
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAA-AATTAGT

                               **       *  *    *        * * 
       3738 GCCTTCCGTCCGGGAAGGGTGTTTTGGGCAATAGCAGGTAAAAATAAAT
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGT

                                           *       *    
       3787 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAAGTGAAAA
          1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAA

       3831 CTGAAAATTG


Statistics
Matches: 273,  Mismatches: 56, Indels: 12
        0.80            0.16        0.04

Matches are distributed among these distances:
  48  116  0.42
  49  157  0.58

ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23


Consensus pattern (49 bp):   
GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGT

Found at i:3528 original size:97 final size:95

Alignment explanation


    Indices: 3426--3817  Score: 351
    Period size: 97  Copynumber: 4.0  Consensus size: 95

       3416 ATGTTAGAAA

                                      *   *                *                 
       3426 AAAAAAATGAGTAAAACTAACGCCTTTCGTTCGGGAAGGGCGTTTTAAGAAAAAGCAAGTAAAAA
          1 AAAAAAA-G-GTAAAA-TAACGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAA

             * *                      *      
       3491 TTAGTGCCTTCCGTCCGGGAAGGGCACTTTGGG
         63 TAAATGCCTTCCGTCCGGGAAGGGCATTTTGGG

                  *               *                  *             *         
       3524 AAAAAGTAGGTATAAATAAGCGTCTTCCGTCCGGGAAGGGCATTTT-GGAAAACAACAAGT-AAA
          1 AAAAA-AAGGTA-AAATAA-CGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAA-AGCAAGTAAAA

              * *                   * *    *  
       3587 ATGAGTGCCTTCCGTCCGGGAAGGACGTTTTAGG
         62 ATAAATGCCTTCCGTCCGGGAAGGGCATTTTGGG

                  *         *  **       *         *                  *       
       3621 AAAAAGCAGGTAAGGATTAGTGCCTTCCATCCGGGAAGTGCGTTTTAGGAAAAA-CAGGTAAAAA
          1 AAAAA-AAGGTAA--AATAACGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAA

             *          *    *               
       3685 TCAATGCCTTCCTTCCGAGAAGGGCATTTTGGG
         63 TAAATGCCTTCCGTCCGGGAAGGGCATTTTGGG

                               **                   *     *  *  *    *       
       3718 AAAAACAA-GTAAAGAATAGTGCCTTCCGTCCGGGAAGGGTGTTTTGGGCAATAGCAGGTAAAAA
          1 AAAAA-AAGGT-AA-AATAACGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAA

                                             
       3782 TAAATGCCTTCCGTCCGGGAAGGGCATTTTGGG
         63 TAAATGCCTTCCGTCCGGGAAGGGCATTTTGGG

               
       3815 AAA
          1 AAA

       3818 TAGCAAGTGA


Statistics
Matches: 244,  Mismatches: 40, Indels: 21
        0.80            0.13        0.07

Matches are distributed among these distances:
  96   40  0.16
  97  157  0.64
  98   46  0.19
  99    1  0.00

ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23


Consensus pattern (95 bp):   
AAAAAAAGGTAAAATAACGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATAA
ATGCCTTCCGTCCGGGAAGGGCATTTTGGG

Found at i:4232 original size:23 final size:23

Alignment explanation


    Indices: 4213--4260  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4203 ACATAAATAT

                         *         
       4213 ATGTAAATGATTTTTTTAAATTA
          1 ATGTAAATGATTTCTTTAAATTA

              *     *               
       4236 ATTTAAATTATTTCTTTAAAGTTA
          1 ATGTAAATGATTTCTTTAAA-TTA

             
       4260 A
          1 A

       4261 ACTTAATATT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  23   17  0.81
  24    4  0.19

ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52


Consensus pattern (23 bp):   
ATGTAAATGATTTCTTTAAATTA

Found at i:5306 original size:11 final size:10

Alignment explanation


    Indices: 5286--5310  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       5276 AAAGAGACCG

                      
       5286 AAAAAGAAAA
          1 AAAAAGAAAA

                      
       5296 AAAAAGAAAA
          1 AAAAAGAAAA

                 
       5306 AAAAA
          1 AAAAA

       5311 CCTTAATTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (10 bp):   
AAAAAGAAAA
Done.