Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004162.1 Corchorus capsularis cultivar CVL-1 contig04170, 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: 1693
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36


Found at i:182 original size:41 final size:40

Alignment explanation


    Indices: 136--353  Score: 276
    Period size: 41  Copynumber: 5.3  Consensus size: 40

        126 CTTCCCAGTT

                                                     
        136 GGAAGGTGTTGTTTAGTTTTCCTGTTTCGCCCTTCCCCATC
          1 GGAAGGTGTTGTTTAGTTTTCCTGTTT-GCCCTTCCCCATC

            *                                        
        177 AGAAGGTGTTGTTTAGTTTTCCTGTTTTGCCCTTCCCCATC
          1 GGAAGGTGTTGTTTAGTTTTCCTG-TTTGCCCTTCCCCATC

                                  * *             * 
        218 GGAAGGTGTTGTTTAGTTTTCCAGCTTGCCCTTCCCCACC
          1 GGAAGGTGTTGTTTAGTTTTCCTGTTTGCCCTTCCCCATC

            *           *   *   *  *            *    
        258 AGAAGGTGTTGTCTACATTTCCCAGTTTGCCCTTCCACATC
          1 GGAAGGTGTTGTTTA-GTTTTCCTGTTTGCCCTTCCCCATC

                                   *            *    
        299 GGAAGGTGTTGTTTAGTTTTCCTATCTTGCCCTTCCACA-C
          1 GGAAGGTGTTGTTTAGTTTTCCTGT-TTGCCCTTCCCCATC

                           
        339 TGGAAGGTGTTGTTT
          1 -GGAAGGTGTTGTTT

        354 GCTCTTTGTT


Statistics
Matches: 155,  Mismatches: 18, Indels: 8
        0.86            0.10        0.04

Matches are distributed among these distances:
  40   34  0.22
  41  118  0.76
  42    3  0.02

ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39


Consensus pattern (40 bp):   
GGAAGGTGTTGTTTAGTTTTCCTGTTTGCCCTTCCCCATC

Found at i:287 original size:81 final size:81

Alignment explanation


    Indices: 104--351  Score: 295
    Period size: 81  Copynumber: 3.0  Consensus size: 81

         94 AAGACTAGCT

                         **     *            *                      * *      
        104 TTGTCTAATTT-CTGGTTTTTCCCTTCC-CAGTTGGAAGGTGTTGTTTAGTTTTCCTGTTTCGCC
          1 TTGTCTAATTTCCCAGTTTTGCCCTTCCACA-TCGGAAGGTGTTGTTTAGTTTTCCAGCTT-GCC

                    *         
        167 CTTCCCCATCAGAAGGTG
         64 CTTCCCCACCAGAAGGTG

                *  *   *  *             *                                    
        185 TTGTTTAGTTTTCCTGTTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCAGCTTGCCCT
          1 TTGTCTAATTTCCCAGTTTTGCCCTTCCACATCGGAAGGTGTTGTTTAGTTTTCCAGCTTGCCCT

                            
        250 TCCCCACCAGAAGGTG
         66 TCCCCACCAGAAGGTG

                                                                      *      
        266 TTGTCTACATTTCCCAG-TTTGCCCTTCCACATCGGAAGGTGTTGTTTAGTTTTCCTATCTTGCC
          1 TTGTCTA-ATTTCCCAGTTTTGCCCTTCCACATCGGAAGGTGTTGTTTAGTTTTCC-AGCTTGCC

                 *   **       
        330 CTTCCACACTGGAAGGTG
         64 CTTCCCCACCAGAAGGTG

                
        348 TTGT
          1 TTGT

        352 TTGCTCTTTG


Statistics
Matches: 145,  Mismatches: 18, Indels: 7
        0.85            0.11        0.04

Matches are distributed among these distances:
  81   72  0.50
  82   71  0.49
  83    2  0.01

ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41


Consensus pattern (81 bp):   
TTGTCTAATTTCCCAGTTTTGCCCTTCCACATCGGAAGGTGTTGTTTAGTTTTCCAGCTTGCCCT
TCCCCACCAGAAGGTG

Found at i:432 original size:50 final size:49

Alignment explanation


    Indices: 360--481  Score: 183
    Period size: 50  Copynumber: 2.4  Consensus size: 49

        350 GTTTGCTCTT

                                                                
        360 TGTTTCAAAAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTT-TCCTTTATC
          1 TGTTTC-AAAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTCT-C-TTATC

                            *                               *
        411 TGTTTCAAAAAATGCCTCTTCCCGGTCGGAAGGTCACTGTTCTCTTATT
          1 TGTTTCAAAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTCTCTTATC

                                  
        460 TGTTTCCAAAAAATGCCCCTTC
          1 TGTTT-CAAAAAATGCCCCTTC

        482 ACCAATTTCG


Statistics
Matches: 66,  Mismatches: 3, Indels: 5
        0.89            0.04        0.07

Matches are distributed among these distances:
  49    9  0.14
  50   50  0.76
  51    7  0.11

ACGTcount: A:0.22, C:0.27, G:0.16, T:0.34


Consensus pattern (49 bp):   
TGTTTCAAAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTCTCTTATC
Done.