Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_968 ID=scaffold_968-JGI_221_v2.0

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: 3335
ACGTcount: A:0.17, C:0.07, G:0.11, T:0.21

Warning! 1487 characters in sequence are not A, C, G, or T


Found at i:2471 original size:43 final size:43

Alignment explanation


    Indices: 2364--2675  Score: 452
    Period size: 43  Copynumber: 7.3  Consensus size: 43

       2354 AGGTTATGTT

                         *  ** *                    *  
       2364 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGAT-
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

                              *                         
       2405 TTATAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
          1 TT-TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

                             *                        *
       2449 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTT
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

                 *                     *               
       2492 TTTAGTGGCGTTTGTGGGAAAAGCGCCTCTAAAGGTCTTGGTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

                          *    *                    *  
       2535 TTTAGCGGCGTTTGCGGGAGAAGCGCCGCTAAAGGTCTTGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

                                                       
       2578 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

                                                        
       2621 TTTAGCGGCGTTTGTGGGAAAA-CGCCGCTAAAGGTC-TGGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGG-TC

                    *    
       2663 TTTAGCGGAGTTT
          1 TTTAGCGGCGTTT

       2676 ATTTCTAAAA


Statistics
Matches: 248,  Mismatches: 19, Indels: 7
        0.91            0.07        0.03

Matches are distributed among these distances:
  41    5  0.02
  42   59  0.24
  43  182  0.73
  44    2  0.01

ACGTcount: A:0.19, C:0.18, G:0.33, T:0.31


Consensus pattern (43 bp):   
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC

Found at i:2764 original size:22 final size:22

Alignment explanation


    Indices: 2736--2778  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2726 TTGTGGCGCT

                            *     
       2736 AAAAAGCACCGCTAAAGGCCTA
          1 AAAAAGCACCGCTAAAAGCCTA

                   *             
       2758 AAAAAGCGCCGCTAAAAGCCT
          1 AAAAAGCACCGCTAAAAGCCT

       2779 GTTTTGGTGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09


Consensus pattern (22 bp):   
AAAAAGCACCGCTAAAAGCCTA
Done.