Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1046

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: 3163
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33


Found at i:2680 original size:110 final size:110

Alignment explanation


    Indices: 2411--2732  Score: 574
    Period size: 110  Copynumber: 2.9  Consensus size: 110

       2401 AAGATTTAGG

                                                                             
       2411 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCTAGCACATTAGTGCACGTTTTCTC
          1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCTAGCACATTAGTGCACGTTTTCTC

                                                 *       
       2476 GAATTTTCGAACGCAAAACATTGCCTTATTTTGAAA-ATTTTAAA
         66 GAATTTTCGAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA

                                                     *          *            
       2520 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
          1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCTAGCACATTAGTGCACGTTTTCTC

                                                         
       2585 GAATTTTCGAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
         66 GAATTTTCGAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA

             *                       *                                       
       2630 ATGATATTTGGCTATTTGGTCGAACAAGAAAAATCGAAACCTAGCACATTAGTGCACGTTTTCTC
          1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCTAGCACATTAGTGCACGTTTTCTC

                  *                        *      
       2695 GAATTTCCGAACGCAAAACATTGCCTTATTTCGAAATT
         66 GAATTTTCGAACGCAAAACATTGCCTTATTTTGAAATT

       2733 AGTATGCGTA


Statistics
Matches: 203,  Mismatches: 9, Indels: 1
        0.95            0.04        0.00

Matches are distributed among these distances:
 109   99  0.49
 110  104  0.51

ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Consensus pattern (110 bp):   
AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCTAGCACATTAGTGCACGTTTTCTC
GAATTTTCGAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA

Found at i:2974 original size:41 final size:41

Alignment explanation


    Indices: 2929--3006  Score: 104
    Period size: 41  Copynumber: 1.9  Consensus size: 41

       2919 AAGAAAATGA

                                   *                  
       2929 ATAGAACTATAAAAATAT-AAGAGATATATATATGTATCTAC
          1 ATAGAACTATAAAAATATGAA-AAATATATATATGTATCTAC

                  *    *                 *       
       2970 ATAGAATTATAGAAATATGAAAAATATATGTATGTAT
          1 ATAGAACTATAAAAATATGAAAAATATATATATGTAT

       3007 AAAATTTTAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  41   30  0.94
  42    2  0.06

ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33


Consensus pattern (41 bp):   
ATAGAACTATAAAAATATGAAAAATATATATATGTATCTAC
Done.