Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1283

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: 18569
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


Found at i:1521 original size:14 final size:15

Alignment explanation


    Indices: 1502--1531  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       1492 GATTCAGCTC

                           
       1502 TTGCACAT-ATATAT
          1 TTGCACATGATATAT

                           
       1516 TTGCACATGATATAT
          1 TTGCACATGATATAT

             
       1531 T
          1 T

       1532 GGTATGACAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    8  0.53
  15    7  0.47

ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43


Consensus pattern (15 bp):   
TTGCACATGATATAT

Found at i:2530 original size:40 final size:40

Alignment explanation


    Indices: 2332--2549  Score: 255
    Period size: 40  Copynumber: 5.5  Consensus size: 40

       2322 TGGATGATAA

                               *        *   *        
       2332 CCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTAGT-T
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT

                 *     **              *       *    
       2372 CCGGGATAAGTTTCGAAGGCATTTGTGTGAGTTACCATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                                     
       2412 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-T
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT

                                                    
       2452 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

            *       *          *     *               
       2492 TCGGGCTATGTCCCGAAGGTATTTGAGCGAG-TAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT

                 *   *         
       2532 CC-GGTTAAATCCCGAAGG
          1 CCGGGCTAAGTCCCGAAGG

       2550 TACTTGGCTT


Statistics
Matches: 153,  Mismatches: 21, Indels: 9
        0.84            0.11        0.05

Matches are distributed among these distances:
  39   17  0.11
  40  135  0.88
  41    1  0.01

ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

Found at i:4422 original size:40 final size:40

Alignment explanation


    Indices: 4374--4640  Score: 480
    Period size: 40  Copynumber: 6.7  Consensus size: 40

       4364 GCAAACACAT

                            *      *                
       4374 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                          * *       
       4414 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *                          
       4454 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                      *             
       4494 TTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
       4534 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
       4574 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                       
       4614 TTGCCTTCGGGTCTTAGCCCGGATATA
          1 TTGCCTTCGGGTCTTAGCCCGGATATA

       4641 ATCCAATGTT


Statistics
Matches: 217,  Mismatches: 10, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40  217  1.00

ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30


Consensus pattern (40 bp):   
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

Found at i:14825 original size:40 final size:40

Alignment explanation


    Indices: 14637--14852  Score: 233
    Period size: 40  Copynumber: 5.4  Consensus size: 40

      14627 GATGATAACT

                   *               *  * * *          
      14637 GGGCTAATTCCCGAAGGCATTTGCGCTACTGACTAGT-TCC
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC

                     **              *       *      
      14677 GGGCTAAGTAACGAAGGCATTTGTGTGAGTTACCATATCC
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC

                                                    *
      14717 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-TCT
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC

                                                    
      14757 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC

                  *          *   * *                 
      14797 GGGCTATGTCCCGAAGGTATTCGAGCGAG-TAGCTATATCC
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC

               *   *         
      14837 -GGTTAAATCCCGAAGG
          1 GGGCTAAGTCCCGAAGG

      14853 TACTTGGCTT


Statistics
Matches: 150,  Mismatches: 22, Indels: 9
        0.83            0.12        0.05

Matches are distributed among these distances:
  39   17  0.11
  40  132  0.88
  41    1  0.01

ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27


Consensus pattern (40 bp):   
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC

Done.