Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_155 ID=scaffold_155-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: 10876
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.26

Warning! 267 characters in sequence are not A, C, G, or T


Found at i:453 original size:27 final size:27

Alignment explanation


    Indices: 421--670  Score: 353
    Period size: 27  Copynumber: 9.3  Consensus size: 27

        411 TATAAAGATC

                       *                
        421 ATTTTACCCTTAG-GGGATATTTCGATA
          1 ATTTTACCCTTCGAGGG-TATTTCGATA

                       *            *  
        448 ATTTTACCCTTTGAGGGTATTTCGGTA
          1 ATTTTACCCTTCGAGGGTATTTCGATA

                       *               
        475 ATTTTACCCTTTGAGGGTATTTCGATA
          1 ATTTTACCCTTCGAGGGTATTTCGATA

                                       
        502 ATTTTACCCTTCGAGGGTATTTCGATA
          1 ATTTTACCCTTCGAGGGTATTTCGATA

                *          *       *    
        529 ATTTAACCCTTCGAGCGTATTT-TAGTA
          1 ATTTTACCCTTCGAGGGTATTTCGA-TA

                                       
        556 ATTTTACCCTTCGAGGGTATTTCGATA
          1 ATTTTACCCTTCGAGGGTATTTCGATA

             *  *                   *  
        583 AATTCACCCTTCGAGGGTATTTCGGTA
          1 ATTTTACCCTTCGAGGGTATTTCGATA

                                        
        610 ATTTTACCCTTCGAGGGTATTTC-AGTA
          1 ATTTTACCCTTCGAGGGTATTTCGA-TA

                        *              
        637 ATTTTACCCTTCAAGGGTATTTCGATA
          1 ATTTTACCCTTCGAGGGTATTTCGATA

                   
        664 ATTTTAC
          1 ATTTTAC

        671 TCATGAATCG


Statistics
Matches: 201,  Mismatches: 17, Indels: 10
        0.88            0.07        0.04

Matches are distributed among these distances:
  26    1  0.00
  27  195  0.97
  28    5  0.02

ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41


Consensus pattern (27 bp):   
ATTTTACCCTTCGAGGGTATTTCGATA

Found at i:7646 original size:27 final size:28

Alignment explanation


    Indices: 7615--7675  Score: 79
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       7605 GTATTTAGTG

                                 *      
       7615 ACAGTA-CAATGAGGGCCTTAGCCCAAT
          1 ACAGTAGCAATGAGGGCCTTAACCCAAT

            *        *  *               
       7642 TCAGTAGCACTGTGGGCCTTAACCCAAT
          1 ACAGTAGCAATGAGGGCCTTAACCCAAT

                  
       7670 ACAGTA
          1 ACAGTA

       7676 TCATTACAGT


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  27    5  0.18
  28   23  0.82

ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21


Consensus pattern (28 bp):   
ACAGTAGCAATGAGGGCCTTAACCCAAT

Found at i:8193 original size:27 final size:27

Alignment explanation


    Indices: 8050--8191  Score: 180
    Period size: 27  Copynumber: 5.3  Consensus size: 27

       8040 TATAAAGATC

                       *            *   
       8050 ATTTTACCCTTCGAGGGTA-TTCTAGTA
          1 ATTTTACCCTTTGAGGGTATTTC-GGTA

                                       
       8077 ATTTTACCCTTTGAGGGTATTTCGGTA
          1 ATTTTACCCTTTGAGGGTATTTCGGTA

                                    *  
       8104 ATTTTACCCTTTGAGGGTATTTCGATA
          1 ATTTTACCCTTTGAGGGTATTTCGGTA

            *          *              * 
       8131 TTTTTACCCTTCGAGGGTATTT-GGACA
          1 ATTTTACCCTTTGAGGGTATTTCGG-TA

             *     *                   
       8158 AATTTACTCTTTGAGGGTATTTCGGTA
          1 ATTTTACCCTTTGAGGGTATTTCGGTA

                   
       8185 ATTTTAC
          1 ATTTTAC

       8192 TCATGAATAG


Statistics
Matches: 99,  Mismatches: 13, Indels: 6
        0.84            0.11        0.05

Matches are distributed among these distances:
  26    1  0.01
  27   93  0.94
  28    5  0.05

ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44


Consensus pattern (27 bp):   
ATTTTACCCTTTGAGGGTATTTCGGTA
Done.