Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_736 ID=scaffold_736-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: 5314
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.25

Warning! 1146 characters in sequence are not A, C, G, or T


Found at i:25 original size:19 final size:19

Alignment explanation


    Indices: 1--153  Score: 270
    Period size: 19  Copynumber: 8.1  Consensus size: 19

                        *      
          1 GCAAACACGTTTAGAAAAC
          1 GCAAACACGTTTCGAAAAC

                               
         20 GCAAACACGTTTCGAAAAC
          1 GCAAACACGTTTCGAAAAC

                        *      
         39 GCAAACACGTTTAGAAAAC
          1 GCAAACACGTTTCGAAAAC

                               
         58 GCAAACACGTTTCGAAAAC
          1 GCAAACACGTTTCGAAAAC

                               
         77 GCAAACACGTTTCGAAAAC
          1 GCAAACACGTTTCGAAAAC

                        *      
         96 GCAAACACGTTTAGAAAAC
          1 GCAAACACGTTTCGAAAAC

                               
        115 GCAAACACGTTTCGAAAAC
          1 GCAAACACGTTTCGAAAAC

                        *      
        134 GCAAACACGTTTGGAAAAC
          1 GCAAACACGTTTCGAAAAC

             
        153 G
          1 G

        154 TCCATGTCTA


Statistics
Matches: 128,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19  128  1.00

ACGTcount: A:0.44, C:0.24, G:0.17, T:0.16


Consensus pattern (19 bp):   
GCAAACACGTTTCGAAAAC

Found at i:1370 original size:22 final size:22

Alignment explanation


    Indices: 1344--1389  Score: 83
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1334 AGGAGACTTA

                              *   
       1344 TTTTGACGAGTCCACTTGGATT
          1 TTTTGACGAGTCCACTTGCATT

                                  
       1366 TTTTGACGAGTCCACTTGCATT
          1 TTTTGACGAGTCCACTTGCATT

              
       1388 TT
          1 TT

       1390 GACTTGCTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43


Consensus pattern (22 bp):   
TTTTGACGAGTCCACTTGCATT

Found at i:4098 original size:22 final size:20

Alignment explanation


    Indices: 4056--4099  Score: 52
    Period size: 22  Copynumber: 2.1  Consensus size: 20

       4046 GCGTTCTTCC

                    *       *   
       4056 GCAAAAATGAGTAAATTTAT
          1 GCAAAAATAAGTAAATATAT

                                  
       4076 GCAAAAACTAAGTCAAATATAT
          1 GCAAAAA-TAAGT-AAATATAT

              
       4098 GC
          1 GC

       4100 TTTATAAACG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    7  0.35
  21    4  0.20
  22    9  0.45

ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25


Consensus pattern (20 bp):   
GCAAAAATAAGTAAATATAT
Done.