Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_117 ID=scaffold_117-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: 13504
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.29

Warning! 1100 characters in sequence are not A, C, G, or T


Found at i:334 original size:15 final size:15

Alignment explanation


    Indices: 298--347  Score: 57
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        288 CTTGGGCATT

                        ** 
        298 GGTTTGGGCTG-AAG
          1 GGTTTGGGCTGTTCG

                            
        312 GGTATTGGGCTGTTCG
          1 GGT-TTGGGCTGTTCG

                      *    
        328 GGTTTGGGCTATTCG
          1 GGTTTGGGCTGTTCG

                 
        343 GGTTT
          1 GGTTT

        348 TGCTAGTTGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  14    3  0.10
  15   24  0.77
  16    4  0.13

ACGTcount: A:0.08, C:0.10, G:0.44, T:0.38


Consensus pattern (15 bp):   
GGTTTGGGCTGTTCG

Found at i:947 original size:46 final size:46

Alignment explanation


    Indices: 889--1008  Score: 133
    Period size: 46  Copynumber: 2.7  Consensus size: 46

        879 TAGGATAGTG

                           *      *               *       
        889 TCTTCGATCTACTCCGCTGTAATCTCAGGGAGACAAGATCTGAAAT
          1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGACAAGACCTGAAAT

                  *                          *            
        935 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG--A-
          1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGACAAGACCTGAAAT

               *                   *    *    
        978 --TGCGATCTACTCCACTGTAACTTCAGAGAGA
          1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGA

       1009 TGAGATCCTT


Statistics
Matches: 65,  Mismatches: 9, Indels: 5
        0.82            0.11        0.06

Matches are distributed among these distances:
  41   27  0.42
  44    1  0.02
  46   37  0.57

ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27


Consensus pattern (46 bp):   
TCTTCGATCTACTCCACTGTAACCTCAGGGAGACAAGACCTGAAAT

Found at i:1071 original size:87 final size:87

Alignment explanation


    Indices: 826--1102  Score: 283
    Period size: 87  Copynumber: 3.2  Consensus size: 87

        816 NNNNNNNNNT

                      *      *              *             *                  
        826 TCAGAGAGATGAGATCCCTTATTTTAATCCGCCCCACTGTAAACTCGGGGAGATAGGATAGTGTC
          1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAAACTCAGGGAGATAGGATAGTGTC

                                  
        891 TTCGATCTACTCCGCTGTAATC
         66 TTCGATCTACTCCGCTGTAATC

                *    *         **       **  **           *            *   ** 
        913 TCAGGGAGACAAGAT-CTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCT
          1 TCAGAGAGATAAGATCCT-TTATT-TT-AATCCGCTCCACTGTAAACTCAGGGAGATAGGATAGT

              * *           *        
        976 G-ATGCGATCTACTCCACTGTAA-C
         63 GTCTTCGATCTACTCCGCTGTAATC

                       *                        *            *               
        999 TTCAGAGAGATGAGATCCTTTATTTTAATCCGCTCCGCTGTAAACTCAGTGAGATAGGATAGTGT
          1 -TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAAACTCAGGGAGATAGGATAGTGT

                                   
       1064 CTTCGATCTACTCCGCTGTAATC
         65 CTTCGATCTACTCCGCTGTAATC

                *           
       1087 TCAGGGAGATAAGATC
          1 TCAGAGAGATAAGATC

       1103 TCTGGCTTCA


Statistics
Matches: 143,  Mismatches: 39, Indels: 16
        0.72            0.20        0.08

Matches are distributed among these distances:
  85   25  0.17
  86    6  0.04
  87   80  0.56
  88    7  0.05
  89   25  0.17

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


Consensus pattern (87 bp):   
TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAAACTCAGGGAGATAGGATAGTGTC
TTCGATCTACTCCGCTGTAATC

Done.