Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_220 ID=scaffold_220-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: 9223
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:1920 original size:19 final size:19

Alignment explanation


    Indices: 1896--1942  Score: 60
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       1886 CTCTTTTTTT

                                
       1896 TTTGCATT-CATTCCATGCA
          1 TTTGCATTACATTCCAT-CA

                         *     
       1915 TTTGCATTACATTGCATCA
          1 TTTGCATTACATTCCATCA

             *       
       1934 TATGCATTA
          1 TTTGCATTA

       1943 GATTTTCACA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  19   18  0.72
  20    7  0.28

ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43


Consensus pattern (19 bp):   
TTTGCATTACATTCCATCA

Found at i:6192 original size:44 final size:44

Alignment explanation


    Indices: 6144--6427  Score: 129
    Period size: 44  Copynumber: 6.5  Consensus size: 44

       6134 CTTGAACAGC

                               *                        
       6144 AGTGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGTAGT
          1 AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT

                   *  * *       ***     *              *   
       6188 AGTGGAGCAGATCGAAGA-CGGTGAATCTTATCTTCCC-AAGGCAGT
          1 AGTGGAGTAGGTTGAAGATCACAG-ATCCTATC-TCCCTAA-GTAGT

              * *     *  *    *   * *            *  **  
       6233 AGAGAAGTAGATTTAAG-CCACTGGTCCTATCTCCCTGAGCGGT
          1 AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT

             *                 **        * *            
       6276 AATGGAGTAGGTTGAAGATTGCAGATCCTGTATCCCTAAGTAGT
          1 AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT

                   * ** *                *                  
       6320 AGTGGAGCAAATCGAAGA-CAGC-GAATCATATCTTCCC-AAGGTAGT
          1 AGTGGAGTAGGTTGAAGATCA-CAG-ATCCTATC-TCCCTAA-GTAGT

                           *                        *      
       6365 AG-GGAAGT-GGATTTAAG-TCACTAG-TCCTATCTCCCTGAGTAGT
          1 AGTGG-AGTAGG-TTGAAGATCAC-AGATCCTATCTCCCTAAGTAGT

                                
       6408 AGTGGAGTAGGTTGAAGATC
          1 AGTGGAGTAGGTTGAAGATC

       6428 GTAGATCTTG


Statistics
Matches: 168,  Mismatches: 53, Indels: 38
        0.65            0.20        0.15

Matches are distributed among these distances:
  43   41  0.24
  44   84  0.50
  45   42  0.25
  46    1  0.01

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26


Consensus pattern (44 bp):   
AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT

Found at i:6301 original size:132 final size:132

Alignment explanation


    Indices: 6120--6426  Score: 452
    Period size: 132  Copynumber: 2.3  Consensus size: 132

       6110 CAGATCAAAA

                           *   *   *                               *         
       6120 ACTGGTCCTATCTCCTTGAACAGCAGTGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGT
          1 ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTATATCCCTAAGT

                        *         * *     *                                  
       6185 AGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG
         66 AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG

              
       6250 CC
        131 CC

                                 *   *                  *        *           
       6252 ACTGGTCCTATCTCCCTGAGCGGTAATGGAGTAGGTTGAAGATTGCAGATCCTGTATCCCTAAGT
          1 ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTATATCCCTAAGT

                                                        *     *     *        
       6317 AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGTAGTAGGGAAGTGGATTTAAG
         66 AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG

            * 
       6382 TC
        131 CC

               *                *                      
       6384 ACTAGTCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAAGAT
          1 ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGAT

       6427 CGTAGATCTT


Statistics
Matches: 155,  Mismatches: 20, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 132  155  1.00

ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26


Consensus pattern (132 bp):   
ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTATATCCCTAAGT
AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG
CC

Found at i:6548 original size:44 final size:44

Alignment explanation


    Indices: 6494--6599  Score: 135
    Period size: 44  Copynumber: 2.4  Consensus size: 44

       6484 CTTGAAATTA

                                        *                
       6494 CAGTGGAGCAGATTGAAAATAC-AAGTCTTATCTCCCTGAAGTTG
          1 CAGTGGAGCAGATTGAAAATACTAA-TCCTATCTCCCTGAAGTTG

                        *    **                *        
       6538 CAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCTTGAAGTTG
          1 CAGTGGAGCAGATTGAAAATACTAATCCTATCTCCCTGAAGTTG

                     *         
       6582 CAGTGGAGCGGATT-AAAA
          1 CAGTGGAGCAGATTGAAAA

       6600 CAATGAATCT


Statistics
Matches: 52,  Mismatches: 9, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  43    2  0.04
  44   48  0.92
  45    2  0.04

ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25


Consensus pattern (44 bp):   
CAGTGGAGCAGATTGAAAATACTAATCCTATCTCCCTGAAGTTG

Found at i:8212 original size:3 final size:3

Alignment explanation


    Indices: 8204--8249  Score: 83
    Period size: 3  Copynumber: 15.3  Consensus size: 3

       8194 TTTAACCTTG

                                                              *          
       8204 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T

       8250 TACTCATTTA


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (3 bp):   
TAT

Done.