Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_344 ID=scaffold_344-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: 8050
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Found at i:1482 original size:132 final size:132

Alignment explanation


    Indices: 1286--2005  Score: 1084
    Period size: 132  Copynumber: 5.5  Consensus size: 132

       1276 ATAAGAATGC

                  *   *                              * *                     
       1286 TGGCTTTAATATACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACT
          1 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT

                                  *                                        * 
       1351 ACTGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAACT
         66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAATT

             *
       1416 AT
        131 AG

                       *              *  *                   *               
       1418 TGGCTTCAATGCACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACT
          1 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT

                *         *        *                  *          *           
       1483 ACTGTTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCATTGCTGCCCAGGGAAGTAGAATT
         66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAATT

              
       1548 AG
        131 AG

                            *                                   *            
       1550 TGGCTTCAATGTACTCTACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTAATCTGCTCCACT
          1 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT

                                *                                            
       1615 ACTGCTTAGGGAGACAAGATATGAAATCTTCAATCTATTCCACTGCTGCCCAG-GAAAGTAGAAT
         66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAG-AAGTAGAAT

               
       1679 TAG
        130 TAG

                                             *        *                      
       1682 TGGCTTCAATGTACTCCACTGTAACCACAGGGATGTAAAATCTGCCATCTTTGATCTGCTCCACT
          1 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT

                                *                          *     *           
       1747 ACTGCTTAGGGAGACAAGATATGAAATCTTCAATCTATTCCACTGCTTCCCAGGGAAGTAGAATT
         66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAATT

             *
       1812 AC
        131 AG

                  *   *                              * * *             *     
       1814 TGGCTTTAATATACTCCACTGTAACCACAGGGAGGTAAAATTCACTATCTTTGATCTGCCCCACT
          1 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT

                     *                                                       
       1879 ACTGCTTAGAGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCA-AGGAAGTAGAAT
         66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGA-GAAGTAGAAT

              *
       1943 TAA
        130 TAG

                                       *             *          *       
       1946 TGGCTTCAATGTACTCCACTGTAACCATAGGGAGGTAAAATTCGCCATCTTTAATCTGCT
          1 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCT

       2006 TCGCTGTCTA


Statistics
Matches: 532,  Mismatches: 53, Indels: 6
        0.90            0.09        0.01

Matches are distributed among these distances:
 131    1  0.00
 132  530  1.00
 133    1  0.00

ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28


Consensus pattern (132 bp):   
TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAATT
AG

Found at i:3162 original size:21 final size:21

Alignment explanation


    Indices: 3138--3186  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3128 TTAGCCTCTC

                     *            
       3138 CATTTTTACTTTTTCAT-TTTT
          1 CATTTTT-CATTTTCATCTTTT

                                 
       3159 CATTTTTCATTTTCATCTTTT
          1 CATTTTTCATTTTCATCTTTT

            *      
       3180 TATTTTT
          1 CATTTTT

       3187 TCACATCACT


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

Matches are distributed among these distances:
  20    8  0.32
  21   17  0.68

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71


Consensus pattern (21 bp):   
CATTTTTCATTTTCATCTTTT

Found at i:3187 original size:7 final size:7

Alignment explanation


    Indices: 3138--3186  Score: 57
    Period size: 7  Copynumber: 7.0  Consensus size: 7

       3128 TTAGCCTCTC

                   
       3138 CATTTTT
          1 CATTTTT

                    
       3145 -ACTTTTT
          1 CA-TTTTT

                   
       3152 CATTTTT
          1 CATTTTT

                   
       3159 CATTTTT
          1 CATTTTT

                   
       3166 CA-TTTT
          1 CATTTTT

                    
       3172 CATCTTTT
          1 CAT-TTTT

            *      
       3180 TATTTTT
          1 CATTTTT

       3187 TCACATCACT


Statistics
Matches: 37,  Mismatches: 1, Indels: 8
        0.80            0.02        0.17

Matches are distributed among these distances:
   6    7  0.19
   7   23  0.62
   8    7  0.19

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71


Consensus pattern (7 bp):   
CATTTTT

Found at i:6107 original size:19 final size:20

Alignment explanation


    Indices: 6083--6122  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       6073 AACTGTTTTT

                  *       *     
       6083 AATGCATATG-ATGTAATGA
          1 AATGCAAATGCATGAAATGA

                                
       6102 AATGCAAATGCATGAAATGA
          1 AATGCAAATGCATGAAATGA

             
       6122 A
          1 A

       6123 TGCGAAAAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  19    9  0.50
  20    9  0.50

ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25


Consensus pattern (20 bp):   
AATGCAAATGCATGAAATGA

Done.