Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_461 ID=scaffold_461-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: 6909
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.32

Warning! 147 characters in sequence are not A, C, G, or T


Found at i:60 original size:2 final size:2

Alignment explanation


    Indices: 53--111  Score: 102
    Period size: 2  Copynumber: 29.5  Consensus size: 2

         43 TTAATTAATA

                                                                           
         53 AT AT AT AT AT AT -T ACT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT

                                     
         95 AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT A

        112 CTCTAGTTTA


Statistics
Matches: 55,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   52  0.95
   3    2  0.04

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:6351 original size:34 final size:34

Alignment explanation


    Indices: 6312--6503  Score: 132
    Period size: 41  Copynumber: 5.0  Consensus size: 34

       6302 AACAGATTCA

                                      *       
       6312 CCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
          1 CCGGCACTTAGCCTGCTAGGCTTATAACCTGATT

                                *                  
       6346 CCGGCACTTAGCCTGCTAGGTTTATAACCTGAATCAGAT
          1 CCGGCACTTAGCCTGCTAGGCTTATAACCTG-AT----T

                 * *              *                  
       6385 CACCGACGCTTAGCCTGCTAGGTTTATAACCTGATTCAGAT
          1 --CCGGCACTTAGCCTGCTAGGCTTATAACCTGA-T----T

                                  *                  
       6426 CACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGAT
          1 --CCGGCACTTAGCCTGCTAGGCTTATAACCTGA-T----T

                                  *             
       6467 CACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
          1 --CCGGCACTTAGCCTGCTAGGCTTATAACCTGATT

             
       6503 C
          1 C

       6504 AGATCACCGG


Statistics
Matches: 144,  Mismatches: 6, Indels: 16
        0.87            0.04        0.10

Matches are distributed among these distances:
  34   30  0.21
  35    2  0.01
  36    1  0.01
  39    1  0.01
  40    2  0.01
  41  108  0.75

ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29


Consensus pattern (34 bp):   
CCGGCACTTAGCCTGCTAGGCTTATAACCTGATT

Found at i:6409 original size:41 final size:41

Alignment explanation


    Indices: 6346--6528  Score: 339
    Period size: 41  Copynumber: 4.5  Consensus size: 41

       6336 TAGCCTGATT

                                            *        
       6346 CCGGCACTTAGCCTGCTAGGTTTATAACCTGAATCAGATCA
          1 CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA

               * *                                   
       6387 CCGACGCTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA
          1 CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA

                                                     
       6428 CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA
          1 CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA

                                                     
       6469 CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA
          1 CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA

                               
       6510 CCGGCACTTAGCCTGCTAG
          1 CCGGCACTTAGCCTGCTAG

       6529 ACGTATAGTC


Statistics
Matches: 137,  Mismatches: 5, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  41  137  1.00

ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28


Consensus pattern (41 bp):   
CCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA

Found at i:6506 original size:123 final size:117

Alignment explanation


    Indices: 6304--6528  Score: 335
    Period size: 123  Copynumber: 1.9  Consensus size: 117

       6294 CTTAATTTAA

                                              *                              
       6304 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCGGCACTTAGCCTGCTAGGTTT
          1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCCGGCACTTAGCCTGCTAGGTTT

                                   *                            
       6369 ATAACCTGAATCAGATCACCGACGCTTAGCCTGCTAGGTTTATAACCTGATT
         66 ATAACCTGAATCAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT

                                        *                                    
       6421 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGC
          1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGA-T----T--CCGGCACTTAGCCTGC

                            *           *               
       6485 TAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAG
         59 TAGGTTTATAACCTGAATCAGATCACCGACACTTAGCCTGCTAG

       6529 ACGTATAGTC


Statistics
Matches: 96,  Mismatches: 5, Indels: 8
        0.88            0.05        0.07

Matches are distributed among these distances:
 116   33  0.34
 117    5  0.05
 121    1  0.01
 123   57  0.59

ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28


Consensus pattern (117 bp):   
CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCCGGCACTTAGCCTGCTAGGTTT
ATAACCTGAATCAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT
Done.