Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_621 ID=scaffold_621-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: 5172
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:3383 original size:1 final size:1

Alignment explanation


    Indices: 3377--3419  Score: 50
    Period size: 1  Copynumber: 43.0  Consensus size: 1

       3367 ATTCAATCAG

                      *          *        *      *     
       3377 AAAAAAAAAATAAAAAAAAAAGAAAAAAAAGAAAAAAGAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       3420 GGAGAGGCCA


Statistics
Matches: 34,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:0.91, C:0.00, G:0.07, T:0.02


Consensus pattern (1 bp):   
A

Found at i:3402 original size:16 final size:16

Alignment explanation


    Indices: 3375--3419  Score: 67
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       3365 AGATTCAATC

                             
       3375 AGAAAAAA-AAAATAAA
          1 AGAAAAAAGAAAA-AAA

                            
       3391 A-AAAAAAGAAAAAAA
          1 AGAAAAAAGAAAAAAA

                          
       3406 AGAAAAAAGAAAAA
          1 AGAAAAAAGAAAAA

       3420 GGAGAGGCCA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  15   10  0.37
  16   17  0.63

ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02


Consensus pattern (16 bp):   
AGAAAAAAGAAAAAAA

Found at i:3403 original size:22 final size:22

Alignment explanation


    Indices: 3375--3420  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3365 AGATTCAATC

                                   
       3375 AGAAAAAAAA-AATAAAAAAAAA
          1 AGAAAAAAAAGAA-AAAAAAAAA

                             *    
       3397 AGAAAAAAAAGAAAAAAGAAAA
          1 AGAAAAAAAAGAAAAAAAAAAA

              
       3419 AG
          1 AG

       3421 GAGAGGCCAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   20  0.91
  23    2  0.09

ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02


Consensus pattern (22 bp):   
AGAAAAAAAAGAAAAAAAAAAA

Found at i:4734 original size:45 final size:45

Alignment explanation


    Indices: 4597--4741  Score: 138
    Period size: 45  Copynumber: 3.3  Consensus size: 45

       4587 ACAGATTAGT

                                        *     *          
       4597 GAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATC
          1 GAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATC

                      *   *             *    *    *     * *
       4642 GAA-A-A-CAAAGTTTTGCCTTCCT-CGGTTG-TAGTGGAGCAGGTT
          1 GAAGATAGCAGA-TCTTGCCTTCCTGC-ATTGACAGTGAAGCAGATC

            *                                            
       4684 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATC
          1 GAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATC

                  *      
       4729 GAAGATGGCAGAT
          1 GAAGATAGCAGAT

       4742 TTTACCTCCT


Statistics
Matches: 74,  Mismatches: 19, Indels: 14
        0.69            0.18        0.13

Matches are distributed among these distances:
  42   15  0.20
  43   15  0.20
  44   16  0.22
  45   28  0.38

ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24


Consensus pattern (45 bp):   
GAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATC

Found at i:4895 original size:132 final size:132

Alignment explanation


    Indices: 4716--5172  Score: 772
    Period size: 132  Copynumber: 3.5  Consensus size: 132

       4706 CTGCATTGAC

                *                              *                             
       4716 AGTGAAGCAGATCGAAGATGGCAGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCA
          1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA

                                                   *                         
       4781 GTAATTCTACTTCCCTGGAAAATAGTGGAATAGATTGAATATTTAAGATCTTATCTCCCTAAGCA
         66 GTAATTCTACTTCCCTGGAAAATAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCA

              
       4846 GT
        131 GT

                                 **                                          
       4848 AGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
          1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA

                                                        *                    
       4913 GTAATTCTACTTCCCTGGAAAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
         66 GTAATTCTACTTCCCTGGAAAATAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCA

              
       4978 GT
        131 GT

                     *                                  *                    
       4980 AGTGGAGCATATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
          1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA

                                   *                     *  *                
       5045 GTAATTCTACTTCCCT-GAACAACAGTGGAATAGATTGAAGATTTTAGGTCTTATCTCCCTAAGC
         66 GTAATTCTACTTCCCTGGAA-AATAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGC

               
       5109 AGT
        130 AGT

                                  *         *           *                
       5112 AGTGGAGCAGATCGAAGATGGCGGATTTTACCACCCTGTGGTTATAGTGGAGTACATTGAA
          1 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAA


Statistics
Matches: 308,  Mismatches: 16, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
 131    3  0.01
 132  305  0.99

ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30


Consensus pattern (132 bp):   
AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTGGAAAATAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCA
GT
Done.