Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_82 ID=scaffold_82-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: 23086
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.21

Warning! 7649 characters in sequence are not A, C, G, or T


Found at i:2152 original size:27 final size:27

Alignment explanation


    Indices: 2129--2316  Score: 240
    Period size: 27  Copynumber: 7.0  Consensus size: 27

       2119 AAGGGTATAA

                               *       
       2129 CAGTCATTTTACCCTATGGTGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                                        
       2156 C-GTTCATTTTACCCTATGGGGGTATTT
          1 CAG-TCATTTTACCCTATGGGGGTATTT

              *                        
       2183 CAATCATTTTACCCTATGGGGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                    *    *             
       2210 CAGTCATTCTACCTTATGGGGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                             **        
       2237 CAGTCATTTTA-CCTATAAGGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                               *        
       2263 C-GATCATTTTACCCTATGAGGGTATTT
          1 CAG-TCATTTTACCCTATGGGGGTATTT

                              **        
       2290 C-GATCATTTTACCCTATAAGGGTATTT
          1 CAG-TCATTTTACCCTATGGGGGTATTT

       2317 TGGTTAATGT


Statistics
Matches: 146,  Mismatches: 11, Indels: 8
        0.88            0.07        0.05

Matches are distributed among these distances:
  25    1  0.01
  26   22  0.15
  27  123  0.84

ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42


Consensus pattern (27 bp):   
CAGTCATTTTACCCTATGGGGGTATTT

Found at i:5099 original size:27 final size:27

Alignment explanation


    Indices: 5076--5263  Score: 240
    Period size: 27  Copynumber: 7.0  Consensus size: 27

       5066 AAGGGTATAA

                               *       
       5076 CAGTCATTTTACCCTATGGTGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                                        
       5103 C-GTTCATTTTACCCTATGGGGGTATTT
          1 CAG-TCATTTTACCCTATGGGGGTATTT

              *                        
       5130 CAATCATTTTACCCTATGGGGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                    *    *             
       5157 CAGTCATTCTACCTTATGGGGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                             **        
       5184 CAGTCATTTTA-CCTATAAGGGTATTT
          1 CAGTCATTTTACCCTATGGGGGTATTT

                               *        
       5210 C-GATCATTTTACCCTATGAGGGTATTT
          1 CAG-TCATTTTACCCTATGGGGGTATTT

                              **        
       5237 C-GATCATTTTACCCTATAAGGGTATTT
          1 CAG-TCATTTTACCCTATGGGGGTATTT

       5264 TGGTTAATGT


Statistics
Matches: 146,  Mismatches: 11, Indels: 8
        0.88            0.07        0.05

Matches are distributed among these distances:
  25    1  0.01
  26   22  0.15
  27  123  0.84

ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42


Consensus pattern (27 bp):   
CAGTCATTTTACCCTATGGGGGTATTT

Found at i:6738 original size:27 final size:27

Alignment explanation


    Indices: 6552--6738  Score: 216
    Period size: 27  Copynumber: 7.0  Consensus size: 27

       6542 GGTATAACAG

                            *         *
       6552 TCATTTTACCCTATGGTGGTATTTCGT
          1 TCATTTTACCCTATGGGGGTATTTCGA

              *                      * 
       6579 TCCTTTTACCCTATGGGGGTATTTCAA
          1 TCATTTTACCCTATGGGGGTATTTCGA

                                       
       6606 TCATTTTACCCTATGGGGGTATTTC-A
          1 TCATTTTACCCTATGGGGGTATTTCGA

                  *  ***               *
       6632 GTCATTCTATTTTATGGGGGTATTTCGG
          1 -TCATTTTACCCTATGGGGGTATTTCGA

                          **           
       6660 TCATTTTA-CCTATAAGGGTATTTCGA
          1 TCATTTTACCCTATGGGGGTATTTCGA

                           *           
       6686 TCATTTTACCCTATGAGGGTATTTCGA
          1 TCATTTTACCCTATGGGGGTATTTCGA

              *           **          
       6713 TCGTTTTACCCTATAAGGGTATTTCG
          1 TCATTTTACCCTATGGGGGTATTTCG

       6739 GTTAATGTAG


Statistics
Matches: 138,  Mismatches: 19, Indels: 6
        0.85            0.12        0.04

Matches are distributed among these distances:
  26   22  0.16
  27  116  0.84

ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43


Consensus pattern (27 bp):   
TCATTTTACCCTATGGGGGTATTTCGA

Found at i:15902 original size:18 final size:20

Alignment explanation


    Indices: 15866--15905  Score: 66
    Period size: 18  Copynumber: 2.1  Consensus size: 20

      15856 ACCTAACACG

                                
      15866 AATTAAATTTAAGACATATT
          1 AATTAAATTTAAGACATATT

                                
      15886 AATTAAA-TTAA-ACATATT
          1 AATTAAATTTAAGACATATT

              
      15904 AA
          1 AA

      15906 CATAACAAGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  18    9  0.45
  19    4  0.20
  20    7  0.35

ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38


Consensus pattern (20 bp):   
AATTAAATTTAAGACATATT
Done.