Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold754

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: 7329
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33


Found at i:4515 original size:84 final size:85

Alignment explanation


    Indices: 4373--4545  Score: 287
    Period size: 84  Copynumber: 2.1  Consensus size: 85

       4363 GATAAACATG

                               *                *           *                
       4373 ATACACTAATAGATCCCTACCCTCTACAATCCGGCCTAGACGTTATGATTGAATCATGAAAGTCA
          1 ATACACTAATAGATCCCTAACCTCTACAATCCGGCCCAGACGTTATGACTGAATCATGAAAGTCA

                 *   *          
       4438 CATTAGCTATTGAAATTGCC
         66 CATTAACTAATGAAATTGCC

                                                                             
       4458 ATACACTAAT-GATCCCTAACCTCTACAATCCGGCCCAGACGTTATGACTGAATCATGAAAGTCA
          1 ATACACTAATAGATCCCTAACCTCTACAATCCGGCCCAGACGTTATGACTGAATCATGAAAGTCA

                                
       4522 CATTAACTAATGAAATTGCC
         66 CATTAACTAATGAAATTGCC

                 
       4542 -TACA
          1 ATACA

       4546 AAAACATTCA


Statistics
Matches: 83,  Mismatches: 5, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  83    4  0.05
  84   69  0.83
  85   10  0.12

ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27


Consensus pattern (85 bp):   
ATACACTAATAGATCCCTAACCTCTACAATCCGGCCCAGACGTTATGACTGAATCATGAAAGTCA
CATTAACTAATGAAATTGCC

Found at i:5974 original size:20 final size:20

Alignment explanation


    Indices: 5935--5976  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       5925 CTGTTAGAGT

                         *      
       5935 TAATATAGTCAAAGCAGTTG
          1 TAATATAGTCAAAACAGTTG

                           *    
       5955 TAATATAGTCAAAACCGTTG
          1 TAATATAGTCAAAACAGTTG

              
       5975 TA
          1 TA

       5977 CCGTTGTAAG


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

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31


Consensus pattern (20 bp):   
TAATATAGTCAAAACAGTTG

Found at i:6005 original size:15 final size:15

Alignment explanation


    Indices: 5985--6015  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5975 TACCGTTGTA

                           
       5985 AGTCTGTTAGCAGTT
          1 AGTCTGTTAGCAGTT

                           
       6000 AGTCTGTTAGCAGTT
          1 AGTCTGTTAGCAGTT

             
       6015 A
          1 A

       6016 AAGATGATAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39


Consensus pattern (15 bp):   
AGTCTGTTAGCAGTT

Found at i:6638 original size:15 final size:15

Alignment explanation


    Indices: 6618--6648  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6608 CTATCATCTT

                           
       6618 TAACTGCTAACAGAC
          1 TAACTGCTAACAGAC

                           
       6633 TAACTGCTAACAGAC
          1 TAACTGCTAACAGAC

             
       6648 T
          1 T

       6649 TACAACGGTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23


Consensus pattern (15 bp):   
TAACTGCTAACAGAC

Found at i:6682 original size:20 final size:20

Alignment explanation


    Indices: 6657--6698  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6647 CTTACAACGG

                    *           
       6657 TACAACAGTTTTGACTATAT
          1 TACAACAGCTTTGACTATAT

                  *             
       6677 TACAACTGCTTTGACTATAT
          1 TACAACAGCTTTGACTATAT

              
       6697 TA
          1 TA

       6699 ACTCTAACAT


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

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40


Consensus pattern (20 bp):   
TACAACAGCTTTGACTATAT
Done.