Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3413

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: 11338
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31


Found at i:1364 original size:39 final size:40

Alignment explanation


    Indices: 1308--1485  Score: 249
    Period size: 39  Copynumber: 4.5  Consensus size: 40

       1298 ACCCAAGTAT

                    *                     *          
       1308 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC

                   *                         **     
       1347 CTTC-GGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

                                                    
       1386 CTTCGGGACTTA-CCCGGATATAGTCACTAGCACAAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

                                     *   *          
       1425 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

                                  
       1465 CTTC-GGACTTAGCCCGGATAT
          1 CTTCGGGACTTAGCCCGGATAT

       1486 CATCCGAATA


Statistics
Matches: 125,  Mismatches: 10, Indels: 8
        0.87            0.07        0.06

Matches are distributed among these distances:
  38    6  0.05
  39   83  0.66
  40   36  0.29

ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25


Consensus pattern (40 bp):   
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

Found at i:2861 original size:38 final size:38

Alignment explanation


    Indices: 2810--2886  Score: 154
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       2800 TGCTAGAAAT

                                                  
       2810 CCAAGAATCATCCTTGAACTTACCTTGATTTAGCTAAC
          1 CCAAGAATCATCCTTGAACTTACCTTGATTTAGCTAAC

                                                  
       2848 CCAAGAATCATCCTTGAACTTACCTTGATTTAGCTAAC
          1 CCAAGAATCATCCTTGAACTTACCTTGATTTAGCTAAC

             
       2886 C
          1 C

       2887 ACCATAGCTG


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31


Consensus pattern (38 bp):   
CCAAGAATCATCCTTGAACTTACCTTGATTTAGCTAAC

Found at i:9542 original size:43 final size:40

Alignment explanation


    Indices: 9374--9555  Score: 230
    Period size: 40  Copynumber: 4.5  Consensus size: 40

       9364 ACCCAAGTAT

                    *                     *          
       9374 CTTC-GGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC

                   *                         **     
       9412 CTTC-GGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

                                                    
       9451 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

                              *                         
       9491 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
          1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC

                                  
       9534 CTTCGGGACTTAGCCCGGATAT
          1 CTTCGGGACTTAGCCCGGATAT

       9556 CATTGCACTA


Statistics
Matches: 127,  Mismatches: 10, Indels: 9
        0.87            0.07        0.06

Matches are distributed among these distances:
  38   10  0.08
  39   26  0.20
  40   60  0.47
  43   31  0.24

ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24


Consensus pattern (40 bp):   
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC

Found at i:9553 original size:83 final size:79

Alignment explanation


    Indices: 9374--9555  Score: 228
    Period size: 83  Copynumber: 2.3  Consensus size: 79

       9364 ACCCAAGTAT

                    *                    *                *                  
       9374 CTTC-GGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGTCTTAGCCCGGATATAGTC
          1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAGTC

                   **     
       9437 ACTAGCATGAATGC
         66 ACTAGCACAAATGC

                                                                       *     
       9451 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG
          1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTC-GGACTTAGCCCGGATATAG

                                
       9515 -CAACTACTCGCACAAATGC
         64 TC-ACTA---GCACAAATGC

                                  
       9534 CTTCGGGACTTAGCCCGGATAT
          1 CTTCGGGACTTAGCCCGGATAT

       9556 CATTGCACTA


Statistics
Matches: 91,  Mismatches: 6, Indels: 10
        0.85            0.06        0.09

Matches are distributed among these distances:
  77    4  0.04
  78    7  0.08
  79   28  0.31
  80   22  0.24
  83   30  0.33

ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24


Consensus pattern (79 bp):   
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Done.