Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2488

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: 10379
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30


Found at i:1515 original size:39 final size:38

Alignment explanation


    Indices: 1404--1521  Score: 195
    Period size: 36  Copynumber: 3.1  Consensus size: 38

       1394 AGATATAGTA

                                                   
       1404 ATATAGTCACTAGCACAAATGCTTCGGGACTTAGCCCGG
          1 ATATAGT-ACTAGCACAAATGCTTCGGGACTTAGCCCGG

                  *                               
       1443 --ATAGCACTAGCACAAATGCTTCGGGACTTAGCCCGG
          1 ATATAGTACTAGCACAAATGCTTCGGGACTTAGCCCGG

                                                   
       1479 ATATAGTACTAGCACAAATGCCTTCGGGACTTAGCCCGG
          1 ATATAGTACTAGCACAAATG-CTTCGGGACTTAGCCCGG

                
       1518 ATAT
          1 ATAT

       1522 CATTCGAATA


Statistics
Matches: 74,  Mismatches: 2, Indels: 6
        0.90            0.02        0.07

Matches are distributed among these distances:
  36   31  0.42
  37    4  0.05
  38   17  0.23
  39   22  0.30

ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23


Consensus pattern (38 bp):   
ATATAGTACTAGCACAAATGCTTCGGGACTTAGCCCGG

Found at i:9420 original size:39 final size:40

Alignment explanation


    Indices: 9330--9508  Score: 269
    Period size: 39  Copynumber: 4.6  Consensus size: 40

       9320 AACCCAAGTA

                     *                     *         
       9330 CCTTCGGGATTTAG-CC-GATATAG-CAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG

                    *                               
       9368 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCAC-AATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

                                        *           
       9407 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

                                        *           
       9447 CCTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

                                   
       9486 CCTTCGGGACTTAGCCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATAT

       9509 CATTCGAATA


Statistics
Matches: 131,  Mismatches: 5, Indels: 8
        0.91            0.03        0.06

Matches are distributed among these distances:
  38   12  0.09
  39   78  0.60
  40   38  0.29
  41    3  0.02

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG

Found at i:9486 original size:79 final size:79

Alignment explanation


    Indices: 9330--9508  Score: 276
    Period size: 79  Copynumber: 2.3  Consensus size: 79

       9320 AACCCAAGTA

                     *                    *                 *                
       9330 CCTTCGGGATTTAG-CC-GATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
          1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG

                          
       9393 TCAATAGCACAATG
         66 TCAATAGCACAATG

                                                                             
       9407 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC-GGACTTAGCCCGGATATA
          1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA

                *           
       9470 GTCACTAGCACAAATG
         65 GTCAATAGCAC-AATG

                                   
       9486 CCTTCGGGACTTAGCCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATAT

       9509 CATTCGAATA


Statistics
Matches: 94,  Mismatches: 4, Indels: 6
        0.90            0.04        0.06

Matches are distributed among these distances:
  77   13  0.14
  78   29  0.31
  79   51  0.54
  80    1  0.01

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24


Consensus pattern (79 bp):   
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCAATAGCACAATG
Done.