Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2110

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: 10953
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29


Found at i:939 original size:40 final size:40

Alignment explanation


    Indices: 857--1073  Score: 239
    Period size: 40  Copynumber: 5.5  Consensus size: 40

        847 ACCCAAGTAT

                  *                **    *       *  
        857 CTTCGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
          1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC

                                  *          *      
        894 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
          1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC

                   *               *  *             
        934 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
          1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC

                                          *          
        974 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
          1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC

                  *      *                   *   *  
       1014 CTT--GATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
          1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC

                   *              
       1052 CTTCGGGACTTAGCCCGGATAT
          1 CTTCGGGTCTTAGCCCGGATAT

       1074 CATTCGATAA


Statistics
Matches: 149,  Mismatches: 24, Indels: 11
        0.81            0.13        0.06

Matches are distributed among these distances:
  37    7  0.05
  38   35  0.23
  39   17  0.11
  40   90  0.60

ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25


Consensus pattern (40 bp):   
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC

Found at i:1064 original size:78 final size:78

Alignment explanation


    Indices: 865--1073  Score: 246
    Period size: 78  Copynumber: 2.7  Consensus size: 78

        855 ATCTTCGGAT

                           *    *       *                        *          *
        865 TTAG-CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCAT
          1 TTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC

                           
        928 AAATGCCTTCGGGAC
         66 AAATGCCTT--GGAC

                             *          *                                *   
        943 TTAGCCCGGATATAATCGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCA
          1 TTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCA

                           
       1007 CAAATGCCTT-GATC
         65 CAAATGCCTTGGA-C

                *         *         *             *              
       1021 TTAGTCCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
          1 TTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT

       1074 CATTCGATAA


Statistics
Matches: 114,  Mismatches: 13, Indels: 8
        0.84            0.10        0.06

Matches are distributed among these distances:
  77    2  0.02
  78   52  0.46
  79   18  0.16
  80   42  0.37

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


Consensus pattern (78 bp):   
TTAGCCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC
AAATGCCTTGGAC

Found at i:1073 original size:118 final size:116

Alignment explanation


    Indices: 857--1073  Score: 319
    Period size: 118  Copynumber: 1.8  Consensus size: 116

        847 ACCCAAGTAT

                                   *                   *               *     
        857 CTTCGGATTTAGCCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAGCCCGGATATGGTCAC
          1 CTTCGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTC-GATCTTAGCCCGGATATAGTCAC

                     *                                          
        922 TAGCATAAATGCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
         65 TAGCATAAAAGCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC

                  *                *             *              *            
        974 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTT-GATCTTAGTCCGGATATAGTC
          1 CTTCGGAT-TTAG-CCGGATATAACAACTCGCAC-AAGGCCTTCGATCTTAGCCCGGATATAGTC

                                                
       1038 ACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
         63 ACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT

       1074 CATTCGATAA


Statistics
Matches: 89,  Mismatches: 8, Indels: 5
        0.87            0.08        0.05

Matches are distributed among these distances:
 117    7  0.08
 118   57  0.64
 119   18  0.20
 120    7  0.08

ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25


Consensus pattern (116 bp):   
CTTCGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCGATCTTAGCCCGGATATAGTCACT
AGCATAAAAGCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC

Found at i:8938 original size:40 final size:40

Alignment explanation


    Indices: 8893--9076  Score: 244
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       8883 CTCACACAAG

                           *        *          *    
       8893 GCCTTCGGGTCTTAGTCCGGATATGGTCACTAGCATAAAT
          1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT

                     *               *  *           
       8933 GCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAAT
          1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT

                                            *        
       8973 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT
          1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT

                    *      *                   *   *
       9013 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
          1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT

                     *              
       9053 GCCTTCGGGACTTAGCCCGGATAT
          1 GCCTTCGGGTCTTAGCCCGGATAT

       9077 CATTCGAATA


Statistics
Matches: 124,  Mismatches: 18, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  39    1  0.01
  40  122  0.98
  41    1  0.01

ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26


Consensus pattern (40 bp):   
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT

Done.