Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2008

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: 5507
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33


Found at i:234 original size:52 final size:53

Alignment explanation


    Indices: 5--303  Score: 245
    Period size: 52  Copynumber: 5.8  Consensus size: 53

          1 TCTC

                                        *      *                   
          5 TAAGTC-AATGTCACTGGCCTTGAATCAACACATTAGCACTCTTCTCA---TCTT
          1 TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCAC-CTT-TCATTTTCTT

                   *  *  **       *   *    *                     
         56 TAAGTCTGATATCGTTGGCCTTTAATTAGCATATTGGCACCTTTCATTTTCTT
          1 TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTCATTTTCTT

             *                                 *    *      **    
        109 TCAGTCTAATGTCACTGGCCTTGAATCAGCACATTAGCACTTTTC-TCATC-T
          1 TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTCATTTTCTT

                   *  *  **         *      *        *            
        160 TAAGTCTGATATCGTTGGCCTTGAGTCAGCATATTGGCA-GTTTCATTTTCTT
          1 TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTCATTTTCTT

                  *         *                   *    *     **    
        212 TAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACACCCTT-ATCATCTT
          1 TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTCATTTTCTT

                    *      **          *            
        264 TAAGTCTAGTGTCACAAGCCTTGAATCTGCACATTGGCAC
          1 TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCAC

        304 ATTTGTCTAG


Statistics
Matches: 191,  Mismatches: 50, Indels: 13
        0.75            0.20        0.05

Matches are distributed among these distances:
  50    7  0.04
  51   44  0.23
  52   99  0.52
  53   41  0.21

ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36


Consensus pattern (53 bp):   
TAAGTCTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTCATTTTCTT

Found at i:268 original size:104 final size:105

Alignment explanation


    Indices: 5--270  Score: 396
    Period size: 103  Copynumber: 2.6  Consensus size: 105

          1 TCTC

                                        *                                    
          5 TAAGT-CAATGTCACTGGCCTTGAATCAACACATTAGCACTCTTCTCATCTTTAAGTCTGATATC
          1 TAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAGCACTCTTCTCATCTTTAAGTCTGATATC

                     *   *                          
         69 GTTGGCCTTTAATTAGCATATTGGCACCTTTCATTTTCTT
         66 GTTGGCCTTGAATCAGCATATTGGCACCTTTCATTTTCTT

             *    *                                  *                       
        109 TCAGTCTAATGTCACTGGCCTTGAATCAGCACATTAGCACTTTTCTCATC-TTAAGTCTGATATC
          1 TAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAGCACTCTTCTCATCTTTAAGTCTGATATC

                       *               *            
        173 GTTGGCCTTGAGTCAGCATATTGGCA-GTTTCATTTTCTT
         66 GTTGGCCTTGAATCAGCATATTGGCACCTTTCATTTTCTT

                            *                        *   *              
        212 TAAGTCCAATGTCACTAGCCTTGAATCAGCACATT-GACACCCTTATCATCTTTAAGTCT
          1 TAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAG-CACTCTTCTCATCTTTAAGTCT

        271 AGTGTCACAA


Statistics
Matches: 145,  Mismatches: 14, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
 102    1  0.01
 103   54  0.37
 104   49  0.34
 105   41  0.28

ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38


Consensus pattern (105 bp):   
TAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAGCACTCTTCTCATCTTTAAGTCTGATATC
GTTGGCCTTGAATCAGCATATTGGCACCTTTCATTTTCTT

Found at i:4452 original size:20 final size:20

Alignment explanation


    Indices: 4429--4481  Score: 63
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       4419 TTCAACGAAT

                  *         *    
       4429 TGTATCAATACAT-AGGGTAA
          1 TGTATCGATACATAAGTG-AA

                     *          
       4449 TGTATCGATGCATAAGTGAA
          1 TGTATCGATACATAAGTGAA

                         
       4469 TGTATCGATACAT
          1 TGTATCGATACAT

       4482 GTCTGAAATG


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  20   25  0.89
  21    3  0.11

ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32


Consensus pattern (20 bp):   
TGTATCGATACATAAGTGAA

Found at i:4655 original size:32 final size:32

Alignment explanation


    Indices: 4564--4668  Score: 133
    Period size: 34  Copynumber: 3.2  Consensus size: 32

       4554 TCATTATATT

                                        *    
       4564 GATACATTCTGGG-TTTTGACCCAAAT-AATTC
          1 GATACATTCTGGGTTTTTGACCCAAATGTA-TC

            *         *                       
       4595 AATACATTCTAGGTTTTGATGACCCAAATGTATC
          1 GATACATTCTGGGTTTT--TGACCCAAATGTATC

                                           *
       4629 GATACATTCTGGGTTTTTGACCCAAATGTATT
          1 GATACATTCTGGGTTTTTGACCCAAATGTATC

                    
       4661 GATACATT
          1 GATACATT

       4669 TTTCAATGTA


Statistics
Matches: 64,  Mismatches: 6, Indels: 7
        0.83            0.08        0.09

Matches are distributed among these distances:
  31   11  0.17
  32   25  0.39
  34   27  0.42
  35    1  0.02

ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37


Consensus pattern (32 bp):   
GATACATTCTGGGTTTTTGACCCAAATGTATC
Done.