Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold360

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: 9317
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31


Found at i:5333 original size:49 final size:49

Alignment explanation


    Indices: 5159--5732  Score: 990
    Period size: 49  Copynumber: 11.9  Consensus size: 49

       5149 CCCTTCGGGA

                                        *      * *     * *   
       5159 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

             * *                                             
       5206 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5253 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5300 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5349 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5398 CTTAT--CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5445 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5494 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                           *                                 
       5543 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5592 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                             
       5641 CTTATCAC--ATATATACACTTTCACATTCATCACATCGG-CATTAGGC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

                                                  *       
       5687 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTA
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA

       5733 CGCCATACTA


Statistics
Matches: 506,  Mismatches: 12, Indels: 16
        0.95            0.02        0.03

Matches are distributed among these distances:
  46   17  0.03
  47  167  0.33
  48   29  0.06
  49  293  0.58

ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32


Consensus pattern (49 bp):   
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC

Found at i:5418 original size:145 final size:144

Alignment explanation


    Indices: 5159--5732  Score: 969
    Period size: 145  Copynumber: 4.0  Consensus size: 144

       5149 CCCTTCGGGA

                                        *      * *     * *    * *            
       5159 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC

                                                   *                         
       5222 ACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATATATACACTTTCACATTCATCAC
         66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATATACACTTTCACATTCATCAC

                          
       5286 ATCGGCCATTAGGC
        131 ATCGGCCATTAGGC

                                                                             
       5300 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT

                                                                             
       5365 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-CATATATATACACTTTCACATTCATC
         64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATATACACTTTCACATTCATC

                            
       5429 ACATCGGCCATTAGGC
        129 ACATCGGCCATTAGGC

                                                                             
       5445 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT

                                                            *                
       5510 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCAT
         64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATATACACTTTCACATTCAT

                             
       5575 CACATCGGCCATTAGGC
        128 CACATCGGCCATTAGGC

                                                                             
       5592 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
          1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC

                                                                             
       5657 ACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
         66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATATACACTTTCACATTCATCA

                *       
       5721 CATCAGCCATTA
        130 CATCGGCCATTA

       5733 CGCCATACTA


Statistics
Matches: 416,  Mismatches: 11, Indels: 9
        0.95            0.03        0.02

Matches are distributed among these distances:
 141   10  0.02
 142    1  0.00
 143   37  0.09
 144   52  0.12
 145  218  0.52
 147   98  0.24

ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32


Consensus pattern (144 bp):   
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGC

Found at i:9215 original size:24 final size:25

Alignment explanation


    Indices: 9186--9235  Score: 75
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       9176 AAGGAATTCG

                                     
       9186 CACACACACAGTGC-CTTAATCATT
          1 CACACACACAGTGCTCTTAATCATT

                    *          *     
       9210 CACACACATAGTGCTCTTATTCATT
          1 CACACACACAGTGCTCTTAATCATT

             
       9235 C
          1 C

       9236 GTTATTACAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24   13  0.57
  25   10  0.43

ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30


Consensus pattern (25 bp):   
CACACACACAGTGCTCTTAATCATT
Done.