Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1017

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: 11199
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1022 original size:48 final size:49

Alignment explanation


    Indices: 869--1059  Score: 289
    Period size: 49  Copynumber: 3.9  Consensus size: 49

        859 TTCGTTTTCT

                       *   **              *              *   
        869 CGATGCCATAGTCCAATTATGGTCTTACACGTAATCACA-ATTCACATAC
          1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATA-TCACTTAC

                                                             
        918 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC
          1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC

                                            *                
        967 CGATGCCATAGCCCAGCTATGGTCTTACACG-GATCACATATCACTTAC
          1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC

                                                          
       1015 CGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATAATCAC
          1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAT-ATCAC

       1060 ATGTTCACAT


Statistics
Matches: 133,  Mismatches: 7, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
  48   54  0.41
  49   78  0.59
  50    1  0.01

ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25


Consensus pattern (49 bp):   
CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC

Found at i:1036 original size:97 final size:98

Alignment explanation


    Indices: 869--1059  Score: 298
    Period size: 97  Copynumber: 2.0  Consensus size: 98

        859 TTCGTTTTCT

                       *    *                                                
        869 CGATGCCATAGTCCAATTATGGTCTTACACGTAATCACAATTCACATACCGATGCCATAGCCCAG
          1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACAATTCACATACCGATGCCATAGCCCAG

                                              
        934 CTATGGTCTTACACGAAATCACAT-ATCACTTAC
         66 CTATGGTCTTACACG-AATCACATAATCACTTAC

                           *                *             *                  
        967 CGATGCCATAGCCCAGCTATGGTCTTACACG-GATCAC-ATATCACTTACCGATGCCATAGCCCA
          1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACAAT-TCACATACCGATGCCATAGCCCA

                                          
       1030 GCTATGGTCTTACACGAATCACATAATCAC
         65 GCTATGGTCTTACACGAATCACATAATCAC

       1060 ATGTTCACAT


Statistics
Matches: 86,  Mismatches: 5, Indels: 5
        0.90            0.05        0.05

Matches are distributed among these distances:
  96   10  0.12
  97   48  0.56
  98   28  0.33

ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25


Consensus pattern (98 bp):   
CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACAATTCACATACCGATGCCATAGCCCAG
CTATGGTCTTACACGAATCACATAATCACTTAC

Found at i:2375 original size:37 final size:37

Alignment explanation


    Indices: 2310--2455  Score: 233
    Period size: 37  Copynumber: 4.0  Consensus size: 37

       2300 TACGTATGAT

                            * *                  
       2310 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
          1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC

               *                     *           
       2345 CACCTATCACTTTGTTTCTTGATCACATAAGTGTAGC
          1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC

                                                 
       2382 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
          1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC

                           *                     
       2419 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
          1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC

       2456 TAAAGCTATC


Statistics
Matches: 102,  Mismatches: 7, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  35    9  0.09
  36    3  0.03
  37   90  0.88

ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37


Consensus pattern (37 bp):   
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC

Found at i:2472 original size:46 final size:46

Alignment explanation


    Indices: 2419--2635  Score: 272
    Period size: 46  Copynumber: 4.6  Consensus size: 46

       2409 TAAGTGTAGC

                            *               *    *        
       2419 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
          1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT

                                                  *       
       2465 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
          1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT

                         *                        *       
       2511 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
          1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT

            *                              *      *    *       *
       2557 TACTTATCACTTTCCACTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAC
          1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT

                         *             
       2609 CACTTATCACTTTATCACTTGATCAGA
          1 CACTTATCACTTTGTCACTTGATCAGA

       2636 AGTACTCAAA


Statistics
Matches: 150,  Mismatches: 15, Indels: 12
        0.85            0.08        0.07

Matches are distributed among these distances:
  46  110  0.73
  48    1  0.01
  50    1  0.01
  52   38  0.25

ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35


Consensus pattern (46 bp):   
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT

Found at i:2593 original size:52 final size:52

Alignment explanation


    Indices: 2508--2621  Score: 140
    Period size: 52  Copynumber: 2.2  Consensus size: 52

       2498 TAGCCGAAGC

                                        *            *      **   
       2508 TATCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
          1 TATCACTT-TCACTTTATCACTTGATCAAATAAGTATAGCCAAAGCTACCACT

                            *                  *    *            
       2561 TATCACTTTCCAC-TTGTCACTTGATCAAATAAGTGTAGCTAAAGCTACCACT
          1 TATCACTTT-CACTTTATCACTTGATCAAATAAGTATAGCCAAAGCTACCACT

                     
       2613 TATCACTTT
          1 TATCACTTT

       2622 ATCACTTGAT


Statistics
Matches: 53,  Mismatches: 7, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  52   42  0.79
  53   11  0.21

ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36


Consensus pattern (52 bp):   
TATCACTTTCACTTTATCACTTGATCAAATAAGTATAGCCAAAGCTACCACT
Done.