Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2180

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: 23152
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31


Found at i:2706 original size:23 final size:24

Alignment explanation


    Indices: 2678--2727  Score: 75
    Period size: 23  Copynumber: 2.1  Consensus size: 24

       2668 ATTCTAGCTA

                                    
       2678 ATATTCAACAAA-ACTAATTCCAC
          1 ATATTCAACAAAGACTAATTCCAC

                          *          
       2701 ATATTCAACAAATGTCTAATTCCAC
          1 ATATTCAACAAA-GACTAATTCCAC

              
       2726 AT
          1 AT

       2728 CAAAATCACC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  23   12  0.50
  25   12  0.50

ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30


Consensus pattern (24 bp):   
ATATTCAACAAAGACTAATTCCAC

Found at i:3260 original size:40 final size:40

Alignment explanation


    Indices: 3124--3382  Score: 262
    Period size: 41  Copynumber: 6.4  Consensus size: 40

       3114 GTTTTATGAC

                   *                                  
       3124 TTTTAGCAGCGTTTTACCAAAAAGCGCCGCTAATGCTCTGAG
          1 TTTTAGCGGCGTTTTACC-AAAAGCGCCGCTAATGCTCTG-G

                                              * *     *
       3166 CTTTTAGC-GCGTTTTACCAAAAGCGCCGCTAATACACTCGTT
          1 -TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-G-G

                             *                      
       3208 TTTTAGC-GCGTTTTACGAAAAGCGCCGCTAATGCT-TGG
          1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG

                               *     *          *     
       3246 TTTTAGCGGCCGTTTTACCCAAAGATG-CGCTAAT-ATCTGG
          1 TTTTAGCGG-CGTTTTACCAAAAG-CGCCGCTAATGCTCTGG

                               *     *         *     
       3286 TTTTTAGCGGCGTTTTACCCAAAGCACCGCTAATGATCTGG
          1 -TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG

                             *                      *
       3327 TTTATAGCGGCGTTTTAACAAAAGCGCCGCTAAT--TCTGT
          1 TTT-TAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG

                             
       3366 TTTTAGCCGGCGTTTTA
          1 TTTTAG-CGGCGTTTTA

       3383 GTTAAAAAAT


Statistics
Matches: 188,  Mismatches: 18, Indels: 24
        0.82            0.08        0.10

Matches are distributed among these distances:
  38   10  0.05
  39   20  0.11
  40   47  0.25
  41   93  0.49
  42   11  0.06
  43    7  0.04

ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32


Consensus pattern (40 bp):   
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG

Found at i:8904 original size:30 final size:30

Alignment explanation


    Indices: 8870--8930  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       8860 TCCTTAACTC

                                          
       8870 AAACTTTGGAAAAATTACAATTTTGCCCCT
          1 AAACTTTGGAAAAATTACAATTTTGCCCCT

                   * * * *     *          
       8900 AAACTTTTGCATATTTACACTTTTGCCCCT
          1 AAACTTTGGAAAAATTACAATTTTGCCCCT

             
       8930 A
          1 A

       8931 GGCTCTAGAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38


Consensus pattern (30 bp):   
AAACTTTGGAAAAATTACAATTTTGCCCCT

Found at i:18246 original size:40 final size:40

Alignment explanation


    Indices: 18209--18393  Score: 189
    Period size: 40  Copynumber: 4.7  Consensus size: 40

      18199 GCTACTCGTT

                            *                        
      18209 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA

                         *     *                    
      18249 CAAATGCCTTCGGAACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA

             *                     *  *      *      
      18289 CCAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA

                         *   *   *      * *  *    *   
      18328 CAAATGCCTTC-GAATCATAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA

                                      
      18369 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

      18394 CATCATTCGA


Statistics
Matches: 117,  Mismatches: 23, Indels: 10
        0.78            0.15        0.07

Matches are distributed among these distances:
  38    1  0.01
  39   31  0.26
  40   73  0.62
  41   12  0.10

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA

Found at i:18353 original size:79 final size:80

Alignment explanation


    Indices: 18211--18391  Score: 199
    Period size: 79  Copynumber: 2.3  Consensus size: 80

      18201 TACTCGTTCA

                          *       **                              *          
      18211 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGGAT
          1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGAACATAACCCGGAT

            *         *     
      18276 TTAGTAAC-TCGCACC
         66 ATAGTAACTTAGCA-C

                                            *                          **    
      18291 AATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTC-GAATCATAGTCCGG
          1 AATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGAA-CATAACCCGG

                *  *         
      18353 ATATGGTCACTTAGCAC
         64 ATATAGTAACTTAGCAC

              *                   
      18370 AAAGCCTTCGGGACTTAGCCCG
          1 AATGCCTTCGGGACTTAGCCCG

      18392 GACATCATTC


Statistics
Matches: 85,  Mismatches: 12, Indels: 9
        0.80            0.11        0.08

Matches are distributed among these distances:
  78    3  0.04
  79   56  0.66
  80   26  0.31

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (80 bp):   
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGAACATAACCCGGAT
ATAGTAACTTAGCAC
Done.