Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold446

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: 9755
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Found at i:1550 original size:79 final size:81

Alignment explanation


    Indices: 1441--1623  Score: 232
    Period size: 79  Copynumber: 2.3  Consensus size: 81

       1431 TACTCGTTCA

                          *         *                                        
       1441 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
          1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG

              *         *     
       1504 ATTTAGTAAC-TCGCACC
         65 ATATAGTAACTTAGCA-C

                                                                      **     
       1521 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
          1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA

               *  *         
       1584 TATGGTCACTTAGCAC
         66 TATAGTAACTTAGCAC

              *                     
       1600 AAAGCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAGCCCGGA

       1624 CATCATTCGA


Statistics
Matches: 90,  Mismatches: 9, Indels: 8
        0.84            0.08        0.07

Matches are distributed among these distances:
  78    3  0.03
  79   59  0.66
  80   28  0.31

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24


Consensus pattern (81 bp):   
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC

Found at i:1623 original size:40 final size:40

Alignment explanation


    Indices: 1420--1623  Score: 238
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       1410 CGGAATTTAA

                              **                *    
       1420 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
          1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC

                *                                 * 
       1460 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *             *                   
       1500 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                                                     *
       1539 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
          1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC

                    *  *    *                        
       1579 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
          1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC

                 
       1619 CCGGA
          1 CCGGA

       1624 CATCATTCGA


Statistics
Matches: 141,  Mismatches: 16, Indels: 14
        0.82            0.09        0.08

Matches are distributed among these distances:
  38    2  0.01
  39   33  0.23
  40   94  0.67
  41   12  0.09

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

Found at i:2958 original size:84 final size:84

Alignment explanation


    Indices: 2785--2961  Score: 338
    Period size: 84  Copynumber: 2.1  Consensus size: 84

       2775 TATTTTATTG

                                                                             
       2785 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTTTTT
          1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTTTTT

                               
       2850 AGCCATAACATCTTGTCCA
         66 AGCCATAACATCTTGTCCA

                                                                             
       2869 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
          1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTA-CCCAACATGTTTATGACATGTTTT

                                
       2934 TAGCCATAACATCTTGTCCA
         65 TAGCCATAACATCTTGTCCA

                     
       2954 -CCATGCTC
          1 CCCATGCTC

       2962 ATGGCCGGCC


Statistics
Matches: 92,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
  84   48  0.52
  85   44  0.48

ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38


Consensus pattern (84 bp):   
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTTTTT
AGCCATAACATCTTGTCCA

Found at i:6110 original size:18 final size:19

Alignment explanation


    Indices: 6079--6121  Score: 72
    Period size: 18  Copynumber: 2.4  Consensus size: 19

       6069 ACCACCGGCA

                               
       6079 TAGATTCGGGTTTCTTTTC
          1 TAGATTCGGGTTTCTTTTC

                               
       6098 TAGATTC-GGTTTCTTTTC
          1 TAGATTCGGGTTTCTTTTC

                   
       6116 TA-ATTC
          1 TAGATTC

       6122 TTTGTCATCA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  17    4  0.17
  18   13  0.54
  19    7  0.29

ACGTcount: A:0.14, C:0.16, G:0.16, T:0.53


Consensus pattern (19 bp):   
TAGATTCGGGTTTCTTTTC

Found at i:9368 original size:40 final size:40

Alignment explanation


    Indices: 9331--9512  Score: 214
    Period size: 39  Copynumber: 4.6  Consensus size: 40

       9321 GCTACTCGTT

                            *                       
       9331 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                               *                     
       9371 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA

             *                        *              
       9411 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA

                                 *    *   *  *   *   
       9450 C-AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAACTCGCA

                                     
       9489 CAAA-GCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGG

       9513 ACATCATTCG


Statistics
Matches: 123,  Mismatches: 11, Indels: 17
        0.81            0.07        0.11

Matches are distributed among these distances:
  37    2  0.02
  38    9  0.07
  39   56  0.46
  40   54  0.44
  41    2  0.02

ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

Done.