Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3349

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, 457

Length: 763
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32


Found at i:557 original size:303 final size:300

Alignment explanation


    Indices: 1--763  Score: 1135
    Period size: 303  Copynumber: 2.5  Consensus size: 300

                                                     *       *         *     
          1 CTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAAGGATATTTTGTCGAATTTCTATTC
          1 CTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTGTATTC

                                                                             
         66 AAATTCGAGGCCCAAGTGCGATAAGAGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGG
         66 AAATTCGAGG-CCAAGTGCGATAAGAGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGG

                                                                             
        131 GTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTCAAGCGTGCTTGGCC
        130 GTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTCAAGCGTGCTTGGCC

                             *                               * *             
        196 GAGAGTAGTACTAGGATTGGTGACCTCCTGGGAAGTCCTCGTGTTGCACGCTTCCCATTTTATTT
        195 GAGAGTAGTACTAGGATAGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT

                                                 *     
        261 CATATAATGTTTTTTTTAGTTGCATTTACTCAACGTGGTGTAA
        260 CATATAA--TTTTTTTTAGTTGCATTTACTCAACGTGATGTAA

                                *     *           *  *                       
        304 CTCATTCGTTATTTGCGTTTCGTGAAGTAAATAATTTGGAATGATATTTGGTCGAATTTGTATTC
          1 CTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTGTATTC

                             *           **                                * 
        369 AAATTCGAGGCGCAAGTACGATAAGAGGCTCCCTTTATATGAATAGATTGCGCAAGAGTTGACAG
         66 AAATTCGAGGC-CAAGTGCGATAAGAGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGG

                                                               *            *
        434 GTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCAG-AGTTAAGCGTGCTTGGG
        130 GTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCC-GCAGTCAAGCGTGCTTGGC

                   *                                                         
        498 CGAGAGTGGTACTAGGATAGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATT
        194 CGAGAGTAGTACTAGGATAGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATT

                                      *   *           
        563 TCATATAATTTTTTTTAGTTGCATTTTCTCGACGTGATGTAA
        259 TCATATAATTTTTTTTAGTTGCATTTACTCAACGTGATGTAA

                   *      *                *  *                  *      *   *
        605 CTCATTCCTTATTTACGTTTTGTGAAATAAACAAATTGAAACGATATTTGGTCAAATTTGCATTT
          1 CTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTGTATTC

                          *         *            *                  * *      
        670 AAATT------CAATTGCGATAAGGGGCAACCTTTATGTGAATAGATTGCGCAAGAATAGACGGG
         66 AAATTCGAGGCCAAGTGCGATAAGAGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGGG

                            *                  
        729 TGCGATCATACCAGCAATAATGCACCGGATCCCAT
        131 TGCGATCATACCAGCACTAATGCACCGGATCCCAT


Statistics
Matches: 418,  Mismatches: 40, Indels: 13
        0.89            0.08        0.03

Matches are distributed among these distances:
 294   79  0.19
 301   90  0.22
 302    1  0.00
 303  247  0.59
 304    1  0.00

ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32


Consensus pattern (300 bp):   
CTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTGTATTC
AAATTCGAGGCCAAGTGCGATAAGAGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGGG
TGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTCAAGCGTGCTTGGCCG
AGAGTAGTACTAGGATAGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTC
ATATAATTTTTTTTAGTTGCATTTACTCAACGTGATGTAA
Done.