Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_73622

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, 930

Length: 1551
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32


Found at i:910 original size:144 final size:144

Alignment explanation


    Indices: 713--976  Score: 474
    Period size: 144  Copynumber: 1.8  Consensus size: 144

        703 AACAATTGGT

                                                           *      *         *
        713 TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTTCCTTCAAAGC
          1 TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGA

                     *                                                       
        778 AACCAACTTGATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGCACTGAATCT
         66 AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGCACTGAATCT

                          
        843 ATCCCCCAGTTATC
        131 ATCCCCCAGTTATC

                               *   *                                         
        857 TTTTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGA
          1 TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGA

                                                                   
        922 AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTG
         66 AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTG

        977 AATTAGATCT


Statistics
Matches: 114,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 144  114  1.00

ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31


Consensus pattern (144 bp):   
TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGA
AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGCACTGAATCT
ATCCCCCAGTTATC

Found at i:1016 original size:144 final size:144

Alignment explanation


    Indices: 718--1009  Score: 433
    Period size: 144  Copynumber: 2.0  Consensus size: 144

        708 TTGGTTTTTT

                                                      *      *         *     
        718 GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTTCCTTCAAAGCAACCA
          1 GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGAAACCA

                *                                             *            * 
        783 ACTTGATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGCACTGAATCTATCCC
         66 ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAACTGAATCTATCAC

               * * *    **
        848 CCAGTTATCTTTTT
        131 CCAATAAGCTTTCA

                          *   *                                              
        862 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGAAACCA
          1 GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGAAACCA

                                                                  *          
        927 ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAA-TTAGATCTATCA
         66 ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAACTGA-ATCTATCA

            *              
        991 TCCAATAAGCTTTCA
        130 CCCAATAAGCTTTCA

                
       1006 GGTC
          1 GGTC

       1010 ACATCCCTTC


Statistics
Matches: 132,  Mismatches: 15, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
 143    2  0.02
 144  130  0.98

ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30


Consensus pattern (144 bp):   
GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCCCGTTGTCCCTTCAAAGAAACCA
ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAACTGAATCTATCAC
CCAATAAGCTTTCA

Done.