Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_00625

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: 1764
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28


Found at i:1641 original size:237 final size:240

Alignment explanation


    Indices: 1220--1667  Score: 742
    Period size: 237  Copynumber: 1.9  Consensus size: 240

       1210 AACATCGGAC

                                                                             
       1220 AGGTTCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGATGAT
          1 AGGTTCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGA-GAT

                       *               *      *                              
       1285 GATGATGATGATGACGACGATGACGATGATCTTTTTAAAGCTATTGATGATGATGGTGATGACGA
         65 GATGATGATGACGACGACGAT-A-GATCATCTTTGTAAAGCTATTGATGATGATGGTGATGACGA

                 *                  *                                        
       1350 CAATGTGGACAATGATGCGCCAGTTGCAGAGTTGTCAATTCTGCCCCGAAATCG-AAACGTCAAC
        128 CAATGAGGACAATGATGCGCCAGTGGCAGAGTTGTCAATTCTGCCCCGAAATCGAAAAC-TCAAC

                *                                            
       1414 TCGACCCTGACCTGGTCTGATGATCTCTCAGCTATTACTTCTTTGCAAA
        192 TCGAACCTGACCTGGTCTGATGATCTCTCAGCTATTACTTCTTTGCAAA

                                *  *                      *                  
       1463 AGGTTCGAAAACGAGCTTCCTGTTGTTTGTTCTCCTTAGATTGGTCGAACGGTGAAGAAGA-A-G
          1 AGGTTCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGAGATG

                                                                             
       1526 ATGATGATGACGACGACGAT-GATCATCTTTGTAAAGCTATTGATGATGATGGTGATGACGACAA
         66 ATGATGATGACGACGACGATAGATCATCTTTGTAAAGCTATTGATGATGATGGTGATGACGACAA

                                                                          *  
       1590 TGAGGACAATGATGCGCCAGTGGCAGAGTTGTCAATTCTGCCCCGAAATCGAAAACTCAACTTGA
        131 TGAGGACAATGATGCGCCAGTGGCAGAGTTGTCAATTCTGCCCCGAAATCGAAAACTCAACTCGA

                         
       1655 ACCTGACCTGGTC
        196 ACCTGACCTGGTC

       1668 CAATGATGAT


Statistics
Matches: 194,  Mismatches: 10, Indels: 8
        0.92            0.05        0.04

Matches are distributed among these distances:
 237  111  0.57
 238    4  0.02
 240   20  0.10
 241    1  0.01
 243   58  0.30

ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28


Consensus pattern (240 bp):   
AGGTTCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGAGATG
ATGATGATGACGACGACGATAGATCATCTTTGTAAAGCTATTGATGATGATGGTGATGACGACAA
TGAGGACAATGATGCGCCAGTGGCAGAGTTGTCAATTCTGCCCCGAAATCGAAAACTCAACTCGA
ACCTGACCTGGTCTGATGATCTCTCAGCTATTACTTCTTTGCAAA

Found at i:1693 original size:18 final size:18

Alignment explanation


    Indices: 1670--1720  Score: 59
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1660 ACCTGGTCCA

                   *        * 
       1670 ATGATGATAATGACGGTG
          1 ATGATGACAATGACGGCG

                         *    
       1688 ATGATGACAATGATGGCG
          1 ATGATGACAATGACGGCG

                            
       1706 ATGAT-AGCAATGACG
          1 ATGATGA-CAATGACG

       1721 ATGCACAAAG


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  17    1  0.04
  18   27  0.96

ACGTcount: A:0.35, C:0.10, G:0.31, T:0.24


Consensus pattern (18 bp):   
ATGATGACAATGACGGCG
Done.