Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006183.1 Kokia drynarioides strain JFW-HI SEQ_120752, whole genome shotgun sequence

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, 853

Length: 1422
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35


Found at i:649 original size:199 final size:197

Alignment explanation


    Indices: 64--867  Score: 702
    Period size: 191  Copynumber: 4.0  Consensus size: 197

         54 TTACATCGCT

                        *        *    *     *                         * * *  
         64 GTTTGTTTCAATTCGCTTCTCCATATTTCATCCGGAAGACGAATTTGGTTAACTTCTCAGAACCT
          1 GTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTTAACTTCTCCGTATCT

                                             *                               
        129 CATCAGGAAGCTAACCTTCTATTGCTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCTGGGGTT
         66 CATCAGGAAGCTAA---T-TA---CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTT

                                      *        *               *        *    
        194 CAAAGACTTTGCTCACTTTGAGCCT-CG--T--TTAGGTCTTCTTCTCAGTGTCTCATCAAGAAG
        124 CAAAGACTTTGCTCA-TTTGAG-CTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAG

                       
        254 ATGACCGCGTC
        187 ATGACCGCGTC

                                  *               *  *        *              
        265 ----G--T---T-CGCTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTTCACTTCT-CGATATC
          1 GTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTTAACTTCTCCG-TATC

                                    **                                       
        319 TCATCAGGAAGCTGACCTTCTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGT
         65 TCATCAGGAAGCT-A------ATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGT

                            *              * *                *        *     
        384 TCAAAGACTTTGCTCGCTTTGAGCGTGGGTTCGATTTGGTCTTCTTCTCAATATCTCATTAGGAA
        123 TCAAAGACTTTGCTC-ATTTGAGC-TGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAA

                        
        449 GATGACCGCGTC
        186 GATGACCGCGTC

                    *     *                                                  
        461 GTTTGTTTTAATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGTCT-ACTTCTCCGTATC
          1 GTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGT-TAACTTCTCCGTATC

                                                  *          *     *         
        525 TCATCAGGAAGCTAATTACTTCGACAC-GCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCAAAG
         65 TCATCAGGAAGCTAATTACTTCGAC-CTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAG

                                                                             
        589 A-TTTGCTCATGTTGAGCATGGGTTTGGTTTGGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
        129 ACTTTGCTCAT-TTGAGC-TGGGTTTGGTTT-GGTCTTCTTCTCAGTATCTCATCAGGAAGATGA

                  *
        653 CCGCGTT
        191 CCGCGTC

               *                  *       *      *                           
        660 GTTCGTTTCAATCC-CTTCTCTGTATCTCACCAGGAATACGAATTTGGTCT-ACTTCTCCGTATC
          1 GTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGT-TAACTTCTCCGTATC

                                *      * * **              *                *
        723 TCATCAGGAAGTTAACCGTTTATTACTCCAATATGCTTCT-AGGTGTGTCATCAGGAAGCTGGGT
         65 TCATCAGGAAG-----C--TAATTACTTCGACCTGCTTCTCA-GTGTCTCATCAGGAAGCTGGGG

               *              * * *                             *            
        787 TTCGAAGAC-TTGCTCACATCGTGC-GTGGTCTTGGTTTGGTCTTCTTCTCAATATCTCATCAGG
        122 TTCAAAGACTTTGCTCA-TTTGAGCTG-GGT-TTGGTTTGGTCTTCTTCTCAGTATCTCATCAGG

                         *
        850 AAGATGACCGCGTT
        184 AAGATGACCGCGTC

                
        864 GTTT
          1 GTTT

        868 TATGGGTATC


Statistics
Matches: 502,  Mismatches: 58, Indels: 83
        0.78            0.09        0.13

Matches are distributed among these distances:
 190    2  0.00
 191  112  0.22
 192    3  0.01
 194    1  0.00
 195    2  0.00
 196   38  0.08
 197    2  0.00
 198   81  0.16
 199   93  0.19
 200    2  0.00
 202    1  0.00
 203    2  0.00
 204   46  0.09
 205   59  0.12
 206   55  0.11
 207    3  0.01

ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35


Consensus pattern (197 bp):   
GTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTTAACTTCTCCGTATCT
CATCAGGAAGCTAATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGAC
TTTGCTCATTTGAGCTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCG
TC

Done.