Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005328.1 Kokia drynarioides strain JFW-HI SEQ_119277, 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, 802

Length: 1337
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30


Found at i:828 original size:28 final size:29

Alignment explanation


    Indices: 797--859  Score: 74
    Period size: 29  Copynumber: 2.2  Consensus size: 29

        787 AAATAAGACT

                                         
        797 TTTTGGATACCCGA-GGGAAAAATGGTAA
          1 TTTTGGATACCCGAGGGGAAAAATGGTAA

                 *  * *        **        
        825 TTTTGAATTCTCGAGGGGAGGAATGGTAA
          1 TTTTGGATACCCGAGGGGAAAAATGGTAA

                  
        854 TTTTGG
          1 TTTTGG

        860 GAAAATTCGG


Statistics
Matches: 28,  Mismatches: 6, Indels: 1
        0.80            0.17        0.03

Matches are distributed among these distances:
  28   11  0.39
  29   17  0.61

ACGTcount: A:0.29, C:0.08, G:0.32, T:0.32


Consensus pattern (29 bp):   
TTTTGGATACCCGAGGGGAAAAATGGTAA

Found at i:994 original size:30 final size:29

Alignment explanation


    Indices: 953--1243  Score: 250
    Period size: 30  Copynumber: 9.8  Consensus size: 29

        943 TTTTTGACAC

                  *                 *     
        953 TCGGGGGCAAAATGGTAATTTTTGAAAGTT
          1 TCGGGGTCAAAATGG-AATTTTTGGAAGTT

                 *            *       *   
        983 TCGGGATCAAAAATGGAAATTTTGGAGGTT
          1 TCGGGGTC-AAAATGGAATTTTTGGAAGTT

                    *    *                
       1013 T-GAGGGTTAAAACGGAATTTTTGGAAGTT
          1 TCG-GGGTCAAAATGGAATTTTTGGAAGTT

               *          *        *      
       1042 TCGAGGTCAAAAATAGAATTTTTTGAAGTT
          1 TCGGGGTC-AAAATGGAATTTTTGGAAGTT

               * *         *       *      
       1072 TCGAGATCAAAAATGAAATTTTTAGAA-TT
          1 TCGGGGTC-AAAATGGAATTTTTGGAAGTT

                     *                     
       1101 TCGAGGGGTAAAAATGGAATTTTTGGAAGTT
          1 TC--GGGGTCAAAATGGAATTTTTGGAAGTT

                        *                 
       1132 TCGGGGTCAAGAGTGGAATTTTTGGAAG-T
          1 TCGGGGTCAA-AATGGAATTTTTGGAAGTT

                    *                     
       1161 TCGGTGGTAAAAATGGAATTTTTGGAAGTT
          1 TCGG-GGTCAAAATGGAATTTTTGGAAGTT

               *                          *
       1191 TCGAGGTCAAAAAT-GAGATTTTTGGAAG-C
          1 TCGGGGTC-AAAATGGA-ATTTTTGGAAGTT

                    *      *        
       1220 TCGAGGGTAAAAATGTAATTTTTG
          1 TCG-GGGTCAAAATGGAATTTTTG

       1244 AATAGTTTAG


Statistics
Matches: 213,  Mismatches: 34, Indels: 29
        0.77            0.12        0.11

Matches are distributed among these distances:
  29   75  0.35
  30  124  0.58
  31   14  0.07

ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33


Consensus pattern (29 bp):   
TCGGGGTCAAAATGGAATTTTTGGAAGTT

Found at i:1103 original size:59 final size:58

Alignment explanation


    Indices: 969--1243  Score: 259
    Period size: 59  Copynumber: 4.6  Consensus size: 58

        959 GCAAAATGGT

                    *                        *       *            *    * *
        969 AATTTTTGAAAGTTTCG-GGATCAAAAATGGAAATTTTGGAGGTTT-GAGGGT-TAAAACGG
          1 AATTTTTGGAA-TTTCGAGG-T-AAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGA

                                        *        *           *          
       1028 AATTTTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTTGAAGTTTCGAGATCAAAAATGA
          1 AATTTTTGGAA-TTTCGAGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGA

                   *                                       *      * *  *
       1088 AATTTTTAGAATTTCGAGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAGAGTGG
          1 AATTTTTGGAATTTCGA--GGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGA

                       *     *                                         
       1148 AATTTTTGGAAGTTCGGTGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGA
          1 AATTTTTGGAATTTC-GAGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGA

            *          **               *        
       1207 GATTTTTGGAAGCTCGAGGGTAAAAATGTAATTTTTG
          1 AATTTTTGGAATTTCGA-GGTAAAAATGGAATTTTTG

       1244 AATAGTTTAG


Statistics
Matches: 181,  Mismatches: 28, Indels: 14
        0.81            0.13        0.06

Matches are distributed among these distances:
  58    1  0.01
  59  113  0.62
  60   63  0.35
  61    4  0.02

ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34


Consensus pattern (58 bp):   
AATTTTTGGAATTTCGAGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGA

Done.