Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008042.1 Kokia drynarioides strain JFW-HI SEQ_122698, 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, 1000

Length: 6907
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:1254 original size:29 final size:27

Alignment explanation


    Indices: 1212--1486  Score: 208
    Period size: 29  Copynumber: 9.5  Consensus size: 27

       1202 AAACTTTCTA

                  *                     
       1212 AAAAATACCATTTTACCCCCGAACTTCC
          1 AAAAATCCCATTTTA-CCCCGAACTTCC

                                         *
       1240 AAAAATCCCATTTTTGACCCCGAACATTCT
          1 AAAAATCCCA-TTTT-ACCCCGAAC-TTCC

                 * *             *       
       1270 AACAATTACCATTTTACCCCCAAACTTCC
          1 AA-AAATCCCATTTTA-CCCCGAACTTCC

                    *       *            *
       1299 AAAAATCCTATTTTTGGCCCCGAACCTTCT
          1 AAAAATCCCA-TTTT-ACCCCGAA-CTTCC

                   **                    
       1329 AAAAATTATCATTTTACCCTCGAACTTCC
          1 AAAAA-TCCCATTTTACCC-CGAACTTCC

                             *           *
       1358 AAAAATCCCATTTTTGATCCCGAACCTTCT
          1 AAAAATCCCA-TTTT-ACCCCGAA-CTTCC

                   * *           *       
       1388 AAAAATTACTATTTTACCCCTAAACTTCC
          1 AAAAA-TCCCATTTTACCCC-GAACTTCC

                           *   *       *
       1417 AAAAATCCCATTTTAACCCTAACCTTCT
          1 AAAAATCCCATTTTACCCCGAA-CTTCC

                   **                   
       1445 AAAAATTATCATTTTACCCCGAACTTCC
          1 AAAAA-TCCCATTTTACCCCGAACTTCC

                          
       1473 AAAAATCCCATTTT
          1 AAAAATCCCATTTT

       1487 TGACTCTGAA


Statistics
Matches: 192,  Mismatches: 38, Indels: 35
        0.72            0.14        0.13

Matches are distributed among these distances:
  27    9  0.05
  28   46  0.24
  29   74  0.39
  30   52  0.27
  31   11  0.06

ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32


Consensus pattern (27 bp):   
AAAAATCCCATTTTACCCCGAACTTCC

Found at i:1299 original size:59 final size:59

Alignment explanation


    Indices: 1207--1516  Score: 412
    Period size: 59  Copynumber: 5.3  Consensus size: 59

       1197 TCCCTAAACT

                     *                                                *
       1207 TTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACA
          1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

                  *                  *               *       *         
       1266 TTCTAACAATTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTGGCCCCGAACC
          1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

                        *          *                          *        
       1325 TTCTAAAAATTATCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGATCCCGAACC
          1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

                         *          **                        *   *    
       1384 TTCTAAAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCA-TTTT-AACCCTAACC
          1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

                        *                                      * *     
       1441 TTCTAAAAATTATCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACTCTGAACC
          1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

            *   *    *         
       1499 CTC-CAAAACTACCATTTT
          1 TTCTAAAAATTACCATTTT

       1517 GGCCCCGTGC


Statistics
Matches: 217,  Mismatches: 32, Indels: 6
        0.85            0.13        0.02

Matches are distributed among these distances:
  56   20  0.09
  57   42  0.19
  58   12  0.06
  59  143  0.66

ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32


Consensus pattern (59 bp):   
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC

Done.