Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010834.1 Kokia drynarioides strain JFW-HI SEQ_125801, 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: 8441
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27


Found at i:477 original size:20 final size:20

Alignment explanation


    Indices: 452--489  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        442 CTGGATGCCT

                                
        452 GAGGTCCCTAGATTATCCAA
          1 GAGGTCCCTAGATTATCCAA

                              
        472 GAGGTCCCTAGATTATCC
          1 GAGGTCCCTAGATTATCC

        490 TTAAATCAGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26


Consensus pattern (20 bp):   
GAGGTCCCTAGATTATCCAA

Found at i:649 original size:59 final size:59

Alignment explanation


    Indices: 573--1156  Score: 816
    Period size: 59  Copynumber: 9.9  Consensus size: 59

        563 CCCTAGATTG

                *                 *                             *      
        573 TCCAGAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCTCGAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                              *                                 *      
        632 TCCAAAAATCCCATTTTTTACCCCGAACCTTCC-AAAATTACCATTTTACCCTCGAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                                   **                           *      
        690 TCCAAAAATCCCATTTTTGACCCTAAACCTTCCAAAAATTACCATTTTACCCTCGAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                                                                        
        749 TCCAAAAATCCCATTTTTGACCCC-AATCCTTCCAAAAATTACCATTTTACCCCCGAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAA-CCTTCCAAAAATTACCATTTTACCCCCGAACT

            *                               *                     *    
        808 ACCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                           *     *          *            *        *    
        867 TCCAAAAATCCCATTCTTGACTCCGAACCTTCTAAAAATTACCATCTTACCCCCAAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

              *                     *       *                         *
        926 TCAAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCCCCGAACA
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                      *             *       **                   **    
        985 TCCAAAAATCTCATTTTTGACCCCAAACCTTCTGAAAATTACCA-TTTACCCCAAAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                             *   *  *       *      *                   
       1043 TCCAAAAATCCCATTTTCGACTCCAAACCTTCTAAAAATAACCATTTTACCCCCGAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

                                  *                *         *      
       1102 TCCAAAAATCCCATTTTTTGACTCCGAACCTTCC-AAAACTACCATTTTGCCCCCG
          1 TCCAAAAATCCCA-TTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCG

       1157 TGCATCTGAA


Statistics
Matches: 479,  Mismatches: 41, Indels: 10
        0.90            0.08        0.02

Matches are distributed among these distances:
  58  107  0.22
  59  353  0.74
  60   19  0.04

ACGTcount: A:0.33, C:0.34, G:0.04, T:0.29


Consensus pattern (59 bp):   
TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACT

Found at i:944 original size:177 final size:175

Alignment explanation


    Indices: 573--1156  Score: 836
    Period size: 176  Copynumber: 3.3  Consensus size: 175

        563 CCCTAGATTG

                *                   *                           *      *     
        573 TCCAGAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAA
          1 TCCAAAAATCCCATTTTTGACC-CCAACCTTCCAAAAATTACCATTTTACCCCCGAACTACCAAA

                        *              *                  * *                
        638 AATCCCATTTTTTACCCCGAACCTTC-CAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCC
         65 AATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCC

                                 *                   *      
        702 ATTTTTGAC-CCTAAACCTTCCAAAAATTACCATTTTACCCTCGAACT
        130 A-TTTTGACTCC-AAACCTTCTAAAAATTACCATTTTACCCCCGAACT

                                                                             
        749 TCCAAAAATCCCATTTTTGACCCCAATCCTTCCAAAAATTACCATTTTACCCCCGAACTACCAAA
          1 TCCAAAAATCCCATTTTTGACCCCAA-CCTTCCAAAAATTACCATTTTACCCCCGAACTACCAAA

                                                                             
        814 AATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCC
         65 AATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCC

                        *                    *        *    
        879 ATTCTTGACTCCGAACCTTCTAAAAATTACCATCTTACCCCCAAACT
        130 ATT-TTGACTCCAAACCTTCTAAAAATTACCATTTTACCCCCGAACT

              *                             *                                
        926 TCAAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCCCCGAAC-ATCCAA
          1 TCCAAAAATCCCATTTTTGACCCC-AACCTTCCAAAAATTACCATTTTACCCCCGAACTA-CCAA

                 *             *        *                   *                
        990 AAATCTCATTTTTGACCCCAAACCTTCTGAAAATTACCA-TTTACCCCAAAACTTCCAAAAATCC
         64 AAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCC

                                        *                   
       1054 CATTTTCGACTCCAAACCTTCTAAAAATAACCATTTTACCCCCGAACT
        129 CATTTT-GACTCCAAACCTTCTAAAAATTACCATTTTACCCCCGAACT

                                     *             *         *      
       1102 TCCAAAAATCCCATTTTTTGACTCCGAACCTTCC-AAAACTACCATTTTGCCCCCG
          1 TCCAAAAATCCCA-TTTTTGAC-CCCAACCTTCCAAAAATTACCATTTTACCCCCG

       1157 TGCATCTGAA


Statistics
Matches: 371,  Mismatches: 28, Indels: 18
        0.89            0.07        0.04

Matches are distributed among these distances:
 175    5  0.01
 176  181  0.49
 177  179  0.48
 178    6  0.02

ACGTcount: A:0.33, C:0.34, G:0.04, T:0.29


Consensus pattern (175 bp):   
TCCAAAAATCCCATTTTTGACCCCAACCTTCCAAAAATTACCATTTTACCCCCGAACTACCAAAA
ATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA
TTTTGACTCCAAACCTTCTAAAAATTACCATTTTACCCCCGAACT
Done.