Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006593.1 Kokia drynarioides strain JFW-HI SEQ_121181, 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: 2419
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37


Found at i:126 original size:12 final size:12

Alignment explanation


    Indices: 109--149  Score: 50
    Period size: 12  Copynumber: 3.4  Consensus size: 12

         99 AGTTTTTTTT

                        
        109 ATATATTTATTA
          1 ATATATTTATTA

                         
        121 ATATATTTACTT-
          1 ATATATTTA-TTA

                        
        133 AT-TATTTATTA
          1 ATATATTTATTA

                  
        144 CATATA
          1 -ATATA

        150 AATATATGTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 7
        0.78            0.00        0.22

Matches are distributed among these distances:
  10    2  0.08
  11    6  0.24
  12   13  0.52
  13    4  0.16

ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56


Consensus pattern (12 bp):   
ATATATTTATTA

Found at i:1270 original size:30 final size:30

Alignment explanation


    Indices: 1236--1638  Score: 383
    Period size: 30  Copynumber: 13.5  Consensus size: 30

       1226 AAGAGGTCCC

                   *  *                   
       1236 TAAACTTCTCAAAAATTACATTTTAACCCT
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                     *    *               
       1266 TAAACTTTTACAAATTTACATTTTAA-CCT
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                 *    *                 *  
       1295 ATAAAATTTTTCAAAATTACATTTTAACAC-
          1 -TAAACTTTTCCAAAATTACATTTTAACCCT

             *  *     *                   
       1325 TGAATTTTTCAAAAATTACATTTTAACCCT
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                *  *          **         *
       1355 TAAAATTGTCCAAAATTATGTTTTAACCCC
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                 *     *             *      
       1385 TAAA-ATTTCTAAAAATTACATTTTGACACC-
          1 TAAACTTTTC-CAAAATTACATTTTAAC-CCT

                      *            *      
       1415 TAAACTTTTCTAAAATTACATTTGAACCCT
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                      *                  *
       1445 TAAACTTTTCTAAAATTACATTTTAACCCA
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                              **          
       1475 TAAACTTTTCCAAAATTATTTTTTAA-CCT
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                    *  *                   
       1504 CTAAACTTCTCTAAAATTACATTTTAA-CCT
          1 -TAAACTTTTCCAAAATTACATTTTAACCCT

                                      *     
       1534 TCAAACTTTTCCAAAATTGA-ATTTTTACCCT
          1 T-AAACTTTTCCAAAATT-ACATTTTAACCCT

                             *      *   * 
       1565 TAAACTTTTCCAAAATTGCATTTTGACCGT
          1 TAAACTTTTCCAAAATTACATTTTAACCCT

                   *        *              
       1595 TAAACTTCTCCAAAATCACATTTTCAA-CCT
          1 TAAACTTTTCCAAAATTACATTTT-AACCCT

            *              
       1625 CAAA-TTTTCCAAAA
          1 TAAACTTTTCCAAAA

       1639 GATTGACTTT


Statistics
Matches: 307,  Mismatches: 53, Indels: 27
        0.79            0.14        0.07

Matches are distributed among these distances:
  29   44  0.14
  30  250  0.81
  31   13  0.04

ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40


Consensus pattern (30 bp):   
TAAACTTTTCCAAAATTACATTTTAACCCT

Found at i:1688 original size:90 final size:91

Alignment explanation


    Indices: 1236--1710  Score: 281
    Period size: 90  Copynumber: 5.3  Consensus size: 91

       1226 AAGAGGTCCC

                                                     *       *   *           
       1236 TAAACTTCTCAAAAATTACATTTT-AACCCTT-AAACTTTTAC-AAATTTACATTTTAA-CCTAT
          1 TAAACTTCTCAAAAATTACATTTTCAA-CCTTCAAACTTTTCCAAAATTGA-ACTTTAACCCT-T

               *    *       *    *    *  
       1297 AAAATTTTTCAAAATTACATTTTAACAC-
         63 AAACTTTTCCAAAATTGCATTGTAACCCT

             *  *  *                            *  *            **        *  
       1325 TGAATTTTTCAAAAATTACATTTT-AACCCTT-AAAATTGTCCAAAATT-ATGTTTTAACCCCTA
          1 TAAACTTCTCAAAAATTACATTTTCAA-CCTTCAAACTTTTCCAAAATTGA-ACTTTAACCCTTA

               *     *      *    * *      
       1387 AA-ATTTCTAAAAATTACATTTTGACACC-
         64 AACTTTTC-CAAAATTGCATTGTAAC-CCT

                   *  *             *                 *          *        *  
       1415 TAAACTTTTCTAAAATTACA-TTTGAACCCTT-AAACTTTTCTAAAATT-ACATTTTAACCCATA
          1 TAAACTTCTCAAAAATTACATTTTCAA-CCTTCAAACTTTTCCAAAATTGA-ACTTTAACCCTTA

                           ***  *       
       1477 AACTTTTCCAAAATTATTTTTTAA-CCT
         64 AACTTTTCCAAAATTGCATTGTAACCCT

                       *                                        *   *        
       1504 CTAAACTTCTCTAAAATTACATTTT-AACCTTCAAACTTTTCCAAAATTGAATTTTTACCCTTAA
          1 -TAAACTTCTCAAAAATTACATTTTCAACCTTCAAACTTTTCCAAAATTGAACTTTAACCCTTAA

                               * *   * 
       1568 ACTTTTCCAAAATTGCATTTTGACCGT
         65 ACTTTTCCAAAATTGCATTGTAACCCT

                      *     *                                          *     
       1595 TAAACTTCTCCAAAATCACATTTTCAACC-TCAAA-TTTTCCAAAAGATTG-ACTTTAATCC-T-
          1 TAAACTTCTCAAAAATTACATTTTCAACCTTCAAACTTTTCC-AAA-ATTGAACTTTAACCCTTA

              *             *             
       1655 AAGTTTTCCAAAAATTTCAATTGTAACCCT
         64 AACTTTTCC-AAAATTGC-ATTGTAACCCT

                               *       
       1685 TAAA-TTCCTCAAAAATTAGATTTTCA
          1 TAAACTT-CTCAAAAATTACATTTTCA

       1711 TCCCTAATTC


Statistics
Matches: 318,  Mismatches: 50, Indels: 35
        0.79            0.12        0.09

Matches are distributed among these distances:
  88   13  0.04
  89   84  0.26
  90  203  0.64
  91   18  0.06

ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40


Consensus pattern (91 bp):   
TAAACTTCTCAAAAATTACATTTTCAACCTTCAAACTTTTCCAAAATTGAACTTTAACCCTTAAA
CTTTTCCAAAATTGCATTGTAACCCT
Done.