Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013496.1 Kokia drynarioides strain JFW-HI SEQ_128522, 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: 9358
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:1151 original size:29 final size:28

Alignment explanation


    Indices: 1116--1457  Score: 248
    Period size: 30  Copynumber: 11.6  Consensus size: 28

       1106 CCCTAAATTA

                                        
       1116 TTCAAAAATTCCATTTTTACCCTCAAAC
          1 TTCAAAAATTCCATTTTTACCCTCAAAC

                       *         *         
       1144 TTCAAAAAAATCCCATTTTTAACCTCAAAAC
          1 TTC--AAAAATTCCATTTTTACCCTC-AAAC

                       ** *        *     
       1175 TTTCAAAAATTATACTTTTACCCCCAAAC
          1 -TTCAAAAATTCCATTTTTACCCTCAAAC

                      *              *    
       1204 TTCAAAAAATCCCATTTTTAACCCTAAAAC
          1 TTC-AAAAATTCCATTTTT-ACCCTCAAAC

                        *                 
       1234 TTTCAAAAATTCTATTTTTACCC-CTAAAC
          1 -TTCAAAAATTCCATTTTTACCCTC-AAAC

                                      *    
       1263 TTCCAAAAATT-CATTTTTTGACCCTAAAAC
          1 TT-CAAAAATTCCA-TTTTT-ACCCTCAAAC

                       **          * *   
       1293 TTTCAAAAATTTTATTTTTACCCCCGAAC
          1 -TTCAAAAATTCCATTTTTACCCTCAAAC

                      *                    
       1322 TTCCAAAAATCCCATTTTTGA-CCTCGAAAC
          1 TT-CAAAAATTCCATTTTT-ACCCTC-AAAC

                                           *
       1352 TTCCAAAAA-TCTCA-TTTTACCC-CTAAATT
          1 TT-CAAAAATTC-CATTTTTACCCTC-AAA-C

                     *                     
       1381 TTCAAAAATCCCATTTTTAACCC-CAAAACC
          1 TTCAAAAATTCCATTTTT-ACCCTC-AAA-C

                      *             *   
       1411 TTCAAAAATTTCATTTTTACCCTCGAAC
          1 TTCAAAAATTCCATTTTTACCCTCAAAC

                      *        
       1439 TTCTAAAAATCCCATTTTT
          1 TTC-AAAAATTCCATTTTT

       1458 GACCACGAAT


Statistics
Matches: 249,  Mismatches: 40, Indels: 49
        0.74            0.12        0.14

Matches are distributed among these distances:
  28   28  0.11
  29   92  0.37
  30  116  0.47
  31   10  0.04
  32    3  0.01

ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35


Consensus pattern (28 bp):   
TTCAAAAATTCCATTTTTACCCTCAAAC

Found at i:1240 original size:59 final size:59

Alignment explanation


    Indices: 1116--1457  Score: 383
    Period size: 59  Copynumber: 5.8  Consensus size: 59

       1106 CCCTAAATTA

                       *          *                                      
       1116 TTCAAAAATTCCATTTTTACCCTCAAACTTCAAAAAAATCCCATTTTTAA-CCTCAAAACT
          1 TTCAAAAATTCTATTTTTACCCCCAAACTTC-AAAAAATCCCATTTTTAACCCT-AAAACT

                      *  *                                             
       1176 TTCAAAAATTATACTTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCTAAAACT
          1 TTCAAAAATTCTATTTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCTAAAACT

                                   *       *       *        *           
       1235 TTCAAAAATTCTATTTTTACCCCTAAACTTCCAAAAAT-TCATTTTTTGACCCTAAAACT
          1 TTCAAAAATTCTATTTTTACCCCCAAACTTCAAAAAATCCCA-TTTTTAACCCTAAAACT

                      *             *      *               *      *     
       1294 TTCAAAAATTTTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACT
          1 TTCAAAAATTCTATTTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCT-AAAACT

             *                      *    *                        *     *
       1353 TCCAAAAA-TCTCA-TTTTACCCCTAAATTTTC-AAAAATCCCATTTTTAACCCCAAAACC
          1 TTCAAAAATTCT-ATTTTTACCCCCAAA-CTTCAAAAAATCCCATTTTTAACCCTAAAACT

                                   * *      *               
       1411 TTCAAAAATT-TCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTT
          1 TTCAAAAATTCT-ATTTTTACCCCCAAACTTCAAAAAATCCCATTTTT

       1458 GACCACGAAT


Statistics
Matches: 243,  Mismatches: 29, Indels: 21
        0.83            0.10        0.07

Matches are distributed among these distances:
  58   51  0.21
  59  160  0.66
  60   32  0.13

ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35


Consensus pattern (59 bp):   
TTCAAAAATTCTATTTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCTAAAACT

Found at i:1499 original size:117 final size:117

Alignment explanation


    Indices: 1149--1466  Score: 293
    Period size: 117  Copynumber: 2.7  Consensus size: 117

       1139 CAAACTTCAA

                               *      *              *          *      *     
       1149 AAAAATCCCATTTTTAACCTCAAAACTTTCAAAAATTAT-ACTTTTACCCCCAAACTTCAAAAAA
          1 AAAAATCCCATTTTTAACCCCAAAACCTTCAAAAATT-TCATTTTTACCCCCGAACTTCCAAAAA

                      *      *      *             * ** ***     *  * 
       1213 TCCCATTTTTAACC-CTAAAACTTTCAAAAAT-TCTATTTTTACCCCTAAACTTCC
         65 TCCCATTTTTGACCAC-GAAACTTCCAAAAATCTC-A-ATCAAAAACTAAATTTTC

                   *        *    *     *           *                         
       1267 AAAAAT-TCATTTTTTGACCCTAAAACTTTCAAAAATTTTATTTTTACCCCCGAACTTCCAAAAA
          1 AAAAATCCCA-TTTTTAACCCCAAAACCTTCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAA

                          *                    * ** ***          
       1331 TCCCATTTTTGACCTCGAAACTTCCAAAAATCTCATTTTACCCCTAAATTTTC
         65 TCCCATTTTTGACCACGAAACTTCCAAAAATCTCAATCAAAAACTAAATTTTC

                                                             *        *      
       1384 AAAAATCCCATTTTTAACCCCAAAACCTTCAAAAATTTCATTTTTACCCTCGAACTTCTAAAAAT
          1 AAAAATCCCATTTTTAACCCCAAAACCTTCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAAT

                              
       1449 CCCATTTTTGACCACGAA
         66 CCCATTTTTGACCACGAA

       1467 TTTTACCAAA


Statistics
Matches: 175,  Mismatches: 20, Indels: 11
        0.85            0.10        0.05

Matches are distributed among these distances:
 117   91  0.52
 118   81  0.46
 119    3  0.02

ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34


Consensus pattern (117 bp):   
AAAAATCCCATTTTTAACCCCAAAACCTTCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAAT
CCCATTTTTGACCACGAAACTTCCAAAAATCTCAATCAAAAACTAAATTTTC
Done.