Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005538.1 Kokia drynarioides strain JFW-HI SEQ_119630, 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, 952

Length: 1588
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36


Found at i:235 original size:17 final size:18

Alignment explanation


    Indices: 213--256  Score: 65
    Period size: 17  Copynumber: 2.6  Consensus size: 18

        203 TAATTTTAAT

                              
        213 GTTTTTATTTAT-TTTTG
          1 GTTTTTATTTATGTTTTG

                      *       
        230 GTTTTT-TTTTTGTTTTG
          1 GTTTTTATTTATGTTTTG

                      
        247 GTTTTTATTT
          1 GTTTTTATTT

        257 GGGCCCAAAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  16    4  0.17
  17   17  0.71
  18    3  0.12

ACGTcount: A:0.07, C:0.00, G:0.14, T:0.80


Consensus pattern (18 bp):   
GTTTTTATTTATGTTTTG

Found at i:671 original size:47 final size:46

Alignment explanation


    Indices: 614--822  Score: 195
    Period size: 47  Copynumber: 4.5  Consensus size: 46

        604 CATAAGAGTT

                             *        *                  * 
        614 ATGTG-TGGCTTTAACCCGCCTCTTTGGATTTGGGGTATAAGATTAG
          1 ATGTGATGGCTTTAACCTGCCT-TTTAGATTTGGGGTATAAGATTGG

            *              *  *             *             *
        660 CTGTGATGGCTTTAATCTACCTTTCTAGATTTAGGGTATAAGATTGA
          1 ATGTGATGGCTTTAACCTGCCTTT-TAGATTTGGGGTATAAGATTGG

                        *  *        *                      
        707 ATGTGATGGCTTAAATCTAGCCTTCTAGATTTGGGGTATAAGATTGG
          1 ATGTGATGGCTTTAACCT-GCCTTTTAGATTTGGGGTATAAGATTGG

                  *    **  *      *                  * *   
        754 ATGTGACGGCTCCAATCTGCCCCTTTAGATTTGGGGTATAAAACTGG
          1 ATGTGATGGCTTTAACCTG-CCTTTTAGATTTGGGGTATAAGATTGG

                        *  *      
        801 ATGTGATGGCTTCAATCTGCCT
          1 ATGTGATGGCTTTAACCTGCCT

        823 GATAGTACTA


Statistics
Matches: 135,  Mismatches: 24, Indels: 8
        0.81            0.14        0.05

Matches are distributed among these distances:
  46    9  0.07
  47  122  0.90
  48    4  0.03

ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36


Consensus pattern (46 bp):   
ATGTGATGGCTTTAACCTGCCTTTTAGATTTGGGGTATAAGATTGG

Found at i:742 original size:94 final size:93

Alignment explanation


    Indices: 640--822  Score: 233
    Period size: 94  Copynumber: 2.0  Consensus size: 93

        630 CGCCTCTTTG

                                *     *    **         *                   * *
        640 GATTTGGGGTATAAGATTAGCTGTGATGGCTTTAATCT-ACCTTTCTAGATTTAGGGTATAAGAT
          1 GATTTGGGGTATAAGATTAGATGTGACGGCTCCAATCTGACCCTT-TAGATTTAGGGTATAAAAC

                                          
        704 TGAATGTGATGGCTTAAATCTAGCCTTCTA
         65 TGAATGTGATGGCTTAAATCT-GCCTTCTA

                              *                    *            *            
        734 GATTTGGGGTATAAGATTGGATGTGACGGCTCCAATCTGCCCCTTTAGATTTGGGGTATAAAACT
          1 GATTTGGGGTATAAGATTAGATGTGACGGCTCCAATCTGACCCTTTAGATTTAGGGTATAAAACT

             *            *         
        799 GGATGTGATGGCTTCAATCTGCCT
         66 GAATGTGATGGCTTAAATCTGCCT

        823 GATAGTACTA


Statistics
Matches: 76,  Mismatches: 12, Indels: 3
        0.84            0.13        0.03

Matches are distributed among these distances:
  93    4  0.05
  94   68  0.89
  95    4  0.05

ACGTcount: A:0.25, C:0.14, G:0.26, T:0.36


Consensus pattern (93 bp):   
GATTTGGGGTATAAGATTAGATGTGACGGCTCCAATCTGACCCTTTAGATTTAGGGTATAAAACT
GAATGTGATGGCTTAAATCTGCCTTCTA

Found at i:1125 original size:52 final size:52

Alignment explanation


    Indices: 1063--1163  Score: 130
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       1053 TCGTTGCGTG

                                 **  *     *                    
       1063 AGCAAGCCCAGAATTATTGTTTTAGGAACTCGTTCAAAATAATCACTGTATA
          1 AGCAAGCCCAGAATTATTGTTGAAGAAACTCATTCAAAATAATCACTGTATA

                *          *                        *   *    
       1115 AGCATGCCCAGAATTGTTGTTGAAGAAACTCATTCAAAATTATCGCTGT
          1 AGCAAGCCCAGAATTATTGTTGAAGAAACTCATTCAAAATAATCACTGT

       1164 GTGATTATGT


Statistics
Matches: 41,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  52   41  1.00

ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Consensus pattern (52 bp):   
AGCAAGCCCAGAATTATTGTTGAAGAAACTCATTCAAAATAATCACTGTATA

Found at i:1176 original size:26 final size:26

Alignment explanation


    Indices: 1147--1209  Score: 63
    Period size: 26  Copynumber: 2.4  Consensus size: 26

       1137 AAGAAACTCA

                             * *  *   
       1147 TTCAAAATTATCGCTGTGTGATTATG
          1 TTCAAAATTATCGCTGTATAATCATG

                * *  *                
       1173 TTCAGAGTTGTCGCTGTATAATCATG
          1 TTCAAAATTATCGCTGTATAATCATG

             *         
       1199 TCCAAAATTAT
          1 TTCAAAATTAT

       1210 GCCCAAAACT


Statistics
Matches: 27,  Mismatches: 10, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40


Consensus pattern (26 bp):   
TTCAAAATTATCGCTGTATAATCATG
Done.