Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011417.1 Kokia drynarioides strain JFW-HI SEQ_126400, 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: 2948
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33


Found at i:143 original size:25 final size:26

Alignment explanation


    Indices: 115--168  Score: 92
    Period size: 25  Copynumber: 2.1  Consensus size: 26

        105 TTATGACTTA

                                      
        115 TAATAAAATTACTAACTAAC-AAATT
          1 TAATAAAATTACTAACTAACAAAATT

                   *                  
        140 TAATAAAGTTACTAACTAACAAAATT
          1 TAATAAAATTACTAACTAACAAAATT

               
        166 TAA
          1 TAA

        169 ACATTATTAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  25   19  0.70
  26    8  0.30

ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31


Consensus pattern (26 bp):   
TAATAAAATTACTAACTAACAAAATT

Found at i:246 original size:20 final size:21

Alignment explanation


    Indices: 221--263  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        211 TACTTACTAC

                                 
        221 TACTAAC-AACAAAATAAAAT
          1 TACTAACTAACAAAATAAAAT

                     *      *    
        241 TACTAACTAGCAAAATTAAAT
          1 TACTAACTAACAAAATAAAAT

              
        262 TA
          1 TA

        264 AAGTAAATTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26


Consensus pattern (21 bp):   
TACTAACTAACAAAATAAAAT

Found at i:644 original size:16 final size:15

Alignment explanation


    Indices: 623--684  Score: 60
    Period size: 16  Copynumber: 4.2  Consensus size: 15

        613 CCTTATTCCC

                            
        623 CTTCTTCTCCTTCTTT
          1 CTTCTTCT-CTTCTTT

                           
        639 CTTCTTCT-TTCTTT
          1 CTTCTTCTCTTCTTT

                           
        653 C-T-TTCT-TTCTTT
          1 CTTCTTCTCTTCTTT

                         *   
        665 CTTTCTTTCTCTTTTTT
          1 C-TTC-TTCTCTTCTTT

               
        682 CTT
          1 CTT

        685 TCTTTTTTCC


Statistics
Matches: 40,  Mismatches: 1, Indels: 10
        0.78            0.02        0.20

Matches are distributed among these distances:
  12   11  0.28
  13    1  0.03
  14    8  0.20
  16   14  0.35
  17    6  0.15

ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71


Consensus pattern (15 bp):   
CTTCTTCTCTTCTTT

Found at i:650 original size:4 final size:4

Alignment explanation


    Indices: 633--693  Score: 83
    Period size: 4  Copynumber: 15.8  Consensus size: 4

        623 CTTCTTCTCC

                                                                      * 
        633 TTCT TTC- TTC- TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT CTTTT
          1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT

                              
        680 TTCT TTCT TT-T TTC
          1 TTCT TTCT TTCT TTC

        694 CTTCATTTTT


Statistics
Matches: 52,  Mismatches: 2, Indels: 6
        0.87            0.03        0.10

Matches are distributed among these distances:
   3    9  0.17
   4   40  0.77
   5    3  0.06

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (4 bp):   
TTCT

Found at i:702 original size:12 final size:11

Alignment explanation


    Indices: 639--704  Score: 55
    Period size: 11  Copynumber: 6.0  Consensus size: 11

        629 CTCCTTCTTT

                  *    
        639 CTTCTTCTTTC
          1 CTTCTTTTTTC

            *           
        650 TTTCTTTCTTTC
          1 CTTCTTT-TTTC

            *           
        662 TTTCTTTCTTT-
          1 CTTCTTT-TTTC

                       
        673 C-TCTTTTTTC
          1 CTTCTTTTTTC

            *          
        683 TTTCTTTTTTC
          1 CTTCTTTTTTC

                *      
        694 CTTCATTTTTC
          1 CTTCTTTTTTC

        705 GTTGGTCCCC


Statistics
Matches: 46,  Mismatches: 6, Indels: 6
        0.79            0.10        0.10

Matches are distributed among these distances:
   9    3  0.07
  10    5  0.11
  11   23  0.50
  12   15  0.33

ACGTcount: A:0.02, C:0.26, G:0.00, T:0.73


Consensus pattern (11 bp):   
CTTCTTTTTTC

Done.