Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009432.1 Kokia drynarioides strain JFW-HI SEQ_124139, 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: 2907
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33


Found at i:100 original size:26 final size:26

Alignment explanation


    Indices: 71--125  Score: 101
    Period size: 26  Copynumber: 2.1  Consensus size: 26

         61 TTATGACTTA

                                      
         71 TAATAAAATTACTAACTAACAAAATT
          1 TAATAAAATTACTAACTAACAAAATT

                   *                  
         97 TAATAAAGTTACTAACTAACAAAATT
          1 TAATAAAATTACTAACTAACAAAATT

               
        123 TAA
          1 TAA

        126 ACATTATTAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   28  1.00

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


Consensus pattern (26 bp):   
TAATAAAATTACTAACTAACAAAATT

Found at i:203 original size:20 final size:21

Alignment explanation


    Indices: 178--220  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        168 TACTTACTAC

                                 
        178 TACTAAC-AACAAAATAAAAT
          1 TACTAACTAACAAAATAAAAT

                     *      *    
        198 TACTAACTAGCAAAATTAAAT
          1 TACTAACTAACAAAATAAAAT

              
        219 TA
          1 TA

        221 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:607 original size:4 final size:4

Alignment explanation


    Indices: 587--646  Score: 72
    Period size: 4  Copynumber: 15.5  Consensus size: 4

        577 CCCCTTATTC

                        *                                            *  
        587 TCTT TC-T TCCT TC-T TCTT TCTT TCTT TCTT TCTT TCTT TCTCT TTTT
          1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT-T TCTT

                             
        634 TCTT TCTT T-TT TC
          1 TCTT TCTT TCTT TC

        647 CTTCATTTTT


Statistics
Matches: 50,  Mismatches: 2, Indels: 8
        0.83            0.03        0.13

Matches are distributed among these distances:
   3    9  0.18
   4   38  0.76
   5    3  0.06

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (4 bp):   
TCTT

Done.