Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003535.1 Kokia drynarioides strain JFW-HI SEQ_116380, 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: 2241
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39


Found at i:1432 original size:28 final size:28

Alignment explanation


    Indices: 1380--1441  Score: 65
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       1370 CAATTATTTT

                                      * 
       1380 TATT-ATTATAATTATTATCAAAATATA
          1 TATTAATTATAATTATTATCAAAATAAA

                                * *      
       1407 TATTAATTAATAA-TATTATTATAATAAA
          1 TATTAATT-ATAATTATTATCAAAATAAA

              *    
       1435 TAATAAT
          1 TATTAAT

       1442 ATTTTATTAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  27    4  0.14
  28   21  0.72
  29    4  0.14

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47


Consensus pattern (28 bp):   
TATTAATTATAATTATTATCAAAATAAA

Found at i:1436 original size:18 final size:18

Alignment explanation


    Indices: 1410--1444  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1400 AAATATATAT

                *       *     
       1410 TAATTAATAATATTATTA
          1 TAATAAATAATAATATTA

                             
       1428 TAATAAATAATAATATT
          1 TAATAAATAATAATATT

       1445 TTATTATTAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (18 bp):   
TAATAAATAATAATATTA

Found at i:1438 original size:21 final size:20

Alignment explanation


    Indices: 1414--1459  Score: 65
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1404 ATATATTAAT

                                 
       1414 TAATAATATTATTATAATAAA
          1 TAATAATATT-TTATAATAAA

                          *  *  
       1435 TAATAATATTTTATTATTAA
          1 TAATAATATTTTATAATAAA

                 
       1455 TAATA
          1 TAATA

       1460 TAAAATATAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   13  0.57
  21   10  0.43

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (20 bp):   
TAATAATATTTTATAATAAA

Found at i:1455 original size:24 final size:23

Alignment explanation


    Indices: 1405--1467  Score: 71
    Period size: 21  Copynumber: 2.8  Consensus size: 23

       1395 TATCAAAATA

                *                  
       1405 TATATTAAT-TAATAATA-TTAT
          1 TATAATAATATAATAATATTTAT

                                    
       1426 TATAATAA-ATAATAATATTTTAT
          1 TATAATAATATAATAATA-TTTAT

                                
       1449 TATTAATAATATAA-AATAT
          1 TA-TAATAATATAATAATAT

       1468 AAGAAAAGAA


Statistics
Matches: 36,  Mismatches: 1, Indels: 8
        0.80            0.02        0.18

Matches are distributed among these distances:
  21   15  0.42
  23    7  0.19
  24   10  0.28
  25    4  0.11

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (23 bp):   
TATAATAATATAATAATATTTAT
Done.