Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001138.1 Kokia drynarioides strain JFW-HI SEQ_112433, 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, 649

Length: 1083
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38


Found at i:584 original size:59 final size:59

Alignment explanation


    Indices: 511--643  Score: 221
    Period size: 59  Copynumber: 2.3  Consensus size: 59

        501 ATTTTGTACA

                                                                       
        511 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT
          1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT

                    *      *                  *                        
        570 ATTTTGGTCAATAATTTGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
          1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT

                 *    *    
        629 ATTTTAGTAATTAAT
          1 ATTTTGGTAAATAAT

        644 TAGCTAAGTT


Statistics
Matches: 68,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  59   68  1.00

ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53


Consensus pattern (59 bp):   
ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT

Found at i:613 original size:29 final size:29

Alignment explanation


    Indices: 511--614  Score: 70
    Period size: 29  Copynumber: 3.6  Consensus size: 29

        501 ATTTTGTACA

                  *   *    *             
        511 ATTTTGGTAAATAATATGATGGGGATATT
          1 ATTTTGATAATTAATTTGATGGGGATATT

                 *               ****       
        540 ATTTTCATAATTAA-TT-ATTTTTTATATTAT
          1 ATTTTGATAATTAATTTGA-TGGGGATA-T-T

                  *                       
        570 ATTTTGGTCAA-TAATTTGATGGGGATATT
          1 ATTTTGAT-AATTAATTTGATGGGGATATT

                            
        599 ATTTTGATAATTAATT
          1 ATTTTGATAATTAATT

        615 ATTTTTTATA


Statistics
Matches: 53,  Mismatches: 15, Indels: 14
        0.65            0.18        0.17

Matches are distributed among these distances:
  27    1  0.02
  28    7  0.13
  29   25  0.47
  30   11  0.21
  31    8  0.15
  32    1  0.02

ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51


Consensus pattern (29 bp):   
ATTTTGATAATTAATTTGATGGGGATATT

Found at i:640 original size:30 final size:28

Alignment explanation


    Indices: 535--645  Score: 82
    Period size: 30  Copynumber: 3.8  Consensus size: 28

        525 TATGATGGGG

                      *                 
        535 ATATTATTTTCATAATTAATTATTTTTT
          1 ATATTATTTTTATAATTAATTATTTTTT

                         *               ****
        563 ATATTATATTTTGGTCAA-TAATT-TGATGGGG
          1 ATATTAT-TTTT-AT-AATTAATTAT--TTTTT

                      *                 
        594 ATATTATTTTGATAATTAATTATTTTTT
          1 ATATTATTTTTATAATTAATTATTTTTT

                                    
        622 ATATTATATTTTAGTAATTAATTA
          1 ATATTAT-TTTTA-TAATTAATTA

        646 GCTAAGTTTA


Statistics
Matches: 61,  Mismatches: 13, Indels: 16
        0.68            0.14        0.18

Matches are distributed among these distances:
  28   17  0.28
  29   14  0.23
  30   20  0.33
  31   10  0.16

ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57


Consensus pattern (28 bp):   
ATATTATTTTTATAATTAATTATTTTTT

Found at i:931 original size:20 final size:21

Alignment explanation


    Indices: 906--948  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        896 TACTTACTAC

                                 
        906 TACTAAC-AACAAAATTAAAT
          1 TACTAACTAACAAAATTAAAT

                     *           
        926 TACTAACTAGCAAAATTAAAT
          1 TACTAACTAACAAAATTAAAT

              
        947 TA
          1 TA

        949 TAGTAAATTA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20    7  0.33
  21   14  0.67

ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28


Consensus pattern (21 bp):   
TACTAACTAACAAAATTAAAT

Done.