Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004555.1 Kokia drynarioides strain JFW-HI SEQ_118029, 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: 2775
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34


Found at i:255 original size:70 final size:71

Alignment explanation


    Indices: 172--315  Score: 227
    Period size: 70  Copynumber: 2.0  Consensus size: 71

        162 TGGGCTTCTC

                  *                        *    *      *                     
        172 ATTCAATATTAGTTGCCACTTTCATCTTGGATTAATGACGTTAGTCAAATTGGTTCATGTGTTTG
          1 ATTCAACATTAGTTGCCACTTTCATCTTGGACTAATAACGTTACTCAAATTGGTTCATGTGTTTG

                  
        237 ACAA-T
         66 ACAAGT

                                                         *         *         
        242 ATTCAACATTAGTTGCCACTTTCATCTTGGACTAATAACGTTACTTAAATTGGTTTATGTGTTTG
          1 ATTCAACATTAGTTGCCACTTTCATCTTGGACTAATAACGTTACTCAAATTGGTTCATGTGTTTG

                  
        307 ACAAGT
         66 ACAAGT

               
        313 ATT
          1 ATT

        316 TATGTAAGAT


Statistics
Matches: 67,  Mismatches: 6, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  70   63  0.94
  71    4  0.06

ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42


Consensus pattern (71 bp):   
ATTCAACATTAGTTGCCACTTTCATCTTGGACTAATAACGTTACTCAAATTGGTTCATGTGTTTG
ACAAGT

Found at i:2641 original size:30 final size:29

Alignment explanation


    Indices: 2607--2691  Score: 98
    Period size: 30  Copynumber: 2.9  Consensus size: 29

       2597 CCAGAACTTC

                 *                        
       2607 TATTTCGACACTCGAATTTTTCAAAAATTA
          1 TATTTTGAC-CTCGAATTTTTCAAAAATTA

                      *  *       *        
       2637 TATTTTGACCCCTAAATTTTTTAAAAATTA
          1 TATTTTGACCTC-GAATTTTTCAAAAATTA

                           *   *     
       2667 TATTTTGACCTCGAACTTTCCAAAA
          1 TATTTTGACCTCGAATTTTTCAAAA

       2692 CTTTGATTGT


Statistics
Matches: 45,  Mismatches: 9, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  29   11  0.24
  30   34  0.76

ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41


Consensus pattern (29 bp):   
TATTTTGACCTCGAATTTTTCAAAAATTA

Found at i:2691 original size:59 final size:59

Alignment explanation


    Indices: 2607--2775  Score: 160
    Period size: 59  Copynumber: 2.8  Consensus size: 59

       2597 CCAGAACTTC

                 *          *   *                         *   *       * 
       2607 TATTTCGACACTCGAATTTTTCAAAAATTATATTTTGACCCCTAAATTTTTTAAAAATTA
          1 TATTTTGAC-CTCGAACTTTCCAAAAATTATATTTTGACCCCTAAACTTTCTAAAAATCA

                                     *        *       *                 
       2667 TATTTTGACCTCGAACTTTCCAAAACTT-TGATTGTGACCCCCAAACTTTCTAAAAATCA
          1 TATTTTGACCTCGAACTTTCCAAAAATTAT-ATTTTGACCCCTAAACTTTCTAAAAATCA

            *     *     * *      *        *        *          
       2726 CATTTTTACCCTTGCACTTTCTAAAAATTACATTTTGACTCCTAAACTTT
          1 TATTTTGA-CCTCGAACTTTCCAAAAATTATATTTTGACCCCTAAACTTT


Statistics
Matches: 87,  Mismatches: 19, Indels: 6
        0.78            0.17        0.05

Matches are distributed among these distances:
  58    1  0.01
  59   46  0.53
  60   40  0.46

ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40


Consensus pattern (59 bp):   
TATTTTGACCTCGAACTTTCCAAAAATTATATTTTGACCCCTAAACTTTCTAAAAATCA

Found at i:2775 original size:30 final size:29

Alignment explanation


    Indices: 2625--2775  Score: 108
    Period size: 30  Copynumber: 5.1  Consensus size: 29

       2615 CACTCGAATT

                         *               *
       2625 TTTC-AAAAATTATATTTTGACCCCTAAAT
          1 TTTCTAAAAATTACATTTTGA-CCCTAAAC

               *         *            *   
       2654 TTTTTAAAAATTATATTTTGA-CCTCGAAC
          1 TTTCTAAAAATTACATTTTGACCCT-AAAC

                *    *  **   *       *    
       2683 TTTCCAAAACTTTGATTGTGACCCCCAAAC
          1 TTTCTAAAAATTACATTTTGA-CCCTAAAC

                       *       *      **  
       2713 TTTCTAAAAATCACATTTTTACCCTTGCAC
          1 TTTCTAAAAATTACATTTTGACCC-TAAAC

                                          
       2743 TTTCTAAAAATTACATTTTGACTCCTAAAC
          1 TTTCTAAAAATTACATTTTGAC-CCTAAAC

               
       2773 TTT
          1 TTT


Statistics
Matches: 91,  Mismatches: 25, Indels: 11
        0.72            0.20        0.09

Matches are distributed among these distances:
  28    3  0.03
  29   23  0.25
  30   61  0.67
  31    4  0.04

ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40


Consensus pattern (29 bp):   
TTTCTAAAAATTACATTTTGACCCTAAAC
Done.