Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007407.1 Kokia drynarioides strain JFW-HI SEQ_122026, 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: 5045
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32


Found at i:1531 original size:31 final size:31

Alignment explanation


    Indices: 1467--1531  Score: 87
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1457 ATATTTACTA

                   *                 *  *  
       1467 AATTAAATATTAAAACTAAATTCGAGTATCG
          1 AATTAAACATTAAAACTAAATTCGACTACCG

                                            
       1498 AATTAAACATTAAAACTAAATTC-ACCTACCG
          1 AATTAAACATTAAAACTAAATTCGA-CTACCG

               
       1529 AAT
          1 AAT

       1532 AGTAGTAACC


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  30    1  0.03
  31   29  0.97

ACGTcount: A:0.49, C:0.15, G:0.06, T:0.29


Consensus pattern (31 bp):   
AATTAAACATTAAAACTAAATTCGACTACCG

Found at i:3255 original size:62 final size:63

Alignment explanation


    Indices: 3115--3261  Score: 192
    Period size: 62  Copynumber: 2.4  Consensus size: 63

       3105 ATATCTGAAC

                                                                           
       3115 TTTTTTTA-ACCCAATTTGGTA-CATGAACTTGACAATTTTTACTAATTTGGTAGCTAAACTT
          1 TTTTTTTAGACCCAATTTGGTACCATGAACTTGACAATTTTTACTAATTTGGTAGCTAAACTT

                   *           *                *     *           *    *   
       3176 TTTTTTTGGACCCAATTTGATACCAT-AACTTGACATTTTTTCCTAATTTGGTATCTAAGCTT
          1 TTTTTTTAGACCCAATTTGGTACCATGAACTTGACAATTTTTACTAATTTGGTAGCTAAACTT

                      ***           
       3238 TTTTTTTAGATTTAATTTGGTACC
          1 TTTTTTTAGACCCAATTTGGTACC

       3262 TAAATTTATT


Statistics
Matches: 73,  Mismatches: 11, Indels: 3
        0.84            0.13        0.03

Matches are distributed among these distances:
  61    7  0.10
  62   63  0.86
  63    3  0.04

ACGTcount: A:0.26, C:0.15, G:0.12, T:0.48


Consensus pattern (63 bp):   
TTTTTTTAGACCCAATTTGGTACCATGAACTTGACAATTTTTACTAATTTGGTAGCTAAACTT

Found at i:4996 original size:29 final size:29

Alignment explanation


    Indices: 4964--5036  Score: 69
    Period size: 30  Copynumber: 2.5  Consensus size: 29

       4954 TGCACGGGGG

                      *        *          
       4964 CAAAATGGTAGTTTTGGTAGGTTTG-GAGT
          1 CAAAATGGTAATTTTGG-AAGTTTGAGAGT

                     * *               *  
       4993 CAAAAATGGGATTTTTGGAAGTTTGAGGGT
          1 C-AAAATGGTAATTTTGGAAGTTTGAGAGT

                           
       5023 -AAAATGGTAATTTT
          1 CAAAATGGTAATTTT

       5037 TGAAAGGTT


Statistics
Matches: 36,  Mismatches: 6, Indels: 5
        0.77            0.13        0.11

Matches are distributed among these distances:
  28   12  0.33
  29    7  0.19
  30   17  0.47

ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37


Consensus pattern (29 bp):   
CAAAATGGTAATTTTGGAAGTTTGAGAGT
Done.