Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004437.1 Kokia drynarioides strain JFW-HI SEQ_117831, 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: 11382
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33


Found at i:495 original size:23 final size:22

Alignment explanation


    Indices: 464--608  Score: 128
    Period size: 23  Copynumber: 6.3  Consensus size: 22

        454 TTAGGGATAT

                                   
        464 AGTAAGCACACACAGTGCAAATC
          1 AGTAAGCACACACAGTGCAAA-C

                *     **           
        487 AGTAGGCACATGCAGTGCAAAAC
          1 AGTAAGCACACACAGTGC-AAAC

                          * *      
        510 AGTAAGCACACACACTACAAATC
          1 AGTAAGCACACACAGTGCAAA-C

                      * *      *   
        533 AGTAAGCACATATAGTGCTGAAC
          1 AGTAAGCACACACAGTGC-AAAC

                  *     *      *   
        556 AGTAAGTACACATAGTGCTGAAC
          1 AGTAAGCACACACAGTGC-AAAC

                                   
        579 AGTAAGCACACACAGTGCTAAAC
          1 AGTAAGCACACACAGTGC-AAAC

             *     
        602 ACTAAGC
          1 AGTAAGC

        609 GCGCTAATGT


Statistics
Matches: 100,  Mismatches: 19, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
  22    3  0.03
  23   92  0.92
  24    5  0.05

ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16


Consensus pattern (22 bp):   
AGTAAGCACACACAGTGCAAAC

Found at i:516 original size:46 final size:46

Alignment explanation


    Indices: 464--608  Score: 166
    Period size: 46  Copynumber: 3.2  Consensus size: 46

        454 TTAGGGATAT

                                       *      *      *    
        464 AGTAAGCACACACAGTGCAAATCAGTAGGCACATGCAGTGCAAAAC
          1 AGTAAGCACACACAGTGCAAATCAGTAAGCACATACAGTGCTAAAC

                          * *                  *      *   
        510 AGTAAGCACACACACTACAAATCAGTAAGCACATATAGTGCTGAAC
          1 AGTAAGCACACACAGTGCAAATCAGTAAGCACATACAGTGCTAAAC

                  *     *      *              *            
        556 AGTAAGTACACATAGTGCTGAA-CAGTAAGCACACACAGTGCTAAAC
          1 AGTAAGCACACACAGTGC-AAATCAGTAAGCACATACAGTGCTAAAC

             *     
        602 ACTAAGC
          1 AGTAAGC

        609 GCGCTAATGT


Statistics
Matches: 81,  Mismatches: 17, Indels: 2
        0.81            0.17        0.02

Matches are distributed among these distances:
  46   79  0.98
  47    2  0.02

ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16


Consensus pattern (46 bp):   
AGTAAGCACACACAGTGCAAATCAGTAAGCACATACAGTGCTAAAC

Found at i:11171 original size:12 final size:12

Alignment explanation


    Indices: 11146--11179  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

      11136 TTAAAAATAT

                  *     
      11146 TTAAAAAATT-A
          1 TTAAAATATTAA

                        
      11157 TTAAAATATTAA
          1 TTAAAATATTAA

                       
      11169 TTAAAATATTA
          1 TTAAAATATTA

      11180 TATTTTTTAT


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

Matches are distributed among these distances:
  11    9  0.43
  12   12  0.57

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (12 bp):   
TTAAAATATTAA

Found at i:11196 original size:25 final size:26

Alignment explanation


    Indices: 11162--11219  Score: 68
    Period size: 25  Copynumber: 2.3  Consensus size: 26

      11152 AATTATTAAA

                             *          
      11162 ATATTAATTAAA-ATATTATATTT-TTT
          1 ATATT-ATTAAACATA-CATATTTATTT

                                      
      11188 ATATTATTAAACATACATATTTATTT
          1 ATATTATTAAACATACATATTTATTT

                   
      11214 AT-TTAT
          1 ATATTAT

      11220 ATTTAATCAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  25   16  0.55
  26   13  0.45

ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55


Consensus pattern (26 bp):   
ATATTATTAAACATACATATTTATTT

Done.