Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010198.1 Kokia drynarioides strain JFW-HI SEQ_125013, 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: 1958
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:375 original size:87 final size:87

Alignment explanation


    Indices: 235--408  Score: 323
    Period size: 87  Copynumber: 2.0  Consensus size: 87

        225 GGCTATTTTT

                                                                    *        
        235 TTTTTTTGAAAGGAAAGGAAAAATGAATTTTTTTTGGGAAATTTCAGCCTTATATATGCCCTTAA
          1 TTTTTTTGAAAGGAAAGGAAAAATGAATTTTTTTTGGGAAATTTCAGCCTTATATAGGCCCTTAA

                                  
        300 AACGACGTCATTTTGAGGGCTA
         66 AACGACGTCATTTTGAGGGCTA

                                                                             
        322 NTTTTTTTGAAAGGAAAGGAAAAATG-ATTTTTTTTGGGAAATTTCAGCCTTATATAGGCCCTTA
          1 -TTTTTTTGAAAGGAAAGGAAAAATGAATTTTTTTTGGGAAATTTCAGCCTTATATAGGCCCTTA

                                   
        386 AAACGACGTCATTTTGAGGGCTA
         65 AAACGACGTCATTTTGAGGGCTA

        409 ATTTCAGCCC


Statistics
Matches: 85,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
  87   60  0.71
  88   25  0.29

ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36


Consensus pattern (87 bp):   
TTTTTTTGAAAGGAAAGGAAAAATGAATTTTTTTTGGGAAATTTCAGCCTTATATAGGCCCTTAA
AACGACGTCATTTTGAGGGCTA

Found at i:885 original size:30 final size:27

Alignment explanation


    Indices: 838--942  Score: 95
    Period size: 29  Copynumber: 3.6  Consensus size: 27

        828 ATAGAAGGTT

                                           
        838 CCTAAA-TTTCCAAAAAATCATGTTTTAACC
          1 CCTAAACTTTCC-AAAAATCA--TTTTAA-C

                                         
        868 CCTAAACTTTCCAAAAATTACATTTTAAC
          1 CCTAAACTTTCCAAAAA-T-CATTTTAAC

               *       *    *           
        897 CCTTAACTTTCTAAAATTACATTTTAAC
          1 CCTAAACTTTCCAAAAAT-CATTTTAAC

                        *     
        925 CCTCAAACTTTCTAAAAA
          1 CCT-AAACTTTCCAAAAA

        943 ATATATTTTG


Statistics
Matches: 66,  Mismatches: 5, Indels: 9
        0.82            0.06        0.11

Matches are distributed among these distances:
  28   14  0.21
  29   27  0.41
  30   17  0.26
  31    6  0.09
  32    2  0.03

ACGTcount: A:0.40, C:0.24, G:0.01, T:0.35


Consensus pattern (27 bp):   
CCTAAACTTTCCAAAAATCATTTTAAC

Found at i:957 original size:30 final size:30

Alignment explanation


    Indices: 850--981  Score: 146
    Period size: 30  Copynumber: 4.5  Consensus size: 30

        840 TAAATTTCCA

                  *  *                    *
        850 AAAAATCATGTTTTAACCC-CTAAACTTTCC
          1 AAAAATTATATTTTAACCCTC-AAACTTTCT

                    *            *        
        880 AAAAATTACATTTTAACCCT-TAACTTTCT
          1 AAAAATTATATTTTAACCCTCAAACTTTCT

                    *                     
        909 -AAAATTACATTTTAACCCTCAAACTTTCT
          1 AAAAATTATATTTTAACCCTCAAACTTTCT

                 *        *                
        938 AAAAAATATATTTTGACCCTCAAAC-TTCTT
          1 AAAAATTATATTTTAACCCTCAAACTTTC-T

                          
        968 AAAAATTATATTTT
          1 AAAAATTATATTTT

        982 TGTTCTTAAA


Statistics
Matches: 88,  Mismatches: 10, Indels: 8
        0.83            0.09        0.08

Matches are distributed among these distances:
  28   19  0.22
  29   18  0.20
  30   51  0.58

ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39


Consensus pattern (30 bp):   
AAAAATTATATTTTAACCCTCAAACTTTCT

Found at i:1081 original size:29 final size:29

Alignment explanation


    Indices: 1033--1109  Score: 104
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       1023 TCGTACCTCC

                                          
       1033 AAAAATCACATTTTTACCCCCAAACTTCTT
          1 AAAAATCACATTTTTACCCCCAAACTTC-T

                  *              *       
       1063 AAAAATTACATTTTT-CCCCCGAACTTCT
          1 AAAAATCACATTTTTACCCCCAAACTTCT

                                
       1091 AAAAATCACCA-TTTTACCC
          1 AAAAATCA-CATTTTTACCC

       1110 TTGAGCATTC


Statistics
Matches: 42,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  28   12  0.29
  29   16  0.38
  30   14  0.33

ACGTcount: A:0.36, C:0.30, G:0.01, T:0.32


Consensus pattern (29 bp):   
AAAAATCACATTTTTACCCCCAAACTTCT
Done.