Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011415.1 Kokia drynarioides strain JFW-HI SEQ_126398, 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: 7735
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:612 original size:41 final size:41

Alignment explanation


    Indices: 555--691  Score: 170
    Period size: 41  Copynumber: 3.3  Consensus size: 41

        545 GGTGCTTATG

                                *       *        *     
        555 ATTGCTCTGACCTTTAGCGGTGCCTT-CTCAAAAGC-ATCGCT
          1 ATTGCTCTGACCTTTAGCGGCG-CTTGCCCAAAAGCGCT-GCT

                    *                     *          
        596 ATTGCTCTAACCTTTAGCGGCGCTTGCCCATAAGCGCTGCT
          1 ATTGCTCTGACCTTTAGCGGCGCTTGCCCAAAAGCGCTGCT

                                          *      **  
        637 ATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCACT
          1 ATTGCTCTGACCTTTAGCGGCGCTTGCCCAAAAGCGCTGCT

                          
        678 ATTGCTCTGACCTT
          1 ATTGCTCTGACCTT

        692 ATTGCTCTAC


Statistics
Matches: 86,  Mismatches: 8, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  40    3  0.03
  41   82  0.95
  42    1  0.01

ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31


Consensus pattern (41 bp):   
ATTGCTCTGACCTTTAGCGGCGCTTGCCCAAAAGCGCTGCT

Found at i:5213 original size:41 final size:40

Alignment explanation


    Indices: 5170--5371  Score: 226
    Period size: 41  Copynumber: 4.9  Consensus size: 40

       5160 GAGAAAGTGC

                      *          *                  *
       5170 CGCTAATGCTATGACCTTTAGTGGCGCTTTCCAATAAACGC
          1 CGCTAATGCTCTGACCTTTAGCGGCGCTTTCC-ATAAACGT

                         *        *                  
       5211 CGCTAATGCTCTGGCCTTTAGCAGCGCTTTTCCATAAACGT
          1 CGCTAATGCTCTGACCTTTAGCGGCGC-TTTCCATAAACGT

                                   **                
       5252 CGCTAATGCTCTGACCTTTAGCGATGCTTCTCCATAAACGT
          1 CGCTAATGCTCTGACCTTTAGCGGCGCTT-TCCATAAACGT

            *         * *                             
       5293 AGCTAATGCTTTAACCTTTAG-GGACGCTTTTCCATAAACGT
          1 CGCTAATGCTCTGACCTTTAGCGG-CGC-TTTCCATAAACGT

            *                 *    *              
       5334 AGCTAATGCTCTGACCTTGAGCGACGCTTTCCCATAAA
          1 CGCTAATGCTCTGACCTTTAGCGGCGCTTT-CCATAAA

       5372 TCCCGTAAAA


Statistics
Matches: 137,  Mismatches: 18, Indels: 12
        0.82            0.11        0.07

Matches are distributed among these distances:
  40    6  0.04
  41  123  0.90
  42    8  0.06

ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31


Consensus pattern (40 bp):   
CGCTAATGCTCTGACCTTTAGCGGCGCTTTCCATAAACGT

Found at i:5289 original size:82 final size:81

Alignment explanation


    Indices: 5170--5371  Score: 253
    Period size: 82  Copynumber: 2.5  Consensus size: 81

       5160 GAGAAAGTGC

                      *          * *                 *           **          
       5170 CGCTAATGCTATGACCTTTAGTGGCGCTTTCCAATAAACGCCGCTAATGCTCTGGCCTTTAGCAG
          1 CGCTAATGCTCTGACCTTTAGCGACGCTTTCC-ATAAACGCAGCTAATGCTCTAACCTTTAG-AG

                              
       5235 -CGCTTTTCCATAAACGT
         64 ACGCTTTTCCATAAACGT

                                    *               *          *          *  
       5252 CGCTAATGCTCTGACCTTTAGCGATGCTTCTCCATAAACGTAGCTAATGCTTTAACCTTTAGGGA
          1 CGCTAATGCTCTGACCTTTAGCGACGCTT-TCCATAAACGCAGCTAATGCTCTAACCTTTAGAGA

                             
       5317 CGCTTTTCCATAAACGT
         65 CGCTTTTCCATAAACGT

            *                 *                   
       5334 AGCTAATGCTCTGACCTTGAGCGACGCTTTCCCATAAA
          1 CGCTAATGCTCTGACCTTTAGCGACGCTTT-CCATAAA

       5372 TCCCGTAAAA


Statistics
Matches: 104,  Mismatches: 13, Indels: 6
        0.85            0.11        0.05

Matches are distributed among these distances:
  81    2  0.02
  82   99  0.95
  83    3  0.03

ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31


Consensus pattern (81 bp):   
CGCTAATGCTCTGACCTTTAGCGACGCTTTCCATAAACGCAGCTAATGCTCTAACCTTTAGAGAC
GCTTTTCCATAAACGT

Found at i:5525 original size:41 final size:41

Alignment explanation


    Indices: 5480--5595  Score: 144
    Period size: 41  Copynumber: 2.9  Consensus size: 41

       5470 CTTTAGCTGT

                   *        *                        
       5480 TTTTTCCTATAAATGCTGCTATTGCTTTACCTTTTGCGACG
          1 TTTTTCCAATAAATGCCGCTATTGCTTTACCTTTTGCGACG

                                                  ** 
       5521 TTTTTCCAATAAATGCCGCTATTGCTTTACCTTTTGCGGGG
          1 TTTTTCCAATAAATGCCGCTATTGCTTTACCTTTTGCGACG

               * **      *               *     
       5562 TTTATGTAA-AAACGCCGCTATTGCTTTATCTTTT
          1 TTTTTCCAATAAATGCCGCTATTGCTTTACCTTTT

       5596 ACGGTTTTTC


Statistics
Matches: 66,  Mismatches: 9, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  40   23  0.35
  41   43  0.65

ACGTcount: A:0.19, C:0.21, G:0.16, T:0.45


Consensus pattern (41 bp):   
TTTTTCCAATAAATGCCGCTATTGCTTTACCTTTTGCGACG

Done.