Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001157.1 Kokia drynarioides strain JFW-HI SEQ_112470, 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: 1981
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37


Found at i:27 original size:18 final size:18

Alignment explanation


    Indices: 4--47  Score: 63
    Period size: 17  Copynumber: 2.5  Consensus size: 18

          1 AAT

                         *    
          4 AAATTTAAATTTTTAAAC
          1 AAATTTAAATTTTAAAAC

                             *
         22 AAATTT-AATTTTAAAAT
          1 AAATTTAAATTTTAAAAC

                     
         39 AAATTTAAA
          1 AAATTTAAA

         48 GGGAGTTTGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  17   15  0.65
  18    8  0.35

ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43


Consensus pattern (18 bp):   
AAATTTAAATTTTAAAAC

Found at i:486 original size:30 final size:30

Alignment explanation


    Indices: 429--487  Score: 73
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        419 TATCACTTGT

                     *        * *         
        429 TTTGATTCATTTCTCTGTGTTTCATCAGGA
          1 TTTGATTCACTTCTCTGTATCTCATCAGGA

                *                 *      
        459 TTTGGTTCACTTCTCTGTATCTGATCAGG
          1 TTTGATTCACTTCTCTGTATCTCATCAGG

        488 GAGCTAACCA


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47


Consensus pattern (30 bp):   
TTTGATTCACTTCTCTGTATCTCATCAGGA

Found at i:890 original size:201 final size:204

Alignment explanation


    Indices: 458--961  Score: 664
    Period size: 201  Copynumber: 2.5  Consensus size: 204

        448 TTTCATCAGG

                            *      *      *         *     *                  
        458 ATTTGGTTCACTTCTCTGTATCTGATCAGGGAGCTAACCACTTTATGGCTTCGACCTACTTCTCA
          1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTACTTCTCA

             *                 *                  **                         
        523 GCGTCTCATCAGGAAGCTGGGGTTCAAAGA-TTTGCTCGTTTTGAGCCTCGTTTAGGTCTTCTTC
         65 GTGTCTCATCAGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTC

                                        *               *                    
        587 TCAGTGCTTCATCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCTCATC
        130 TCAGTGCTTCATCAGGAAGATGATTACAGCGCTGTTTGTTTCAACTCGCTCCTCCGTATCTCATC

            * *       
        652 CGGAAGACGA
        195 AGAAAGACGA

                                *            *         *                     
        662 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTTTGTTGCTTCGACCTACTTCTCAG
          1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAG

                                                                 *           
        727 TGTCTCATCAGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
         66 TGTCTCATCAGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTCT

            *                                                  *  **         
        792 TAGTG-TCTCATCAGGAAGATGA-T-C-GCG-TCGTTTGTTTCAACTCGCTTCTTTGTATCTCAT
        131 CAGTGCT-TCATCAGGAAGATGATTACAGCGCT-GTTTGTTTCAACTCGCTCCTCCGTATCTCAT

                   *   
        852 CAGAAAGGCGA
        194 CAGAAAGACGA

                                        *                     *     *        
        863 ATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAG
          1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAG

             *                        *         
        928 TATCTTC-TCAGGAAGCT-AGGGTTCGAAGATTTTG
         66 TGTC-TCATCAGGAAGCTGA-GGTTCAAAGATTTTG

        962 TTTGCTTTAA


Statistics
Matches: 265,  Mismatches: 30, Indels: 13
        0.86            0.10        0.04

Matches are distributed among these distances:
 200    2  0.01
 201  123  0.46
 202    3  0.01
 203   52  0.20
 204   85  0.32

ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36


Consensus pattern (204 bp):   
ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAG
TGTCTCATCAGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTCT
CAGTGCTTCATCAGGAAGATGATTACAGCGCTGTTTGTTTCAACTCGCTCCTCCGTATCTCATCA
GAAAGACGA
Done.