Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005685.1 Kokia drynarioides strain JFW-HI SEQ_119880, 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: 11478
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Found at i:2523 original size:16 final size:16

Alignment explanation


    Indices: 2499--2532  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2489 GCTCTGCTGA

                            
       2499 ATAGAGTCTTGAGTTT
          1 ATAGAGTCTTGAGTTT

                *           
       2515 ATAGGGTCTTGAGTTT
          1 ATAGAGTCTTGAGTTT

              
       2531 AT
          1 AT

       2533 GGCAGCTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44


Consensus pattern (16 bp):   
ATAGAGTCTTGAGTTT

Found at i:4020 original size:30 final size:30

Alignment explanation


    Indices: 3979--4181  Score: 187
    Period size: 30  Copynumber: 6.8  Consensus size: 30

       3969 AAAAATGAAA

                *         *          *     
       3979 TTTTAGAAAATTTGGGGGTC-AAATTTAAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATAT-AAT

                         *                
       4009 TTTTGGAAAATTTAAGGGTCAAAATATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                 *      *                 
       4039 TTTTGAAAAATTAGAGGGTCAAAATATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                      *           *      * 
       4069 TTTTGGAAATTTTTG-GGGTCACAATATATT
          1 TTTTGGAAA-ATTTGAGGGTCAAAATATAAT

                *       *  *       *      
       4099 TTTTAGAAAATTCGAAGGTCAAACTATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                     *  *  * *            
       4129 TTTTGGAAAGTTCGAAGTTCAAAATATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                *    *              
       4159 TTTTTGAAAGTTTG-GGGATCAAA
          1 TTTTGGAAAATTTGAGGG-TCAAA

       4182 TTTTAAATAA


Statistics
Matches: 142,  Mismatches: 27, Indels: 8
        0.80            0.15        0.05

Matches are distributed among these distances:
  29    4  0.03
  30  130  0.92
  31    8  0.06

ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38


Consensus pattern (30 bp):   
TTTTGGAAAATTTGAGGGTCAAAATATAAT

Found at i:4127 original size:90 final size:89

Alignment explanation


    Indices: 4008--4175  Score: 221
    Period size: 90  Copynumber: 1.9  Consensus size: 89

       3998 CAAATTTAAA

                 *       *                                *                  
       4008 TTTTTGGAAAATTTAAGGGTCAAAATATAATTTTTGAAAAATTAGAGGGTCAAAATATAATTTTT
          1 TTTTTAGAAAATTGAAGGGTCAAAATATAATTTTTGAAAAATTAGAAGGTCAAAATATAATTTTT

                  *                  
       4073 GGAAATTTTTGGGGTCACAATATAT
         66 GGAAA-GTTTGGGGTCACAATATAT

                                     *           *   *  *    *               
       4098 TTTTTAGAAAATTCGAA-GGTCAAACTATAATTTTTGGAAAGTTCGAAGTTCAAAATATAATTTT
          1 TTTTTAGAAAATT-GAAGGGTCAAAATATAATTTTTGAAAAATTAGAAGGTCAAAATATAATTTT

             *            
       4162 TTGAAAGTTTGGGG
         65 TGGAAAGTTTGGGG

       4176 ATCAAATTTT


Statistics
Matches: 67,  Mismatches: 10, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  89    7  0.10
  90   58  0.87
  91    2  0.03

ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39


Consensus pattern (89 bp):   
TTTTTAGAAAATTGAAGGGTCAAAATATAATTTTTGAAAAATTAGAAGGTCAAAATATAATTTTT
GGAAAGTTTGGGGTCACAATATAT

Found at i:10098 original size:17 final size:17

Alignment explanation


    Indices: 10076--10113  Score: 76
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      10066 CACAAAGAGT

                             
      10076 CTGTTTCTTTATATGGA
          1 CTGTTTCTTTATATGGA

                             
      10093 CTGTTTCTTTATATGGA
          1 CTGTTTCTTTATATGGA

                
      10110 CTGT
          1 CTGT

      10114 CCTACAGCAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53


Consensus pattern (17 bp):   
CTGTTTCTTTATATGGA
Done.