Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010187.1 Kokia drynarioides strain JFW-HI SEQ_124998, 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: 22441
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:149 original size:25 final size:25

Alignment explanation


    Indices: 99--168  Score: 65
    Period size: 25  Copynumber: 2.8  Consensus size: 25

         89 TACTTTTTTT

                           *           
         99 TTTCTCCTTCTTCCCCTTC-TTC-TTC
          1 TTTCTCCTTCTT--CTTTCTTTCATTC

                                      
        124 -TTCTTCCTTCTTCTTTCTTTCATTC
          1 TTTC-TCCTTCTTCTTTCTTTCATTC

                  *  *          
        149 TTTCTCTTTTTTCTTTCTTT
          1 TTTCTCCTTCTTCTTTCTTT

        169 TTTCCTTCAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  23    4  0.11
  24    6  0.16
  25   25  0.66
  26    3  0.08

ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66


Consensus pattern (25 bp):   
TTTCTCCTTCTTCTTTCTTTCATTC

Found at i:1096 original size:30 final size:30

Alignment explanation


    Indices: 1043--1101  Score: 75
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1033 AAACCTTGAT

                                    *     
       1043 ATTTAAATAAAAACTTTCAAATAATTCAAA
          1 ATTTAAATAAAAACTTTCAAATAACTCAAA

                    * *                   
       1073 ATTTAAATGATAACTTTTC-AATAACTCAA
          1 ATTTAAATAAAAAC-TTTCAAATAACTCAA

       1102 CGATCATTTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  30   21  0.84
  31    4  0.16

ACGTcount: A:0.51, C:0.12, G:0.02, T:0.36


Consensus pattern (30 bp):   
ATTTAAATAAAAACTTTCAAATAACTCAAA

Found at i:1900 original size:2 final size:2

Alignment explanation


    Indices: 1893--1920  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1883 CAGAACAGGT

                                                     
       1893 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC

       1921 GTGAGATATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:14607 original size:29 final size:27

Alignment explanation


    Indices: 14575--14641  Score: 71
    Period size: 29  Copynumber: 2.4  Consensus size: 27

      14565 AATTTCCATC

                               *   * *   
      14575 AAATAAAAAAAGTGAGAATTATACTCAAA
          1 AAATAAAAAAAG-GAGAATCA-AATAAAA

                          *             
      14604 AAATAAAGAAAAGGGGAATCAAATAAAA
          1 AAATAAA-AAAAGGAGAATCAAATAAAA

                      
      14632 AAATAAAAAA
          1 AAATAAAAAA

      14642 CATATAGCAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  27    3  0.09
  28   12  0.36
  29   13  0.39
  30    5  0.15

ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15


Consensus pattern (27 bp):   
AAATAAAAAAAGGAGAATCAAATAAAA

Found at i:17978 original size:19 final size:19

Alignment explanation


    Indices: 17954--17993  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      17944 ATGGCCATGT

                               
      17954 AAGCATCACCTTCGACTTC
          1 AAGCATCACCTTCGACTTC

                               
      17973 AAGCATCACCTTCGACTTC
          1 AAGCATCACCTTCGACTTC

              
      17992 AA
          1 AA

      17994 CGTATTGGAA


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

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.30, C:0.35, G:0.10, T:0.25


Consensus pattern (19 bp):   
AAGCATCACCTTCGACTTC

Found at i:22388 original size:23 final size:23

Alignment explanation


    Indices: 22362--22441  Score: 97
    Period size: 23  Copynumber: 3.5  Consensus size: 23

      22352 AGTGCAGGGC

                           *       
      22362 AACAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

                *    *         *   
      22385 AACAAAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACAAAGTGCTA

            **                     
      22408 GTCAGAGAGCACACAAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *         
      22431 ATCAGAGAGCA
          1 AACAGAGAGCA


Statistics
Matches: 47,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   47  1.00

ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11


Consensus pattern (23 bp):   
AACAGAGAGCACACAAAGTGCTA

Done.