Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006730.1 Kokia drynarioides strain JFW-HI SEQ_121328, 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: 17412
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34


Found at i:1199 original size:19 final size:19

Alignment explanation


    Indices: 1160--1202  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       1150 TTTATATAAG

                         *     
       1160 TTTTAAAATTTAATAAATT
          1 TTTTAAAATTTAAGAAATT

                       *    *  
       1179 TTTTAAAATTTTAGAATTT
          1 TTTTAAAATTTAAGAAATT

                 
       1198 TTTTA
          1 TTTTA

       1203 GTTTATATAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58


Consensus pattern (19 bp):   
TTTTAAAATTTAAGAAATT

Found at i:1217 original size:19 final size:19

Alignment explanation


    Indices: 1150--1217  Score: 54
    Period size: 18  Copynumber: 3.7  Consensus size: 19

       1140 TTTATTTTAG

                           *   
       1150 TTTATATAAG-TTTTAAAA
          1 TTTATATAAGTTTTTTAAA

                     *          
       1168 TTTA-ATAAATTTTTTAAAA
          1 TTTATATAAGTTTTTT-AAA

                  *         * *
       1187 TTT-TAGAA-TTTTTTTAG
          1 TTTATATAAGTTTTTTAAA

                          
       1204 TTTATATAAGTTTT
          1 TTTATATAAGTTTT

       1218 AAAATAATCG


Statistics
Matches: 39,  Mismatches: 6, Indels: 9
        0.72            0.11        0.17

Matches are distributed among these distances:
  17    8  0.21
  18   18  0.46
  19   13  0.33

ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57


Consensus pattern (19 bp):   
TTTATATAAGTTTTTTAAA

Found at i:1433 original size:41 final size:41

Alignment explanation


    Indices: 1383--1501  Score: 184
    Period size: 41  Copynumber: 2.9  Consensus size: 41

       1373 TGCTTGCCTG

                *                          *         
       1383 TAAGTGTCGCTATTGCTCTGACCTTTAGCGGTGTTTTTCCA
          1 TAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTTCCA

                             *    *          *       
       1424 TAAGCGTCGCTATTGCTTTGACTTTTAGCGGCGCTTTTCCA
          1 TAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTTCCA

                                      *          
       1465 TAAGCGTCGCTATTGCTCTGACCTTTTGCGGCGTTTT
          1 TAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTT

       1502 CTGTCCAAAC


Statistics
Matches: 69,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  41   69  1.00

ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40


Consensus pattern (41 bp):   
TAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTTCCA

Found at i:1435 original size:82 final size:82

Alignment explanation


    Indices: 1344--1501  Score: 201
    Period size: 82  Copynumber: 1.9  Consensus size: 82

       1334 CCAGATCATT

                               *         *         *    *                    
       1344 AGCGACGCTAATGCACTGATTTTTAGCGGTGC-TTGCCTGTAAGTGTCGCTATTGCTCTGACCTT
          1 AGCGACGCTAATGCACTGACTTTTAGCGGCGCTTTGCC-ATAAGCGTCGCTATTGCTCTGACCTT

                  *           
       1408 TAGCGGTGTTTTTCCATA
         65 TAGCGGCGTTTTTCCATA

                *     *   **                   *                             
       1426 AGCGTCGCTATTGCTTTGACTTTTAGCGGCGCTTTTCCATAAGCGTCGCTATTGCTCTGACCTTT
          1 AGCGACGCTAATGCACTGACTTTTAGCGGCGCTTTGCCATAAGCGTCGCTATTGCTCTGACCTTT

            *          
       1491 TGCGGCGTTTT
         66 AGCGGCGTTTT

       1502 CTGTCCAAAC


Statistics
Matches: 64,  Mismatches: 11, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  82   60  0.94
  83    4  0.06

ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38


Consensus pattern (82 bp):   
AGCGACGCTAATGCACTGACTTTTAGCGGCGCTTTGCCATAAGCGTCGCTATTGCTCTGACCTTT
AGCGGCGTTTTTCCATA

Found at i:3784 original size:157 final size:157

Alignment explanation


    Indices: 3511--3963  Score: 525
    Period size: 157  Copynumber: 2.9  Consensus size: 157

       3501 TGTAATGCTT

                  * *       *     **      *                                  
       3511 ACACGAGCTGTGAAATGGGCCTGTTCACACAAGCTATGGGTCGGGATGTTAAGCTACACGATGCT
          1 ACACGATCAGTGAAATAGGCCTACTCACACGAGCTATGGGTCGGGATGTTAAGCTACACGATG-T

            *          *            * *           *      * *                 
       3576 GA-TCACACGACCTGTGGAGAATCAGCAACAATTGCAAAATCTCAACTATCGGTAGGACATCCAA
         65 TACTCACACGAGCTGTGGAGAATCTGTAACAATTGCAAGATCTCAGCCATCGGTAGGACATCCAA

             **   *           *    * *   
       3640 -TTCAGTACCCTTATATCTTGTATGGCTC
        130 GACCAGCACCC-TATATCCTGTACGACTC

               *            *                              *                 
       3668 ACATGATCAGTGAAATCGGCCTACTCACACGAGCTATGGGTCGGGATCTTAAGCTACACGATGTT
          1 ACACGATCAGTGAAATAGGCCTACTCACACGAGCTATGGGTCGGGATGTTAAGCTACACGATGTT

                                        *          *                    **   
       3733 ACTCACACGAGCTGTGGAGAATCTGTAATAATTGCAAGACCTCAGCCATCGGTAGGACATTTAAG
         66 ACTCACACGAGCTGTGGAGAATCTGTAACAATTGCAAGATCTCAGCCATCGGTAGGACATCCAAG

                    *                  
       3798 ACCAGCACTCTATATCCTGTACGACTC
        131 ACCAGCACCCTATATCCTGTACGACTC

                    *                        * *  *    *                   * 
       3825 ACACGATCTGTGAAATAGGCCTACTCACACGAGTTTTGAGTCGAGATGTTAAGCTACACGATGCT
          1 ACACGATCAGTGAAATAGGCCTACTCACACGAGCTATGGGTCGGGATGTTAAGCTACACGATGTT

            *    *                                    *           *          
       3890 GCTCATACGAGCT-TGGAGAATCTGTAACAATTGCAAGATCTTAGCCATCGGTAAGACATCCAAG
         66 ACTCACACGAGCTGTGGAGAATCTGTAACAATTGCAAGATCTCAGCCATCGGTAGGACATCCAAG

                *     
       3954 ACCAACACCC
        131 ACCAGCACCC

       3964 AAAAACATGT


Statistics
Matches: 249,  Mismatches: 45, Indels: 5
        0.83            0.15        0.02

Matches are distributed among these distances:
 156   55  0.22
 157  188  0.76
 158    6  0.02

ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24


Consensus pattern (157 bp):   
ACACGATCAGTGAAATAGGCCTACTCACACGAGCTATGGGTCGGGATGTTAAGCTACACGATGTT
ACTCACACGAGCTGTGGAGAATCTGTAACAATTGCAAGATCTCAGCCATCGGTAGGACATCCAAG
ACCAGCACCCTATATCCTGTACGACTC
Done.