Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005698.1 Kokia drynarioides strain JFW-HI SEQ_119908, 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: 6083
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35


Found at i:1151 original size:24 final size:24

Alignment explanation


    Indices: 1113--1229  Score: 117
    Period size: 24  Copynumber: 4.9  Consensus size: 24

       1103 AATGTTTCTT

                   *       *      * 
       1113 ATATTAGTTGGCGAGAGTAAACAC
          1 ATATTAGCTGGCGAGCGTAAACGC

                      *          * *
       1137 ATATTAGCTGACGAGCGTAAATGT
          1 ATATTAGCTGGCGAGCGTAAACGC

                   *       *     *  
       1161 ATATTAGATGGCGAGAGTAAATGC
          1 ATATTAGCTGGCGAGCGTAAACGC

                                   *
       1185 ATATTAGCTGGCGAGCGTAAACGT
          1 ATATTAGCTGGCGAGCGTAAACGC

              *       **         
       1209 ATCTTAGCTGATGAGCGTAAA
          1 ATATTAGCTGGCGAGCGTAAA

       1230 TGTACTGAAC


Statistics
Matches: 76,  Mismatches: 17, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   76  1.00

ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26


Consensus pattern (24 bp):   
ATATTAGCTGGCGAGCGTAAACGC

Found at i:1179 original size:48 final size:48

Alignment explanation


    Indices: 1112--1215  Score: 154
    Period size: 48  Copynumber: 2.2  Consensus size: 48

       1102 CAATGTTTCT

                    *                                     * 
       1112 TATATTAGTTGGCGAGAGTAAACACATATTAGCTGACGAGCGTAAATG
          1 TATATTAGATGGCGAGAGTAAACACATATTAGCTGACGAGCGTAAACG

                                  **           *            
       1160 TATATTAGATGGCGAGAGTAAATGCATATTAGCTGGCGAGCGTAAACG
          1 TATATTAGATGGCGAGAGTAAACACATATTAGCTGACGAGCGTAAACG

               *    
       1208 TATCTTAG
          1 TATATTAG

       1216 CTGATGAGCG


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  48   50  1.00

ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28


Consensus pattern (48 bp):   
TATATTAGATGGCGAGAGTAAACACATATTAGCTGACGAGCGTAAACG

Found at i:1229 original size:48 final size:48

Alignment explanation


    Indices: 1112--1231  Score: 141
    Period size: 48  Copynumber: 2.5  Consensus size: 48

       1102 CAATGTTTCT

                    *  *          **                      * 
       1112 TATATTAGTTGGCGAGAGTAAACACATATTAGCTGACGAGCGTAAATG
          1 TATATTAGATGACGAGAGTAAATGCATATTAGCTGACGAGCGTAAACG

                       *                       *            
       1160 TATATTAGATGGCGAGAGTAAATGCATATTAGCTGGCGAGCGTAAACG
          1 TATATTAGATGACGAGAGTAAATGCATATTAGCTGACGAGCGTAAACG

               *    *   *   *       
       1208 TATCTTAGCTGATGAGCGTAAATG
          1 TATATTAGATGACGAGAGTAAATG

       1232 TACTGAACTT


Statistics
Matches: 62,  Mismatches: 10, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  48   62  1.00

ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28


Consensus pattern (48 bp):   
TATATTAGATGACGAGAGTAAATGCATATTAGCTGACGAGCGTAAACG

Found at i:1657 original size:12 final size:12

Alignment explanation


    Indices: 1640--1664  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       1630 AATTATTACA

                        
       1640 TGAAATTATATG
          1 TGAAATTATATG

                        
       1652 TGAAATTATATG
          1 TGAAATTATATG

             
       1664 T
          1 T

       1665 ATAAATTGAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44


Consensus pattern (12 bp):   
TGAAATTATATG

Found at i:2808 original size:30 final size:29

Alignment explanation


    Indices: 2768--2827  Score: 111
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       2758 AAAAATTGTT

                                         
       2768 TATAATAGGAATGTAGTATAATATATATA
          1 TATAATAGGAATGTAGTATAATATATATA

                                          
       2797 TATATATAGGAATGTAGTATAATATATATA
          1 TATA-ATAGGAATGTAGTATAATATATATA

             
       2827 T
          1 T

       2828 TGAATAAATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  29    4  0.13
  30   26  0.87

ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40


Consensus pattern (29 bp):   
TATAATAGGAATGTAGTATAATATATATA
Done.