Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005228.1 Kokia drynarioides strain JFW-HI SEQ_119111, 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: 2782
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:595 original size:29 final size:29

Alignment explanation


    Indices: 563--651  Score: 81
    Period size: 29  Copynumber: 3.0  Consensus size: 29

        553 TTGATTTAAT

                                         
        563 GTGCAATTATATACATGAACTTTAATTTG
          1 GTGCAATTATATACATGAACTTTAATTTG

                       *  *    *           
        592 GTGCAATTATACACGTGAATTTCTAATTATG
          1 GTGCAATTATATACATGAACTT-TAATT-TG

              *      *      *             
        623 GTTCACA-TGTATACACGAAACTTTAATTT
          1 GTGCA-ATTATATACATG-AACTTTAATTT

        652 TGATTTAATT


Statistics
Matches: 47,  Mismatches: 9, Indels: 7
        0.75            0.14        0.11

Matches are distributed among these distances:
  29   19  0.40
  30    6  0.13
  31   17  0.36
  32    5  0.11

ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39


Consensus pattern (29 bp):   
GTGCAATTATATACATGAACTTTAATTTG

Found at i:1034 original size:41 final size:41

Alignment explanation


    Indices: 958--1134  Score: 196
    Period size: 41  Copynumber: 4.3  Consensus size: 41

        948 CTATTGCTTA

                       *                ** *          *
        958 ACCTTTAGCGGTGTTTTTCCT-ATAAACACCACTAATGCTCTT
          1 ACCTTTAGCGGCG--TTTCCTCATAAACGTCGCTAATGCTCTG

                     *      *                         
       1000 ACCTTTAGCAGCGTTTTCT-AGTAAACGTCGCTAATGCTCTG
          1 ACCTTTAGCGGCGTTTCCTCA-TAAACGTCGCTAATGCTCTG

                    *  *                *            
       1041 ACCTTTAGTGGTGTTTCCTCATAAACGTTGCTAATGCTCTG
          1 ACCTTTAGCGGCGTTTCCTCATAAACGTCGCTAATGCTCTG

                                  *    *             
       1082 ACCTTTAGCGGCGTTTCCTCATTAACGCCGCTAATGCTCTG
          1 ACCTTTAGCGGCGTTTCCTCATAAACGTCGCTAATGCTCTG

              *         
       1123 ACTTTTAGCGGC
          1 ACCTTTAGCGGC

       1135 ATTTTTCCTA


Statistics
Matches: 115,  Mismatches: 18, Indels: 5
        0.83            0.13        0.04

Matches are distributed among these distances:
  40    6  0.05
  41   97  0.84
  42   12  0.10

ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36


Consensus pattern (41 bp):   
ACCTTTAGCGGCGTTTCCTCATAAACGTCGCTAATGCTCTG

Found at i:1168 original size:82 final size:81

Alignment explanation


    Indices: 945--1179  Score: 219
    Period size: 82  Copynumber: 2.9  Consensus size: 81

        935 TGGGAAAATC

                  *      *                      *        *                   
        945 CCGCTATTGCT-TAACCTTTAGCGGTGTTTTTCCTATAAACA-CCACTAATGCTCTTACCTTTAG
          1 CCGCTAATGCTCTGACCTTTAGC-G-GTTTTTCCTACAAA-AGCCGCTAATGCTCTTACCTTTAG

             *      *          
       1008 CAGCGTTTTCTAGTAAACG
         63 CGGCGTTTCCTAGTAAACG

            *                     *   *               **           *         
       1027 TCGCTAATGCTCTGACCTTTAGTGGTGTTTCCT-CATAAACGTTGCTAATGCTCTGACCTTTAGC
          1 CCGCTAATGCTCTGACCTTTAGCGGTTTTTCCTACA-AAA-GCCGCTAATGCTCTTACCTTTAGC

                          *    
       1091 GGCGTTTCCTCA-TTAACG
         64 GGCGTTTCCT-AGTAAACG

                            *                               *             *  
       1109 CCGCTAATGCTCTGACTTTTAGCGGCATTTTTCCTACAAAAGCCGCTATTGCT-TTACCTTTTGC
          1 CCGCTAATGCTCTGACCTTTAGCGG--TTTTTCCTACAAAAGCCGCTAATGCTCTTACCTTTAGC

                   
       1173 GGCGTTT
         64 GGCGTTT

       1180 TTAAAAAAAA


Statistics
Matches: 123,  Mismatches: 22, Indels: 16
        0.76            0.14        0.10

Matches are distributed among these distances:
  80    2  0.02
  81   10  0.08
  82   80  0.65
  83   19  0.15
  84   10  0.08
  85    2  0.02

ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37


Consensus pattern (81 bp):   
CCGCTAATGCTCTGACCTTTAGCGGTTTTTCCTACAAAAGCCGCTAATGCTCTTACCTTTAGCGG
CGTTTCCTAGTAAACG

Found at i:1228 original size:40 final size:40

Alignment explanation


    Indices: 1146--1221  Score: 134
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       1136 TTTTTCCTAC

                  *                           *     
       1146 AAAAGCCGCTATTGCTTTACCTTTTGCGGCGTTTTTAAAA
          1 AAAAGCAGCTATTGCTTTACCTTTTGCGGCGTTTATAAAA

                                                
       1186 AAAAGCAGCTATTGCTTTACCTTTTGCGGCGTTTAT
          1 AAAAGCAGCTATTGCTTTACCTTTTGCGGCGTTTAT

       1222 GGAAAAACGC


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  40   34  1.00

ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38


Consensus pattern (40 bp):   
AAAAGCAGCTATTGCTTTACCTTTTGCGGCGTTTATAAAA

Found at i:2133 original size:15 final size:14

Alignment explanation


    Indices: 2109--2160  Score: 52
    Period size: 16  Copynumber: 3.5  Consensus size: 14

       2099 TCAGAATAAC

                          
       2109 ACAA-TTGTTCTAA
          1 ACAAGTTGTTCTAA

                        *  
       2122 TACAAGTTGTTCCAA
          1 -ACAAGTTGTTCTAA

                            
       2137 ACAATGATTGTTCTAA
          1 ACAA-G-TTGTTCTAA

                    
       2153 ACATAGTT
          1 ACA-AGTT

       2161 ATTCCTGAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 7
        0.78            0.05        0.17

Matches are distributed among these distances:
  14    8  0.25
  15   11  0.34
  16   12  0.38
  17    1  0.03

ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37


Consensus pattern (14 bp):   
ACAAGTTGTTCTAA
Done.