Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003778.1 Kokia drynarioides strain JFW-HI SEQ_116756, 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: 2762
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1327 original size:59 final size:59

Alignment explanation


    Indices: 1192--1326  Score: 186
    Period size: 59  Copynumber: 2.3  Consensus size: 59

       1182 AAAACGACGT

                               *                                        
       1192 GGTAAAATGGTAATTTTTAAAAAAATCGAGGTAAAAAATAGAATTTTTTGGAAGTTCGGA
          1 GGTAAAATGGTAATTTTTAGAAAAATCGAGGTAAAAAATAGAA-TTTTTGGAAGTTCGGA

                                            *      *                   *
       1252 GGT-AAATGGTAATTTTTAGAAAAATCGAGGTCAAAAATGGAA-TTTTGGAATGTTCGGG
          1 GGTAAAATGGTAATTTTTAGAAAAATCGAGGTAAAAAATAGAATTTTTGGAA-GTTCGGA

                    *         
       1310 GGTAAAATTG-AATTTTT
          1 GGTAAAATGGTAATTTTT

       1327 TTAGAAAGTT


Statistics
Matches: 68,  Mismatches: 5, Indels: 6
        0.86            0.06        0.08

Matches are distributed among these distances:
  57    8  0.12
  58   16  0.24
  59   41  0.60
  60    3  0.04

ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33


Consensus pattern (59 bp):   
GGTAAAATGGTAATTTTTAGAAAAATCGAGGTAAAAAATAGAATTTTTGGAAGTTCGGA

Found at i:1379 original size:30 final size:29

Alignment explanation


    Indices: 1325--1401  Score: 93
    Period size: 30  Copynumber: 2.6  Consensus size: 29

       1315 AATTGAATTT

                                         
       1325 TTTTAGAAAGTTTAGGGTTAAAAATATAA
          1 TTTTAGAAAGTTTAGGGTTAAAAATATAA

                                 *         
       1354 TTTTAGAGAAGTTTGAGGG-TCAAAATATAA
          1 TTTTAGA-AAGTTT-AGGGTTAAAAATATAA

                 *  *         
       1384 TTTTTGGATAGTTTAGGG
          1 -TTTTAGAAAGTTTAGGG

       1402 ACCTTTAGGG


Statistics
Matches: 42,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  29   11  0.26
  30   21  0.50
  31   10  0.24

ACGTcount: A:0.36, C:0.01, G:0.23, T:0.39


Consensus pattern (29 bp):   
TTTTAGAAAGTTTAGGGTTAAAAATATAA

Found at i:2367 original size:59 final size:59

Alignment explanation


    Indices: 2293--2540  Score: 296
    Period size: 58  Copynumber: 4.3  Consensus size: 59

       2283 ATCTATTTTC

                                                         *             
       2293 AAAAT-GTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTCGAAGTTCGAGGGT
          1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT

                                                 *       *        *      
       2351 AAAATGGTAATTTTTGG-AAAATC-ATGGTCAAAAATTGAATTTTGGGAAGTT-TAGGGGT
          1 AAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGT

                                         *                               
       2409 AAAATGGT-ATTTTTGGAAAAATCGAGGTAAAAAATGGAATTTTTTGGAAGTTCG-GAGGT
          1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAA-TTTTTGGAAGTTCGAG-GGT

                           *       * *                  * *     *      
       2468 -AAATGGTAATTTTTAGAAAAATTGGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGT
          1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT

                            
       2526 AAAAAT-GTAATTTTT
          1 -AAAATGGTAATTTTT

       2541 TTGAAAATTT


Statistics
Matches: 163,  Mismatches: 15, Indels: 23
        0.81            0.07        0.11

Matches are distributed among these distances:
  57   10  0.06
  58   86  0.53
  59   63  0.39
  60    4  0.02

ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33


Consensus pattern (59 bp):   
AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT

Found at i:2512 original size:29 final size:29

Alignment explanation


    Indices: 2468--2539  Score: 83
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       2458 GTTCGGAGGT

                                            
       2468 AAATGGTAATTTTTAGAAAAATTG-GGGTCAA
          1 AAATGG-AA-TTTTAGAAAAATTGAGGGT-AA

                             **          
       2499 AAATGGAATTTTAGAAAGTTTGAGGGTAA
          1 AAATGGAATTTTAGAAAAATTGAGGGTAA

                 *      
       2528 AAATGTAATTTT
          1 AAATGGAATTTT

       2540 TTTGAAAATT


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  29   25  0.68
  30    6  0.16
  31    6  0.16

ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35


Consensus pattern (29 bp):   
AAATGGAATTTTAGAAAAATTGAGGGTAA

Found at i:2561 original size:31 final size:30

Alignment explanation


    Indices: 2468--2570  Score: 102
    Period size: 31  Copynumber: 3.4  Consensus size: 30

       2458 GTTCGGAGGT

                                *  *    *  
       2468 AAATGGTAATTTTTAGAAAAATTGGGGTCAA
          1 AAAT-GTAATTTTTAGAAAATTTAGGGTTAA

                 *            *            
       2499 AAATGGAA-TTTTAGAAAGTTTGAGGG-TAA
          1 AAATGTAATTTTTAGAAAATTT-AGGGTTAA

                          *                
       2528 AAATGTAATTTTTTTGAAAATTTAGGGTTAA
          1 AAATGTAA-TTTTTAGAAAATTTAGGGTTAA

                *       
       2559 AAATATAATTTT
          1 AAATGTAATTTT

       2571 GGAGAATTTT


Statistics
Matches: 59,  Mismatches: 9, Indels: 9
        0.77            0.12        0.12

Matches are distributed among these distances:
  29   20  0.34
  30   14  0.24
  31   25  0.42

ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38


Consensus pattern (30 bp):   
AAATGTAATTTTTAGAAAATTTAGGGTTAA
Done.