Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006589.1 Kokia drynarioides strain JFW-HI SEQ_121177, 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: 20205
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:9165 original size:40 final size:40

Alignment explanation


    Indices: 9108--9190  Score: 121
    Period size: 40  Copynumber: 2.1  Consensus size: 40

       9098 AAGAAGTGCT

                                                 *  
       9108 CTGTTTGCACATCTATGCCCCTATATACACTTCGGTGTCC
          1 CTGTTTGCACATCTATGCCCCTATATACACTTCGGTGCCC

                        *       *   * *             
       9148 CTGTTTGCACATTTATGCCCTTATTTGCACTTCGGTGCCC
          1 CTGTTTGCACATCTATGCCCCTATATACACTTCGGTGCCC

               
       9188 CTG
          1 CTG

       9191 ACTGCACGTA


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  40   38  1.00

ACGTcount: A:0.14, C:0.31, G:0.17, T:0.37


Consensus pattern (40 bp):   
CTGTTTGCACATCTATGCCCCTATATACACTTCGGTGCCC

Found at i:14176 original size:17 final size:18

Alignment explanation


    Indices: 14138--14177  Score: 57
    Period size: 17  Copynumber: 2.3  Consensus size: 18

      14128 GCAAATGTGT

                   *          
      14138 TGACAAATAAAATGTAGA
          1 TGACAAACAAAATGTAGA

                              
      14156 -GACAAACAAAATGTA-A
          1 TGACAAACAAAATGTAGA

                  
      14172 TGACAA
          1 TGACAA

      14178 CTAAATGAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  16    1  0.05
  17   19  0.95

ACGTcount: A:0.57, C:0.10, G:0.15, T:0.17


Consensus pattern (18 bp):   
TGACAAACAAAATGTAGA

Found at i:17312 original size:12 final size:12

Alignment explanation


    Indices: 17275--17312  Score: 60
    Period size: 12  Copynumber: 3.2  Consensus size: 12

      17265 CTTTTCTTCA

                        
      17275 TTCTT-CTTCTC
          1 TTCTTCCTTCTC

              *         
      17286 TTATTCCTTCTC
          1 TTCTTCCTTCTC

                        
      17298 TTCTTCCTTCTC
          1 TTCTTCCTTCTC

               
      17310 TTC
          1 TTC

      17313 CTCATTTTCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  11    4  0.17
  12   20  0.83

ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61


Consensus pattern (12 bp):   
TTCTTCCTTCTC

Found at i:17340 original size:18 final size:18

Alignment explanation


    Indices: 17301--17347  Score: 51
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      17291 CCTTCTCTTC

                             **
      17301 TTCCTTC-TCTTCCTCATT
          1 TTCCTTCTTC-TCCTCAAG

                              
      17319 TTCCTTCTTCTCCTCAAG
          1 TTCCTTCTTCTCCTCAAG

                 *     
      17337 TTCCTCCTTCT
          1 TTCCTTCTTCT

      17348 TAGCTATGTT


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

Matches are distributed among these distances:
  18   23  0.92
  19    2  0.08

ACGTcount: A:0.06, C:0.40, G:0.02, T:0.51


Consensus pattern (18 bp):   
TTCCTTCTTCTCCTCAAG
Done.