Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010807.1 Kokia drynarioides strain JFW-HI SEQ_125774, 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: 35223
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37

Warning! 53 characters in sequence are not A, C, G, or T


Found at i:3898 original size:37 final size:37

Alignment explanation


    Indices: 3855--3934  Score: 126
    Period size: 37  Copynumber: 2.2  Consensus size: 37

       3845 TGTATCTTTG

                                *            *    
       3855 TCTTTTCTTTACAGAGAATCTTTATTATTCA-TCTTCA
          1 TCTTTTCTTTACAGAGAATCATTATTATT-ATTATTCA

                                                 
       3892 TCTTTTCTTTACAGAGAATCATTATTATTATTATTCA
          1 TCTTTTCTTTACAGAGAATCATTATTATTATTATTCA

                  
       3929 TCTTTT
          1 TCTTTT

       3935 GTCTTCTAGG


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  36    1  0.03
  37   39  0.98

ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54


Consensus pattern (37 bp):   
TCTTTTCTTTACAGAGAATCATTATTATTATTATTCA

Found at i:7556 original size:21 final size:21

Alignment explanation


    Indices: 7531--7574  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       7521 AGTAGAATAG

                                 
       7531 AGATATTTGAGAATGAGTTTT
          1 AGATATTTGAGAATGAGTTTT

                                 
       7552 AGATATTTGAGAATGAGTTTT
          1 AGATATTTGAGAATGAGTTTT

              
       7573 AG
          1 AG

       7575 GAATGCTTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41


Consensus pattern (21 bp):   
AGATATTTGAGAATGAGTTTT

Found at i:19527 original size:3 final size:3

Alignment explanation


    Indices: 19519--19550  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

      19509 TTAAAAGAAA

                                                      
      19519 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
          1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC

      19551 ACTTGTAATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31


Consensus pattern (3 bp):   
GCT

Found at i:25569 original size:14 final size:14

Alignment explanation


    Indices: 25526--25570  Score: 51
    Period size: 13  Copynumber: 3.4  Consensus size: 14

      25516 TTAAATGTGC

                          
      25526 TTTTG-AAAAGTG-
          1 TTTTGAAAAAGTGA

                *         
      25538 TTTTTAAAAAGT-A
          1 TTTTGAAAAAGTGA

            *             
      25551 CTTTGAAAAAGTGA
          1 TTTTGAAAAAGTGA

                  
      25565 TTTTGA
          1 TTTTGA

      25571 TATGTACTTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  12    4  0.15
  13   16  0.62
  14    6  0.23

ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42


Consensus pattern (14 bp):   
TTTTGAAAAAGTGA

Found at i:25587 original size:26 final size:26

Alignment explanation


    Indices: 25518--25587  Score: 79
    Period size: 26  Copynumber: 2.7  Consensus size: 26

      25508 TGGTGGGTTT

                  *             *     
      25518 AAATGTGCTTTTGAAAAGTGTTTTTA
          1 AAATGTACTTTTGAAAAGTGATTTTA

               *                      *
      25544 AAAAGTAC-TTTGAAAAAGTGATTTTG
          1 AAATGTACTTTTG-AAAAGTGATTTTA

             *                
      25570 ATATGTACTTTTGAAAAG
          1 AAATGTACTTTTGAAAAG

      25588 CTTGGTTTAA


Statistics
Matches: 36,  Mismatches: 6, Indels: 4
        0.78            0.13        0.09

Matches are distributed among these distances:
  25    4  0.11
  26   28  0.78
  27    4  0.11

ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40


Consensus pattern (26 bp):   
AAATGTACTTTTGAAAAGTGATTTTA

Found at i:27993 original size:3 final size:3

Alignment explanation


    Indices: 27985--28041  Score: 105
    Period size: 3  Copynumber: 19.0  Consensus size: 3

      27975 CTTAACATAA

                                 *                                         
      27985 AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

                       
      28033 AAG AAG AAG
          1 AAG AAG AAG

      28042 TATTTATTAA


Statistics
Matches: 52,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   52  1.00

ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:28579 original size:2 final size:2

Alignment explanation


    Indices: 28572--28608  Score: 67
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      28562 ATAATTTTAC

                                                                    
      28572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      28609 CACAGAAGTA


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

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.