Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012437.1 Kokia drynarioides strain JFW-HI SEQ_127441, 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: 10251
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35


Found at i:6577 original size:23 final size:24

Alignment explanation


    Indices: 6529--6579  Score: 70
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       6519 TATATTGCTA

                                 *  
       6529 TTTTTTGTTGTTTCTGGTGTATGT
          1 TTTTTTGTTGTTTCTGGTGTAGGT

                                     
       6553 TTTTTTGTTGTTT-TGGTGCT-GGT
          1 TTTTTTGTTGTTTCTGGTG-TAGGT

                
       6576 TTTT
          1 TTTT

       6580 ACTGTTTTGG


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  23   11  0.44
  24   14  0.56

ACGTcount: A:0.02, C:0.04, G:0.25, T:0.69


Consensus pattern (24 bp):   
TTTTTTGTTGTTTCTGGTGTAGGT

Found at i:6578 original size:21 final size:23

Alignment explanation


    Indices: 6530--6591  Score: 65
    Period size: 21  Copynumber: 2.7  Consensus size: 23

       6520 ATATTGCTAT

                                   *
       6530 TTTTTGTTGTTTCTGGTGTATGTT
          1 TTTTTGTTGTTT-TGGTGTATGTG

                              *    
       6554 TTTTTGTTGTTTTGGTG-CTG-G
          1 TTTTTGTTGTTTTGGTGTATGTG

                 **          
       6575 TTTTTACTGTTTTGGTG
          1 TTTTTGTTGTTTTGGTG

       6592 ATGCTTTTGC


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  21   15  0.44
  22    2  0.06
  23    5  0.15
  24   12  0.35

ACGTcount: A:0.03, C:0.05, G:0.27, T:0.65


Consensus pattern (23 bp):   
TTTTTGTTGTTTTGGTGTATGTG

Found at i:6679 original size:34 final size:34

Alignment explanation


    Indices: 6633--6757  Score: 196
    Period size: 34  Copynumber: 3.6  Consensus size: 34

       6623 TATTGTGTTT

                  *                           
       6633 GTTGTTTTTTGCTGTTATTTTTACTGCTATTTTG
          1 GTTGTTGTTTGCTGTTATTTTTACTGCTATTTTG

                   *              *           
       6667 GTTGTTGATTGCTGTTATTTTTTCTGCTATTTTG
          1 GTTGTTGTTTGCTGTTATTTTTACTGCTATTTTG

                                     *        
       6701 GTTGTTGTTTGCTGTTATTTTTACTACTATTTTG
          1 GTTGTTGTTTGCTGTTATTTTTACTGCTATTTTG

                        *          
       6735 GTTGTTGTTTAGATGTTATTTTT
          1 GTTGTTGTTT-GCTGTTATTTTT

       6758 TATACGTTTT


Statistics
Matches: 83,  Mismatches: 7, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  34   72  0.87
  35   11  0.13

ACGTcount: A:0.10, C:0.07, G:0.19, T:0.63


Consensus pattern (34 bp):   
GTTGTTGTTTGCTGTTATTTTTACTGCTATTTTG

Found at i:6790 original size:68 final size:68

Alignment explanation


    Indices: 6640--6778  Score: 174
    Period size: 68  Copynumber: 2.0  Consensus size: 68

       6630 TTTGTTGTTT

                              *                   *           * *        ** *
       6640 TTTGCTGTTATTTTTACTGCTATTTTGGTTGTTGATTGCTGTTATTTTTTCTGCTATTTTGGTTG
          1 TTTGCTGTTATTTTTACTACTATTTTGGTTGTTGATTGATGTTATTTTTTATACTATTTTGACTA

               
       6705 TTG
         66 TTG

                                              *                              
       6708 TTTGCTGTTATTTTTACTACTATTTTGGTTGTTGTTTAGATGTTATTTTTTATACGT-TTTT-AC
          1 TTTGCTGTTATTTTTACTACTATTTTGGTTGTTGATT-GATGTTATTTTTTATAC-TATTTTGAC

                 
       6771 TATTG
         64 TATTG

               
       6776 TTT
          1 TTT

       6779 CGTTGTATTT


Statistics
Matches: 61,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  68   42  0.69
  69   18  0.30
  70    1  0.02

ACGTcount: A:0.12, C:0.08, G:0.17, T:0.63


Consensus pattern (68 bp):   
TTTGCTGTTATTTTTACTACTATTTTGGTTGTTGATTGATGTTATTTTTTATACTATTTTGACTA
TTG

Found at i:8106 original size:3 final size:3

Alignment explanation


    Indices: 8098--8134  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       8088 GATTAAATTA

                                                             
       8098 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

       8135 AATTGATTAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

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


Consensus pattern (3 bp):   
ATT

Found at i:8143 original size:12 final size:10

Alignment explanation


    Indices: 8094--8135  Score: 63
    Period size: 9  Copynumber: 4.5  Consensus size: 10

       8084 ATTTGATTAA

                      
       8094 ATTAATTATT
          1 ATTAATTATT

                      
       8104 ATT-ATTATT
          1 ATTAATTATT

                      
       8113 ATT-ATTATT
          1 ATTAATTATT

                      
       8122 ATT-ATTATT
          1 ATTAATTATT

                 
       8131 ATTAA
          1 ATTAA

       8136 ATTGATTAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   9   27  0.87
  10    4  0.13

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (10 bp):   
ATTAATTATT
Done.