Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008891.1 Kokia drynarioides strain JFW-HI SEQ_123578, 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: 28340
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35

Warning! 115 characters in sequence are not A, C, G, or T


Found at i:5050 original size:58 final size:57

Alignment explanation


    Indices: 4957--5080  Score: 187
    Period size: 58  Copynumber: 2.2  Consensus size: 57

       4947 TGTTGGCTAT

                  *                                                  
       4957 ACACCCTTTTTTGTCAAATAAAAATATAATTTTTTGGTGTTGGCCATGCAATAGCCG
          1 ACACCCCTTTTTGTCAAATAAAAATATAATTTTTTGGTGTTGGCCATGCAATAGCCG

                                                                  * ** 
       5014 ACACCCCTTTTTGTCAAATAAAAA-ATGCAATTTTTTGGTGTTGGCCATGCAATGGTTG
          1 ACACCCCTTTTTGTCAAATAAAAATAT--AATTTTTTGGTGTTGGCCATGCAATAGCCG

                     
       5072 ACACCCCTT
          1 ACACCCCTT

       5081 GTTCTCGGAT


Statistics
Matches: 61,  Mismatches: 4, Indels: 3
        0.90            0.06        0.04

Matches are distributed among these distances:
  56    2  0.03
  57   23  0.38
  58   36  0.59

ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35


Consensus pattern (57 bp):   
ACACCCCTTTTTGTCAAATAAAAATATAATTTTTTGGTGTTGGCCATGCAATAGCCG

Found at i:5093 original size:58 final size:58

Alignment explanation


    Indices: 4970--5097  Score: 170
    Period size: 58  Copynumber: 2.2  Consensus size: 58

       4960 CCCTTTTTTG

                                                                   *  *
       4970 TCAAATAAAAATAT--AATTTTTTGGTGTTGGCCATGCAATAGCCGACACCCCTTTTTG
          1 TCAAATAAAAA-ATGCAATTTTTTGGTGTTGGCCATGCAATAGCCGACACCCCTTGTTC

                                                    * **              
       5027 TCAAATAAAAAATGCAATTTTTTGGTGTTGGCCATGCAATGGTTGACACCCCTTGTTC
          1 TCAAATAAAAAATGCAATTTTTTGGTGTTGGCCATGCAATAGCCGACACCCCTTGTTC

              **         
       5085 TCGGATAAAAAAT
          1 TCAAATAAAAAAT

       5098 TTTCAAATTT


Statistics
Matches: 62,  Mismatches: 7, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  56    2  0.03
  57   11  0.18
  58   49  0.79

ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Consensus pattern (58 bp):   
TCAAATAAAAAATGCAATTTTTTGGTGTTGGCCATGCAATAGCCGACACCCCTTGTTC

Found at i:5699 original size:115 final size:116

Alignment explanation


    Indices: 5496--5726  Score: 367
    Period size: 115  Copynumber: 2.0  Consensus size: 116

       5486 GTGTCGGCCA

                   *                        *                                
       5496 TTAGATGGCCAATATCAATTTTTACTGTTCATTTCAGGTAATTTTGGTATATATTTTTTAACTTG
          1 TTAGATGACCAATATCAATTTTTACTGTTCATATCAGGTAATTTTGGTATATATTTTTTAACTTG

                                                                
       5561 GCTCATTTTCGTAAATAATCAAAATTTTT-GAGTTATTTCGATAAATTACTC
         66 GCTCATTTTCGTAAATAATCAAAATTTTTAGA-TTATTTCGATAAATTACTC

                                         *         *        *                
       5612 TTAGATGACCAATATCAA-TTTTACTGTTTATATCAGGTCATTTTGGTGTATATTTTTTAACTTG
          1 TTAGATGACCAATATCAATTTTTACTGTTCATATCAGGTAATTTTGGTATATATTTTTTAACTTG

             * *     *                                         
       5676 GGTTATTTTTGTAAATAATCAAAATTTTTAGATTATTTCGATAAATTACTC
         66 GCTCATTTTCGTAAATAATCAAAATTTTTAGATTATTTCGATAAATTACTC

       5727 GAGTATTAGT


Statistics
Matches: 106,  Mismatches: 8, Indels: 3
        0.91            0.07        0.03

Matches are distributed among these distances:
 115   87  0.82
 116   19  0.18

ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47


Consensus pattern (116 bp):   
TTAGATGACCAATATCAATTTTTACTGTTCATATCAGGTAATTTTGGTATATATTTTTTAACTTG
GCTCATTTTCGTAAATAATCAAAATTTTTAGATTATTTCGATAAATTACTC

Found at i:6230 original size:15 final size:17

Alignment explanation


    Indices: 6200--6232  Score: 52
    Period size: 15  Copynumber: 2.1  Consensus size: 17

       6190 AAATTTCTTC

                             
       6200 AAAAATAATAAAATTAT
          1 AAAAATAATAAAATTAT

                             
       6217 AAAAA-AAT-AAATTAT
          1 AAAAATAATAAAATTAT

             
       6232 A
          1 A

       6233 TATTCATATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    8  0.50
  16    3  0.19
  17    5  0.31

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (17 bp):   
AAAAATAATAAAATTAT

Found at i:6805 original size:5 final size:5

Alignment explanation


    Indices: 6790--6825  Score: 63
    Period size: 5  Copynumber: 7.0  Consensus size: 5

       6780 AATTATATAT

                                                      
       6790 TTTATA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
          1 TTTA-A TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA

       6826 AATATAAATC


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5   26  0.87
   6    4  0.13

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (5 bp):   
TTTAA

Done.