Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000107.1 Kokia drynarioides strain JFW-HI SEQ_110744, 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: 8052
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37


Found at i:346 original size:21 final size:21

Alignment explanation


    Indices: 318--412  Score: 85
    Period size: 21  Copynumber: 4.8  Consensus size: 21

        308 TGTGCCTAGT

                                 
        318 AGGCTTTGTGCCGGTGTTTTC
          1 AGGCTTTGTGCCGGTGTTTTC

             *        *           
        339 AAGCTTTGTGAC--TAG---T-
          1 AGGCTTTGTGCCGGT-GTTTTC

                  *    *    *    
        355 AGGCTTGGTGCAGGTGATTTC
          1 AGGCTTTGTGCCGGTGTTTTC

                                 
        376 AGGCTTTGTGCCGGTGTTTTC
          1 AGGCTTTGTGCCGGTGTTTTC

                   *        
        397 AGGCTTTATGCCGGTG
          1 AGGCTTTGTGCCGGTG

        413 ATTCAATAAC


Statistics
Matches: 57,  Mismatches: 10, Indels: 14
        0.70            0.12        0.17

Matches are distributed among these distances:
  16    8  0.14
  17    2  0.04
  18    1  0.02
  19    1  0.02
  20    2  0.04
  21   43  0.75

ACGTcount: A:0.12, C:0.17, G:0.34, T:0.38


Consensus pattern (21 bp):   
AGGCTTTGTGCCGGTGTTTTC

Found at i:354 original size:37 final size:37

Alignment explanation


    Indices: 299--385  Score: 129
    Period size: 37  Copynumber: 2.4  Consensus size: 37

        289 CTTACACAAA

                         *           *    *    * 
        299 TTCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTT
          1 TTCAGGCTTTGTGACTAGTAGGCTTGGTGCAGGTGAT

                *                                
        336 TTCAAGCTTTGTGACTAGTAGGCTTGGTGCAGGTGAT
          1 TTCAGGCTTTGTGACTAGTAGGCTTGGTGCAGGTGAT

                         
        373 TTCAGGCTTTGTG
          1 TTCAGGCTTTGTG

        386 CCGGTGTTTT


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   44  1.00

ACGTcount: A:0.13, C:0.16, G:0.32, T:0.39


Consensus pattern (37 bp):   
TTCAGGCTTTGTGACTAGTAGGCTTGGTGCAGGTGAT

Found at i:1616 original size:104 final size:103

Alignment explanation


    Indices: 1459--1782  Score: 373
    Period size: 104  Copynumber: 3.1  Consensus size: 103

       1449 TAATATTAGT

                       *              *                                      
       1459 TGTGAACGTAGGTCAGTGAGCTGTTAGGAGTTGCGATATTAAATCAACGAACTCAAATAATCAGA
          1 TGTGAACGTAGATCAGTGAGCTGTTAAGAGTTGCGATATTAAATCAACGAACTCAAATAATC-GA

             *       *      *       *              
       1524 GACTGCGATCTTAAATTAGCTAGCTTTAATAACATCAAC
         65 GGCTGCGATATTAAATCAGCTAGCCTTAATAACATCAAC

                           **                 *  *        ***                
       1563 TGTGAACGTAGATCAACGAGCTGTTAAGAGTTGCAATCTTAAATCAGTTAACTCAAATAATCGAA
          1 TGTGAACGTAGATCAGTGAGCTGTTAAGAGTTGCGATATTAAATCAACGAACTCAAATAATCG-A

              * * *  *         *                   
       1628 GGTTACAATTTTAAATCAGTTAGCCTTAATAACATCAAC
         65 GGCTGCGATATTAAATCAGCTAGCCTTAATAACATCAAC

            *                      *           *                             
       1667 CGTGAACGTA-AGTCAGTGAGCTATT-AGAAGTTGTGATATTAAATCAACGAACTCAAATAATCG
          1 TGTGAACGTAGA-TCAGTGAGCTGTTAAG-AGTTGCGATATTAAATCAACGAACTCAAATAATC-

                                *                  **
       1730 GAGGCTGCGATATTAAATCAACTAGCCTTAATAACATCAGT
         63 GAGGCTGCGATATTAAATCAGCTAGCCTTAATAACATCAAC

                        
       1771 TGTGAACGTAGA
          1 TGTGAACGTAGA

       1783 AATAACAATA


Statistics
Matches: 179,  Mismatches: 36, Indels: 9
        0.80            0.16        0.04

Matches are distributed among these distances:
 103    4  0.02
 104  173  0.97
 105    2  0.01

ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28


Consensus pattern (103 bp):   
TGTGAACGTAGATCAGTGAGCTGTTAAGAGTTGCGATATTAAATCAACGAACTCAAATAATCGAG
GCTGCGATATTAAATCAGCTAGCCTTAATAACATCAAC

Found at i:7016 original size:19 final size:19

Alignment explanation


    Indices: 6975--7017  Score: 52
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       6965 CTATGCGTGG

                        * *    
       6975 AATTTTATTTATTTTTAAT
          1 AATTTTATTTATATATAAT

                                
       6994 AATTTTATTTATAATATAA-
          1 AATTTTATTTAT-ATATAAT

                 
       7013 AATTT
          1 AATTT

       7018 AAATATAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  19   17  0.81
  20    4  0.19

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (19 bp):   
AATTTTATTTATATATAAT
Done.