Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009236.1 Kokia drynarioides strain JFW-HI SEQ_123941, 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: 16111
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:6692 original size:15 final size:14

Alignment explanation


    Indices: 6671--6704  Score: 59
    Period size: 15  Copynumber: 2.4  Consensus size: 14

       6661 AATTTCTTAC

                          
       6671 AACAAGGGAGTTAT
          1 AACAAGGGAGTTAT

                           
       6685 AGACAAGGGAGTTAT
          1 A-ACAAGGGAGTTAT

                 
       6700 AACAA
          1 AACAA

       6705 CAATCAGCAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    5  0.26
  15   14  0.74

ACGTcount: A:0.47, C:0.09, G:0.26, T:0.18


Consensus pattern (14 bp):   
AACAAGGGAGTTAT

Found at i:8406 original size:189 final size:190

Alignment explanation


    Indices: 8084--8464  Score: 719
    Period size: 189  Copynumber: 2.0  Consensus size: 190

       8074 TATCCTAACT

                                                        *                    
       8084 AAATGTGACCACAGAGCTGAGGCTAATAATTGTGAGCTAAGACGGGATTGGCAATTAGAACCTTG
          1 AAATGTGACCACAGAGCT-AGGCTAATAATTGTGAGCTAAGACGAGATTGGCAATTAGAACCTTG

                *                                                            
       8149 GATTTTTCTAACAAAACGATCCCTATGTTTAAACCATCAATTGAACAAGATCCTATCTTGGAGTT
         65 GATTATTCTAACAAAACGATCCCTATGTTTAAACCATCAATTGAACAAGATCCTATCTTGGAGTT

                                                                         
       8214 AAAGCCATTACCGATGCATTTGAAGTATGTCTTTTTGGGTGACAATGACACATTACCCGTG
        130 AAAGCCATTACCGATGCATTTGAAGTATGTCTTTTTGGGTGACAATGACACATTACCCGTG

                                       *                                     
       8275 AAATGTGACCACAGAGCT-GGCTAATAGTTGTGAGCTAAGACGAGATTGGCAATTAGAACCTTGG
          1 AAATGTGACCACAGAGCTAGGCTAATAATTGTGAGCTAAGACGAGATTGGCAATTAGAACCTTGG

                                                                             
       8339 ATTATTCTAACAAAACGATCCCTATGTTTAAACCATCAATTGAACAAGATCCTATCTTGGAGTTA
         66 ATTATTCTAACAAAACGATCCCTATGTTTAAACCATCAATTGAACAAGATCCTATCTTGGAGTTA

                                                                        
       8404 AAGCCATTACCGATGCATTTGAAGTATGTCTTTTTGGGTGACAATGACACATTACCCGTG
        131 AAGCCATTACCGATGCATTTGAAGTATGTCTTTTTGGGTGACAATGACACATTACCCGTG

             
       8464 A
          1 A

       8465 TTGTCAGTGC


Statistics
Matches: 187,  Mismatches: 3, Indels: 2
        0.97            0.02        0.01

Matches are distributed among these distances:
 189  169  0.90
 191   18  0.10

ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29


Consensus pattern (190 bp):   
AAATGTGACCACAGAGCTAGGCTAATAATTGTGAGCTAAGACGAGATTGGCAATTAGAACCTTGG
ATTATTCTAACAAAACGATCCCTATGTTTAAACCATCAATTGAACAAGATCCTATCTTGGAGTTA
AAGCCATTACCGATGCATTTGAAGTATGTCTTTTTGGGTGACAATGACACATTACCCGTG

Found at i:11335 original size:17 final size:16

Alignment explanation


    Indices: 11313--11356  Score: 52
    Period size: 17  Copynumber: 2.7  Consensus size: 16

      11303 CATTTATGTC

                            *
      11313 TATTTCTTTTTTTACTT
          1 TATTTCTTTTTTTA-TA

                    *       
      11330 TATTTCTTCTTTTATA
          1 TATTTCTTTTTTTATA

             *         
      11346 TGTTTCTTTTT
          1 TATTTCTTTTT

      11357 AGATTCTATG


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  16   10  0.43
  17   13  0.57

ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75


Consensus pattern (16 bp):   
TATTTCTTTTTTTATA
Done.