Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005419.1 Kokia drynarioides strain JFW-HI SEQ_119440, 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: 2399
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38


Found at i:771 original size:197 final size:197

Alignment explanation


    Indices: 431--834  Score: 632
    Period size: 197  Copynumber: 2.0  Consensus size: 197

        421 ACCACACCGC

                                         *             *          *          
        431 CATTACCAATAGACTCCTCGTCACCTTACGAACCTAACCCTTCTTTCTCCTTCTTCTTTAACGTT
          1 CATT-CCAATAGACTCCTCGTCACCTTACAAACCTAACCCTTCCTTCTCCTTCTCCTTTAACGTT

                         *                             *                     
        496 GCTATTCGTGAGAGCCAGTGCTAGAACAAACTTGTTTCACTTCTTTTTAGCCACACTCCGTCACG
         65 GCTATTCGTGAGAACCAGTGCTAGAACAAACTTGTTTCACTTCGTTTTAGCCACACTCCGTCACG

                 *                                                           
        561 AACTTTGCTCCTTACCTCTAATCTTGAT-GTGGGTATGTGAAAAGGATCATTTTCTTCCGTTTTT
        130 AACTTCGCTCCTTACCTCTAATCTTG-TCGTGGGTATGTGAAAAGGATCATTTTCTTCCGTTTTT

                
        625 GTGT
        194 GTGT

                                      *                                      
        629 CATTCCAATAGACTCCTCGTCACCTTGCAAACCTAACCCTTCCTTCTCCTTCTCCTTTAACGTTG
          1 CATTCCAATAGACTCCTCGTCACCTTACAAACCTAACCCTTCCTTCTCCTTCTCCTTTAACGTTG

            *            **           *  *                 *         *       
        694 TTATTCGTGAGAATTAGTGCTAGAACCAATTTGTTTCACTTCGTTTTCGCCACACTCTGTCAC-A
         66 CTATTCGTGAGAACCAGTGCTAGAACAAACTTGTTTCACTTCGTTTTAGCCACACTCCGTCACGA

                                                                    *        
        758 AGCTTCGCTCCTTACCTCTAATCTTGTCGTGGGTATGTGAAAAGGATCATTTTCTTTCGTTTTTG
        131 A-CTTCGCTCCTTACCTCTAATCTTGTCGTGGGTATGTGAAAAGGATCATTTTCTTCCGTTTTTG

               
        823 TGT
        195 TGT

                     
        826 CATTCCAAT
          1 CATTCCAAT

        835 GAGCTTGTGC


Statistics
Matches: 189,  Mismatches: 15, Indels: 5
        0.90            0.07        0.02

Matches are distributed among these distances:
 196    3  0.02
 197  182  0.96
 198    4  0.02

ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38


Consensus pattern (197 bp):   
CATTCCAATAGACTCCTCGTCACCTTACAAACCTAACCCTTCCTTCTCCTTCTCCTTTAACGTTG
CTATTCGTGAGAACCAGTGCTAGAACAAACTTGTTTCACTTCGTTTTAGCCACACTCCGTCACGA
ACTTCGCTCCTTACCTCTAATCTTGTCGTGGGTATGTGAAAAGGATCATTTTCTTCCGTTTTTGT
GT

Found at i:1193 original size:26 final size:26

Alignment explanation


    Indices: 1162--1211  Score: 66
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       1152 CCTATTCACT

                               *       
       1162 TTGACC-AGACTTGTTGACTTTGACCG
          1 TTGACCTAGA-TTGTTGACATTGACCG

                   *                
       1188 TTGACCTTGATTGTTGACATTGAC
          1 TTGACCTAGATTGTTGACATTGAC

       1212 TTTGATCGTT


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

Matches are distributed among these distances:
  26   19  0.90
  27    2  0.10

ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38


Consensus pattern (26 bp):   
TTGACCTAGATTGTTGACATTGACCG

Found at i:1210 original size:19 final size:19

Alignment explanation


    Indices: 1188--1224  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       1178 ACTTTGACCG

                       *       
       1188 TTGACCTTGATTGTTGACA
          1 TTGACCTTGATCGTTGACA

                 *            
       1207 TTGACTTTGATCGTTGAC
          1 TTGACCTTGATCGTTGAC

       1225 TTTTTTGGCC


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

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43


Consensus pattern (19 bp):   
TTGACCTTGATCGTTGACA
Done.