Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004409.1 Kokia drynarioides strain JFW-HI SEQ_117789, 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: 17026
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:8447 original size:140 final size:140

Alignment explanation


    Indices: 8171--8435  Score: 422
    Period size: 140  Copynumber: 1.9  Consensus size: 140

       8161 AATAATTGGT

                                                                   *         
       8171 AATTAATAAAGTGGAACCAGACCTTGCTTTGCACGGTGAGGAATCGACGATGCATTGTATAGTTA
          1 AATTAATAAAGTGGAACCAGACCTTGCTTTGCACGGTGAGGAATCGACGATGCATGGTATAGTTA

                       *   *                  *                              
       8236 TTGGGATTGTTGCCTGTCCAGATGGCACCATCAATGCATAAATCACTCATTAACATGTCAGCTCC
         66 TTGGGATTGTTACCTATCCAGATGGCACCATCAACGCATAAATCACTCATTAACATGTCAGCTCC

                      
       8301 CTCTTCAATC
        131 CTCTTCAATC

                            *                         * *                    
       8311 AATTAATAAAGTGGAATCAGACCTTGCTTTGCACGGTGAGGACTTGACGATGCATGGTATAGTTA
          1 AATTAATAAAGTGGAACCAGACCTTGCTTTGCACGGTGAGGAATCGACGATGCATGGTATAGTTA

                 *            *              *  *              *        
       8376 TTGGGGTTGTTACCTATCTAGATGGCACCATCAGCGGATAAATCACTCATTGACATGTCA
         66 TTGGGATTGTTACCTATCCAGATGGCACCATCAACGCATAAATCACTCATTAACATGTCA

       8436 TTGCCCTCTT


Statistics
Matches: 113,  Mismatches: 12, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 140  113  1.00

ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Consensus pattern (140 bp):   
AATTAATAAAGTGGAACCAGACCTTGCTTTGCACGGTGAGGAATCGACGATGCATGGTATAGTTA
TTGGGATTGTTACCTATCCAGATGGCACCATCAACGCATAAATCACTCATTAACATGTCAGCTCC
CTCTTCAATC

Found at i:16592 original size:26 final size:26

Alignment explanation


    Indices: 16563--16648  Score: 77
    Period size: 26  Copynumber: 3.2  Consensus size: 26

      16553 CTCCTCTGAA

                                      
      16563 TCAAATAAACTTAATTCTTCTCTCAT
          1 TCAAATAAACTTAATTCTTCTCTCAT

                    *    **               *
      16589 TCAAACT-TA-TTTTTCTCTTCTCTCGTCAA
          1 TCAAA-TAAACTTAAT-TC-T-TCTC-TCAT

                                      
      16618 TCAAATAAACTTAATTCTTCTCTCAT
          1 TCAAATAAACTTAATTCTTCTCTCAT

                 
      16644 TCAAA
          1 TCAAA

      16649 CTTATTTTTC


Statistics
Matches: 45,  Mismatches: 8, Indels: 14
        0.67            0.12        0.21

Matches are distributed among these distances:
  25    3  0.07
  26   16  0.36
  27    6  0.13
  28    6  0.13
  29   11  0.24
  30    3  0.07

ACGTcount: A:0.31, C:0.24, G:0.01, T:0.43


Consensus pattern (26 bp):   
TCAAATAAACTTAATTCTTCTCTCAT

Found at i:16622 original size:55 final size:55

Alignment explanation


    Indices: 16561--16667  Score: 214
    Period size: 55  Copynumber: 1.9  Consensus size: 55

      16551 CTCTCCTCTG

                                                                   
      16561 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTCGTC
          1 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTCGTC

                                                                
      16616 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTC
          1 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTC

      16668 ATTTCTTCAT


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   52  1.00

ACGTcount: A:0.28, C:0.25, G:0.01, T:0.46


Consensus pattern (55 bp):   
AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTCGTC

Found at i:16662 original size:26 final size:26

Alignment explanation


    Indices: 16578--16670  Score: 91
    Period size: 26  Copynumber: 3.5  Consensus size: 26

      16568 TAAACTTAAT

                                      
      16578 TCTTCTCTCATTCAAACTTATTTTTC
          1 TCTTCTCTCATTCAAACTTATTTTTC

                         *        *    **  
      16604 TCTTCTCTCGTCAATCAAA-TAAACTTAAT-
          1 TC-T-TCTC-TCATTCAAACT-TA-TTTTTC

                                      
      16633 TCTTCTCTCATTCAAACTTATTTTTC
          1 TCTTCTCTCATTCAAACTTATTTTTC

                        
      16659 TCTTCTCTCATT
          1 TCTTCTCTCATT

      16671 TCTTCATCTT


Statistics
Matches: 52,  Mismatches: 8, Indels: 14
        0.70            0.11        0.19

Matches are distributed among these distances:
  25    3  0.06
  26   23  0.44
  27    6  0.12
  28    6  0.12
  29   11  0.21
  30    3  0.06

ACGTcount: A:0.23, C:0.27, G:0.01, T:0.49


Consensus pattern (26 bp):   
TCTTCTCTCATTCAAACTTATTTTTC
Done.