Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004770.1 Kokia drynarioides strain JFW-HI SEQ_118376, 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: 15671
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35


Found at i:1091 original size:142 final size:142

Alignment explanation


    Indices: 870--1207  Score: 487
    Period size: 142  Copynumber: 2.4  Consensus size: 142

        860 AAATATTATT

                                        *        *                           
        870 AAACTAAATTGCTTGACAAGTGCACATTATTAAGAAGACACTAAATTCTTAAAAATAAAAATATT
          1 AAACT-AATTGCTTGACAAGTGCACATTGTTAAG-AGGCACTAAATTCTTAAAAATAAAAATATT

            *                           *                              *     
        935 GGGATTTGAAAATGTCCAAAGAATATAAGTAGTCAGACCATATTTTGACTTTTAAATTTTACACC
         64 AGGATTTGAAAATGTCCAAAGAATATAAATAGTCAGACCATATTTTGACTTTTAAATTTAACACC

               *          
       1000 ATAGCTTGCTCCAA
        129 ATAACTTGCTCCAA

               *                    *   **          *    *            *      
       1014 AAATTAATTGCTTGACAAGTGCACGTTGCCAAGAGGCACTGAATTTTTAAAAATAAAAGTATTAG
          1 AAACTAATTGCTTGACAAGTGCACATTGTTAAGAGGCACTAAATTCTTAAAAATAAAAATATTAG

                          *                               *             *    
       1079 GATTTGAAAATGTCTAAAGAATATAAATAGTCAGACCATATTTTGATTTTTAAATTTAACTCCAT
         66 GATTTGAAAATGTCCAAAGAATATAAATAGTCAGACCATATTTTGACTTTTAAATTTAACACCAT

              *         
       1144 AATTTGCTCCAA
        131 AACTTGCTCCAA

                                 *                        *     
       1156 AAACTAATTGCTTGACAAGTGTACATTGTTAAGAGGCACTAAATTCCTAAAA
          1 AAACTAATTGCTTGACAAGTGCACATTGTTAAGAGGCACTAAATTCTTAAAA

       1208 GATTTGAAAA


Statistics
Matches: 169,  Mismatches: 25, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
 142  141  0.83
 143   24  0.14
 144    4  0.02

ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32


Consensus pattern (142 bp):   
AAACTAATTGCTTGACAAGTGCACATTGTTAAGAGGCACTAAATTCTTAAAAATAAAAATATTAG
GATTTGAAAATGTCCAAAGAATATAAATAGTCAGACCATATTTTGACTTTTAAATTTAACACCAT
AACTTGCTCCAA

Found at i:5285 original size:30 final size:30

Alignment explanation


    Indices: 5244--5301  Score: 82
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       5234 ACTCCAAACT

                *            *             
       5244 TTTTTACTTTTCTC-CTGAAACTTTTACTCA
          1 TTTTCACTTTTCTCTC-AAAACTTTTACTCA

                                        
       5274 TTTTCACTTTTCTCTCAAAACTTTTACT
          1 TTTTCACTTTTCTCTCAAAACTTTTACT

       5302 TCCCTCCTAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  30   24  0.96
  31    1  0.04

ACGTcount: A:0.21, C:0.24, G:0.02, T:0.53


Consensus pattern (30 bp):   
TTTTCACTTTTCTCTCAAAACTTTTACTCA

Found at i:7141 original size:18 final size:18

Alignment explanation


    Indices: 7118--7156  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       7108 AAAAAGGTTT

                       *       
       7118 TTTTCAGATTTTAT-CTTC
          1 TTTTCA-ATTTAATCCTTC

                              
       7136 TTTTCAATTTAATCCTTC
          1 TTTTCAATTTAATCCTTC

               
       7154 TTT
          1 TTT

       7157 ATCTTTTTCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    6  0.32
  18   13  0.68

ACGTcount: A:0.18, C:0.18, G:0.03, T:0.62


Consensus pattern (18 bp):   
TTTTCAATTTAATCCTTC

Found at i:8319 original size:5 final size:5

Alignment explanation


    Indices: 8309--8351  Score: 52
    Period size: 5  Copynumber: 8.4  Consensus size: 5

       8299 AAATTCCAAA

                                                    *           
       8309 TTATT TTATT TTATT TTATT TTACTT TT-TT CTTCTT TTATT TT
          1 TTATT TTATT TTATT TTATT TTA-TT TTATT -TTATT TTATT TT

       8352 TGTCAAACCA


Statistics
Matches: 34,  Mismatches: 1, Indels: 6
        0.83            0.02        0.15

Matches are distributed among these distances:
   4    2  0.06
   5   26  0.76
   6    6  0.18

ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79


Consensus pattern (5 bp):   
TTATT

Found at i:11453 original size:31 final size:29

Alignment explanation


    Indices: 11416--11475  Score: 75
    Period size: 31  Copynumber: 2.0  Consensus size: 29

      11406 AAATTTAAAA

                    *                      
      11416 ATATACATTAATTATGATTTAATGTGTAATT
          1 ATATACATGAATTATGATTT--TGTGTAATT

                     *   *               
      11447 ATATACATGGATTTTGATTTTGTGTAATT
          1 ATATACATGAATTATGATTTTGTGTAATT

      11476 TTAAATATGA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    9  0.35
  31   17  0.65

ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50


Consensus pattern (29 bp):   
ATATACATGAATTATGATTTTGTGTAATT

Found at i:14786 original size:42 final size:42

Alignment explanation


    Indices: 14721--14803  Score: 105
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      14711 ACCACAGCAT

                    *       ***                        
      14721 AACAACAACAAACTCTGTTCACCAGAATAA-AGGAAAGCCAAC
          1 AACAACAAAAAACTCTAAACACCAGAATAAGA-GAAAGCCAAC

                                     *               
      14763 AACAACAAAAAACTCTAAACACCAGTATAAGAGAAAGCCAA
          1 AACAACAAAAAACTCTAAACACCAGAATAAGAGAAAGCCAA

      14804 ACCCGACCCT


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  42   34  0.97
  43    1  0.03

ACGTcount: A:0.54, C:0.24, G:0.11, T:0.11


Consensus pattern (42 bp):   
AACAACAAAAAACTCTAAACACCAGAATAAGAGAAAGCCAAC
Done.