Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014201.1 Kokia drynarioides strain JFW-HI SEQ_129234, 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: 10431
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33

Warning! 7 characters in sequence are not A, C, G, or T


Found at i:82 original size:3 final size:3

Alignment explanation


    Indices: 74--157  Score: 53
    Period size: 3  Copynumber: 28.0  Consensus size: 3

         64 ATATCATTAG

                          * **          * *               *         * *     
         74 TAA TAA TAA TAG CCA TAA TAA CAT TAA TAA TAA TAC TAA TAA CAT TAAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA

                          *          *            *        
        123 TAA TAA T-A TAT TAA TAA TTA TAA TAA TAT TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

        158 ATATAAAAAA


Statistics
Matches: 57,  Mismatches: 22, Indels: 4
        0.69            0.27        0.05

Matches are distributed among these distances:
   2    2  0.04
   3   53  0.93
   4    2  0.04

ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36


Consensus pattern (3 bp):   
TAA

Found at i:1250 original size:29 final size:29

Alignment explanation


    Indices: 1217--1441  Score: 93
    Period size: 29  Copynumber: 7.6  Consensus size: 29

       1207 GACTCGAAGA

                                         
       1217 TTCTAAAAATTACATTTTTACCCCCGAAC
          1 TTCTAAAAATTACATTTTTACCCCCGAAC

                       *      *     **   
       1246 TTCTAAAAATTCCATTTTGACCCCAAAAC
          1 TTCTAAAAATTACATTTTTACCCCCGAAC

                          **        *    *
       1275 TT-TCAAAAATTACCCTTTTACCCTCG-AG
          1 TTCT-AAAAATTACATTTTTACCCCCGAAC

                *       *       *  *     **
       1303 TGTCCAAAAATTCCAATTTTGA-TCCCGATT
          1 T-TCTAAAAATTAC-ATTTTTACCCCCGAAC

                        *          *      **
       1333 TTCCTAAAAATTCCATTTTTGA-TCCCGATTT
          1 TT-CTAAAAATTACATTTTT-ACCCCCGA-AC

              *     *    **             *
       1364 TTTTAAAAGTTACCGTTTTACCCCCG-AG
          1 TTCTAAAAATTACATTTTTACCCCCGAAC

                        *        *        
       1392 TGTCTAAAAATTTCATTTTTAACCCCGAAC
          1 T-TCTAAAAATTACATTTTTACCCCCGAAC

                                 
       1422 TTTTCT-AAAATTACCATTTT
          1 --TTCTAAAAATTA-CATTTT

       1442 GCCCCCAAAG


Statistics
Matches: 143,  Mismatches: 39, Indels: 26
        0.69            0.19        0.12

Matches are distributed among these distances:
  28    4  0.03
  29   80  0.56
  30   45  0.31
  31   13  0.09
  32    1  0.01

ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38


Consensus pattern (29 bp):   
TTCTAAAAATTACATTTTTACCCCCGAAC

Found at i:1371 original size:30 final size:30

Alignment explanation


    Indices: 1308--1364  Score: 105
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1298 TCGAGTGTCC

                                          
       1308 AAAAATTCCAATTTTGATCCCGATTTTCCT
          1 AAAAATTCCAATTTTGATCCCGATTTTCCT

                      *                
       1338 AAAAATTCCATTTTTGATCCCGATTTT
          1 AAAAATTCCAATTTTGATCCCGATTTT

       1365 TTTAAAAGTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42


Consensus pattern (30 bp):   
AAAAATTCCAATTTTGATCCCGATTTTCCT

Found at i:1401 original size:59 final size:59

Alignment explanation


    Indices: 1336--1447  Score: 145
    Period size: 59  Copynumber: 1.9  Consensus size: 59

       1326 CCCGATTTTC

                             * *      *    *           *                
       1336 CTAAAAATTCCATTTTTGATCCCG-ATTTTTTTAAAAGTTACCGTTTTACCCCCGAGTGT
          1 CTAAAAATTCCATTTTTAACCCCGAACTTTTCTAAAA-TTACCATTTTACCCCCGAGTGT

                     *                                     *     
       1395 CTAAAAATTTCATTTTTAACCCCGAACTTTTCTAAAATTACCATTTTGCCCCC
          1 CTAAAAATTCCATTTTTAACCCCGAACTTTTCTAAAATTACCATTTTACCCCC

       1448 AAAGTCCAAA


Statistics
Matches: 45,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  59   35  0.78
  60   10  0.22

ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39


Consensus pattern (59 bp):   
CTAAAAATTCCATTTTTAACCCCGAACTTTTCTAAAATTACCATTTTACCCCCGAGTGT

Found at i:6481 original size:21 final size:22

Alignment explanation


    Indices: 6440--6481  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6430 ACCTAAAAGT

                            *     
       6440 TAAAAAAACAATATATCAAATC
          1 TAAAAAAACAATATATAAAATC

                                  
       6462 TAAAAAACACAA-ATA-AAAAT
          1 TAAAAAA-ACAATATATAAAAT

       6482 TATTAAGATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 3
        0.82            0.05        0.14

Matches are distributed among these distances:
  21    4  0.22
  22   10  0.56
  23    4  0.22

ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19


Consensus pattern (22 bp):   
TAAAAAAACAATATATAAAATC

Found at i:10129 original size:16 final size:14

Alignment explanation


    Indices: 10088--10121  Score: 52
    Period size: 13  Copynumber: 2.4  Consensus size: 14

      10078 GGAAAAAAAA

                          
      10088 AAAGAAA-AAAGAG
          1 AAAGAAAGAAAGAG

                          
      10101 AAAGAAAGAAAGAG
          1 AAAGAAAGAAAGAG

                   
      10115 AGAAGAA
          1 A-AAGAA

      10122 GGAGAAGAAG


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

Matches are distributed among these distances:
  13    7  0.37
  14    7  0.37
  15    5  0.26

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (14 bp):   
AAAGAAAGAAAGAG
Done.