Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012481.1 Kokia drynarioides strain JFW-HI SEQ_127485, 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: 4084
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:74 original size:3 final size:3

Alignment explanation


    Indices: 66--113  Score: 78
    Period size: 3  Copynumber: 15.7  Consensus size: 3

         56 GTATTAAATG

                                         *                              
         66 AAT AAT AAT AAT AAT AAT AAT ATT AGAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT

              
        112 AA
          1 AA

        114 ATCGAAAGGT


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   3   40  0.95
   4    2  0.05

ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:1166 original size:59 final size:58

Alignment explanation


    Indices: 1063--1265  Score: 194
    Period size: 59  Copynumber: 3.4  Consensus size: 58

       1053 GAAGGTCCCG

                              *    *    *                               
       1063 AAATTTCCAAAAATCCCAATTTTAACCCTAAAACTTCCAAAAATCCCATTTTTGACCCCA
          1 AAATTTCCAAAAAT-CCATTTTTGACCCCAAAACTTCCAAAAATCCCA-TTTTGACCCCA

                   *                    *                          * *
       1123 AAATTTCTAAAAATCCATTTTTGACCCCGAAACTTCCAAAAATCCCATTTTGACCTCT
          1 AAATTTCCAAAAATCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTGACCCCA

               *                  *     *   *    *       *              *
       1181 AAACTTCCAAAAATCTCATTTTCGACCCTAAACCTTCTAAAAATTACCATTTT-ACCCTCG
          1 AAATTTCCAAAAATC-CATTTTTGACCCCAAAACTTCCAAAAA-TCCCATTTTGACCC-CA

              *              *        
       1241 AACTTT-CAAAAATCCCGTTTTTGAC
          1 AAATTTCCAAAAAT-CCATTTTTGAC

       1266 TCTGAACCTT


Statistics
Matches: 118,  Mismatches: 21, Indels: 9
        0.80            0.14        0.06

Matches are distributed among these distances:
  58   22  0.19
  59   69  0.58
  60   27  0.23

ACGTcount: A:0.36, C:0.29, G:0.04, T:0.32


Consensus pattern (58 bp):   
AAATTTCCAAAAATCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTGACCCCA

Found at i:1272 original size:29 final size:29

Alignment explanation


    Indices: 1067--1265  Score: 190
    Period size: 29  Copynumber: 6.8  Consensus size: 29

       1057 GTCCCGAAAT

                          *    *          
       1067 TTCCAAAAATCCCAATTTTAACCCTAAAAC
          1 TTCCAAAAATCCCATTTTTGACCCT-AAAC

                                     *   *
       1097 TTCCAAAAATCCCATTTTTGACCCCAAAAT
          1 TTCCAAAAATCCCATTTTTGA-CCCTAAAC

               *                     *    
       1127 TTCTAAAAAT-CCATTTTTGACCCCGAAAC
          1 TTCCAAAAATCCCATTTTTGA-CCCTAAAC

                                          
       1156 TTCCAAAAATCCCA-TTTTGACCTCTAAAC
          1 TTCCAAAAATCCCATTTTTGACC-CTAAAC

                       *      *           
       1185 TTCCAAAAATCTCATTTTCGACCCTAAACC
          1 TTCCAAAAATCCCATTTTTGACCCTAAA-C

               *       *               *   
       1215 TTCTAAAAATTACCA-TTTT-ACCCTCGAAC
          1 TTCCAAAAA-TCCCATTTTTGACCCT-AAAC

              *          *        
       1244 TTTCAAAAATCCCGTTTTTGAC
          1 TTCCAAAAATCCCATTTTTGAC

       1266 TCTGAACCTT


Statistics
Matches: 140,  Mismatches: 20, Indels: 18
        0.79            0.11        0.10

Matches are distributed among these distances:
  28    5  0.04
  29   72  0.51
  30   57  0.41
  31    6  0.04

ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32


Consensus pattern (29 bp):   
TTCCAAAAATCCCATTTTTGACCCTAAAC

Found at i:1274 original size:59 final size:59

Alignment explanation


    Indices: 1070--1291  Score: 191
    Period size: 59  Copynumber: 3.8  Consensus size: 59

       1060 CCGAAATTTC

                       *    *     *  *           *              *   *   
       1070 CAAAAATCCCAATTTTAACCCTAAAACTTCCAAAAATCCCATTTTTGACC-CCAAAATTT
          1 CAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAATACCA-TTTTGACCTCTAAACTTT

                                  *   *           *                    *
       1129 CTAAAAAT-CCATTTTTGACCCCGAAACTTCCAAAAATCCCATTTTGACCTCTAAACTTC
          1 C-AAAAATCCCATTTTTGACCCTGAACCTTCCAAAAATACCATTTTGACCTCTAAACTTT

                    *      *      *       *                       *      
       1188 CAAAAATCTCATTTTCGACCCTAAACCTTCTAAAAATTACCATTTT-ACC-CTCGAACTTT
          1 CAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAA-TACCATTTTGACCTCT-AAACTTT

                      *        *           *  **         
       1247 CAAAAATCCCGTTTTTGACTCTGAACCTTCCGAATCTACCATTTT
          1 CAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAATACCATTTT

       1292 ACCCCCGTGC


Statistics
Matches: 133,  Mismatches: 25, Indels: 11
        0.79            0.15        0.07

Matches are distributed among these distances:
  58   25  0.19
  59   94  0.71
  60   14  0.11

ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32


Consensus pattern (59 bp):   
CAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAATACCATTTTGACCTCTAAACTTT

Found at i:3631 original size:110 final size:110

Alignment explanation


    Indices: 3450--3678  Score: 296
    Period size: 110  Copynumber: 2.1  Consensus size: 110

       3440 CACTAATCGA

                  *  *                         *       *                     
       3450 ATAAACCGATGATATAAAAGGTGAGCCCAACTCTAGTTGGATATACCAACAAATATTACGCCCAG
          1 ATAAACTGACGATATAAAAGGTGAGCCCAACTCTAATTGGATAAACCAACAAATATTACGCCCAG

                                     *                   
       3515 CGTTAGTCGGATAAACCGACAAGTTGTGTGCCCAGCACTAGTCAG
         66 CGTTAGTCGGATAAACCGACAAGTTATGTGCCCAGCACTAGTCAG

                                     *   *                   ** * *  *       
       3560 ATAAACTGACGATATAAAAGGTGAGTCCAGCTCTAATTGGATAAACCAATGATTTTTGCGCCCAG
          1 ATAAACTGACGATATAAAAGGTGAGCCCAACTCTAATTGGATAAACCAACAAATATTACGCCCAG

                            *   * *            *      *  
       3625 CGTTAGTCGGATAAACTGACGATTTATGTGCCCAGTACTAGTTAG
         66 CGTTAGTCGGATAAACCGACAAGTTATGTGCCCAGCACTAGTCAG

              *      
       3670 ATTAACTGA
          1 ATAAACTGA

       3679 TGAAGATTAC


Statistics
Matches: 101,  Mismatches: 18, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
 110  101  1.00

ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25


Consensus pattern (110 bp):   
ATAAACTGACGATATAAAAGGTGAGCCCAACTCTAATTGGATAAACCAACAAATATTACGCCCAG
CGTTAGTCGGATAAACCGACAAGTTATGTGCCCAGCACTAGTCAG
Done.