Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005986.1 Kokia drynarioides strain JFW-HI SEQ_120406, 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, 820

Length: 1367
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40


Found at i:1061 original size:16 final size:16

Alignment explanation


    Indices: 1042--1076  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1032 ATAAAATAAA

                            
       1042 TTTTTAATGTTGTTTT
          1 TTTTTAATGTTGTTTT

                 *  *       
       1058 TTTTTTATTTTGTTTT
          1 TTTTTAATGTTGTTTT

               
       1074 TTT
          1 TTT

       1077 ATTTTATTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.09, C:0.00, G:0.09, T:0.83


Consensus pattern (16 bp):   
TTTTTAATGTTGTTTT

Found at i:1073 original size:13 final size:13

Alignment explanation


    Indices: 1057--1089  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1047 AATGTTGTTT

                        *
       1057 TTTTTTTATTTTG
          1 TTTTTTTATTTTA

                         
       1070 TTTTTTTATTTTA
          1 TTTTTTTATTTTA

                   
       1083 TTTTTTT
          1 TTTTTTT

       1090 GGTTTTTGAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88


Consensus pattern (13 bp):   
TTTTTTTATTTTA

Found at i:1075 original size:18 final size:19

Alignment explanation


    Indices: 1049--1101  Score: 63
    Period size: 18  Copynumber: 2.7  Consensus size: 19

       1039 AAATTTTTAA

                      *        
       1049 TGTTGTTTTTTTTTTATTT
          1 TGTTGTTTTTATTTTATTT

                               
       1068 TGTT-TTTTTATTTTATTT
          1 TGTTGTTTTTATTTTATTT

             *              
       1086 TTTTGGTTTTTGATTT
          1 TGTT-GTTTTT-ATTT

       1102 GTTTTATTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  18   16  0.55
  19    4  0.14
  20    5  0.17
  21    4  0.14

ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81


Consensus pattern (19 bp):   
TGTTGTTTTTATTTTATTT

Found at i:1111 original size:16 final size:16

Alignment explanation


    Indices: 1041--1113  Score: 51
    Period size: 16  Copynumber: 4.4  Consensus size: 16

       1031 AATAAAATAA

                  *          
       1041 ATTTTTAATGTTGTTTT
          1 ATTTTTGAT-TTGTTTT

                  *          
       1058 -TTTTTTATTTTGTTTT
          1 ATTTTTGA-TTTGTTTT

            *      *         
       1074 TTTATTTTATTT-TTTT
          1 ATT-TTTGATTTGTTTT

             *               
       1090 GGTTTTTGATTTGTTTT
          1 -ATTTTTGATTTGTTTT

                   
       1107 ATTTTTG
          1 ATTTTTG

       1114 GTCAGTCAAA


Statistics
Matches: 47,  Mismatches: 4, Indels: 11
        0.76            0.06        0.18

Matches are distributed among these distances:
  16   30  0.64
  17   12  0.26
  18    5  0.11

ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78


Consensus pattern (16 bp):   
ATTTTTGATTTGTTTT
Done.