Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021381.1 Corchorus olitorius cultivar O-4 contig21414, 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, 990

Length: 1650
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36


Found at i:1319 original size:17 final size:17

Alignment explanation


    Indices: 1297--1330  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1287 ACAAAAATTG

                             
       1297 AAATTGTTCATAAACAA
          1 AAATTGTTCATAAACAA

                       *     
       1314 AAATTGTTCATGAACAA
          1 AAATTGTTCATAAACAA

       1331 TATAATAATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29


Consensus pattern (17 bp):   
AAATTGTTCATAAACAA

Found at i:1471 original size:16 final size:16

Alignment explanation


    Indices: 1450--1481  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1440 TATTATTATT

                            
       1450 TTATTAATAATATATA
          1 TTATTAATAATATATA

                  *         
       1466 TTATTATTAATATATA
          1 TTATTAATAATATATA

       1482 AATAATTATA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (16 bp):   
TTATTAATAATATATA

Found at i:1471 original size:24 final size:26

Alignment explanation


    Indices: 1425--1473  Score: 75
    Period size: 24  Copynumber: 2.0  Consensus size: 26

       1415 AATTTAAATA

                                      
       1425 TATTAGATAATAGAATATTATTATTT
          1 TATTAGATAATAGAATATTATTATTT

                         *           
       1451 TATTA-ATAATA-TATATTATTATT
          1 TATTAGATAATAGAATATTATTATT

       1474 AATATATAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   11  0.50
  25    6  0.27
  26    5  0.23

ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53


Consensus pattern (26 bp):   
TATTAGATAATAGAATATTATTATTT

Found at i:1569 original size:35 final size:35

Alignment explanation


    Indices: 1523--1597  Score: 141
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       1513 TTATATAAAC

                                      *        
       1523 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
          1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT

                                               
       1558 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
          1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT

                 
       1593 GAACA
          1 GAACA

       1598 TAAACGAACT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  35   39  1.00

ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23


Consensus pattern (35 bp):   
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Done.