Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019295.1 Corchorus olitorius cultivar O-4 contig19328, 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: 17334
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32


Found at i:1931 original size:21 final size:21

Alignment explanation


    Indices: 1907--1998  Score: 148
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       1897 TGCTAGGAGT

                       *      *  
       1907 TCATTGGAGAAAGTTCCATGC
          1 TCATTGGAGAAGGTTCCAAGC

                 *               
       1928 TCATTAGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       1949 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1970 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       1991 TCATTGGA
          1 TCATTGGA

       1999 ATTGCCTAAG


Statistics
Matches: 66,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   66  1.00

ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:3832 original size:15 final size:15

Alignment explanation


    Indices: 3812--3840  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       3802 TGGATGTTCG

                           
       3812 AAATCAACAAGCTCA
          1 AAATCAACAAGCTCA

                          
       3827 AAATCAACAAGCTC
          1 AAATCAACAAGCTC

       3841 GACTTAGTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14


Consensus pattern (15 bp):   
AAATCAACAAGCTCA

Found at i:7553 original size:21 final size:22

Alignment explanation


    Indices: 7529--7571  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       7519 TTTGCCTCAT

                                  
       7529 GCATTCATTCAT-CATGCCATG
          1 GCATTCATTCATGCATGCCATG

                  *         *     
       7550 GCATTCGTTCATGCATTCCATG
          1 GCATTCATTCATGCATGCCATG

       7572 AAGCCTTAGC


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

Matches are distributed among these distances:
  21   11  0.58
  22    8  0.42

ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35


Consensus pattern (22 bp):   
GCATTCATTCATGCATGCCATG

Found at i:9237 original size:76 final size:74

Alignment explanation


    Indices: 9102--9251  Score: 212
    Period size: 76  Copynumber: 2.0  Consensus size: 74

       9092 TTTATCTGGA

                              *                                           *  
       9102 CTGTGAGCAAAGGAATGATGAGTTCTAATCAAAAAATTTTCAAAATCAGTTTTAATCAAAACTAT
          1 CTGTGAGCAAAGGAATGACGAGTTCTAATCAAAAAATTTTCAAAATCAGTTTTAATCAAAACAAT

             *       
       9167 GGTTTCGAG
         66 GATTTCGAG

                                                *                   **       
       9176 CTGTGAGCAAAGGAATGACGATGATT-TAATCAAAAGATGTTTCAAAATCAGTTTTGGTCAAAAC
          1 CTGTGAGCAAAGGAATGACGA-G-TTCTAATCAAAAAAT-TTTCAAAATCAGTTTTAATCAAAAC

                        
       9240 AATGATTTCGAG
         63 AATGATTTCGAG

       9252 GTGACTAAAT


Statistics
Matches: 67,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  74   20  0.30
  75   12  0.18
  76   35  0.52

ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30


Consensus pattern (74 bp):   
CTGTGAGCAAAGGAATGACGAGTTCTAATCAAAAAATTTTCAAAATCAGTTTTAATCAAAACAAT
GATTTCGAG

Found at i:10357 original size:23 final size:26

Alignment explanation


    Indices: 10327--10376  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      10317 CTATCCTTCT

                                      
      10327 ATCCATCT-AT-CATC-AAGTTTTTC
          1 ATCCATCTCATCCATCAAAGTTTTTC

                     *                
      10350 ATCCATCTCGTCCATCAAAGTTTTTC
          1 ATCCATCTCATCCATCAAAGTTTTTC

             
      10376 A
          1 A

      10377 ATTTTTCAAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  23    8  0.35
  24    1  0.04
  25    4  0.17
  26   10  0.43

ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40


Consensus pattern (26 bp):   
ATCCATCTCATCCATCAAAGTTTTTC
Done.