Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012938.1 Corchorus olitorius cultivar O-4 contig12971, 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: 8925
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:1570 original size:24 final size:24

Alignment explanation


    Indices: 1538--1590  Score: 79
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1528 TATAAAGTCT

                *      *            
       1538 CTTTTTTTTCAGTAAAATATATTC
          1 CTTTCTTTTCAATAAAATATATTC

                          *         
       1562 CTTTCTTTTCAATAGAATATATTC
          1 CTTTCTTTTCAATAAAATATATTC

                 
       1586 CTTTC
          1 CTTTC

       1591 CTTTAGAATA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53


Consensus pattern (24 bp):   
CTTTCTTTTCAATAAAATATATTC

Found at i:1673 original size:51 final size:51

Alignment explanation


    Indices: 1595--1704  Score: 184
    Period size: 51  Copynumber: 2.2  Consensus size: 51

       1585 CCTTTCCTTT

                               *                        *      
       1595 AGAATATATTCGTTTGAATTCAATGTCATTGTATGACAAAAAAAGAGAAGA
          1 AGAATATATTCGTTTGAATACAATGTCATTGTATGACAAAAAAAAAGAAGA

                                  *                        *   
       1646 AGAATATATTCGTTTGAATACATTGTCATTGTATGACAAAAAAAAAGCAGA
          1 AGAATATATTCGTTTGAATACAATGTCATTGTATGACAAAAAAAAAGAAGA

                    
       1697 AGAATATA
          1 AGAATATA

       1705 ATGTCATTCA


Statistics
Matches: 55,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  51   55  1.00

ACGTcount: A:0.46, C:0.08, G:0.16, T:0.29


Consensus pattern (51 bp):   
AGAATATATTCGTTTGAATACAATGTCATTGTATGACAAAAAAAAAGAAGA

Found at i:3262 original size:25 final size:25

Alignment explanation


    Indices: 3228--3275  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       3218 GTAATTGTCT

                 *                   
       3228 ACTAGTATTCTCATGTTTAGTTAAA
          1 ACTAGCATTCTCATGTTTAGTTAAA

                                   
       3253 ACTAGCATTCTCATGTTTAGTTA
          1 ACTAGCATTCTCATGTTTAGTTA

       3276 TTTTAATTGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44


Consensus pattern (25 bp):   
ACTAGCATTCTCATGTTTAGTTAAA

Found at i:3352 original size:36 final size:36

Alignment explanation


    Indices: 3259--3350  Score: 141
    Period size: 36  Copynumber: 2.6  Consensus size: 36

       3249 TAAAACTAGC

                            *             *     
       3259 ATTCTCATGTTTAGTTATTTTAATTGTCTATTACGT
          1 ATTCTCATGTTTAGTTGTTTTAATTGTCTAATACGT

                                       *        
       3295 ATTCTCATGTTTAGTTGTTTTAATTGTGTAATAC-T
          1 ATTCTCATGTTTAGTTGTTTTAATTGTCTAATACGT

               *                 
       3330 ATTGTCATGTTTAGTTGTTTT
          1 ATTCTCATGTTTAGTTGTTTT

       3351 TATAGTTTAT


Statistics
Matches: 52,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  35   21  0.40
  36   31  0.60

ACGTcount: A:0.21, C:0.09, G:0.14, T:0.57


Consensus pattern (36 bp):   
ATTCTCATGTTTAGTTGTTTTAATTGTCTAATACGT

Found at i:5054 original size:27 final size:26

Alignment explanation


    Indices: 5024--5078  Score: 83
    Period size: 27  Copynumber: 2.1  Consensus size: 26

       5014 AAATCAAGCG

                 *                  *  
       5024 TATGAGATGATAGTTCTTAACTTCTAT
          1 TATGAAATGATAGTTCTT-ACTTCCAT

                                      
       5051 TATGAAATGATAGTTCTTACTTCCAT
          1 TATGAAATGATAGTTCTTACTTCCAT

              
       5077 TA
          1 TA

       5079 ATTAAGTTCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  26    9  0.35
  27   17  0.65

ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44


Consensus pattern (26 bp):   
TATGAAATGATAGTTCTTACTTCCAT
Done.