Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023906.1 Corchorus olitorius cultivar O-4 contig23939, 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: 8868
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:3045 original size:12 final size:13

Alignment explanation


    Indices: 3030--3058  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       3020 ATCAATAAAA

                         
       3030 AAAATCAAAAT-C
          1 AAAATCAAAATCC

                         
       3042 AAAATCAAAATCC
          1 AAAATCAAAATCC

                
       3055 AAAA
          1 AAAA

       3059 GGGAATTGAT


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

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14


Consensus pattern (13 bp):   
AAAATCAAAATCC

Found at i:5078 original size:143 final size:144

Alignment explanation


    Indices: 4819--5098  Score: 409
    Period size: 143  Copynumber: 2.0  Consensus size: 144

       4809 TTCCAATTGA

                              *       *                               *      
       4819 TAAAACCTCCGGGTACCATTTCATTTTATCAAGTTTTTCATTAAAAATCCATATTTAAGTTAAAA
          1 TAAAACCTCCGGGTACCACTTCATTTCATCAAGTTTTTCATTAAAAATCCATATTTAAATTAAAA

                                                    *           **           
       4884 ATCCTTGTTCAAGGTCTCAATTCAAAGTTTGCATTGGTAAGTCCTCCGGGCATGAATTCAGAAAC
         66 ATCCTTGTTCAAGGTCTCAATTCAAAGTTTGCATTGGTAAATCCTCCGGGCACAAATTCAGAAAC

                          
       4949 CTCCGGGCAATCGG
        131 CTCCGGGCAATCGG

                          *                           *     *   *        *   
       4963 TAAAACCTCCGGGTGCCACTTCATTTCATCAAGTTTTTCA-TCAAAATTCATGTTTAAATTTAAA
          1 TAAAACCTCCGGGTACCACTTCATTTCATCAAGTTTTTCATTAAAAATCCATATTTAAATTAAAA

                     *       **     *                                   *    
       5027 ATCCTTGTTTAAGGTCTTTATTCAGAGTTTGCATTGGTAAATCCTCCGGGCACAAATTCATAAAC
         66 ATCCTTGTTCAAGGTCTCAATTCAAAGTTTGCATTGGTAAATCCTCCGGGCACAAATTCAGAAAC

                   
       5092 CTCCGGG
        131 CTCCGGG

       5099 TATTAATTAT


Statistics
Matches: 120,  Mismatches: 16, Indels: 1
        0.88            0.12        0.01

Matches are distributed among these distances:
 143   83  0.69
 144   37  0.31

ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34


Consensus pattern (144 bp):   
TAAAACCTCCGGGTACCACTTCATTTCATCAAGTTTTTCATTAAAAATCCATATTTAAATTAAAA
ATCCTTGTTCAAGGTCTCAATTCAAAGTTTGCATTGGTAAATCCTCCGGGCACAAATTCAGAAAC
CTCCGGGCAATCGG

Found at i:5365 original size:30 final size:30

Alignment explanation


    Indices: 5330--5696  Score: 511
    Period size: 30  Copynumber: 12.2  Consensus size: 30

       5320 GCTTTATCAT

                                        * 
       5330 CTTTATTTTAATCCTGGTTGAGGATCATCG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                  *         *             
       5360 CTTTATGTTAATCCTGTTTGAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                               *          
       5390 CTTTATTTTAATCCTGGTTTAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                               *   *      
       5420 CTTTATTTTAATCCTGGTTTAGGGTCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                                          
       5450 CTTTATTTTAATCCTGGTTGAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                      *     *  *          
       5480 CTTTATTTTAGTCCTGATTTAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                                          
       5510 CTTTATTTTAATCCTGGTTGAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

              **                  *       
       5540 CTGCATTTTAATCCTGGTTGAGAATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                   *           *        *  
       5570 CTTTATTCTAATCCTGGTTTAGGAAT-ACTG
          1 CTTTATTTTAATCCTGGTTGAGG-ATCATTG

                                          
       5600 CTTTATTTTAATCCTGGTTGAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

            *  **  *          *           
       5630 ATTCCTTCTAATCCTGGTGGAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

            *   *              *          
       5660 GTTTGTTTTAATCCTGGTTTAGGATCATTG
          1 CTTTATTTTAATCCTGGTTGAGGATCATTG

                   
       5690 CTTTATT
          1 CTTTATT

       5697 GCTTTATTTT


Statistics
Matches: 295,  Mismatches: 40, Indels: 4
        0.87            0.12        0.01

Matches are distributed among these distances:
  29    2  0.01
  30  291  0.99
  31    2  0.01

ACGTcount: A:0.20, C:0.14, G:0.19, T:0.46


Consensus pattern (30 bp):   
CTTTATTTTAATCCTGGTTGAGGATCATTG

Found at i:5716 original size:38 final size:38

Alignment explanation


    Indices: 5656--5730  Score: 123
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       5646 GTGGAGGATC

                *   *                             
       5656 ATTGGTTTGTTTTAATCCTGGTTTAGGATCATTGCTTT
          1 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTT

                             *                   
       5694 ATTGCTTTATTTTAATCTTGGTTTAGGATCATTGCTT
          1 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTT

       5731 CATCAGTTAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  38   34  1.00

ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53


Consensus pattern (38 bp):   
ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTT
Done.