Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010107.1 Corchorus capsularis cultivar CVL-1 contig10128, 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: 8083
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3902 original size:222 final size:223

Alignment explanation


    Indices: 3507--3921  Score: 573
    Period size: 222  Copynumber: 1.9  Consensus size: 223

       3497 GACTAGAATA

                                                        *                    
       3507 GCGAAAATCAAACTGTAAAATTCATTAAGCAACGACTAACACAATAGTCGTTGCGAAAAGAGTAA
          1 GCGAAAATCAAACTGTAAAATTCATTAAGCAACGACTAACACAAAAGTCGTTGCGAAAAGAGTAA

                     *         **  *          *              *            *  
       3572 GATTTCGCAGCGACTTAATTTGTGGCTTCAAAAGTAATCATGTTTTTAGTAGCGACTTTCAAGGT
         66 GATTTCGCAACGACTTAATCGGTCGCTTCAAAAGCAATCATGTTTTTAGCAGCGACTTTCAAAGT

                    *                 *     *   *                            
       3637 CGCTGCGATAATCAATTTGTAAAATATATTAAGCAAGGACTAACAAAAGTCGTTGCGAAAAGAGT
        131 CGCTGCGAAAATCAATTTGTAAAATAAATTAAACAACGACTAACAAAAGTCGTTGCGAAAAGAGT

                                        
       3702 AAGATTCCGCAGCAAGTTCAAGGTCGCT
        196 AAGATTCCGCAGCAAGTTCAAGGTCGCT

                       **                    *                    *    * **  
       3730 GCGAAAATCAATTTGTAAAATAT-ATTAAGCAATGACTAACA-AAAAGTCGTTGTGAAATGTTTA
          1 GCGAAAATCAAACTGTAAAAT-TCATTAAGCAACGACTAACACAAAAGTCGTTGCGAAAAGAGTA

                                      *                     *                
       3793 AGATTTCGCAACGACTTAATCGGTCGTTTCAAAAGCAATCATGTTTTTTGCAGCGACTTTCAAAG
         65 AGATTTCGCAACGACTTAATCGGTCGCTTCAAAAGCAATCATGTTTTTAGCAGCGACTTTCAAAG

             *   * *                                      *            *    
       3858 TTGCTTCTAAAATCAATTTGTAAAATAAATTAAACAACGACTAACAGAAGTCGTTGCGAGAAGA
        130 TCGCTGCGAAAATCAATTTGTAAAATAAATTAAACAACGACTAACAAAAGTCGTTGCGAAAAGA

       3922 CTATGAATTC


Statistics
Matches: 165,  Mismatches: 26, Indels: 3
        0.85            0.13        0.02

Matches are distributed among these distances:
 222  128  0.78
 223   36  0.22
 224    1  0.01

ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28


Consensus pattern (223 bp):   
GCGAAAATCAAACTGTAAAATTCATTAAGCAACGACTAACACAAAAGTCGTTGCGAAAAGAGTAA
GATTTCGCAACGACTTAATCGGTCGCTTCAAAAGCAATCATGTTTTTAGCAGCGACTTTCAAAGT
CGCTGCGAAAATCAATTTGTAAAATAAATTAAACAACGACTAACAAAAGTCGTTGCGAAAAGAGT
AAGATTCCGCAGCAAGTTCAAGGTCGCT

Found at i:4720 original size:23 final size:23

Alignment explanation


    Indices: 4667--4721  Score: 60
    Period size: 21  Copynumber: 2.5  Consensus size: 23

       4657 CGTTTCTGAA

                       *  *      * 
       4667 AATGATCATTTTAGGATATAACG
          1 AATGATCATTTCAGAATATAAAG

               *                   
       4690 --TTATCATTTCAGAATATAAAG
          1 AATGATCATTTCAGAATATAAAG

                       
       4711 AATGATCATTT
          1 AATGATCATTT

       4722 TATTTTTTTT


Statistics
Matches: 25,  Mismatches: 5, Indels: 4
        0.74            0.15        0.12

Matches are distributed among these distances:
  21   17  0.68
  23    8  0.32

ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38


Consensus pattern (23 bp):   
AATGATCATTTCAGAATATAAAG

Found at i:4879 original size:29 final size:31

Alignment explanation


    Indices: 4813--4880  Score: 86
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       4803 TTCCGTCAGA

                       *    *         *    
       4813 TTATATCCTGATTTGATCGTTTCAAGTAACG
          1 TTATATCCTGAATTGAGCGTTTCAAGAAACG

                                    *      
       4844 TTATATCCTGAATTG-GCGTTTC-TGAAACG
          1 TTATATCCTGAATTGAGCGTTTCAAGAAACG

                    
       4873 TTATATCC
          1 TTATATCC

       4881 CAAATTGATC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  29   13  0.39
  30    6  0.18
  31   14  0.42

ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41


Consensus pattern (31 bp):   
TTATATCCTGAATTGAGCGTTTCAAGAAACG
Done.