Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010947.1 Corchorus capsularis cultivar CVL-1 contig10968, 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: 7926
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:265 original size:42 final size:41

Alignment explanation


    Indices: 193--345  Score: 137
    Period size: 42  Copynumber: 3.7  Consensus size: 41

        183 TCTAATATTC

                     *   *    * *    *                
        193 TAACATTTTTAAGTGTTATAGATTGGATTGGTTGGCAAATTT
          1 TAACATTTTCAAGCGTTACAAATTGTATTGGTTGGC-AATTT

                                                 * * *
        235 TAACATTTTCAAGCGTTACAAATTGTATTGGTTGGCTGAGTC
          1 TAACATTTTCAAGCGTTACAAATTGTATTGGTTGGC-AATTT

              *                  *             * *    
        277 TATCATTTTCAA-CTGTTACAGATTGTATTGGTTGACTATTT
          1 TAACATTTTCAAGC-GTTACAAATTGTATTGGTTGGCAATTT

                 *    *                 
        318 TCAACGTTTTTAAGCGTTACAAATTGTA
          1 T-AACATTTTCAAGCGTTACAAATTGTA

        346 CTGTTTGAAT


Statistics
Matches: 89,  Mismatches: 19, Indels: 6
        0.78            0.17        0.05

Matches are distributed among these distances:
  41    4  0.04
  42   84  0.94
  43    1  0.01

ACGTcount: A:0.27, C:0.11, G:0.18, T:0.43


Consensus pattern (41 bp):   
TAACATTTTCAAGCGTTACAAATTGTATTGGTTGGCAATTT

Found at i:337 original size:84 final size:84

Alignment explanation


    Indices: 191--345  Score: 213
    Period size: 84  Copynumber: 1.8  Consensus size: 84

        181 TTTCTAATAT

                       *  *     *               *                            
        191 TCTAACATTTTTAAGTGTTATAGATTGGATTGGTTGGCAAATTTTAACATTTTCAAGCGTTACAA
          1 TCTAACATTTTCAACTGTTACAGATTGGATTGGTTGACAAATTTTAACATTTTCAAGCGTTACAA

                               
        256 ATTGTATTGGTTGGCTGAG
         66 ATTGTATTGGTTGGCTGAG

                *                      *           *         *    *          
        275 TCTATCATTTTCAACTGTTACAGATTGTATTGGTTGAC-TATTTTCAACGTTTTTAAGCGTTACA
          1 TCTAACATTTTCAACTGTTACAGATTGGATTGGTTGACAAATTTT-AACATTTTCAAGCGTTACA

                   
        339 AATTGTA
         65 AATTGTA

        346 CTGTTTGAAT


Statistics
Matches: 61,  Mismatches: 9, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  83    5  0.08
  84   56  0.92

ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43


Consensus pattern (84 bp):   
TCTAACATTTTCAACTGTTACAGATTGGATTGGTTGACAAATTTTAACATTTTCAAGCGTTACAA
ATTGTATTGGTTGGCTGAG

Found at i:2864 original size:21 final size:21

Alignment explanation


    Indices: 2839--2881  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2829 ATACTTCCCC

                                 
       2839 ACTTAAGCATAAATTAATTAT
          1 ACTTAAGCATAAATTAATTAT

                                 
       2860 ACTTAAGCATAAATTAATTAT
          1 ACTTAAGCATAAATTAATTAT

             
       2881 A
          1 A

       2882 AACACCATGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37


Consensus pattern (21 bp):   
ACTTAAGCATAAATTAATTAT

Found at i:5239 original size:12 final size:12

Alignment explanation


    Indices: 5222--5261  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

       5212 GATGGCCGGT

                        
       5222 CATGTGTCTGGC
          1 CATGTGTCTGGC

                    *  *
       5234 CATGTGTCCGGT
          1 CATGTGTCTGGC

                  *     
       5246 CATGTGCCTGGC
          1 CATGTGTCTGGC

                
       5258 CATG
          1 CATG

       5262 CGATGGATGG


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  12   23  1.00

ACGTcount: A:0.10, C:0.28, G:0.33, T:0.30


Consensus pattern (12 bp):   
CATGTGTCTGGC

Found at i:7726 original size:21 final size:21

Alignment explanation


    Indices: 7701--7740  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7691 ACCATGGACG

                                 
       7701 AGACAGATACAAAAATGAAAA
          1 AGACAGATACAAAAATGAAAA

                    *  *       
       7722 AGACAGATTCAGAAATGAA
          1 AGACAGATACAAAAATGAA

       7741 GAAGTTCAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.60, C:0.10, G:0.17, T:0.12


Consensus pattern (21 bp):   
AGACAGATACAAAAATGAAAA
Done.