Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015823.1 Corchorus capsularis cultivar CVL-1 contig15844, 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: 20298
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:9256 original size:24 final size:24

Alignment explanation


    Indices: 9218--9281  Score: 74
    Period size: 24  Copynumber: 2.7  Consensus size: 24

       9208 GAAGGAAAGG

                 *    *        *   *
       9218 AACCCCATCAGAGGGAGAATCGGG
          1 AACCCTATCACAGGGAGAAACGGA

             *                      
       9242 AGCCCTATCACAGGGAGAAACGGA
          1 AACCCTATCACAGGGAGAAACGGA

                     *      
       9266 AACCCTATCGCAGGGA
          1 AACCCTATCACAGGGA

       9282 AAAGAAAAGA


Statistics
Matches: 33,  Mismatches: 7, Indels: 0
        0.82            0.17        0.00

Matches are distributed among these distances:
  24   33  1.00

ACGTcount: A:0.34, C:0.27, G:0.30, T:0.09


Consensus pattern (24 bp):   
AACCCTATCACAGGGAGAAACGGA

Found at i:14046 original size:18 final size:18

Alignment explanation


    Indices: 14019--14054  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      14009 TATCACCCCT

                 *            
      14019 CTGCTGTATCAGGTGTAG
          1 CTGCTCTATCAGGTGTAG

                              
      14037 CTGCTCTATCAGGTGTAG
          1 CTGCTCTATCAGGTGTAG

      14055 TCCCTGTTGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33


Consensus pattern (18 bp):   
CTGCTCTATCAGGTGTAG

Found at i:14612 original size:154 final size:155

Alignment explanation


    Indices: 14454--14749  Score: 361
    Period size: 154  Copynumber: 1.9  Consensus size: 155

      14444 CACCAGTAGG

                            *                  *               *         **  
      14454 CTTAGATTA-CATCCATAAGAC-TATGGAAAAAATTCTAAGTAAAA-CAGAGCTTCCCT-TGGTA
          1 CTTAGATTATC-TCCACAA-ACTTATGGAAAAAATACTAAGTAAAACCA-AAC-TCCCTATCATA

                              *              *                               
      14515 GTGAACCGACTTCACACCTCAAA-TGTCCTTAACTGAAAAACTAGCATAAGTTTTTCAT-TCTAA
         62 GTGAACCGACTTCACACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCT-TAA

               *       *                  
      14578 GTCTGTTTGAGGTGAAACTTGGCCAAGACA
        126 GTCCGTTTGAGATGAAACTTGGCCAAGACA

                                                                        *    
      14608 CTTAGATTATCTCCACAAACTTATGGAAAAAATACTAAGTAAAACCAAACTCCCTATCATGGTGA
          1 CTTAGATTATCTCCACAAACTTATGGAAAAAATACTAAGTAAAACCAAACTCCCTATCATAGTGA

             ** **   *                           *                           
      14673 AGTGGTTTCTCACCCCAAATTGTCCTTAAATGAAAAAGTAGCATAAGTTTTTCATCTTAAGTCCG
         66 ACCGACTTCACACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCTTAAGTCCG

                        
      14738 TTTGAGATGAAA
        131 TTTGAGATGAAA

      14750 TTTAGCGAAG


Statistics
Matches: 120,  Mismatches: 16, Indels: 11
        0.82            0.11        0.07

Matches are distributed among these distances:
 153    7  0.06
 154   58  0.48
 155   54  0.45
 156    1  0.01

ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29


Consensus pattern (155 bp):   
CTTAGATTATCTCCACAAACTTATGGAAAAAATACTAAGTAAAACCAAACTCCCTATCATAGTGA
ACCGACTTCACACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCTTAAGTCCG
TTTGAGATGAAACTTGGCCAAGACA

Found at i:19954 original size:33 final size:32

Alignment explanation


    Indices: 19917--20004  Score: 115
    Period size: 33  Copynumber: 2.7  Consensus size: 32

      19907 AAAGGATCGT

                                              
      19917 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
          1 GTGGCCGG-TGTGGCCGGGCATGGCC-ATGTCAA

                                           **
      19950 GTGGCCGGGTGTGGCCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGTGGCCGGGCATGGCCATGTCAA

                                  
      19983 GTGGCCGGTGATGGCCGGGCAT
          1 GTGGCCGGTG-TGGCCGGGCAT

      20005 CTCCATATCG


Statistics
Matches: 50,  Mismatches: 2, Indels: 6
        0.86            0.03        0.10

Matches are distributed among these distances:
  32    5  0.10
  33   43  0.86
  34    2  0.04

ACGTcount: A:0.09, C:0.25, G:0.48, T:0.18


Consensus pattern (32 bp):   
GTGGCCGGTGTGGCCGGGCATGGCCATGTCAA

Found at i:20021 original size:33 final size:32

Alignment explanation


    Indices: 19950--20057  Score: 119
    Period size: 33  Copynumber: 3.3  Consensus size: 32

      19940 GCCGAGTCAA

                                  **    *    
      19950 GTGGCCGGGTGTGGCCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGTGGCCGGGCATCTCCATATCGC

                                             
      19983 GTGGCCGGTGATGGCCGGGCATCTCCATATCGC
          1 GTGGCCGGTG-TGGCCGGGCATCTCCATATCGC

            *          *         *            
      20016 ATGGCCGGTGTTGCGCGGGCAACTCCA-AGTCGC
          1 GTGGCCGGTGTGGC-CGGGCATCTCCATA-TCGC

                     
      20049 GTGGCCGGT
          1 GTGGCCGGT

      20058 CACTCGCGCC


Statistics
Matches: 65,  Mismatches: 7, Indels: 6
        0.83            0.09        0.08

Matches are distributed among these distances:
  32    8  0.12
  33   57  0.88

ACGTcount: A:0.10, C:0.29, G:0.42, T:0.19


Consensus pattern (32 bp):   
GTGGCCGGTGTGGCCGGGCATCTCCATATCGC
Done.