Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016285.1 Corchorus olitorius cultivar O-4 contig16318, 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: 23557
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:7317 original size:21 final size:21

Alignment explanation


    Indices: 7288--7338  Score: 93
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       7278 GGGTTGCGAG

                                 
       7288 TTTGGGCTCATGTATTAGTCT
          1 TTTGGGCTCATGTATTAGTCT

                *                
       7309 TTTGAGCTCATGTATTAGTCT
          1 TTTGGGCTCATGTATTAGTCT

                     
       7330 TTTGGGCTC
          1 TTTGGGCTC

       7339 TTTGAGACTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.14, C:0.16, G:0.24, T:0.47


Consensus pattern (21 bp):   
TTTGGGCTCATGTATTAGTCT

Found at i:7428 original size:30 final size:29

Alignment explanation


    Indices: 7393--7452  Score: 75
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       7383 TCCCTCTGTT

                    *     *               
       7393 TACAAAAAGGGATCGATTTGGTCCCCCTAC
          1 TACAAAAACGG-TCAATTTGGTCCCCCTAC

                     *              *    
       7423 TACAAAAACTGTCAATTTGGTCCCTCTAC
          1 TACAAAAACGGTCAATTTGGTCCCCCTAC

             
       7452 T
          1 T

       7453 TATAATTCGG


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  29   17  0.65
  30    9  0.35

ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28


Consensus pattern (29 bp):   
TACAAAAACGGTCAATTTGGTCCCCCTAC

Found at i:7816 original size:29 final size:29

Alignment explanation


    Indices: 7762--7817  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       7752 CCAAATTGTA

                  *              *       
       7762 AGTAGATGGACCAAATTGACAGTTTTTAT
          1 AGTAGAGGGACCAAATTGACACTTTTTAT

                                        
       7791 AGTAGAGGGACCAAATTGATC-CTTTTT
          1 AGTAGAGGGACCAAATTGA-CACTTTTT

       7818 TTGTAAATAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   23  0.96
  30    1  0.04

ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34


Consensus pattern (29 bp):   
AGTAGAGGGACCAAATTGACACTTTTTAT

Found at i:9978 original size:31 final size:30

Alignment explanation


    Indices: 9922--9979  Score: 73
    Period size: 31  Copynumber: 1.9  Consensus size: 30

       9912 GTGTATGTTT

                    *                     
       9922 TATTGGGCCCTTTTGAGTGGTTGTGAAGCA
          1 TATTGGGCACTTTTGAGTGGTTGTGAAGCA

                           *             
       9952 TATTGGGCTACTTTTTAGT-GTGTGTGAA
          1 TATTGGGC-ACTTTTGAGTGGT-TGTGAA

       9980 ATATGTTGGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  30   10  0.42
  31   14  0.58

ACGTcount: A:0.17, C:0.10, G:0.31, T:0.41


Consensus pattern (30 bp):   
TATTGGGCACTTTTGAGTGGTTGTGAAGCA

Found at i:10904 original size:224 final size:224

Alignment explanation


    Indices: 10512--10956  Score: 836
    Period size: 224  Copynumber: 2.0  Consensus size: 224

      10502 CCGCGCCACA

                                  *                                     *    
      10512 TGGCGCGGGCTGTATCTTTTGCTTTTTCTTTTTTCTTTCATTATACTATATAATATTTGGTTAAA
          1 TGGCGCGGGCTGTATCTTTTGCCTTTTCTTTTTTCTTTCATTATACTATATAATATTTGGCTAAA

                                                                  *          
      10577 TTTGTAATTTTGTTTACATATATTCTTATTGGCTAAAAAAGCAAACGTGTCAATTTGTGGGAGCC
         66 TTTGTAATTTTGTTTACATATATTCTTATTGGCTAAAAAAGCAAACGTGTCAATCTGTGGGAGCC

                  *                        *                      *          
      10642 TTAGGGGAAATCCAGGTGTCAAAGAGGGATGGGGCCACGCGGCAGAAGGAGGGAGCCTCACGGGA
        131 TTAGGGAAAATCCAGGTGTCAAAGAGGGATGAGGCCACGCGGCAGAAGGAGGGAACCTCACGGGA

                                         
      10707 CTCCTTTTAATGGGAAAGAGGTTTGAATG
        196 CTCCTTTTAATGGGAAAGAGGTTTGAATG

                                                                             
      10736 TGGCGCGGGCTGTATCTTTTGCCTTTTCTTTTTTCTTTCATTATACTATATAATATTTGGCTAAA
          1 TGGCGCGGGCTGTATCTTTTGCCTTTTCTTTTTTCTTTCATTATACTATATAATATTTGGCTAAA

                                                                             
      10801 TTTGTAATTTTGTTTACATATATTCTTATTGGCTAAAAAAGCAAACGTGTCAATCTGTGGGAGCC
         66 TTTGTAATTTTGTTTACATATATTCTTATTGGCTAAAAAAGCAAACGTGTCAATCTGTGGGAGCC

                                                                             
      10866 TTAGGGAAAATCCAGGTGTCAAAGAGGGATGAGGCCACGCGGCAGAAGGAGGGAACCTCACGGGA
        131 TTAGGGAAAATCCAGGTGTCAAAGAGGGATGAGGCCACGCGGCAGAAGGAGGGAACCTCACGGGA

                                      
      10931 CTCCTTTTAATGGGAAAGAGGTTTGA
        196 CTCCTTTTAATGGGAAAGAGGTTTGA

      10957 TGTTTAGTCG


Statistics
Matches: 215,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 224  215  1.00

ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34


Consensus pattern (224 bp):   
TGGCGCGGGCTGTATCTTTTGCCTTTTCTTTTTTCTTTCATTATACTATATAATATTTGGCTAAA
TTTGTAATTTTGTTTACATATATTCTTATTGGCTAAAAAAGCAAACGTGTCAATCTGTGGGAGCC
TTAGGGAAAATCCAGGTGTCAAAGAGGGATGAGGCCACGCGGCAGAAGGAGGGAACCTCACGGGA
CTCCTTTTAATGGGAAAGAGGTTTGAATG

Found at i:23479 original size:2 final size:2

Alignment explanation


    Indices: 23472--23554  Score: 148
    Period size: 2  Copynumber: 41.5  Consensus size: 2

      23462 AGATGAAGTG

                        *  *                                              
      23472 GA GA GA GA AA TA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                                         
      23514 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

      23555 TAG


Statistics
Matches: 78,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   78  1.00

ACGTcount: A:0.51, C:0.00, G:0.48, T:0.01


Consensus pattern (2 bp):   
GA

Done.