Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024037.1 Corchorus olitorius cultivar O-4 contig24070, 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: 11996
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:716 original size:112 final size:112

Alignment explanation


    Indices: 518--721  Score: 372
    Period size: 112  Copynumber: 1.8  Consensus size: 112

        508 CCTCACGCCA

                 *  *                                                        
        518 TGCCATATGTGAAATTCAATTACATAACAATAATTGATTTTAGATAATTAATTTTAAATTCAAAC
          1 TGCCACATATGAAATTCAATTACATAACAATAATTGATTTTAGATAATTAATTTTAAATTCAAAC

                                                           
        583 AACTTTCTTCTGCCAAAATAAAGCAAATCATGCCACATAGGATTGCT
         66 AACTTTCTTCTGCCAAAATAAAGCAAATCATGCCACATAGGATTGCT

                                   *                                         
        630 TGCCACATATGAAATTCAATTACGTAACAATAATTGATTTTAGATAATTAATTTTAAATTCAAAC
          1 TGCCACATATGAAATTCAATTACATAACAATAATTGATTTTAGATAATTAATTTTAAATTCAAAC

                            *          
        695 AACTTTCTTCTGCCAAGATAAAGCAAA
         66 AACTTTCTTCTGCCAAAATAAAGCAAA

        722 AGTTTAGAAT


Statistics
Matches: 88,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 112   88  1.00

ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34


Consensus pattern (112 bp):   
TGCCACATATGAAATTCAATTACATAACAATAATTGATTTTAGATAATTAATTTTAAATTCAAAC
AACTTTCTTCTGCCAAAATAAAGCAAATCATGCCACATAGGATTGCT

Found at i:6718 original size:15 final size:16

Alignment explanation


    Indices: 6685--6724  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       6675 TTACTTTGCT

                            
       6685 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       6701 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
       6716 TTGCTTTCT
          1 TTGTTTTCT

       6725 TTCAAGCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:7078 original size:45 final size:46

Alignment explanation


    Indices: 6988--7078  Score: 114
    Period size: 45  Copynumber: 2.0  Consensus size: 46

       6978 TCTCTTTGTG

                                         *         **     
       6988 TCTGCGTTTTGATCTAAAAAAAAAAATTTGTTTTTCTTTTTTCTTT
          1 TCTGCGTTTTGATCTAAAAAAAAAAATTTATTTTTCTTTCGTCTTT

                       *   *                               
       7034 TCTGCGTTTT-TTCTGAAAAAAAAAA-TTATTTTTCTTTGCGTCTTT
          1 TCTGCGTTTTGATCTAAAAAAAAAAATTTATTTTTCTTT-CGTCTTT

       7079 AATAAAAAAA


Statistics
Matches: 39,  Mismatches: 5, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  44   11  0.28
  45   18  0.46
  46   10  0.26

ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53


Consensus pattern (46 bp):   
TCTGCGTTTTGATCTAAAAAAAAAAATTTATTTTTCTTTCGTCTTT

Found at i:7194 original size:26 final size:25

Alignment explanation


    Indices: 7136--7183  Score: 71
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       7126 TTTGAAAAAG

                  *                  
       7136 AAAAAAGAGTTTTCGTTTTTGCGAT
          1 AAAAAAAAGTTTTCGTTTTTGCGAT

                                    
       7161 AAAAAAAAGTTTT-GTGTTTTGCG
          1 AAAAAAAAGTTTTCGT-TTTTGCG

       7184 TCAAGAAAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24    2  0.10
  25   19  0.90

ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40


Consensus pattern (25 bp):   
AAAAAAAAGTTTTCGTTTTTGCGAT

Found at i:7221 original size:29 final size:29

Alignment explanation


    Indices: 7161--7230  Score: 81
    Period size: 28  Copynumber: 2.4  Consensus size: 29

       7151 TTTTTGCGAT

                    *                    
       7161 AAAAAAAAGTTTTGTGTTTTGCGTCAAGA
          1 AAAAAAAAATTTTGTGTTTTGCGTCAAGA

                                      * * 
       7190 AAAAAAAAATTTT-TGTTTCTGCGT-TATA
          1 AAAAAAAAATTTTGTGTTT-TGCGTCAAGA

                   *     
       7218 AAAAAAATATTTT
          1 AAAAAAAAATTTT

       7231 CTTTTATTTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  28   19  0.53
  29   17  0.47

ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39


Consensus pattern (29 bp):   
AAAAAAAAATTTTGTGTTTTGCGTCAAGA
Done.