Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013253.1 Corchorus olitorius cultivar O-4 contig13286, 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: 41288
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:5989 original size:15 final size:16

Alignment explanation


    Indices: 5960--5989  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       5950 GTGTGAATTC

                            
       5960 AAATTGATCTTTTGAA
          1 AAATTGATCTTTTGAA

                           
       5976 AAATTGAT-TTTTGA
          1 AAATTGATCTTTTGA

       5990 TAAACTTACA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47


Consensus pattern (16 bp):   
AAATTGATCTTTTGAA

Found at i:7623 original size:22 final size:22

Alignment explanation


    Indices: 7581--7623  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7571 TTTCTAATTA

                           **     
       7581 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
       7603 ATTGTTTTC-TTAGATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

       7624 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG

Found at i:11471 original size:22 final size:21

Alignment explanation


    Indices: 11421--11472  Score: 59
    Period size: 22  Copynumber: 2.4  Consensus size: 21

      11411 GGCTTGGAAT

                *         *   *  
      11421 GGTGATGGCACGGGCATGGCC
          1 GGTGGTGGCACGGGAATGACC

                                  
      11442 GGTGGTGGCACGGTGAATGACC
          1 GGTGGTGGCACGG-GAATGACC

               *     
      11464 GGTTGTGGC
          1 GGTGGTGGC

      11473 TTGGTAGTGG


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

Matches are distributed among these distances:
  21   12  0.46
  22   14  0.54

ACGTcount: A:0.13, C:0.19, G:0.48, T:0.19


Consensus pattern (21 bp):   
GGTGGTGGCACGGGAATGACC

Found at i:14748 original size:28 final size:29

Alignment explanation


    Indices: 14688--14750  Score: 74
    Period size: 29  Copynumber: 2.2  Consensus size: 29

      14678 AAAAATAATT

                       *     **          
      14688 TTTTTTCTTTTTGAAAACGCGGAAACAAA
          1 TTTTTTCTTTTAGAAAAAACGGAAACAAA

                                 *      *
      14717 TTTTTTCTTTTAGAAAAAACGTAAA-AAC
          1 TTTTTTCTTTTAGAAAAAACGGAAACAAA

                  
      14745 TTTTTT
          1 TTTTTT

      14751 TTATCGCAAA


Statistics
Matches: 29,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  28    8  0.28
  29   21  0.72

ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44


Consensus pattern (29 bp):   
TTTTTTCTTTTAGAAAAAACGGAAACAAA

Found at i:16556 original size:11 final size:11

Alignment explanation


    Indices: 16513--16561  Score: 61
    Period size: 11  Copynumber: 4.7  Consensus size: 11

      16503 TTGAATTAAT

                       
      16513 TCTTC-AATAG
          1 TCTTCAAATAG

                       
      16523 TCTTC--A-AG
          1 TCTTCAAATAG

                        
      16531 TCTTCAAATTAG
          1 TCTTCAAA-TAG

                       
      16543 TCTTCAAATAG
          1 TCTTCAAATAG

                    
      16554 TCTTCAAA
          1 TCTTCAAA

      16562 CACGAACTTC


Statistics
Matches: 35,  Mismatches: 0, Indels: 7
        0.83            0.00        0.17

Matches are distributed among these distances:
   8    7  0.20
   9    1  0.03
  10    6  0.17
  11   11  0.31
  12   10  0.29

ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39


Consensus pattern (11 bp):   
TCTTCAAATAG

Found at i:27990 original size:18 final size:18

Alignment explanation


    Indices: 27967--28005  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      27957 GATGGCGTAG

                  *    *      
      27967 ATTGCCGTTTCTGATGCC
          1 ATTGCCATTTCCGATGCC

                         *    
      27985 ATTGCCATTTCCGTTGCC
          1 ATTGCCATTTCCGATGCC

               
      28003 ATT
          1 ATT

      28006 TCTGACATGT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41


Consensus pattern (18 bp):   
ATTGCCATTTCCGATGCC

Found at i:29503 original size:16 final size:16

Alignment explanation


    Indices: 29484--29514  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      29474 GCAAAAAAAA

                            
      29484 TGAAAATAAAAAGAAG
          1 TGAAAATAAAAAGAAG

                 *         
      29500 TGAAAGTAAAAAGAA
          1 TGAAAATAAAAAGAA

      29515 AACCTTTAAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13


Consensus pattern (16 bp):   
TGAAAATAAAAAGAAG
Done.