Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013799.1 Corchorus olitorius cultivar O-4 contig13832, 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: 28199
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:9282 original size:17 final size:17

Alignment explanation


    Indices: 9262--9300  Score: 53
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       9252 CCTCTTTTAA

                           * 
       9262 TTTTCTG-ATTTTTTTT
          1 TTTTCTGAATTTTTTCT

                *            
       9278 TTTTTTGAATTTTTTCT
          1 TTTTCTGAATTTTTTCT

                  
       9295 TTTTCT
          1 TTTTCT

       9301 ATCTCTAATA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  16    6  0.32
  17   13  0.68

ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79


Consensus pattern (17 bp):   
TTTTCTGAATTTTTTCT

Found at i:13178 original size:27 final size:28

Alignment explanation


    Indices: 13140--13213  Score: 114
    Period size: 28  Copynumber: 2.7  Consensus size: 28

      13130 AGTGGACTTG

                                        
      13140 AAATGACCAAAATGCCCCT-GAATGTGC
          1 AAATGACCAAAATGCCCCTGGAATGTGC

                *                 * *   
      13167 AAATTACCAAAATGCCCCTGGATTTTGC
          1 AAATGACCAAAATGCCCCTGGAATGTGC

                               
      13195 AAATGACCAAAATGCCCCT
          1 AAATGACCAAAATGCCCCT

      13214 AGTTGATACT


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  27   18  0.43
  28   24  0.57

ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGGAATGTGC

Found at i:13723 original size:21 final size:22

Alignment explanation


    Indices: 13699--13739  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      13689 AAGCCCGCAC

                         *        
      13699 GCCAGCACCCG-GGCAGCACCA
          1 GCCAGCACCCGCGCCAGCACCA

                  *             
      13720 GCCAGCCCCCGCGCCAGCAC
          1 GCCAGCACCCGCGCCAGCAC

      13740 GGGGCTGCTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.20, C:0.54, G:0.27, T:0.00


Consensus pattern (22 bp):   
GCCAGCACCCGCGCCAGCACCA

Found at i:16720 original size:18 final size:19

Alignment explanation


    Indices: 16686--16721  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      16676 TGAAGACTCA

                               
      16686 TTAAAGATAATTTGAAGAT
          1 TTAAAGATAATTTGAAGAT

                    *         
      16705 TTAAAGATCA-TTGAAGA
          1 TTAAAGATAATTTGAAGA

      16722 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33


Consensus pattern (19 bp):   
TTAAAGATAATTTGAAGAT

Found at i:19474 original size:18 final size:19

Alignment explanation


    Indices: 19447--19485  Score: 53
    Period size: 18  Copynumber: 2.1  Consensus size: 19

      19437 GATTCTTGTT

                 *             
      19447 TTTGTGCAATT-GACCTAA
          1 TTTGTCCAATTAGACCTAA

                         *     
      19465 TTTGTCCAATTAGCCCTAA
          1 TTTGTCCAATTAGACCTAA

              
      19484 TT
          1 TT

      19486 GGAGATATTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   10  0.56
  19    8  0.44

ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41


Consensus pattern (19 bp):   
TTTGTCCAATTAGACCTAA

Found at i:26210 original size:3 final size:3

Alignment explanation


    Indices: 26202--26236  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      26192 ATCGTACAAC

                                                          
      26202 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

      26237 TAAATTCAGC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:27851 original size:12 final size:12

Alignment explanation


    Indices: 27834--27858  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      27824 GGGTACATAA

                        
      27834 ATAATACAGGTT
          1 ATAATACAGGTT

                        
      27846 ATAATACAGGTT
          1 ATAATACAGGTT

             
      27858 A
          1 A

      27859 ACGCGGGTCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32


Consensus pattern (12 bp):   
ATAATACAGGTT
Done.