Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017387.1 Corchorus olitorius cultivar O-4 contig17420, 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: 22113
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:2276 original size:27 final size:27

Alignment explanation


    Indices: 2246--2320  Score: 107
    Period size: 28  Copynumber: 2.7  Consensus size: 27

       2236 AGGGTCACCT

                                *       
       2246 AGGGGCATTTTGGTCATTTTTA-AGTTC
          1 AGGGGCATTTTGGTCATTTTCACA-TTC

                                *       
       2273 AGGGGCATTTTGGTCATTTGGCACATTC
          1 AGGGGCATTTTGGTCATTT-TCACATTC

                                
       2301 AGGGGCATTTTGGTCATTTT
          1 AGGGGCATTTTGGTCATTTT

       2321 AAGATTAGCT


Statistics
Matches: 43,  Mismatches: 3, Indels: 4
        0.86            0.06        0.08

Matches are distributed among these distances:
  27   19  0.44
  28   23  0.53
  29    1  0.02

ACGTcount: A:0.17, C:0.13, G:0.28, T:0.41


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTTCACATTC

Found at i:4512 original size:22 final size:21

Alignment explanation


    Indices: 4482--4532  Score: 66
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       4472 AGGTATATTT

                                * 
       4482 CCTGATTTAATGCAATTTGATC
          1 CCTGATTT-ATGCAATTTGACC

                *     *          
       4504 CCTGCTTTATTCAATTTGACC
          1 CCTGATTTATGCAATTTGACC

                    
       4525 CCTGATTT
          1 CCTGATTT

       4533 TAGAAATTAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  21   18  0.72
  22    7  0.28

ACGTcount: A:0.22, C:0.24, G:0.12, T:0.43


Consensus pattern (21 bp):   
CCTGATTTATGCAATTTGACC

Found at i:5641 original size:15 final size:15

Alignment explanation


    Indices: 5621--5651  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5611 AAGAAGCAAT

                           
       5621 AAAAGGTGTTTTCAA
          1 AAAAGGTGTTTTCAA

                   *       
       5636 AAAAGGTTTTTTCAA
          1 AAAAGGTGTTTTCAA

             
       5651 A
          1 A

       5652 TCATGTTCTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35


Consensus pattern (15 bp):   
AAAAGGTGTTTTCAA

Found at i:7664 original size:4 final size:4

Alignment explanation


    Indices: 7657--7683  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       7647 TTTGAAAAAA

                                             
       7657 AATT AATT AATT AATT AATT AATT AAT
          1 AATT AATT AATT AATT AATT AATT AAT

       7684 AAAAAGAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (4 bp):   
AATT

Found at i:16709 original size:19 final size:18

Alignment explanation


    Indices: 16676--16711  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      16666 TGGAAATAAT

                              
      16676 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
      16694 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

      16712 TAAGTCTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:17565 original size:18 final size:18

Alignment explanation


    Indices: 17544--17580  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      17534 AGGGTAATTT

                              
      17544 TAAAAAAAAATGTTTTCA
          1 TAAAAAAAAATGTTTTCA

                  *  *        
      17562 TAAAAAGAAGTGTTTTCA
          1 TAAAAAAAAATGTTTTCA

             
      17580 T
          1 T

      17581 GATAGATGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35


Consensus pattern (18 bp):   
TAAAAAAAAATGTTTTCA
Done.