Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012322.1 Corchorus olitorius cultivar O-4 contig12355, 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: 10349
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32


Found at i:1918 original size:84 final size:85

Alignment explanation


    Indices: 1755--2048  Score: 416
    Period size: 84  Copynumber: 3.5  Consensus size: 85

       1745 TTTGCCATAT

                                        *                             *      
       1755 AGAGAATTGCCCCTGTGTTATAATTGTGGTTGGGGAC-TTTGATATAGATGCCTCTGTATTATAA
          1 AGAGAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTTGATATAGATGCCTCTGTGTTATAA

                 *              
       1819 ATGTGCTTGAGGACTTTAG-
         66 ATGTGTTTGAGGACTTTAGA

                 *     *                                          *          
       1838 AGAGAGTTGCCTCTGTGTTATAATTGTGTTTGGGGACTTTTGATATAGATGCCTATGTGTTATAA
          1 AGAGAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTTGATATAGATGCCTCTGTGTTATAA

                             *  
       1903 ATGTGTTTGAGGACTTTGGA
         66 ATGTGTTTGAGGACTTTAGA

             *     *        *       *                      *     *           
       1923 ATA-AAGGTGCCCCTGAGTTATAAATGTGTTTGGGGACTTTTG-TATTGATGCTTCTGTGTTATA
          1 AGAGAA-TTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTTGATATAGATGCCTCTGTGTTATA

                                  
       1986 AATGTGTTTGAGGACTTTAGAA
         65 AATGTGTTTGAGGACTTTAG-A

                                  *                  
       2008 AGAGAATTGCCCCTGTGTTATAGTTGTGTTTGGGGACTTTT
          1 AGAGAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTT

       2049 ATTTATTGGG


Statistics
Matches: 184,  Mismatches: 22, Indels: 8
        0.86            0.10        0.04

Matches are distributed among these distances:
  83   34  0.18
  84   80  0.43
  85   68  0.37
  86    2  0.01

ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40


Consensus pattern (85 bp):   
AGAGAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTTGATATAGATGCCTCTGTGTTATAA
ATGTGTTTGAGGACTTTAGA

Found at i:6640 original size:19 final size:18

Alignment explanation


    Indices: 6616--6651  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6606 TGAAGACTAA

                               
       6616 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       6635 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       6652 ATTATCTCAA


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:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:8640 original size:21 final size:21

Alignment explanation


    Indices: 8614--8655  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8604 TTGAATCCCT

                                  
       8614 ATTGGATAC-AAGTGGTACTAG
          1 ATTGGAT-CTAAGTGGTACTAG

                                 
       8635 ATTGGATCTAAGTGGTACTAG
          1 ATTGGATCTAAGTGGTACTAG

       8656 GGTTTCTAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20    1  0.05
  21   19  0.95

ACGTcount: A:0.31, C:0.10, G:0.29, T:0.31


Consensus pattern (21 bp):   
ATTGGATCTAAGTGGTACTAG

Found at i:9763 original size:33 final size:33

Alignment explanation


    Indices: 9726--9872  Score: 127
    Period size: 33  Copynumber: 4.5  Consensus size: 33

       9716 CTAATTTGAG

                      *       *              
       9726 TGTTGTTTGTAATGACACGAAATCTGTTTTAGA
          1 TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

                   *       *      *  **      
       9759 TGTTGTTAGTGATGATACTAAACCTAATTT-GA
          1 TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

              *       *                      *
       9791 GTATTGTTTGCGATGACACTAAATCTGTTTTAGG
          1 -TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

             *             *               *  
       9825 TATTGTTTGTGATGAAAC-AAATTCTGTTTTGGA
          1 TGTTGTTTGTGATGACACTAAA-TCTGTTTTAGA

                **         
       9858 TGTTAATTGTGATGA
          1 TGTTGTTTGTGATGA

       9873 AAACAAATCT


Statistics
Matches: 89,  Mismatches: 22, Indels: 6
        0.76            0.19        0.05

Matches are distributed among these distances:
  32    5  0.06
  33   83  0.93
  34    1  0.01

ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

Found at i:9790 original size:66 final size:66

Alignment explanation


    Indices: 9713--9839  Score: 191
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       9703 AGTAATTCTG

                          *       *                        *                 
       9713 AACCTAATTTGAGTGTTGTTTGTAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTATTGTTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT

             
       9778 A
         66 A

                                   *       *             *       *       
       9779 AACCTAATTTGAGTATTGTTTGCGATGACACTAAATCTGTTTTAGGTATTGTTTGTGATGA
          1 AACCTAATTTGAGTATTGTTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGA

       9840 AACAAATTCT


Statistics
Matches: 54,  Mismatches: 7, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  66   54  1.00

ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42


Consensus pattern (66 bp):   
AACCTAATTTGAGTATTGTTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT
A
Done.