Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024829.1 Corchorus olitorius cultivar O-4 contig24862, 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: 23703
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:296 original size:33 final size:31

Alignment explanation


    Indices: 190--335  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

        180 GAGTAATTCT

                         *         *         
        190 AAATCTGTTTTAGATGTTGTTTGCGAT-AATAC
          1 AAATCTGTTTT-GGTGTTGTTTGTGATGAA-AC

                *  **                     *  
        222 TAAACCTAATTTGAGTGTTGTTTGTGATGACAC
          1 -AAATCTGTTTTG-GTGTTGTTTGTGATGAAAC

                                             
        255 TAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
          1 -AAATCTGTTTT-GGTGTTGTTTGTGATGAAAC

                             * **             
        288 AAATTCTGTTTTGGATGCTAATTGTGATGAAAAC
          1 AAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAAC

                          
        322 AAATCTGTTTTGGT
          1 AAATCTGTTTTGGT

        336 TGATCATAGC


Statistics
Matches: 94,  Mismatches: 13, Indels: 13
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    7  0.07
  33   78  0.83
  34    9  0.10

ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42


Consensus pattern (31 bp):   
AAATCTGTTTTGGTGTTGTTTGTGATGAAAC

Found at i:2165 original size:21 final size:21

Alignment explanation


    Indices: 2139--2251  Score: 167
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       2129 TGCTAGAAGT

                                  
       2139 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       2160 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
       2181 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       2202 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       2223 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       2244 TCATTGGA
          1 TCATTGGA

       2252 ATTGCCAAAG


Statistics
Matches: 87,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   85  0.98

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:9656 original size:23 final size:23

Alignment explanation


    Indices: 9612--9656  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       9602 ACTCAATTAG

                  *     *  * *     
       9612 TGTTCATGAACACGTTCGTTTAT
          1 TGTTCACGAACAAGTCCATTTAT

                                  
       9635 TGTTCACGAACAAGTCCATTTA
          1 TGTTCACGAACAAGTCCATTTA

       9657 AATGAGCCGA


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38


Consensus pattern (23 bp):   
TGTTCACGAACAAGTCCATTTAT

Found at i:14391 original size:22 final size:22

Alignment explanation


    Indices: 14360--14403  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      14350 TTCTTTCCGC

                       *          
      14360 AACAACTTCTGTCCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

                 *      *         
      14382 AACAAGTTCTGGGCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

      14404 TCCTGCGCAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25


Consensus pattern (22 bp):   
AACAACTTCTGGCCCGAAGTTG
Done.