Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001429.1 Corchorus olitorius cultivar O-4 contig01429, 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, 650

Length: 1084
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31


Found at i:182 original size:21 final size:20

Alignment explanation


    Indices: 158--227  Score: 61
    Period size: 21  Copynumber: 3.2  Consensus size: 20

        148 TCTCACAGAG

                                  
        158 AGGTTATCAACAA-TCATAGGA
          1 AGGTTA-CAA-AATTCATAGGA

                                 
        179 AGGTTACAAAATTTCATAGGA
          1 AGGTTACAAAA-TTCATAGGA

                    *       *      
        200 AGGTTTATTAAAATTTTATAGGA
          1 AGG-TTA-CAAAA-TTCATAGGA

                 
        223 AGGTT
          1 AGGTT

        228 TATTAAAATT


Statistics
Matches: 43,  Mismatches: 2, Indels: 7
        0.83            0.04        0.13

Matches are distributed among these distances:
  19    2  0.05
  20    3  0.07
  21   17  0.40
  22    5  0.12
  23   16  0.37

ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33


Consensus pattern (20 bp):   
AGGTTACAAAATTCATAGGA

Found at i:250 original size:23 final size:23

Alignment explanation


    Indices: 171--243  Score: 114
    Period size: 23  Copynumber: 3.3  Consensus size: 23

        161 TTATCAACAA

                            *      
        171 TCATAGGAAGG-TTA-CAAAATT
          1 TCATAGGAAGGTTTATTAAAATT

                                   
        192 TCATAGGAAGGTTTATTAAAATT
          1 TCATAGGAAGGTTTATTAAAATT

             *                     
        215 TTATAGGAAGGTTTATTAAAATT
          1 TCATAGGAAGGTTTATTAAAATT

                  
        238 TCATAG
          1 TCATAG

        244 TTAGGTTATC


Statistics
Matches: 47,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  21   11  0.23
  22    3  0.06
  23   33  0.70

ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37


Consensus pattern (23 bp):   
TCATAGGAAGGTTTATTAAAATT

Found at i:293 original size:29 final size:29

Alignment explanation


    Indices: 235--293  Score: 66
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        225 GTTTATTAAA

                     *  **           *   
        235 ATTTCATAGTTAGGTTATCAAAGTTTCAT
          1 ATTTCATAGGTAAATTATCAAAGTTGCAT

                                          
        264 ATTTCATAGGTAAATTATCGAAA-TTGCAT
          1 ATTTCATAGGTAAATTATC-AAAGTTGCAT

             
        293 A
          1 A

        294 ACGTGGTTAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  29   22  0.88
  30    3  0.12

ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41


Consensus pattern (29 bp):   
ATTTCATAGGTAAATTATCAAAGTTGCAT

Found at i:303 original size:22 final size:22

Alignment explanation


    Indices: 278--339  Score: 79
    Period size: 22  Copynumber: 2.8  Consensus size: 22

        268 CATAGGTAAA

                 *     *     *  * 
        278 TTATCGAAATTGCATAACGTGG
          1 TTATCAAAATTTCATAAAGTAG

                        *         
        300 TTATCAAAATTTAATAAAGTAG
          1 TTATCAAAATTTCATAAAGTAG

                              
        322 TTATCAAAATTTCATAAA
          1 TTATCAAAATTTCATAAA

        340 AATATTCAAT


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   34  1.00

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


Consensus pattern (22 bp):   
TTATCAAAATTTCATAAAGTAG
Done.