Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017815.1 Corchorus olitorius cultivar O-4 contig17848, 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: 3112
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:391 original size:22 final size:22

Alignment explanation


    Indices: 363--464  Score: 66
    Period size: 22  Copynumber: 4.6  Consensus size: 22

        353 CAAATTATTG

                                  
        363 AAATTTCATAGTGTGGCTATCA
          1 AAATTTCATAGTGTGGCTATCA

                      *    *         
        385 AAATTTCATAATGT-ACTAGTTACA
          1 AAATTTCATAGTGTGGCTA--T-CA

               *        **         
        409 AAAATTCATAG-AAGG-TAATCA
          1 AAATTTCATAGTGTGGCT-ATCA

              *       *    **     
        430 AAGTTTCATATTGTGTTTATCA
          1 AAATTTCATAGTGTGGCTATCA

                         
        452 AAATTTCATAGTG
          1 AAATTTCATAGTG

        465 AGATTAACAC


Statistics
Matches: 58,  Mismatches: 15, Indels: 14
        0.67            0.17        0.16

Matches are distributed among these distances:
  21   13  0.22
  22   30  0.52
  23    3  0.05
  24   12  0.21

ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37


Consensus pattern (22 bp):   
AAATTTCATAGTGTGGCTATCA

Found at i:526 original size:21 final size:22

Alignment explanation


    Indices: 483--529  Score: 69
    Period size: 21  Copynumber: 2.2  Consensus size: 22

        473 ACTAAATTCT

                            *     
        483 ATAGGGAAGTTATTAACATTTC
          1 ATAGGGAAGTTATTAAAATTTC

                   *              
        505 ATAGGGAGGTTA-TAAAATTTC
          1 ATAGGGAAGTTATTAAAATTTC

                
        526 ATAG
          1 ATAG

        530 TTTGATTATC


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   12  0.52
  22   11  0.48

ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34


Consensus pattern (22 bp):   
ATAGGGAAGTTATTAAAATTTC

Found at i:616 original size:22 final size:22

Alignment explanation


    Indices: 591--671  Score: 67
    Period size: 22  Copynumber: 3.5  Consensus size: 22

        581 TATGTGGTAT

                                  
        591 TCAAAATTTTATATTAAGGTTA
          1 TCAAAATTTTATATTAAGGTTA

                                       
        613 TCAAAATTAATT-TCATATAGAGGTTA
          1 TCAAAATT--TTAT-AT-TA-AGGTTA

                          * **     
        639 TCACAAA-TTTATACTGTGGTTA
          1 TCA-AAATTTTATATTAAGGTTA

                       
        661 TCAAAATTTTA
          1 TCAAAATTTTA

        672 GAGTGTGGTG


Statistics
Matches: 48,  Mismatches: 3, Indels: 16
        0.72            0.04        0.24

Matches are distributed among these distances:
  21    3  0.06
  22   20  0.42
  23    2  0.04
  24    7  0.15
  25    3  0.06
  26   10  0.21
  27    3  0.06

ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42


Consensus pattern (22 bp):   
TCAAAATTTTATATTAAGGTTA

Found at i:678 original size:22 final size:22

Alignment explanation


    Indices: 621--777  Score: 97
    Period size: 22  Copynumber: 7.1  Consensus size: 22

        611 TATCAAAATT

                         *          
        621 AATTTCATA-TAGAGGTTATCACA
          1 AATTTCATAGT-GTGGTTATCA-A

                     *            
        644 AATTT-ATACTGTGGTTATCAA
          1 AATTTCATAGTGTGGTTATCAA

                 * *        * *   
        665 AATTTTAGAGTGTGGTGACCAA
          1 AATTTCATAGTGTGGTTATCAA

                                  *
        687 AATTTCATAG-GATGGTTATCAT
          1 AATTTCATAGTG-TGGTTATCAA

                         *     *  
        709 AATTTCATAGTGTAGTTATTAA
          1 AATTTCATAGTGTGGTTATCAA

             *  *  *  * *        *
        731 AGTTCCACAGGGAGGTTATCAC
          1 AATTTCATAGTGTGGTTATCAA

                  *      *         
        753 AATTTCTTAAG-GAGGTTATCAA
          1 AATTTCAT-AGTGTGGTTATCAA

               
        775 AAT
          1 AAT

        778 AATATAGCAA


Statistics
Matches: 103,  Mismatches: 26, Indels: 11
        0.74            0.19        0.08

Matches are distributed among these distances:
  21    7  0.07
  22   87  0.84
  23    9  0.09

ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36


Consensus pattern (22 bp):   
AATTTCATAGTGTGGTTATCAA

Found at i:3005 original size:22 final size:22

Alignment explanation


    Indices: 2980--3057  Score: 77
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       2970 AATAATTAGG

                           *      *
       2980 TTATCAAAATTTTATTGGG-AGT
          1 TTATCAAAATTTTATAGGGTA-A

                  *               
       3002 TTATCAGAATTTTATAGGGTAA
          1 TTATCAAAATTTTATAGGGTAA

                        * *  *  * 
       3024 TTATCAAAATTTCACAGTGTGA
          1 TTATCAAAATTTTATAGGGTAA

                        
       3046 TTATCAAAATTT
          1 TTATCAAAATTT

       3058 AATAAAAATA


Statistics
Matches: 47,  Mismatches: 8, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  22   46  0.98
  23    1  0.02

ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42


Consensus pattern (22 bp):   
TTATCAAAATTTTATAGGGTAA
Done.