Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023506.1 Corchorus olitorius cultivar O-4 contig23539, 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: 5715
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2518 original size:21 final size:22

Alignment explanation


    Indices: 2466--2519  Score: 60
    Period size: 21  Copynumber: 2.6  Consensus size: 22

       2456 GGGATTGGAG

                           *      
       2466 TATTTA-TTTATTTTGTTGCTT
          1 TATTTATTTTATTTTCTTGCTT

            *      *              
       2487 AATTT-TATTATTTTCTTG-TT
          1 TATTTATTTTATTTTCTTGCTT

                         
       2507 TATTTATTTTATT
          1 TATTTATTTTATT

       2520 GTTCACATAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 4
        0.74            0.14        0.11

Matches are distributed among these distances:
  20    6  0.23
  21   20  0.77

ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72


Consensus pattern (22 bp):   
TATTTATTTTATTTTCTTGCTT

Found at i:3362 original size:21 final size:22

Alignment explanation


    Indices: 3338--3415  Score: 79
    Period size: 22  Copynumber: 3.6  Consensus size: 22

       3328 AGTTTAGTTT

                 *                
       3338 TCAAATTTTCATAGGGGGT-AA
          1 TCAAAATTTCATAGGGGGTAAA

                          * *     
       3359 TCAAAATTTCATAGTGTGTAAA
          1 TCAAAATTTCATAGGGGGTAAA

                      *     *   *  
       3381 TCAAAATTTCTTAGGTAGGTTAA
          1 TCAAAATTTCATAGG-GGGTAAA

                         
       3404 T-AAAATTTCATA
          1 TCAAAATTTCATA

       3416 ACTATCAAAA


Statistics
Matches: 46,  Mismatches: 9, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  21   16  0.35
  22   25  0.54
  23    5  0.11

ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37


Consensus pattern (22 bp):   
TCAAAATTTCATAGGGGGTAAA

Found at i:3365 original size:22 final size:23

Alignment explanation


    Indices: 3340--3389  Score: 68
    Period size: 21  Copynumber: 2.3  Consensus size: 23

       3330 TTTAGTTTTC

                                   
       3340 AAATTTTCATAGGGGGT-AATCA
          1 AAATTTTCATAGGGGGTAAATCA

                        * *        
       3362 AAA-TTTCATAGTGTGTAAATCA
          1 AAATTTTCATAGGGGGTAAATCA

                  
       3384 AAATTT
          1 AAATTT

       3390 CTTAGGTAGG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  21   11  0.46
  22   11  0.46
  23    2  0.08

ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36


Consensus pattern (23 bp):   
AAATTTTCATAGGGGGTAAATCA

Found at i:3388 original size:44 final size:44

Alignment explanation


    Indices: 3292--3415  Score: 112
    Period size: 43  Copynumber: 2.8  Consensus size: 44

       3282 TATAAACATT

                              *  *          *      *    *
       3292 ATCAAAATTTTCATGAGGAGGAAATCAAAATTCCATAGTTTAGTT
          1 ATCAAAATTTTCAT-AGGGGGTAATCAAAATTTCATAGTGTAGTA

            *                                            
       3337 TTC-AAATTTTCATAGGGGGTAATCAAAATTTCATAGTGT-GTAA
          1 ATCAAAATTTTCATAGGGGGTAATCAAAATTTCATAGTGTAGT-A

                        *        *                
       3380 ATCAAAA-TTTCTTAGGTAGGTTAAT-AAAATTTCATA
          1 ATCAAAATTTTCATAGG--GGGTAATCAAAATTTCATA

       3416 ACTATCAAAA


Statistics
Matches: 66,  Mismatches: 9, Indels: 9
        0.79            0.11        0.11

Matches are distributed among these distances:
  42    2  0.03
  43   32  0.48
  44   24  0.36
  45    8  0.12

ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36


Consensus pattern (44 bp):   
ATCAAAATTTTCATAGGGGGTAATCAAAATTTCATAGTGTAGTA

Done.