Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024339.1 Corchorus olitorius cultivar O-4 contig24372, 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: 8650
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:983 original size:17 final size:17

Alignment explanation


    Indices: 961--996  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        951 ATACAAAGAG

                             
        961 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
        978 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
        995 CT
          1 CT

        997 TTACAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA

Found at i:2699 original size:13 final size:13

Alignment explanation


    Indices: 2678--2713  Score: 54
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       2668 CTAACCCCAA

                *        
       2678 TTTTAAAAAGCAC
          1 TTTTCAAAAGCAC

                         
       2691 TTTTCAAAAGCAC
          1 TTTTCAAAAGCAC

                      
       2704 TTCTTCAAAA
          1 TT-TTCAAAA

       2714 CCAAGTTTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  13   14  0.67
  14    7  0.33

ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33


Consensus pattern (13 bp):   
TTTTCAAAAGCAC

Found at i:3474 original size:226 final size:227

Alignment explanation


    Indices: 3078--3520  Score: 721
    Period size: 226  Copynumber: 2.0  Consensus size: 227

       3068 TTATACATAA

                                           *                  *             *
       3078 TATTTTTGTAACCAGGTGAAATTACTAAATGGTCCTTCTAACTTTTAACTTGGGACGACCTTATT
          1 TATTTTTGTAACCAGGTGAAATTACTAAATGCTCCTTCTAACTTTTAACTAGGGACGACCTTATC

                                                     **                      
       3143 GCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGGTTCGTATTCCATCACTCTATAA
         66 GCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCGTATTCCATCACTCTATAA

                  *             *        *   *                    *          
       3208 CCTCATTAATCATATTTATTGTATCTAAATCCACAGAAAACGCGTTCACATTTATAGAG-AAAAA
        131 CCTCATAAATCATATTTATTATATCTAAACCCAAAGAAAACGCGTTCACATTTACAGAGCAAAAA

                                             
       3272 AACAA-TCTATAAAAATTGACTCTACATATTAT
        196 AACAATTC-ATAAAAATTGACTCTACATATTAT

                                                                    *  *     
       3304 TATTTTTGTAACCAGGTGAAATTACTAAATGCTCCTTCTAACTTTTAACCTAGGG-TGATCTTAT
          1 TATTTTTGTAACCAGGTGAAATTACTAAATGCTCCTTCTAACTTTTAA-CTAGGGACGACCTTAT

                                                                             
       3368 CGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCGTATTCCATCACTCTATA
         65 CGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCGTATTCCATCACTCTATA

                                     *                       *               
       3433 ACCTCATAAATCATATTTATTATATTTAAACCCAAAGAAAACGCGTTCATATTTACAGAGCAAAA
        130 ACCTCATAAATCATATTTATTATATCTAAACCCAAAGAAAACGCGTTCACATTTACAGAGCAAAA

                                   
       3498 AAACAATTCATAAAAATTGACTC
        195 AAACAATTCATAAAAATTGACTC

       3521 ATATGATAAT


Statistics
Matches: 200,  Mismatches: 14, Indels: 5
        0.91            0.06        0.02

Matches are distributed among these distances:
 226  169  0.85
 227   29  0.14
 228    2  0.01

ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35


Consensus pattern (227 bp):   
TATTTTTGTAACCAGGTGAAATTACTAAATGCTCCTTCTAACTTTTAACTAGGGACGACCTTATC
GCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCAATTCGTATTCCATCACTCTATAA
CCTCATAAATCATATTTATTATATCTAAACCCAAAGAAAACGCGTTCACATTTACAGAGCAAAAA
AACAATTCATAAAAATTGACTCTACATATTAT

Found at i:4283 original size:19 final size:20

Alignment explanation


    Indices: 4259--4306  Score: 59
    Period size: 19  Copynumber: 2.6  Consensus size: 20

       4249 TTAGGTGTGG

                                
       4259 AAACAAGTATACACATGCA-
          1 AAACAAGTATACACATGCAT

                                
       4278 AAACAA--ATA-ACATGCAT
          1 AAACAAGTATACACATGCAT

               *        
       4295 AAAAAAGTATAC
          1 AAACAAGTATAC

       4307 CCACATTAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 7
        0.75            0.03        0.22

Matches are distributed among these distances:
  16    7  0.29
  17    8  0.33
  19    9  0.38

ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17


Consensus pattern (20 bp):   
AAACAAGTATACACATGCAT

Found at i:5544 original size:40 final size:41

Alignment explanation


    Indices: 5429--5551  Score: 153
    Period size: 40  Copynumber: 3.0  Consensus size: 41

       5419 TTATACCTTG

                     *  *                            
       5429 GGACTAAACTTGCATTTAATTTATTAACTTAATTATTAGG-
          1 GGACTAAACCTGAATTTAATTTATTAACTTAATTATTAGGA

                                       *              
       5469 GGACTAAACCT-AGATTTAATTTATTACCTTAATTATTAGGA
          1 GGACTAAACCTGA-ATTTAATTTATTAACTTAATTATTAGGA

                                     **   *       *  
       5510 GG-CTAAACCTGAATTTAATTTATTTTCTTGATTATTAAGA
          1 GGACTAAACCTGAATTTAATTTATTAACTTAATTATTAGGA

              
       5550 GG
          1 GG

       5552 GTCAAGTTAG


Statistics
Matches: 73,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  40   70  0.96
  41    3  0.04

ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41


Consensus pattern (41 bp):   
GGACTAAACCTGAATTTAATTTATTAACTTAATTATTAGGA
Done.