Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012129.1 Corchorus capsularis cultivar CVL-1 contig12150, 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: 28572
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:24338 original size:171 final size:161

Alignment explanation


    Indices: 23932--24353  Score: 420
    Period size: 171  Copynumber: 2.6  Consensus size: 161

      23922 TAAGTGGAGT

                                            *  *      *                *     
      23932 ACTTTT-AACTGCACAAGATTTTTAGCAACCGGCGCTGGAAATAGAGATTTCAGGCTAAAACATA
          1 ACTTTTCAACTGCACAAGATTTTTAGCAACCGACGGTGGAAAGAGAGATTTCAGGCTAACACATA

            **    *                   *                                      
      23996 AGCTTACCTCCAAAGTTTCCAACTTTTGTAGCACCTGATCATTAGCACCTTCCATCTCGAAAATT
         66 CCCTTATCTCCAAAGTTTCCAAC-TTCGTAGCACCTGATCATTAGCACCTTCCATCTCGAAAATT

                              *  *    * *  *
      24061 TCCTCCAACATACTGCAGTCATTTATTTGGAG
        130 TCCTCCAACATACTGCAGCCAGTTATCTCGAC

            *     *                                     *    * *      *      
      24093 GCTTTTTAACTGCACAAGATTTTTAGCAACCGACGGTGGAAAGATAGATGTGAGGCTACCACA-A
          1 ACTTTTCAACTGCACAAGATTTTTAGCAACCGACGGTGGAAAGAGAGATTTCAGGCTAACACATA

                                               *                             
      24157 CCCTTTATCTCCAAAGTTTCCAACTTCGATAGCACTTGATCATTAGCACCTTCCAATTCCATCTC
         66 CCC-TTATCTCCAAAGTTTCCAACTTCG-TAGCACCTGATCATTAGCA----CC--TTCCA--T-

                       *           *                   
      24222 CTCGAAAATTTGCTCCATA-ATATTGCAGCCAGTTATCTCGAC
        120 CTCGAAAATTTCCTCCA-ACATACTGCAGCCAGTTATCTCGAC

                     *  *         *   *      *                        *     *
      24264 ACTTTTCAATTGTACAAGATTTCTAGTAACCGATGGTGGAAAGAGAGATTTCAGGCTATCACATT
          1 ACTTTTCAACTGCACAAGATTTTTAGCAACCGACGGTGGAAAGAGAGATTTCAGGCTAACACATA

                      *               
      24329 CCCTTATCTCTAAA-TGTTCCAACTT
         66 CCCTTATCTCCAAAGT-TTCCAACTT

      24354 TTTCAGCAAC


Statistics
Matches: 212,  Mismatches: 34, Indels: 20
        0.80            0.13        0.08

Matches are distributed among these distances:
 161   10  0.05
 162   85  0.40
 166    2  0.01
 168    5  0.02
 170    2  0.01
 171  104  0.49
 172    4  0.02

ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31


Consensus pattern (161 bp):   
ACTTTTCAACTGCACAAGATTTTTAGCAACCGACGGTGGAAAGAGAGATTTCAGGCTAACACATA
CCCTTATCTCCAAAGTTTCCAACTTCGTAGCACCTGATCATTAGCACCTTCCATCTCGAAAATTT
CCTCCAACATACTGCAGCCAGTTATCTCGAC

Found at i:27724 original size:11 final size:11

Alignment explanation


    Indices: 27708--27733  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      27698 CATCGTGTTT

                       
      27708 AAATTAAAATA
          1 AAATTAAAATA

                       
      27719 AAATTAAAATA
          1 AAATTAAAATA

                
      27730 AAAT
          1 AAAT

      27734 AGAGAAGTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (11 bp):   
AAATTAAAATA

Found at i:27774 original size:17 final size:17

Alignment explanation


    Indices: 27752--27786  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      27742 ATAGTGAATA

                        *    
      27752 TAAAATTTCATCTATAT
          1 TAAAATTTCATCCATAT

                             
      27769 TAAAATTTCATCCATAT
          1 TAAAATTTCATCCATAT

             
      27786 T
          1 T

      27787 GTATAGTAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46


Consensus pattern (17 bp):   
TAAAATTTCATCCATAT
Done.