Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022336.1 Corchorus olitorius cultivar O-4 contig22369, 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: 2542
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31


Found at i:475 original size:33 final size:31

Alignment explanation


    Indices: 402--547  Score: 121
    Period size: 33  Copynumber: 4.5  Consensus size: 31

        392 GCTATGATCA

                                       ** * 
        402 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGATTTG-TTTCATCACAAACAAC

                                             
        434 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *              
        467 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   **  *      *     *        
        500 ACTCAAATTAGGTTTAGTATCATCGCAAACAAC
          1 AC-CAAAACAGATTT-GTTTCATCACAAACAAC

              **           
        533 ATTTAAAACAGATTT
          1 A-CCAAAACAGATTT

        548 AGAATTACTC


Statistics
Matches: 94,  Mismatches: 14, Indels: 11
        0.79            0.12        0.09

Matches are distributed among these distances:
  32    7  0.07
  33   81  0.86
  34    6  0.06

ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27


Consensus pattern (31 bp):   
ACCAAAACAGATTTGTTTCATCACAAACAAC

Found at i:549 original size:33 final size:33

Alignment explanation


    Indices: 438--549  Score: 127
    Period size: 33  Copynumber: 3.4  Consensus size: 33

        428 ATTAGCATCC

                           *                * 
        438 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTATCATCACAAACAACACTT

                          *                 *
        471 AAAACAGATTTAGTGTCATCACAAACAACACTC
          1 AAAACAGATTTAGTATCATCACAAACAACACTT

               **  *            *         *  
        504 AAATTAGGTTTAGTATCATCGCAAACAACATTT
          1 AAAACAGATTTAGTATCATCACAAACAACACTT

                         
        537 AAAACAGATTTAG
          1 AAAACAGATTTAG

        550 AATTACTCTT


Statistics
Matches: 65,  Mismatches: 13, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  32    4  0.06
  33   61  0.94

ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCACAAACAACACTT
Done.