Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015421.1 Corchorus capsularis cultivar CVL-1 contig15442, 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, 966

Length: 1611
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30


Found at i:1039 original size:33 final size:33

Alignment explanation


    Indices: 973--1080  Score: 107
    Period size: 33  Copynumber: 3.4  Consensus size: 33

        963 TCTCGTCACA

                     *   *            *      
        973 CAAAACAGATTTATTTTCAATGC---CATCAAC
          1 CAAAACAGAATTAATTTCAATGCTATAATCAAC

                    *                         
       1003 CAAAACAGGATT-ATTTGCAATGCTATAATCAAC
          1 CAAAACAGAATTAATTT-CAATGCTATAATCAAC

                   *         *        **     
       1036 CAAAACAAAATTAATTTTAATGCTATGTTCAAC
          1 CAAAACAGAATTAATTTCAATGCTATAATCAAC

                        
       1069 CAAAACAGAATT
          1 CAAAACAGAATT

       1081 GTTTTCATCA


Statistics
Matches: 63,  Mismatches: 10, Indels: 7
        0.79            0.12        0.09

Matches are distributed among these distances:
  29    3  0.05
  30   16  0.25
  33   40  0.63
  34    4  0.06

ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29


Consensus pattern (33 bp):   
CAAAACAGAATTAATTTCAATGCTATAATCAAC

Found at i:1143 original size:33 final size:33

Alignment explanation


    Indices: 1106--1240  Score: 114
    Period size: 33  Copynumber: 4.1  Consensus size: 33

       1096 AGCATCCAAG

                                              
       1106 ACAGATTTAGTTTCATCACAAACAACAC-CTAAA
          1 ACAGATTTAGTTTCATCACAAACAACACTC-AAA

                       *    *                
       1139 ACAGATTTAGTGTCATTACAAACAACACTCAAA
          1 ACAGATTTAGTTTCATCACAAACAACACTCAAA

            **  *      *    **               
       1172 TTAGGTTTAGTATCATTGCAAACAACACTCAAA
          1 ACAGATTTAGTTTCATCACAAACAACACTCAAA

            **  *             *                
       1205 TTAGGTTTAGTATT-ATCGCAAACAACA-TCTAAA
          1 ACAGATTTAGT-TTCATCACAAACAACACTC-AAA

               
       1238 ACA
          1 ACA

       1241 TTCTTTGCAA


Statistics
Matches: 88,  Mismatches: 11, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  32    2  0.02
  33   84  0.95
  34    2  0.02

ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27


Consensus pattern (33 bp):   
ACAGATTTAGTTTCATCACAAACAACACTCAAA
Done.