Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001763.1 Corchorus olitorius cultivar O-4 contig01763, 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, 986

Length: 1644
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30


Found at i:968 original size:153 final size:153

Alignment explanation


    Indices: 690--1092  Score: 698
    Period size: 153  Copynumber: 2.6  Consensus size: 153

        680 ATTCGTATCA

                                         *                                   
        690 ACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGATTTGC
          1 ACTAATCTTACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATTGTGATTTGC

                                                 **                          
        755 CAAATCGAAGATGATTCAGAACCGAACTAATGGGCCCTGAATGGCCCAAAATAACAAGTGTTCAA
         66 CAAATCGAAGATGATTCAGAACCGAACTAATGGGCCCCAAATGGCCCAAAATAACAAGTGTTCAA

                                   
        820 AATGAGCTAAAAATTCACAATGG
        131 AATGAGCTAAAAATTCACAATGG

                                         *         *                         
        843 ACTAATCTTACCAAAATGATTATAGTTAGTCCATAAACATTGGAAAGAAAAGCATTGTGATTTGC
          1 ACTAATCTTACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATTGTGATTTGC

                                                                             
        908 CAAATCGAAGATGATTCAGAACCGAACTAATGGGCCCCAAATGGCCCAAAATAACAAGTGTTCAA
         66 CAAATCGAAGATGATTCAGAACCGAACTAATGGGCCCCAAATGGCCCAAAATAACAAGTGTTCAA

                                   
        973 AATGAGCTAAAAATTCACAATGG
        131 AATGAGCTAAAAATTCACAATGG

                                      *            *                   *  *  
        996 ACTAATCTTACCAAAATGATTATAGTGAGCCCATAAACAGTGGAAAGAAAAGCATTGTGGTTCGC
          1 ACTAATCTTACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATTGTGATTTGC

                       **     *             
       1061 CAAATCGAAGACAATTCAAAACCGAACTAATG
         66 CAAATCGAAGATGATTCAGAACCGAACTAATG

       1093 TGATGCGCCA


Statistics
Matches: 238,  Mismatches: 12, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 153  238  1.00

ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23


Consensus pattern (153 bp):   
ACTAATCTTACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATTGTGATTTGC
CAAATCGAAGATGATTCAGAACCGAACTAATGGGCCCCAAATGGCCCAAAATAACAAGTGTTCAA
AATGAGCTAAAAATTCACAATGG

Found at i:1225 original size:21 final size:21

Alignment explanation


    Indices: 1199--1332  Score: 191
    Period size: 21  Copynumber: 6.4  Consensus size: 21

       1189 TGCTAGAAGT

                                  
       1199 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                               *  
       1220 TCATTGGAGCAA-GTTCCACGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
       1241 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       1262 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       1283 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1304 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       1325 TCATTGGA
          1 TCATTGGA

       1333 ATTGCCTAAG


Statistics
Matches: 106,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  104  0.98

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.