Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011947.1 Corchorus olitorius cultivar O-4 contig11980, 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: 9702
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:375 original size:19 final size:20

Alignment explanation


    Indices: 338--376  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        328 AGCAATTTTG

                        *       
        338 CAGGGAGATCAAGACACAAA
          1 CAGGGAGATCAACACACAAA

                          *     
        358 CAGGG-GATCAACATACAAA
          1 CAGGGAGATCAACACACAAA

        377 TGACCAAAGG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   12  0.71
  20    5  0.29

ACGTcount: A:0.49, C:0.21, G:0.23, T:0.08


Consensus pattern (20 bp):   
CAGGGAGATCAACACACAAA

Found at i:5307 original size:84 final size:84

Alignment explanation


    Indices: 5166--5333  Score: 282
    Period size: 84  Copynumber: 2.0  Consensus size: 84

       5156 ACTAATGCTT

                                                        *      **            
       5166 CCTCTTCAGTGCCACTAATTCCACAGGAAAATCAATCTGATTCTGTGGCCATTCATGGTTCTTTA
          1 CCTCTTCAGTGCCACTAATTCCACAGGAAAATCAATCTGATTCTCTGGCCACACATGGTTCTTTA

                               
       5231 GTGCCACTAGCTCCACAGA
         66 GTGCCACTAGCTCCACAGA

                                            ***                              
       5250 CCTCTTCAGTGCCACTAATTCCACAGGAAAATTGTTCTGATTCTCTGGCCACACATGGTTCTTTA
          1 CCTCTTCAGTGCCACTAATTCCACAGGAAAATCAATCTGATTCTCTGGCCACACATGGTTCTTTA

                               
       5315 GTGCCACTAGCTCCACAGA
         66 GTGCCACTAGCTCCACAGA

       5334 ATAGTCGCAC


Statistics
Matches: 78,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  84   78  1.00

ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30


Consensus pattern (84 bp):   
CCTCTTCAGTGCCACTAATTCCACAGGAAAATCAATCTGATTCTCTGGCCACACATGGTTCTTTA
GTGCCACTAGCTCCACAGA

Found at i:7031 original size:27 final size:28

Alignment explanation


    Indices: 6989--7068  Score: 89
    Period size: 27  Copynumber: 3.0  Consensus size: 28

       6979 GGATAATTCA

                              *          
       6989 AAGTCAG-TCTCTCATTCCAAGTC-AGTC
          1 AAGTCAGTTCTC-CATTCAAAGTCTAGTC

                                        
       7016 AAGTCAGTTCTCCATTCAAAG-CTAGTC
          1 AAGTCAGTTCTCCATTCAAAGTCTAGTC

                *                       
       7043 AAGTTAGTT-TCCCATTCAAAGT-TAGT
          1 AAGTCAGTTCT-CCATTCAAAGTCTAGT

       7069 TCCCTAGGAT


Statistics
Matches: 47,  Mismatches: 2, Indels: 8
        0.82            0.04        0.14

Matches are distributed among these distances:
  26    2  0.04
  27   41  0.87
  28    4  0.09

ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33


Consensus pattern (28 bp):   
AAGTCAGTTCTCCATTCAAAGTCTAGTC

Found at i:8054 original size:3 final size:3

Alignment explanation


    Indices: 8046--8089  Score: 79
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       8036 CAGACCCTTG

                                 *                                    
       8046 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC

       8090 ATTTCTCAGA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TCT

Done.