Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010335.1 Corchorus capsularis cultivar CVL-1 contig10356, 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: 6381
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:4306 original size:200 final size:200

Alignment explanation


    Indices: 3956--4356  Score: 642
    Period size: 200  Copynumber: 2.0  Consensus size: 200

       3946 TGTTTGGTGC

                             *             *                                 
       3956 ACCGTTAGGGTCGATTGGGTCCGTCAGTGGCTCAAACGGCCTACCAAACATTATTTAGGGTGGGA
          1 ACCGTTAGGGTCGATTGAGTCCGTCAGTGGCCCAAACGGCCTACCAAACATTATTTAGGGTGGGA

                   *                          *   *                  *       
       4021 TCAATTGTCCTCCATTAAACACATATATTACAACTACCGAGAATATTCTCATATGTATAGTAACA
         66 TCAATTGGCCTCCATTAAACACATATATTACAACCACCAAGAATATTCTCATATGTACAGTAACA

               *     *                                         *             
       4086 AATCTAACCTGTACAGTAACCAATTTTACTCTCACCGAA-CTGATCTCACCGGTGTACCAAACAG
        131 AATATAACCCGTACAGTAACCAATTTTACTCTCACCGAATC-GATCTCACCAGTGTACCAAACAG

                  
       4150 GGCCTT
        195 GGCCTT

                  *              *                              *            
       4156 ACCGTTTGGGTCGATTGAGTCGGTCAGTGGCCCAAACGGCCTACCAAACATTTTTTAGGGTGGGA
          1 ACCGTTAGGGTCGATTGAGTCCGTCAGTGGCCCAAACGGCCTACCAAACATTATTTAGGGTGGGA

               *                      *                         *            
       4221 TCAGTTGGCCTCCATTAAACACATATTTTACAACCACCAAGAATATTCTCATCTGTACAGTAACA
         66 TCAATTGGCCTCCATTAAACACATATATTACAACCACCAAGAATATTCTCATATGTACAGTAACA

                                              *                              
       4286 AATATAACCCGTACAGTAACCAATTTTACTCTCATCGAATCGATCTCACCAGTGTACCAAACAGG
        131 AATATAACCCGTACAGTAACCAATTTTACTCTCACCGAATCGATCTCACCAGTGTACCAAACAGG

                 
       4351 GCCTT
        196 GCCTT

             
       4356 A
          1 A

       4357 GTCTTTAAAG


Statistics
Matches: 184,  Mismatches: 16, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 200  183  0.99
 201    1  0.01

ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27


Consensus pattern (200 bp):   
ACCGTTAGGGTCGATTGAGTCCGTCAGTGGCCCAAACGGCCTACCAAACATTATTTAGGGTGGGA
TCAATTGGCCTCCATTAAACACATATATTACAACCACCAAGAATATTCTCATATGTACAGTAACA
AATATAACCCGTACAGTAACCAATTTTACTCTCACCGAATCGATCTCACCAGTGTACCAAACAGG
GCCTT

Found at i:4902 original size:21 final size:22

Alignment explanation


    Indices: 4867--4911  Score: 65
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       4857 TTAATAGAAG

                                  
       4867 ATAAAAAAAGTACAAAACCCAC
          1 ATAAAAAAAGTACAAAACCCAC

                  *            *  
       4889 ATAAAACAAG-ACAAAACCTAC
          1 ATAAAAAAAGTACAAAACCCAC

              
       4910 AT
          1 AT

       4912 GCAGTGAGAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.62, C:0.22, G:0.04, T:0.11


Consensus pattern (22 bp):   
ATAAAAAAAGTACAAAACCCAC

Found at i:5059 original size:2 final size:2

Alignment explanation


    Indices: 5052--5080  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5042 ATTCGGATGT

                                                       
       5052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5081 TGACTACTAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:5668 original size:46 final size:46

Alignment explanation


    Indices: 5583--5673  Score: 119
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       5573 CAATTTAATA

                             *       *  *                 
       5583 AAAAATCACAAATACAATCCACATCGACTACTTACAATCAAATATC
          1 AAAAATCACAAATACAAACCACATCCACGACTTACAATCAAATATC

                                  *      **   *          
       5629 AAAAATCACAAATACAAACCACGTCCACGGTTTAGAATCAAATAT
          1 AAAAATCACAAATACAAACCACATCCACGACTTACAATCAAATAT

       5674 ATCTATATAT


Statistics
Matches: 38,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  46   38  1.00

ACGTcount: A:0.49, C:0.24, G:0.05, T:0.21


Consensus pattern (46 bp):   
AAAAATCACAAATACAAACCACATCCACGACTTACAATCAAATATC
Done.