Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012132.1 Corchorus capsularis cultivar CVL-1 contig12153, 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: 10518
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24


Found at i:4261 original size:8 final size:8

Alignment explanation


    Indices: 4243--4287  Score: 67
    Period size: 8  Copynumber: 5.9  Consensus size: 8

       4233 TCATACATAC

                    
       4243 CCAAATA-
          1 CCAAATAT

                    
       4250 CCAAATAT
          1 CCAAATAT

                    
       4258 CCAAATA-
          1 CCAAATAT

                    
       4265 CCAAATAT
          1 CCAAATAT

                    
       4273 CCAAATAT
          1 CCAAATAT

            *      
       4281 TCAAATA
          1 CCAAATA

       4288 CTCGTCAGAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
   7   14  0.40
   8   21  0.60

ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22


Consensus pattern (8 bp):   
CCAAATAT

Found at i:4263 original size:15 final size:15

Alignment explanation


    Indices: 4243--4279  Score: 74
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       4233 TCATACATAC

                           
       4243 CCAAATACCAAATAT
          1 CCAAATACCAAATAT

                           
       4258 CCAAATACCAAATAT
          1 CCAAATACCAAATAT

                   
       4273 CCAAATA
          1 CCAAATA

       4280 TTCAAATACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19


Consensus pattern (15 bp):   
CCAAATACCAAATAT

Found at i:4266 original size:23 final size:24

Alignment explanation


    Indices: 4239--4288  Score: 77
    Period size: 23  Copynumber: 2.2  Consensus size: 24

       4229 ATATTCATAC

                                    
       4239 ATACCCAAATA-CCAAATATCCAA
          1 ATACCCAAATATCCAAATATCCAA

                                *   
       4262 ATA-CCAAATATCCAAATATTCAA
          1 ATACCCAAATATCCAAATATCCAA

                
       4285 ATAC
          1 ATAC

       4289 TCGTCAGATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  22    7  0.29
  23   17  0.71

ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22


Consensus pattern (24 bp):   
ATACCCAAATATCCAAATATCCAA

Found at i:9213 original size:53 final size:53

Alignment explanation


    Indices: 9117--9270  Score: 229
    Period size: 53  Copynumber: 2.9  Consensus size: 53

       9107 CATTTATAAG

                        *                    *    *           *    
       9117 TCCCTAAACACAAAGGCAATTCTATATCAAAAGACCTCGAACACAAGGGTGTTCA
          1 TCCCTAAACACAGAGGC-A-TCTATATCAAAAGTCCTCAAACACAAGGGTATTCA

                                                                 
       9172 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
          1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA

                                  *               *        
       9225 TCCCTAAACACAGAGGCATCTACATC-AAAGTCCTCAAGCACAAGGG
          1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGG

       9271 CATCCATACT


Statistics
Matches: 93,  Mismatches: 6, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  52   19  0.20
  53   57  0.61
  54    1  0.01
  55   16  0.17

ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19


Consensus pattern (53 bp):   
TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA

Found at i:9324 original size:30 final size:30

Alignment explanation


    Indices: 9225--9326  Score: 102
    Period size: 30  Copynumber: 3.4  Consensus size: 30

       9215 AGGGTATTCA

                *                 *        
       9225 TCCCTAAACACAGAGGCATCTACA-TCAAAG
          1 TCCCCAAACACAGAGGCATCTATACT-AAAG

               *   *             *         
       9255 TCCTCAAGCACA-AGGGCATCCATACTAAAG
          1 TCCCCAAACACAGA-GGCATCTATACTAAAG

                 *                         
       9285 -CCCGTAAACACAGAGGCATCTATACTAAAG
          1 TCCC-CAAACACAGAGGCATCTATACTAAAG

                        
       9315 TCCCCAAACACA
          1 TCCCCAAACACA

       9327 TGTCACACAG


Statistics
Matches: 57,  Mismatches: 10, Indels: 10
        0.74            0.13        0.13

Matches are distributed among these distances:
  29    3  0.05
  30   49  0.86
  31    5  0.09

ACGTcount: A:0.39, C:0.31, G:0.14, T:0.16


Consensus pattern (30 bp):   
TCCCCAAACACAGAGGCATCTATACTAAAG
Done.