Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021181.1 Corchorus olitorius cultivar O-4 contig21214, 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: 20033
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28


Found at i:19155 original size:41 final size:41

Alignment explanation


    Indices: 19108--19351  Score: 303
    Period size: 41  Copynumber: 5.9  Consensus size: 41

      19098 TCTCTCTCTC

                                                     
      19108 CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT
          1 CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT

                                          *       *    
      19149 CAAAGTCC-CTAAACACATTTATAACACAGGGGCATCTCTATT
          1 CAAAGTCCTC-AAACACATTTATAACACAGAGGCATCTATA-T

                          *                **         
      19191 CCAAAGTCCTCAAATACATTTATAACACAGAAACATCTATAT
          1 -CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT

                    *        *                      * * 
      19233 CAAAGTCCCCAAACACAATTATAACACA-AGGGCAATTCTCTCT
          1 CAAAGTCCTCAAACACATTTATAACACAGA-GGC-A-TCTATAT

            *                         *    *         
      19276 AAAAGTCCTCAAACACATTTATAACATAGAGACATCTATAT
          1 CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT

                                        *      
      19317 CAAAGTCCTCAAACACATTTATAACACAAAGGCAT
          1 CAAAGTCCTCAAACACATTTATAACACAGAGGCAT

      19352 TTCTCTTTAT


Statistics
Matches: 170,  Mismatches: 25, Indels: 16
        0.81            0.12        0.08

Matches are distributed among these distances:
  40    2  0.01
  41   98  0.58
  42    4  0.02
  43   64  0.38
  44    2  0.01

ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24


Consensus pattern (41 bp):   
CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT

Found at i:19345 original size:84 final size:84

Alignment explanation


    Indices: 19064--19357  Score: 396
    Period size: 84  Copynumber: 3.5  Consensus size: 84

      19054 TTAATAACCA

                    *                 *                                      
      19064 AAAGTCCCCAACACAATTATAACACAGGGGCAATTCTCTCTCTCCAAAGTCCTCAAACACATTTA
          1 AAAGTCCCAAACACAATTATAACACAAGGGCAA-T-TCTCTCTCCAAAGTCCTCAAACACATTTA

                      *          
      19129 TAACACAGAGGCATCTATATC
         64 TAACACAGAGACATCTATATC

                            *          *             *               *       
      19150 AAAGTCCCTAAACACATTTATAACACAGGGGC-A-TCTCTATTCCAAAGTCCTCAAATACATTTA
          1 AAAGTCCC-AAACACAATTATAACACAAGGGCAATTCTCT-CTCCAAAGTCCTCAAACACATTTA

                     *           
      19213 TAACACAGAAACATCTATATC
         64 TAACACAGAGACATCTATATC

                                                       *                     
      19234 AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTCTCT-AAAAGTCCTCAAACACATTTAT
          1 AAAGT-CCCAAACACAATTATAACACAAGGGCAATTCTCTCTCCAAAGTCCTCAAACACATTTAT

                *               
      19298 AACATAGAGACATCTATATC
         65 AACACAGAGACATCTATATC

                            *           *    *      
      19318 AAAGTCCTCAAACACATTTATAACACAAAGGCATTTCTCT
          1 AAAGTCC-CAAACACAATTATAACACAAGGGCAATTCTCT

      19358 TTATGGCAAA


Statistics
Matches: 186,  Mismatches: 16, Indels: 14
        0.86            0.07        0.06

Matches are distributed among these distances:
  83    7  0.04
  84  139  0.75
  85    5  0.03
  86   14  0.08
  87   21  0.11

ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25


Consensus pattern (84 bp):   
AAAGTCCCAAACACAATTATAACACAAGGGCAATTCTCTCTCCAAAGTCCTCAAACACATTTATA
ACACAGAGACATCTATATC

Found at i:19425 original size:2 final size:2

Alignment explanation


    Indices: 19418--19456  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      19408 TCCTATCTTG

                                                                      
      19418 TA TA TA TA TA 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 TA TA TA TA TA T

      19457 GTGTGTGTGT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:19461 original size:2 final size:2

Alignment explanation


    Indices: 19456--19494  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      19446 TATATATATA

                                                                      
      19456 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T

      19495 AGCAAAGGCC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51


Consensus pattern (2 bp):   
TG

Done.