Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015500.1 Corchorus olitorius cultivar O-4 contig15533, 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: 6694
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Found at i:1522 original size:36 final size:36

Alignment explanation


    Indices: 1468--1537  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1458 TTCAATAACC

                       * *      *               
       1468 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTCTAATTTTGATTATCATATTTCTTA

                  *                           
       1504 TTACATTTTTTCTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTCTAATTTTGATTATCATATTTCT

       1538 CCAAAATCTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.21, C:0.11, G:0.07, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTCTAATTTTGATTATCATATTTCTTA

Found at i:2411 original size:204 final size:201

Alignment explanation


    Indices: 2023--2432  Score: 712
    Period size: 204  Copynumber: 2.0  Consensus size: 201

       2013 GCTTAAAAAC

                                *                                            
       2023 TTTATCAAAGGTGAATGTTACTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAAAGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                          *                                                  
       2088 GATACAACACATTATTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
         66 GATACAACACATTACTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG

                                         *             *                     
       2153 ATTTATTAAATTAAATTAGATCAATGTCAGACAAAATTTCAAATTTATAAAAGATATTAAAGATC
        131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC

                   
       2218 CGATTTA
        195 CGATTTA

                    *                                                        
       2225 TTTATCAATGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAAAGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                                        *        *     *  *                  
       2290 GATACAACACATTACTATTATATATATCGAACTATACCAAAAACAATTAGTTGAACATTAGTGGT
         66 GATACAACACATTACTATTATATATA--AAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGT

                                                                             
       2355 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
        129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT

                    
       2420 CCGATTTA
        194 CCGATTTA

                 
       2428 TTTAT
          1 TTTAT

       2433 TATTAAGGAA


Statistics
Matches: 197,  Mismatches: 9, Indels: 3
        0.94            0.04        0.01

Matches are distributed among these distances:
 202   88  0.45
 203   18  0.09
 204   91  0.46

ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36


Consensus pattern (201 bp):   
TTTATCAAAGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA

Found at i:2598 original size:39 final size:40

Alignment explanation


    Indices: 2544--2624  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       2534 ATACCTATGA

                                             *      
       2544 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
       2583 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
       2623 AT
          1 AT

       2625 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:3428 original size:16 final size:16

Alignment explanation


    Indices: 3407--3439  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3397 GATGTCCTAA

                            
       3407 TAAATAATCCTTCTTT
          1 TAAATAATCCTTCTTT

                            
       3423 TAAATAATCCTTCTTT
          1 TAAATAATCCTTCTTT

             
       3439 T
          1 T

       3440 TTCCCCATCG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52


Consensus pattern (16 bp):   
TAAATAATCCTTCTTT

Found at i:6245 original size:24 final size:25

Alignment explanation


    Indices: 6218--6266  Score: 64
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       6208 ATATATATAC

                                     
       6218 TATATA-TATGCTATTGAGACATGG
          1 TATATAGTATGCTATTGAGACATGG

                     *  *            
       6242 TATATATGTGTGTTATTGAGACATG
          1 TATATA-GTATGCTATTGAGACATG

       6267 CATGGGTCAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    6  0.29
  26   15  0.71

ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41


Consensus pattern (25 bp):   
TATATAGTATGCTATTGAGACATGG
Done.