Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012644.1 Corchorus olitorius cultivar O-4 contig12677, 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: 7603
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28


Found at i:787 original size:21 final size:22

Alignment explanation


    Indices: 758--809  Score: 70
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        748 AATCATCAAA

                *          *      
        758 GGTGATGGCACGG-GCATGGCC
          1 GGTGGTGGCACGGTGAATGGCC

                                  
        779 GGTGGTGGCACGGTGAATGGCC
          1 GGTGGTGGCACGGTGAATGGCC

               *     
        801 GGTTGTGGC
          1 GGTGGTGGC

        810 TTGGTAGTGG


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  21   12  0.44
  22   15  0.56

ACGTcount: A:0.12, C:0.19, G:0.50, T:0.19


Consensus pattern (22 bp):   
GGTGGTGGCACGGTGAATGGCC

Found at i:966 original size:33 final size:32

Alignment explanation


    Indices: 929--992  Score: 83
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        919 GCACTTGACT

                  *                          
        929 CGGCTGTGGCTGGTCCTAGCCGGGCATGAGGCG
          1 CGGCTGGGGCTGGTCCT-GCCGGGCATGAGGCG

                       *  **               
        962 CGGCTGGGGCTTGTGGTGCCGGGCATGAGGC
          1 CGGCTGGGGCTGGTCCTGCCGGGCATGAGGC

        993 TCGGATGAAG


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  32   14  0.52
  33   13  0.48

ACGTcount: A:0.08, C:0.25, G:0.48, T:0.19


Consensus pattern (32 bp):   
CGGCTGGGGCTGGTCCTGCCGGGCATGAGGCG

Found at i:1572 original size:28 final size:29

Alignment explanation


    Indices: 1532--1605  Score: 125
    Period size: 28  Copynumber: 2.6  Consensus size: 29

       1522 TTAAAATTTA

                                         
       1532 TCAGGGGCATTTTGGTCA-TTTTTTCGCC
          1 TCAGGGGCATTTTGGTCATTTTTTTCGCC

                                         
       1560 TCAGGGGCATTTTGGTCATTTTTTTCGCC
          1 TCAGGGGCATTTTGGTCATTTTTTTCGCC

                        *     
       1589 TCA-GGGCATTTAGGTCA
          1 TCAGGGGCATTTTGGTCA

       1606 AAATTACTGG


Statistics
Matches: 44,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  28   31  0.70
  29   13  0.30

ACGTcount: A:0.14, C:0.20, G:0.26, T:0.41


Consensus pattern (29 bp):   
TCAGGGGCATTTTGGTCATTTTTTTCGCC

Found at i:2349 original size:17 final size:18

Alignment explanation


    Indices: 2322--2355  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       2312 CAAACAAATA

                        *     
       2322 AAAGAAAACATGCAAGAC
          1 AAAGAAAACATGAAAGAC

                             
       2340 AAAG-AAACATGAAAGA
          1 AAAGAAAACATGAAAGA

       2356 AATGGAACCA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   11  0.73
  18    4  0.27

ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06


Consensus pattern (18 bp):   
AAAGAAAACATGAAAGAC

Found at i:6072 original size:47 final size:47

Alignment explanation


    Indices: 5464--6050  Score: 1032
    Period size: 47  Copynumber: 12.5  Consensus size: 47

       5454 AGTAAATAGA

                                                           
       5464 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                      *                    
       5511 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                                           
       5558 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                                           
       5605 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                                           
       5652 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                                           
       5699 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                                           
       5746 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

             *                     *                       
       5793 AAGTAATTAAACTAAGTAGTAAAGGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                                           
       5840 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                             *             
       5887 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAAATTAGTTTAATTCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                                      *      *    *         
       5934 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGCTTAA-TCTT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTC-T

                                      * *    **  *      *  
       5981 AGGTAATTAAACTAAGTAGTAAAAGAAGTAGAACCTATTTTAATCCT
          1 AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

                 *                 
       6028 AGGTAGTTAAACTAAGTAGTAAA
          1 AGGTAATTAAACTAAGTAGTAAA

       6051 GAGTAGTCAA


Statistics
Matches: 522,  Mismatches: 16, Indels: 4
        0.96            0.03        0.01

Matches are distributed among these distances:
  46    2  0.00
  47  519  0.99
  48    1  0.00

ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31


Consensus pattern (47 bp):   
AGGTAATTAAACTAAGTAGTAAAAGAGGAAGAATTTAGTTTAATTCT

Done.