Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024530.1 Corchorus olitorius cultivar O-4 contig24563, 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: 13455
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32


Found at i:2605 original size:28 final size:28

Alignment explanation


    Indices: 2574--2643  Score: 131
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       2564 AGTGCACTCG

                             *          
       2574 AAATGACCAAAATGCCCTTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                                        
       2602 AAATGACCAAAATGCCCCTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                          
       2630 AAATGACCAAAATG
          1 AAATGACCAAAATG

       2644 AGAAGTAAAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  28   41  1.00

ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGGAGATGAA

Found at i:2925 original size:23 final size:23

Alignment explanation


    Indices: 2899--3028  Score: 75
    Period size: 23  Copynumber: 5.3  Consensus size: 23

       2889 TAAAAGGACC

                                   
       2899 GTCTTCCGCTTATCCTTCGAACT
          1 GTCTTCCGCTTATCCTTCGAACT

                   **             * *   
       2922 GTCTTCCAATTCAAT-CTTAAAAGGACT
          1 GTCTTCCGCTT--ATCCTT---CGAACT

                                   
       2949 GTCTTCCGCTTATCCTTCGAACT
          1 GTCTTCCGCTTATCCTTCGAACT

                   **             * *  *
       2972 GTCTTCCAATTCAAT-CTTAAAAGGACC
          1 GTCTTCCGCTT--ATCCTT---CGAACT

                                   
       2999 GTCTTCCGCTTATCCTTCGAACT
          1 GTCTTCCGCTTATCCTTCGAACT

                   
       3022 GTCTTCC
          1 GTCTTCC

       3029 AATTCAATCT


Statistics
Matches: 77,  Mismatches: 18, Indels: 24
        0.65            0.15        0.20

Matches are distributed among these distances:
  23   32  0.42
  24    6  0.08
  25    8  0.10
  26    6  0.08
  27   25  0.32

ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36


Consensus pattern (23 bp):   
GTCTTCCGCTTATCCTTCGAACT

Found at i:2925 original size:50 final size:50

Alignment explanation


    Indices: 2863--3189  Score: 600
    Period size: 50  Copynumber: 6.5  Consensus size: 50

       2853 CGATCAACTT

                   *             *                            
       2863 CTTCGAATTGTCTTCCAATTCTATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                               *              
       2913 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACTGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                              
       2963 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                       *      
       3013 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                              
       3063 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                *                             *               
       3113 CTTCTAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                       
       3163 CTTCGAACTGTCTTCCAATTCAATCTT
          1 CTTCGAACTGTCTTCCAATTCAATCTT

       3190 GATATCTGGT


Statistics
Matches: 268,  Mismatches: 9, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  50  268  1.00

ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36


Consensus pattern (50 bp):   
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

Found at i:4064 original size:27 final size:27

Alignment explanation


    Indices: 4034--4117  Score: 82
    Period size: 27  Copynumber: 3.1  Consensus size: 27

       4024 TCTTTTACCT

                                       
       4034 AAGCCGCCCTTTTCGGGTTTTCAACTC
          1 AAGCCGCCCTTTTCGGGTTTTCAACTC

                  *         **  *       *
       4061 AAGCTCTCCCTTTTC-CATCCTTC-ACTT
          1 AAGC-CGCCCTTTTCGGGT-TTTCAACTC

            *                          
       4088 GAGCCGCCCTTTTCGGGTTTTCAACTC
          1 AAGCCGCCCTTTTCGGGTTTTCAACTC

               
       4115 AAG
          1 AAG

       4118 TGACCCCCAA


Statistics
Matches: 41,  Mismatches: 12, Indels: 8
        0.67            0.20        0.13

Matches are distributed among these distances:
  26   12  0.29
  27   17  0.41
  28   12  0.29

ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35


Consensus pattern (27 bp):   
AAGCCGCCCTTTTCGGGTTTTCAACTC
Done.