Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023047.1 Corchorus olitorius cultivar O-4 contig23080, 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: 25021
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35


Found at i:22 original size:2 final size:2

Alignment explanation


    Indices: 17--51  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          7 TTCTTTTTCT

                                                                
         17 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         52 TCTTCTTCTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:64 original size:12 final size:14

Alignment explanation


    Indices: 13--67  Score: 68
    Period size: 12  Copynumber: 4.4  Consensus size: 14

          3 TTTTTTCTTT

                          
         13 TTCTTCTCTCTCTC
          1 TTCTTCTCTCTCTC

                          
         27 -TC-TCTCTCTCTC
          1 TTCTTCTCTCTCTC

                          
         39 -TC-TCTCTCTCTC
          1 TTCTTCTCTCTCTC

                          
         51 TTCTTCT-TCT-TC
          1 TTCTTCTCTCTCTC

                 
         63 TTCTT
          1 TTCTT

         68 TTTTTTTCTT


Statistics
Matches: 39,  Mismatches: 0, Indels: 6
        0.87            0.00        0.13

Matches are distributed among these distances:
  12   29  0.74
  13    7  0.18
  14    3  0.08

ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58


Consensus pattern (14 bp):   
TTCTTCTCTCTCTC

Found at i:12448 original size:15 final size:16

Alignment explanation


    Indices: 12417--12460  Score: 54
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      12407 CGTTTAAAAC

                             
      12417 TTCTTTGTTA-TATTTT
          1 TTCTTT-TTATTATTTT

                            
      12433 TTCTTTTTATTATTTT
          1 TTCTTTTTATTATTTT

             *     *    
      12449 TACTTTTAATTA
          1 TTCTTTTTATTA

      12461 ATTAAATATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  15    3  0.12
  16   22  0.88

ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73


Consensus pattern (16 bp):   
TTCTTTTTATTATTTT

Found at i:12656 original size:30 final size:31

Alignment explanation


    Indices: 12622--12702  Score: 112
    Period size: 31  Copynumber: 2.6  Consensus size: 31

      12612 TCCATCCCGA

                                            
      12622 TAACGTTAGATCCTAAATTG-A-CACAAGAGC
          1 TAACGTTAGATCCTAAATTGTAGCACAAGA-C

                                    **     
      12652 TAACGTTAGATCCTAAATTGTAGCTTAAGAC
          1 TAACGTTAGATCCTAAATTGTAGCACAAGAC

            *                   
      12683 AAACGTTAGATCCTAAATTG
          1 TAACGTTAGATCCTAAATTG

      12703 CGCATTTAGC


Statistics
Matches: 46,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  30   20  0.43
  31   21  0.46
  32    5  0.11

ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28


Consensus pattern (31 bp):   
TAACGTTAGATCCTAAATTGTAGCACAAGAC

Found at i:23789 original size:14 final size:14

Alignment explanation


    Indices: 23770--23797  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      23760 AACACACACC

                          
      23770 ATTAGGGTTTGTTT
          1 ATTAGGGTTTGTTT

                          
      23784 ATTAGGGTTTGTTT
          1 ATTAGGGTTTGTTT

      23798 GGTAGGAAGG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57


Consensus pattern (14 bp):   
ATTAGGGTTTGTTT
Done.