Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019805.1 Corchorus olitorius cultivar O-4 contig19838, 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: 3145
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Found at i:2276 original size:52 final size:50

Alignment explanation


    Indices: 2212--2333  Score: 172
    Period size: 50  Copynumber: 2.4  Consensus size: 50

       2202 CGATCAATTT

                   *     *   *                                  
       2212 CTTTGAATTGTCTTCCACTCTAATATATTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAAT-TAA-ATATTAAAAGGACCGTCTTCCGCTTATC

                                *   *         *               
       2264 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATTAAATATTAAAAGGACCGTCTTCCGCTTATC

                                
       2314 CTTTGAACTGTCTACCAATT
          1 CTTTGAACTGTCTACCAATT

       2334 CAATTCTATA


Statistics
Matches: 64,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  50   46  0.72
  51    2  0.03
  52   16  0.25

ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38


Consensus pattern (50 bp):   
CTTTGAACTGTCTACCAATTAAATATTAAAAGGACCGTCTTCCGCTTATC

Found at i:2303 original size:50 final size:51

Alignment explanation


    Indices: 2239--2346  Score: 191
    Period size: 50  Copynumber: 2.1  Consensus size: 51

       2229 CTCTAATATA

                                                               
       2239 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TC
          1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC

                     *                                         
       2289 TTAAAAGGATCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC
          1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC

                   
       2340 TATAAAA
          1 T-TAAAA

       2347 AAGGTAATGC


Statistics
Matches: 55,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  50   47  0.85
  51    3  0.05
  52    5  0.09

ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35


Consensus pattern (51 bp):   
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC

Found at i:2428 original size:48 final size:49

Alignment explanation


    Indices: 2389--2489  Score: 143
    Period size: 50  Copynumber: 2.0  Consensus size: 49

       2379 TTAGATGAAA

                                                               
       2389 CCAAGGTTTGA-AA-TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAG
          1 CCAAGG-TTGATAATTGACTCGTATGGAAACGAGTT-GGCTTGTGGAAAAG

              * *                                             
       2438 CCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
          1 CCAAGGTTGATAATTGACTCGTATGGAAACGAG-TTGGCTTGTGGAAAAG

              
       2488 CC
          1 CC

       2490 TAAAGCATTC


Statistics
Matches: 47,  Mismatches: 2, Indels: 5
        0.87            0.04        0.09

Matches are distributed among these distances:
  48    4  0.09
  49    6  0.13
  50   35  0.74
  51    2  0.04

ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28


Consensus pattern (49 bp):   
CCAAGGTTGATAATTGACTCGTATGGAAACGAGTTGGCTTGTGGAAAAG
Done.