Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023280.1 Corchorus olitorius cultivar O-4 contig23313, 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: 13383
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:7535 original size:19 final size:18

Alignment explanation


    Indices: 7511--7546  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7501 TGAAGACTTA

                               
       7511 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       7530 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       7547 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:13279 original size:59 final size:58

Alignment explanation


    Indices: 13112--13381  Score: 398
    Period size: 59  Copynumber: 4.6  Consensus size: 58

      13102 TTTTATCTAA

                                            **                        
      13112 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAG

                                 * *                                        
      13170 AGAGTTTTCAATTCAAAATCTCATCTTGTTTTTCTTTTAAAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTG------TTTTAAAATCCTGTTCGAGGTCTCTGTTAG

                                 *                                     
      13234 AGAGTTTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTT-TAAAATCCTGTTCGAGGTCTCTGTTAG

               *                   *         *                        
      13293 AGAATTTTCAATTCAAAATCTTATCTTGTTTT-TAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAG

                                            
      13350 AGAGTTTTCAATTCAAAATCTTACCTTGTTTT
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTTT

      13382 TT


Statistics
Matches: 193,  Mismatches: 12, Indels: 15
        0.88            0.05        0.07

Matches are distributed among these distances:
  57   54  0.28
  58   30  0.16
  59   55  0.28
  64   54  0.28

ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44


Consensus pattern (58 bp):   
AGAGTTTTCAATTCAAAATCTTACCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAG

Found at i:13358 original size:57 final size:57

Alignment explanation


    Indices: 13112--13382  Score: 398
    Period size: 57  Copynumber: 4.6  Consensus size: 57

      13102 TTTTATCTAA

                                                                      
      13112 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTG-TTTTTAATCCTGTTCGAGGTCTCTGTTAG

                                 * *                                        
      13170 AGAGTTTTCAATTCAAAATCTCATCTTGTTTTTCTTTTAAAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTG----T-TTTT--AATCCTGTTCGAGGTCTCTGTTAG

                                 *            *                        
      13234 AGAGTTTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTT-T-TAATCCTGTTCGAGGTCTCTGTTAG

               *                   *                                 
      13293 AGAATTTTCAATTCAAAATCTTATCTTGTTTTTAATCCTGTTCGAGGTCTCTGTTAG
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTTAATCCTGTTCGAGGTCTCTGTTAG

                                             
      13350 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTT
          1 AGAGTTTTCAATTCAAAATCTTACCTTGTTTTT

      13383 T


Statistics
Matches: 194,  Mismatches: 11, Indels: 17
        0.87            0.05        0.08

Matches are distributed among these distances:
  57   55  0.28
  58   27  0.14
  59   54  0.28
  60    2  0.01
  61    2  0.01
  62    4  0.02
  64   50  0.26

ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44


Consensus pattern (57 bp):   
AGAGTTTTCAATTCAAAATCTTACCTTGTTTTTAATCCTGTTCGAGGTCTCTGTTAG
Done.