Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006035.1 Corchorus olitorius cultivar O-4 contig06060, 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: 1689
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38


Found at i:521 original size:36 final size:36

Alignment explanation


    Indices: 474--543  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        464 TTCAATAACC

                         *      *               
        474 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
        510 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

        544 CCAAAAACTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:1387 original size:204 final size:203

Alignment explanation


    Indices: 1034--1431  Score: 699
    Period size: 204  Copynumber: 2.0  Consensus size: 203

       1024 TTAATAACTT

                                                                             
       1034 TATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
          1 TATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA

                *                                                            
       1099 TACAGCACATTATTATTATTATACATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTG
         66 TACAACACATTATTATTATTATACATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTG

                   *                 *                                       
       1164 ATTTATTGAATTAAATTAGATCAATTTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
        131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC

                     
       1229 TGATTTATC
        195 TGATTTATC

                                                                             
       1238 TATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
          1 TATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA

                                   *   *  *              *                   
       1303 TACAACACATTATTATTA-TATATATAGAATTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
         66 TACAACACATTATTATTATTATACATAAAACTATACC-AAAAAAAGTAGTTGAACATTAGTGGTT

                         *                                                   
       1367 GATTTATTAAATTTAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
        130 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC

       1432 CAATTTATTT


Statistics
Matches: 185,  Mismatches: 8, Indels: 3
        0.94            0.04        0.02

Matches are distributed among these distances:
 203   21  0.11
 204  164  0.89

ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36


Consensus pattern (203 bp):   
TATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
TACAACACATTATTATTATTATACATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCT
GATTTATC

Found at i:1624 original size:68 final size:67

Alignment explanation


    Indices: 1522--1678  Score: 305
    Period size: 68  Copynumber: 2.3  Consensus size: 67

       1512 AAACCTAAGA

                                                                             
       1522 ATTTAATTAATGTAAGTATTTTTTTTTTGGTCAAATAATGTAAGTATTTCAGTTATTATAGTATT
          1 ATTTAATTAATGTAAGTATTTTTTTTTTGGTCAAATAATGTAAGTATTTCAGTTATTATAGTATT

              
       1587 CC
         66 CC

                                                                             
       1589 ATTTAATTAATGTAAGTACTTTTTTTTTTGGTCAAATAATGTAAGTATTTCAGTTATTATAGTAT
          1 ATTTAATTAATGTAAGTA-TTTTTTTTTTGGTCAAATAATGTAAGTATTTCAGTTATTATAGTAT

               
       1654 TCC
         65 TCC

                                  
       1657 ATTTAATTAATGTAAGTATTTT
          1 ATTTAATTAATGTAAGTATTTT

       1679 AGTTATTATA


Statistics
Matches: 89,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
  67   22  0.25
  68   67  0.75

ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51


Consensus pattern (67 bp):   
ATTTAATTAATGTAAGTATTTTTTTTTTGGTCAAATAATGTAAGTATTTCAGTTATTATAGTATT
CC
Done.