Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010548.1 Corchorus olitorius cultivar O-4 contig10580, 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: 2780
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:1759 original size:214 final size:217

Alignment explanation


    Indices: 1376--1811  Score: 693
    Period size: 214  Copynumber: 2.0  Consensus size: 217

       1366 AGAATTATTA

                                        *  *                  *              
       1376 ATTTCTTTATTTTTCAATTAAAATCTTATAAGTTTGTAAGAGAAATTATTGTTCTTTCTTAAAAT
          1 ATTTCTTTATTTTTCAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTATTCTTTCTTAAAAT

                                               *                             
       1441 ATACCAAAGGCTTTTTTCTAATCAAAATATCAATATAATGAATATTAGAATTAATTAGAGACACG
         66 ATACCAAAGGCTTTTTTCTAATC-AAATAT-AATACAATGAATATTAGAATTAATTAGAGACACG

                 *          *               *                                
       1506 TGTCGTGATTTGGAGGTCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATT
        129 TGTCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATTTGTAGTGTACATTGTTATCATT

                                    
       1571 ATATATATATG-ATATGATATATG
        194 ATATATATATGAATATGATATATG

                          *                                                  
       1594 ATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTATTCTTTCTTAAAAA
          1 ATTTCTTTATTTTTCAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTATTCTTTCTT-AAAA

                *    *                                                 *     
       1659 TATAGCAAATGCGTTTTTTCTAATC-AATAT-AT-CAA-GAATATTAGAATTAATTAGATACACG
         65 TATACCAAAGGC-TTTTTTCTAATCAAATATAATACAATGAATATTAGAATTAATTAGAGACACG

                                                                             
       1720 TGTCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATTTGTAGTGTACATTGTTATCATT
        129 TGTCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATTTGTAGTGTACATTGTTATCATT

                                     
       1785 ATATATATATGATATATGATATATG
        194 ATATATATATGA-ATATGATATATG

              
       1810 AT
          1 AT

       1812 ATATGATATA


Statistics
Matches: 203,  Mismatches: 11, Indels: 10
        0.91            0.05        0.04

Matches are distributed among these distances:
 214   98  0.48
 215    2  0.01
 216   16  0.08
 218   61  0.30
 219   14  0.07
 220   12  0.06

ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42


Consensus pattern (217 bp):   
ATTTCTTTATTTTTCAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTATTCTTTCTTAAAAT
ATACCAAAGGCTTTTTTCTAATCAAATATAATACAATGAATATTAGAATTAATTAGAGACACGTG
TCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATTTGTAGTGTACATTGTTATCATTAT
ATATATATGAATATGATATATG

Found at i:1801 original size:7 final size:7

Alignment explanation


    Indices: 1784--1863  Score: 103
    Period size: 7  Copynumber: 11.3  Consensus size: 7

       1774 TTGTTATCAT

                   
       1784 TATAT-A
          1 TATATGA

                   
       1790 TATATGA
          1 TATATGA

                   
       1797 TATATGA
          1 TATATGA

                   
       1804 TATATGA
          1 TATATGA

                   
       1811 TATATGA
          1 TATATGA

                     
       1818 TATATGATA
          1 TATATG--A

                   
       1827 TATATGA
          1 TATATGA

                   
       1834 TATATGA
          1 TATATGA

                   
       1841 TATAT-A
          1 TATATGA

                    
       1847 TATGAT-A
          1 TAT-ATGA

                    
       1854 TGATATGA
          1 T-ATATGA

              
       1862 TA
          1 TA

       1864 CTACCTCCAT


Statistics
Matches: 68,  Mismatches: 0, Indels: 11
        0.86            0.00        0.14

Matches are distributed among these distances:
   6    9  0.13
   7   48  0.71
   8    4  0.06
   9    7  0.10

ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44


Consensus pattern (7 bp):   
TATATGA

Found at i:1808 original size:16 final size:16

Alignment explanation


    Indices: 1784--1859  Score: 101
    Period size: 16  Copynumber: 5.1  Consensus size: 16

       1774 TTGTTATCAT

                            
       1784 TATAT-ATATATG--A
          1 TATATGATATATGATA

                            
       1797 TATATGATATATG--A
          1 TATATGATATATGATA

                            
       1811 TATATGATATATGATA
          1 TATATGATATATGATA

                            
       1827 TATATGATATATGATA
          1 TATATGATATATGATA

                             
       1843 TATAT-ATGATATGATA
          1 TATATGAT-ATATGATA

             
       1859 T
          1 T

       1860 GATACTACCT


Statistics
Matches: 59,  Mismatches: 0, Indels: 5
        0.92            0.00        0.08

Matches are distributed among these distances:
  13    5  0.08
  14   21  0.36
  15    2  0.03
  16   31  0.53

ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45


Consensus pattern (16 bp):   
TATATGATATATGATA
Done.