Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013246.1 Corchorus olitorius cultivar O-4 contig13279, 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: 2742
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33


Found at i:446 original size:1 final size:1

Alignment explanation


    Indices: 440--464  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

        430 TCAGAGAGTC

                                     
        440 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

        465 GTATCTGGGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:2191 original size:50 final size:50

Alignment explanation


    Indices: 2067--2357  Score: 478
    Period size: 50  Copynumber: 5.8  Consensus size: 50

       2057 CGGAATGGAT

                             *           *                     
       2067 CGTC-TCCTGCTTATCCGTTGAACTGTCTTCCAATTCAATCTTAAAAGGA-
          1 CGTCTTCC-GCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC

                 *                     *               *      
       2116 CGTCTCCCGCTTATCCTTTGAACTGTCAACCAATTCAATCTTAGAAGGAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC

                                                              
       2166 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC

                                                              
       2216 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC

                                    *                 *        
       2266 CGTCTTCCGCTTATCCTTTGAACTATCTACCAATTCAATCTGAAAAAGGAC
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT-TAAAAGGAC

                                        *            
       2317 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCT
          1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT

       2358 CGAGAAAAAC


Statistics
Matches: 227,  Mismatches: 12, Indels: 4
        0.93            0.05        0.02

Matches are distributed among these distances:
  49   41  0.18
  50  139  0.61
  51   47  0.21

ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34


Consensus pattern (50 bp):   
CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGAC

Found at i:2356 original size:151 final size:149

Alignment explanation


    Indices: 2067--2357  Score: 476
    Period size: 151  Copynumber: 1.9  Consensus size: 149

       2057 CGGAATGGAT

                                        *                                    
       2067 CGTCTCCTGCTTATCCGTTGAACTGTCTTCCAATTCAATCTTAAAAGGACGTCTCCCGCTTATCC
          1 CGTCTCCTGCTTATCCGTTGAACTGTCTACCAATTCAATCTTAAAAGGACGTCTCCCGCTTATCC

                    *                * *                                     
       2132 TTTGAACTGTCAACCAATTCAATCTTAGAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACC
         66 TTTGAACTATCAACCAATTCAATCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACC

                               
       2197 AATTCAATCTTAAAAGGAC
        131 AATTCAATCTTAAAAGGAC

                             *                                      *        
       2216 CGTCTTCC-GCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTAT
          1 CGTC-TCCTGCTTATCCGTTGAACTGTCTACCAATTCAATCTTAAAAGGA-CGTCTCCCGCTTAT

                         *                                                   
       2280 CCTTTGAACTATCTACCAATTCAATCTGAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
         64 CCTTTGAACTATCAACCAATTCAATCT-AAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT

            *            
       2345 TCCAATTCAATCT
        128 ACCAATTCAATCT

       2358 CGAGAAAAAC


Statistics
Matches: 131,  Mismatches: 8, Indels: 4
        0.92            0.06        0.03

Matches are distributed among these distances:
 149   43  0.33
 150   41  0.31
 151   47  0.36

ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34


Consensus pattern (149 bp):   
CGTCTCCTGCTTATCCGTTGAACTGTCTACCAATTCAATCTTAAAAGGACGTCTCCCGCTTATCC
TTTGAACTATCAACCAATTCAATCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACC
AATTCAATCTTAAAAGGAC

Found at i:2733 original size:63 final size:65

Alignment explanation


    Indices: 2587--2736  Score: 162
    Period size: 63  Copynumber: 2.3  Consensus size: 65

       2577 CCGGTGCATC

                                                *            *         *     
       2587 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAACCTTTTCGAGAAACTATCTTCTGATGTGCT
          1 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAACATTTTCGAGAAACCATCTTCTGACGTGCT

             *         * *          *    *                 *          *      
       2652 TTTTAACAAGAGCATCTTCCGACCGACTTTTGAAA-ATTTT-GAGAATCCATCTTCTGGCGTAG-
          1 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAACATTTTCGAGAAACCATCTTCTGACGT-GC

             
       2714 T
         65 T

                **                
       2715 TCTTGGCAAGATCGTCTTCCGA
          1 TCTTAACAAGATCGTCTTCCGA

       2737 TCAACT


Statistics
Matches: 69,  Mismatches: 15, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
  63   34  0.49
  64    5  0.07
  65   30  0.43

ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34


Consensus pattern (65 bp):   
TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAACATTTTCGAGAAACCATCTTCTGACGTGCT
Done.