Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007954.1 Corchorus capsularis cultivar CVL-1 contig07975, 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: 13318
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:9080 original size:31 final size:31

Alignment explanation


    Indices: 9044--9103  Score: 102
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       9034 TGTTCATAAG

                        *                  
       9044 TGAACAATTATGTAGAAACTTATTTGTCTTA
          1 TGAACAATTATGAAGAAACTTATTTGTCTTA

                            *            
       9075 TGAACAATTATGAAGAGACTTATTTGTCT
          1 TGAACAATTATGAAGAAACTTATTTGTCT

       9104 ATAAAAGGTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40


Consensus pattern (31 bp):   
TGAACAATTATGAAGAAACTTATTTGTCTTA

Found at i:9182 original size:37 final size:37

Alignment explanation


    Indices: 9132--9202  Score: 124
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       9122 ATATAATTAT

                              *  *               
       9132 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
          1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA

                                              
       9169 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
          1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT

       9203 GTTGATCAAG


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  37   32  1.00

ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37


Consensus pattern (37 bp):   
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA

Found at i:9324 original size:42 final size:43

Alignment explanation


    Indices: 9277--9359  Score: 116
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       9267 CGTGTTTGGC

                                          *             
       9277 TTATCGTGTCTCATGTC-TGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCATGTCGT-AATCGTGTCAAGACACGATTAAGA

                     *  *                            
       9319 TTATCGTGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCATGTCGTAATCGTGTCAAGACACGATTAA

       9360 CACGTTTAAG


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  42   24  0.67
  43   12  0.33

ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCATGTCGTAATCGTGTCAAGACACGATTAAGA

Found at i:9782 original size:12 final size:12

Alignment explanation


    Indices: 9765--9795  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       9755 TACCCTATGT

                        
       9765 AAACACGACACG
          1 AAACACGACACG

                  *     
       9777 AAACACAACACG
          1 AAACACGACACG

                   
       9789 AAACACG
          1 AAACACG

       9796 GATTGCTAGG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.55, C:0.32, G:0.13, T:0.00


Consensus pattern (12 bp):   
AAACACGACACG

Found at i:12073 original size:13 final size:13

Alignment explanation


    Indices: 12055--12089  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      12045 GATGAAGAGA

                         
      12055 ATATTTATAATTG
          1 ATATTTATAATTG

                        *
      12068 ATATTTATAATTT
          1 ATATTTATAATTG

                *    
      12081 ATATATATA
          1 ATATTTATA

      12090 TATATTATAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54


Consensus pattern (13 bp):   
ATATTTATAATTG
Done.