Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002988.1 Corchorus capsularis cultivar CVL-1 contig02996, 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: 5270
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:490 original size:10 final size:10

Alignment explanation


    Indices: 475--499  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

        465 GAGGACTCTA

                      
        475 GAATTTTCTG
          1 GAATTTTCTG

                      
        485 GAATTTTCTG
          1 GAATTTTCTG

                 
        495 GAATT
          1 GAATT

        500 GTGCAGCAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48


Consensus pattern (10 bp):   
GAATTTTCTG

Found at i:1529 original size:50 final size:50

Alignment explanation


    Indices: 1454--1553  Score: 191
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       1444 GAGGGGTTCC

                                                              
       1454 CTGAAAAGAGAAAGTCTAAGCTCTTACCTCGTGGAGATGATCCATTCCAA
          1 CTGAAAAGAGAAAGTCTAAGCTCTTACCTCGTGGAGATGATCCATTCCAA

                                                   *          
       1504 CTGAAAAGAGAAAGTCTAAGCTCTTACCTCGTGGAGATGGTCCATTCCAA
          1 CTGAAAAGAGAAAGTCTAAGCTCTTACCTCGTGGAGATGATCCATTCCAA

       1554 GTCTTGGAGA


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  50   49  1.00

ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24


Consensus pattern (50 bp):   
CTGAAAAGAGAAAGTCTAAGCTCTTACCTCGTGGAGATGATCCATTCCAA

Found at i:5010 original size:45 final size:45

Alignment explanation


    Indices: 4960--5049  Score: 162
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       4950 GATTACTTCT

                                 *                       
       4960 CCAGCTCATCATTAATACGGGGTAGGGATCTTTTAGTAATTCCAC
          1 CCAGCTCATCATTAATACGGGATAGGGATCTTTTAGTAATTCCAC

                            *                            
       5005 CCAGCTCATCATTAATTCGGGATAGGGATCTTTTAGTAATTCCAC
          1 CCAGCTCATCATTAATACGGGATAGGGATCTTTTAGTAATTCCAC

       5050 TACACTATTA


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32


Consensus pattern (45 bp):   
CCAGCTCATCATTAATACGGGATAGGGATCTTTTAGTAATTCCAC

Found at i:5247 original size:2 final size:2

Alignment explanation


    Indices: 5240--5268  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5230 TAATATGTAG

                                                       
       5240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5269 TA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.