Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001318.1 Corchorus capsularis cultivar CVL-1 contig01318, 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: 7053
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29


Found at i:1331 original size:190 final size:190

Alignment explanation


    Indices: 1008--1383  Score: 680
    Period size: 190  Copynumber: 2.0  Consensus size: 190

        998 AGATCAAACA

                                                                        *    
       1008 ATAAACCCATAACTAAACTAAAGATTTCTCATTAAAATAATGCTAACAAGTTGATTGGTCTACGC
          1 ATAAACCCATAACTAAACTAAAGATTTCTCATTAAAATAATGCTAACAAGTTGATTGGTCCACGC

                        *                          *                         
       1073 TGGCGCTACGAGCATTATTTTTTTAGAATCGTTACTTATTATCATACATATATTAAAAGATTTTC
         66 TGGCGCTACGAGAATTATTTTTTTAGAATCGTTACTTATCATCATACATATATTAAAAGATTTTC

                                            *                           
       1138 GCCGTAAATTTAAAATGGAGACATTGCTTTGATATGTTTATTGGGATTGTTCTATTAACG
        131 GCCGTAAATTTAAAATGGAGACATTGCTTTGACATGTTTATTGGGATTGTTCTATTAACG

                                                                          *  
       1198 ATAAACCCATAACTAAACTAAAGATTTCTCATTAAAATAATGCTAACAAGTTGATTGGTCCATGC
          1 ATAAACCCATAACTAAACTAAAGATTTCTCATTAAAATAATGCTAACAAGTTGATTGGTCCACGC

                      *     *                            *                   
       1263 TGGCGCTACGGGAATTTTTTTTTTAGAATCGTTACTTATCATCATGCATATATTAAAAGATTTTC
         66 TGGCGCTACGAGAATTATTTTTTTAGAATCGTTACTTATCATCATACATATATTAAAAGATTTTC

                                                                    
       1328 GCCGTAAATTTAAAATGGAGACATTGCTTTGACATGTTTATTGGGATTGTTCTATT
        131 GCCGTAAATTTAAAATGGAGACATTGCTTTGACATGTTTATTGGGATTGTTCTATT

       1384 TCCTTTTTTA


Statistics
Matches: 178,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 190  178  1.00

ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38


Consensus pattern (190 bp):   
ATAAACCCATAACTAAACTAAAGATTTCTCATTAAAATAATGCTAACAAGTTGATTGGTCCACGC
TGGCGCTACGAGAATTATTTTTTTAGAATCGTTACTTATCATCATACATATATTAAAAGATTTTC
GCCGTAAATTTAAAATGGAGACATTGCTTTGACATGTTTATTGGGATTGTTCTATTAACG

Found at i:5623 original size:15 final size:13

Alignment explanation


    Indices: 5591--5615  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5581 ATGAAGAAAA

                         
       5591 AAATATATCAAGC
          1 AAATATATCAAGC

                        
       5604 AAATATATCAAG
          1 AAATATATCAAG

       5616 GCACAATACG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24


Consensus pattern (13 bp):   
AAATATATCAAGC
Done.