Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014220.1 Corchorus olitorius cultivar O-4 contig14253, 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, 811

Length: 1352
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32


Found at i:825 original size:334 final size:334

Alignment explanation


    Indices: 6--1345  Score: 2262
    Period size: 334  Copynumber: 4.0  Consensus size: 334

          1 AGAAA

                                                   *          *              
          6 AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCTACAATACTCAAAAAAATCATATAAT
          1 AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAAT

             *                                                      *        
         71 TAAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAAT
         66 TCAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT

                                                                     *       
        136 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATTCATTGTG
        131 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG

                                                    *                        
        201 GCTTAGAGATTTGATTAGATATATATAGATATTTCGAGAATTCTTACTGCCAAAAATCATGCAAA
        196 GCTTAGAGATTTGATTAGATATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAAA

                                 *                           *               
        266 ACTGAGTCAGGGCCCCGAAACACATTTTTAGCCAAAAATCGTGAT-G--CGTACACGATTTCGGC
        261 ACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGC

                     
        328 TAAAATTTG
        326 TAAAATTTG

                                                                             
        337 AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAAT
          1 AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAAT

                                     *                                       
        402 TCAACGCCAAAAATATTTTAGGGTGGTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT
         66 TCAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT

                                        *                                    
        467 TTATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG
        131 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG

                 *                                   *                       
        532 GCTTACAGATTTGATTAGATGA-ATATAGATATTTCGAGAAATCTTACTGCCAAAAATCATGCAA
        196 GCTTAGAGATTTGATTAGAT-ATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAA

                                          *                                  
        596 AACTGAGTCAGGGCCCCGAAACGCATTTTTCGCCAAAAATCGTGATGGTTAGTACACGATTTCGG
        260 AACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGG

                      
        661 CTAAAATTTG
        325 CTAAAATTTG

            *       **                           *                           
        671 GAAAAAACTAACCCGAAAAGTTTTTCCCCAATTTTTTTCGACAATACTCAGAAAAATCATATAAT
          1 AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAAT

                                    *                               *   *    
        736 TCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCAGAAT
         66 TCAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT

                                                                             
        801 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG
        131 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG

             *          *          *           *          *    *           * 
        866 GTTTAGAGATTTCATTAGATGA-GTATAGATATTTTGAGAAGTCTTTCTGCTAAAAAT-ATTGGA
        196 GCTTAGAGATTTGATTAGAT-ATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCA-TGCA

                          **                                                 
        929 AAACTGAG-CTAGGATCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTC
        259 AAACTGAGTC-AGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTC

                        
        993 GGCTAAAATTTG
        323 GGCTAAAATTTG

            *           *              *                                     
       1005 CAAAAAACCGACGCGAAAAGTTTTTCCACAATTTTTTGCGACAATACTCAGAAAAATCATATAAT
          1 AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAAT

                                                                             
       1070 TCAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT
         66 TCAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT

                      *                                                      
       1135 TTATTTCTAAATAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG
        131 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG

                                                                             
       1200 GCTTAGAGATTTGATTAGATATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAAA
        196 GCTTAGAGATTTGATTAGATATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAAA

                  *               *        *                    *            
       1265 ACTGAGACAGGGCCCCGAAACGTATTTTTAGTCAAAAATCGTGATGGTTAGTGCACGATTTCGGC
        261 ACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGC

                     
       1330 TAAAATTTG
        326 TAAAATTTG

                   
       1339 AAAAAAA
          1 AAAAAAA

       1346 AAAAAAA


Statistics
Matches: 944,  Mismatches: 56, Indels: 15
        0.93            0.06        0.01

Matches are distributed among these distances:
 331  292  0.31
 332    2  0.00
 333    3  0.00
 334  645  0.68
 335    2  0.00

ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Consensus pattern (334 bp):   
AAAAAAACCGACCCGAAAAGTTTTTCCCCAATTTTTTGCGACAATACTCAGAAAAATCATATAAT
TCAACGCCAAAAATATTTTAGGGTGTTTCACGCTTCTAATATCGTTTTTCCATTTTCTTCTGAAT
TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTG
GCTTAGAGATTTGATTAGATATATATAGATATTTCGAGAAGTCTTACTGCCAAAAATCATGCAAA
ACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGC
TAAAATTTG

Done.