Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018354.1 Corchorus olitorius cultivar O-4 contig18387, 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: 4190
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29


Found at i:1026 original size:324 final size:323

Alignment explanation


    Indices: 1--1370  Score: 2219
    Period size: 323  Copynumber: 4.2  Consensus size: 323

                          *                       ***             *          
          1 GTTTTTAGCCAAAATCCGTGATGGTTAGTACACGATTTCAACTAAAAACTGACCTGAAAAATTTT
          1 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGAAAAATTTT

                                      *                                      
         66 TTCTCAATTTTTTGCAACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGA
         66 TTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGA

                  *         *                 *    *                         
        131 TTTTCATGCTTCTAAAAATCGTTTTCGCATTTTTCTCCCTAATTAATTTCTAATTAAATTGAAAC
        131 TTTTCAAGCTTCTAAATATCGTTTTCGCATTTTTTTCCCGAATTAATTTCTAATTAAATTGAAAC

                                                                  *          
        196 AAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGATTAGATAAAT
        196 AAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATAAAT

                                                                            
        261 ATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTAGAGCCGGGCTCCGGAACGC
        261 ATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATT-GAGCCGGGCTCCGGAACGC

                                                                             
        325 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAAAAATTT
          1 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTT-GGCTAAAAACTGACCCGAAAAATTT

                                                                             
        390 TTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGG
         65 TTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGG

                   *                                *                        
        455 ATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCCTAATTAATTTCTAATTAAATTGAAA
        130 ATTTTCAAGCTTCTAAATATCGTTTTCGCATTTTTTTCCCGAATTAATTTCTAATTAAATTGAAA

                                   *                                        *
        520 CAAGATTCAGATACTCGTAAAGATAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATTAT
        195 CAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA-TAA

                                                                             
        585 ATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGGAACGC
        259 ATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGGAACGC

                                                  *                      *   
        650 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAAACTGACCCGAAAATGTTT
          1 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGAAAA-ATTT

                    *       * *                    *                         
        714 TTTCTCAAATTTTTGCGATAATACTCAGAAAAAATATATGATTCAACGCCAAAAAGATTGACGGG
         65 TTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGG

                 *   *                     *               *               * 
        779 ATTTTAAAGATTCTAAATATCGTTTTCGCATATTTTT-CCGAATTAAGTTCTAATTAAATTGATA
        130 ATTTTCAAGCTTCTAAATATCGTTTTCGCATTTTTTTCCCGAATTAATTTCTAATTAAATTGAAA

                *                                                           *
        843 CAAGCTTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATTAT
        195 CAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA-TAA

                      *                                      *      *        
        908 ATATAGAAACATTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGTCGGGCTACGGAACGC
        259 ATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGGAACGC

                                                                        *    
        973 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGAAAATTTTT
          1 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGAAAAATTTT

                                                         *            *      
       1038 TTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTCACGGGA
         66 TTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGA

                                                                             
       1103 TTTTCAAGCTTCTAAATATCGTTTTCGCATTTTTTT-CCGAATTAATTTCTAATTAAATTGAAAC
        131 TTTTCAAGCTTCTAAATATCGTTTTCGCATTTTTTTCCCGAATTAATTTCTAATTAAATTGAAAC

               *                  *                                  *       
       1167 AAGCTTCAGATACTCGTAAA-AAAAATCCTTATATCGAATGTGGCTGAGATTTGGTTGGATAAAT
        196 AAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATAAAT

                              *     *       *               *      *     * 
       1231 ATAGAAACTTTTAGGAGTATTTGCACCCAAAATCATGCAAAATTGAGCTGGGCTCTGGAACAC
        261 ATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGGAACGC

            *       *            *                            *              
       1294 ATTTTTAGTCAAAAACCGTGACGGTTAGTACACGATTTTGGCTAAAAACTTACCCGAAAAGA-TT
          1 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGAAAA-ATTT

              *          
       1358 TTACTCAATTTTT
         65 TTTCTCAATTTTT

       1371 ACCACAGAGC


Statistics
Matches: 980,  Mismatches: 61, Indels: 13
        0.93            0.06        0.01

Matches are distributed among these distances:
 321  128  0.13
 322   37  0.04
 323  349  0.36
 324  154  0.16
 325  264  0.27
 326   48  0.05

ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Consensus pattern (323 bp):   
GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCCGAAAAATTTT
TTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGA
TTTTCAAGCTTCTAAATATCGTTTTCGCATTTTTTTCCCGAATTAATTTCTAATTAAATTGAAAC
AAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATAAAT
ATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGGAACGC

Found at i:4159 original size:2 final size:2

Alignment explanation


    Indices: 4152--4190  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       4142 AAAACTGGAA

                                                                      
       4152 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.