Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014158.1 Corchorus capsularis cultivar CVL-1 contig14179, 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, 684

Length: 1140
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:668 original size:322 final size:322

Alignment explanation


    Indices: 4--787  Score: 1184
    Period size: 322  Copynumber: 2.4  Consensus size: 322

          1 AGT

                                                                             
          4 TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACACGTTTTTAGCAAAAAACTGT
          1 TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAAC-CGTTTTTAGCAAAAAACTGT

                               *           *    *    *                       
         69 GATTGTTAGTACACGATTTGGGACT-AAAATCGA-CGGAAAGGTTTTTCCTCAA-TTTTTGCGAC
         65 GATTGTTAGTACACGATTTCGG-CTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTGCGAC

                                                                             
        131 AAAGTACTCATAAAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCTAATA
        129 -AA-TACTCATAAAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCTAATA

                                                               **            
        196 TAGTTTTTCCATTTTTTTTCCAAACTTTTATTTCAAATTAAATCGAAACAATTTTCAGATGCTCG
        192 TAGTTTTTCCATTTTTTTTCCAAAC-TTTATTTCAAATTAAATCGAAACAAAATTCAGATGCTCG

                                                                             
        261 TAAAAAGAAATCCTTAAATCCATTGTAGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGA
        256 TAAAAAGAAATCCTTAAATCCATTGTAGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGA

             *
        326 GT
        321 GA

                                                 *                           
        328 TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTTCGGAACGCGTTTTTAGCAAAAAACTGT
          1 TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAAC-CGTTTTTAGCAAAAAACTGT

                                  *                                          
        393 GATTGTTAGTACACGATTTCGGTTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTGCGACA
         65 GATTGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTGCGACA

                                                                         * * 
        458 ATACTCAT-AAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCTAATCTTG
        130 ATACTCATAAAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCTAATATAG

                              **           *                                *
        522 TTTTTTCCATTTTTTTTCTGAA-TTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAG
        195 -TTTTTCCATTTTTTTTCCAAACTTTATTTCAAATTAAATCGAAACAAAATTCAGATGCTCGTAA

                             *     *   *       *                            
        586 AAAGAAATCCTTAAATCTATTGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGA
        259 AAAGAAATCCTTAAATCCATTGTAGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGA

                                       *  *     *                            
        650 TTTTCTGCAAAAAATCATGCAAAATTGCGCTGGGTCACCGGAATCCGTTTTTAGCCAAAAAAAAC
          1 TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAA-CCGTTTTTAG-C--AAAAAAC

                  *                                *                         
        715 -GTGATAGTTAAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGC
         62 TGTGATTGTT-AGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTGC

            * *      
        779 CATAATACT
        126 GACAATACT

        788 AAGATCGTAA


Statistics
Matches: 422,  Mismatches: 29, Indels: 17
        0.90            0.06        0.04

Matches are distributed among these distances:
 322  145  0.34
 323   57  0.14
 324  125  0.30
 325   85  0.20
 326   10  0.02

ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Consensus pattern (322 bp):   
TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACCGTTTTTAGCAAAAAACTGTG
ATTGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTGCGACAA
TACTCATAAAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCTAATATAGT
TTTTCCATTTTTTTTCCAAACTTTATTTCAAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
AGAAATCCTTAAATCCATTGTAGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGA

Found at i:973 original size:207 final size:210

Alignment explanation


    Indices: 580--994  Score: 628
    Period size: 207  Copynumber: 2.0  Consensus size: 210

        570 ATTCAGATGC

                 *                 *           *                             
        580 TCGTAGAAAGAAATCCTTAAATCTATTGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
          1 TCGTAAAAAGAAATCCTTAAATCCATTGTTGCTGAAATTTGGTTAGATGAATATAGATATTT-AA

                                            *  *        *                    
        645 GGAGATTTTCTGCAAAAAATCATGCAAAATTGCGCTGGGTCACCGGAATCCGTTTTTAGCCAAAA
         65 GGAGATTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCACCAGAATCCGTTTTTAGCC-AAA

                                                                             
        710 AAAACGTGATAGTTAAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCC-TCAATTT
        129 AAAACGTGATAGTTAAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCAT-AATTT

                   *          
        774 TTTGCCATAATACTAAGA
        193 TTTGCCACAATACTAAGA

                                                                   *         
        792 TCGTAAAAAGAAATCCTTAAATCCATTG-TGACTGAAATTTGGTTAGATGAATATGGATATTT-A
          1 TCGTAAAAAGAAATCCTTAAATCCATTGTTG-CTGAAATTTGGTTAGATGAATATAGATATTTAA

                                                      *                      
        855 GGAG-TCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCAGAA-CGCGTTTTTAGCC-A
         65 GGAGAT-TTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCACCAGAATC-CGTTTTTAGCCAA

            *          *                                                     
        917 GAAAACGTGATGGTT-AGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCATAATTT
        128 AAAAACGTGATAGTTAAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCATAATTT

                          
        981 TTTGCCACAATACT
        193 TTTGCCACAATACT

        995 CAGAAAAAGT


Statistics
Matches: 188,  Mismatches: 11, Indels: 13
        0.89            0.05        0.06

Matches are distributed among these distances:
 207   60  0.32
 208   15  0.08
 209    2  0.01
 210   54  0.29
 211    2  0.01
 212   55  0.29

ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31


Consensus pattern (210 bp):   
TCGTAAAAAGAAATCCTTAAATCCATTGTTGCTGAAATTTGGTTAGATGAATATAGATATTTAAG
GAGATTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCACCAGAATCCGTTTTTAGCCAAAAA
AACGTGATAGTTAAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCATAATTTTTT
GCCACAATACTAAGA
Done.