Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010314.1 Corchorus capsularis cultivar CVL-1 contig10335, 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: 3443
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Found at i:2148 original size:432 final size:429

Alignment explanation


    Indices: 1350--2331  Score: 1009
    Period size: 432  Copynumber: 2.3  Consensus size: 429

       1340 TTTCAAAAGT

                    *   **      * *                *  *                      
       1350 ATTTTTTAGAATTGAAACATGACAATTAGCTTTTGAGTCTTTTATG-AAAGTTGTAGATCATAAA
          1 ATTTTTTAAAATCAAAACATTAAAATTAGCTTTTGAGTCCTTCATGAAAAGTTGTAGATCATAAA

                 *                  * *      *                             * 
       1414 ATTACTTTTTAATAGAC-CTGAATTATCTTAATTGGATAAATAGAACAAAG----AAAAAAATGA
         66 ATTACCTTTTAATAGACACTGAATCAACTTAATCGGATAAATAGAACAAAGAATAAAAAAAATAA

                    *     *                                                * 
       1474 AGCGTTAATCGAGTGAGATAGAATTTGTAAAGAACTAAGTAACATGCAATATAAAATAGAAAAGT
        131 AGCGTTAAACGAGTAAGATAGAATTTGTAAAGAACTAAGT-A-ATG--ATATAAAATAGAAAAAT

                              *                   *          * *             
       1539 ATGAGGGTCATTTGATAACTAATCCAAATAAGAAAATATTTTCTTAATGGATATCTTGAAACATA
        192 ATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATAGTTTCTTAATGAAGATCTTGAAACATA

                                           *                                 
       1604 AAAATTCCCTTTTGAACTAAAACTCGTAGATCAAATTAACTTTCGGATACTTCATGAAAGTCATA
        257 AAAATTCCCTTTTGAACTAAAACTCGTAGATAAAATTAACTTTCGGATACTTCATGAAAGTCATA

            *        *       *    *       *                        * *       
       1669 GATCATACAGTAACCTTTTAACTGACACTTGAATAACTTTAATCGGACATGTGGATCGAAAATTA
        322 AATCATACAATAACCTTCTAACCGACACTTCAAT-AC--T-ATCGGACATGTGGACCAAAAATTA

              * *                     *                       
       1734 TATGGTATTAAATAGACCAACAATTGGAAAGA-C-CAAA-TTTAGGAAGC
        383 TACGATATTAAATAGACCAACAA-T-CAAA-ACCACAAAGTTTAGGAAGC

                     *   * *            *                                  * 
       1781 ATTCTTTT-GAATTATAACATTAAAATTTGCTTTTGAGTCCTTCATGAAAAGTTGTAGATCATGA
          1 ATT-TTTTAAAATCAAAACATTAAAATTAGCTTTTGAGTCCTTCATGAAAAGTTGTAGATCATAA

                                                *  *                         
       1845 AATTACCTTTTAATAGACACATGAATCAACTTAATCAGACAAATAGAACAAAGAATAAAAAAAAT
         65 AATTACCTTTTAATAGACAC-TGAATCAACTTAATCGGATAAATAGAACAAAGAATAAAAAAAAT

               *                     *            *                  *       
       1910 AAATC-TTAAACGTTAGATTAAGATGGAATTTGTAAAGGACTAAGT-A-G-TATAAAGTAGAAAA
        129 AAAGCGTTAAACG--AG--TAAGATAGAATTTGTAAAGAACTAAGTAATGATATAAAATAGAAAA

                                                        *           *        
       1971 ATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAAT-GTTTGTTAATGAAGATTTTG-AACA
        190 ATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATAGTTTCTTAATGAAGATCTTGAAACA

                                                            *       * *      
       2034 TAAAAACTT-CCTTTTGAACCCTTCATGAAACTCGTAGATAAAATTTAGCTTTCGGGTCCTTCAT
        255 TAAAAA-TTCCCTTTTGAA--C-T-A--AAACTCGTAGATAAAA-TTAACTTTCGGATACTTCAT

              *    *        *            *                                   
       2098 GAGAGTCGTAAATCATGCAATAACCTTCTGACCGACAC-TCAAT-C-ATCGGACATGTGGACCAA
        312 GAAAGTCATAAATCATACAATAACCTTCTAACCGACACTTCAATACTATCGGACATGTGGACCAA

                               *    **                    *     *
       2160 AAATTATACGATATTAAATTGACCGGCAATCAAAACCACAAAGTTTCGGAAGT
        377 AAATTATACGATATTAAATAGACCAACAATCAAAACCACAAAGTTTAGGAAGC

                             *         * *        *                 *        
       2213 ATTTTTTAAAATCAAAATATTAAAATTGGTTTTTGAGTTCTTCATGAAAA-TTGTAAATCATAAA
          1 ATTTTTTAAAATCAAAACATTAAAATTAGCTTTTGAGTCCTTCATGAAAAGTTGTAGATCATAAA

              *                        *                       *    
       2277 ATCACCTTTTAATAGACACTTGAATCACCTTAATCGGATAAATAGAA-AAAAAATA
         66 ATTACCTTTTAATAGACAC-TGAATCAACTTAATCGGATAAATAGAACAAAGAATA

       2332 CAATAATAAA


Statistics
Matches: 461,  Mismatches: 66, Indels: 49
        0.80            0.11        0.09

Matches are distributed among these distances:
 429    1  0.00
 430   11  0.02
 431   97  0.21
 432  142  0.31
 433   18  0.04
 434   78  0.17
 435    1  0.00
 436    2  0.00
 437    7  0.02
 438   31  0.07
 439   49  0.11
 441   24  0.05

ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31


Consensus pattern (429 bp):   
ATTTTTTAAAATCAAAACATTAAAATTAGCTTTTGAGTCCTTCATGAAAAGTTGTAGATCATAAA
ATTACCTTTTAATAGACACTGAATCAACTTAATCGGATAAATAGAACAAAGAATAAAAAAAATAA
AGCGTTAAACGAGTAAGATAGAATTTGTAAAGAACTAAGTAATGATATAAAATAGAAAAATATGA
GGGTCATTTGATAAATAATCCAAATAAGAAAATAGTTTCTTAATGAAGATCTTGAAACATAAAAA
TTCCCTTTTGAACTAAAACTCGTAGATAAAATTAACTTTCGGATACTTCATGAAAGTCATAAATC
ATACAATAACCTTCTAACCGACACTTCAATACTATCGGACATGTGGACCAAAAATTATACGATAT
TAAATAGACCAACAATCAAAACCACAAAGTTTAGGAAGC

Found at i:2646 original size:9 final size:10

Alignment explanation


    Indices: 2625--2660  Score: 65
    Period size: 10  Copynumber: 3.7  Consensus size: 10

       2615 TCACTCCCTA

                      
       2625 TTCTTATTGT
          1 TTCTTATTGT

                      
       2635 TTCTTA-TGT
          1 TTCTTATTGT

                      
       2644 TTCTTATTGT
          1 TTCTTATTGT

                   
       2654 TTCTTAT
          1 TTCTTAT

       2661 AATATGCCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   9    9  0.36
  10   16  0.64

ACGTcount: A:0.11, C:0.11, G:0.08, T:0.69


Consensus pattern (10 bp):   
TTCTTATTGT
Done.