Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008731.1 Corchorus olitorius cultivar O-4 contig08758, 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, 808

Length: 1348
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:762 original size:326 final size:320

Alignment explanation


    Indices: 65--1326  Score: 1121
    Period size: 320  Copynumber: 3.9  Consensus size: 320

         55 TCCCAGCAAC

                         *              *                   *                
         65 ATTGGATTTAAGGGTTTGTTTTTACGAGTAT-TGAATCTTGTTTCGATATAATTAGAAATAAATT
          1 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT

                                       *   *                 *              *
        129 C--AAAAAAATGGAAAAAACGATATTAAAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTGAAT
         66 CGAAAAAAAATGG--AAAACGATATTAGAAGAGTGAAAAACCCTTCAATCTTTTTGGCGTTGAAA

              *   **    *   *               *      *      *         *        
        191 TACATAGATTTTCTGAGTA-TTGTGGCAAAGAAATTGAGGAA-AAACTTTTCGGGTAAGTTTTTG
        129 TATATATTTTTTATGACTATTTGTGG-AAA-ATATTGAGAAATAAAATTTTCGGGTCAG---TT-

                                    *                  *       **    *    *  
        254 GAAAATATTAGCCGAAATCGTGTAATAACCATCACCGTTTTTGGCTAAAAATGCGTTTCGG-TCC
        188 -----T-TTAGCCGAAATCGTGTACTAACCATCA-CGTTTTTGACTAAAAACACGTTCCGGAGCC

                     *    *           *    * *      *                     *  
        318 GCCAGCTCAGTTTTACATGATTTTTGTCAGAGACACTCCTGGAAATATCAATA-T-------TCA
        246 -CCAGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATACTAACCGAACCA

               *       
        375 AATGTCAGCCA
        310 AATCTCAGCCA

              *                       *                                      
        386 TAATGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
          1 -ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT

                                                                             
        451 TCGAAAAAAAATGGAAACACGATATTAGAAGAGTGAAAAACCCTTCAATCTTTTTGGCGTTGAAA
         65 TCGAAAAAAAATGGAAA-ACGATATTAGAAGAGTGAAAAACCCTTCAATCTTTTTGGCGTTGAAA

                             *                                       *       
        516 TATATATTTTTTATGACCATTTGTGGTAAAATATTGAGAAATAAAATTTT-GGGTCATTTTTTAG
        129 TATATATTTTTTATGACTATTTGTGG-AAAATATTGAGAAATAAAATTTTCGGGTCAGTTTTTAG

             *                               *      *                *       
        580 CTGAAATCGTGTACTAACCATCACGATTTTTTGTCTAAAAGCACGTTCCGGAGCCCCGGCTCAAT
        193 CCGAAATCGTGTACTAACCATCACG--TTTTTGACTAAAAACACGTTCCGGAGCCCCAGCTCAAT

                                                     *    *   *              
        645 TTTGCATGATTTTTGG-AGCAAAGACTCCTTGAAATAT-ATCTAGGTTAATCGAA-CAGAATCTC
        256 TTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCA-ATA--CTAACCGAACCA-AATCTC

                 
        707 AGCCA
        316 AGCCA

                    *                         *      *          **           
        712 CATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAGCTAGAAATAAAT
          1 -ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT

                      *          *                *   *                     *
        777 TCGGAAAAAATATGGATAAACAATATTAGAAGCA-TG-GAAAGCCTGTCAATCTTTTTGGCGTTA
         65 TC-GAAAAAAAATGGA-AAACGATATTAGAAG-AGTGAAAAACCCT-TCAATCTTTTTGGCGTTG

                           *** *             *                     *      *  
        840 AAATATATATTTTTTCCCAATATTT-T-GAAAAAATTGAGAAA-AAAACTTTTCGTGTCAGTGTT
        126 AAATATATATTTTTTATGACTATTTGTGGAAAATATTGAGAAATAAAA-TTTTCGGGTCAGTTTT

                                *                       *    *   *  * *      
        902 TAGCCGAAATCGTGTACTAATCATCATCGTTTTTGACTAAAAACGCGTTTCGGTGCGCTAGCTCA
        190 TAGCCGAAATCGTGTACTAACCATCA-CGTTTTTGACTAAAAACACGTTCCGGAGCCCCAGCTCA

            *        *            *     *                 *   *        *     
        967 GTTTTGCATTATTTTTGGCAGAGAGACTTCTTGAAATATCAATACTCACCTAACCAAATGTCAG-
        254 ATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATACTAACCGAACCAAATCTCAGC

              
       1031 CA
        319 CA

              *          *                                                   
       1033 ATAGCGAATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
          1 ATTG-G-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA

              *                             *                                
       1098 TTAG-AAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAA
         64 TTCGAAAAAAAATGG-AAAACGATATTAGAAGAGTGAAAAACCCTTCAATCTTTTTGGCGTTGAA

            *                                        *               *       
       1161 TTATATATTTTTTATGACTA-TTGTGGCAAAATATTGAG--TTAAAATTCTTCGGGTTAGTTTTT
        128 ATATATATTTTTTATGACTATTTGTGG-AAAATATTGAGAAATAAAATT-TTCGGGTCAGTTTTT

                     *    *                    *           *   *       *  *  
       1223 AGCCGAAATTGTGCAAC-AACCATCACGGTTTTTGGCTAAAAACACATTTCAGGA-CCCAAGATC
        191 AGCCGAAATCGTG-TACTAACCATCAC-GTTTTTGACTAAAAACAC-GTTCCGGAGCCCCAGCTC

             *     *               **        *       
       1286 AGTTTTGGATGATTTTTGGCAGAGGGACTCCTTAAAATATC
        253 AATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATC

       1327 TATATTTATC


Statistics
Matches: 773,  Mismatches: 121, Indels: 94
        0.78            0.12        0.10

Matches are distributed among these distances:
 314    2  0.00
 315   28  0.04
 316   59  0.08
 317    2  0.00
 318    2  0.00
 319   57  0.07
 320  110  0.14
 321   20  0.03
 322   95  0.12
 323   42  0.05
 324   94  0.12
 325  102  0.13
 326   94  0.12
 327   63  0.08
 328    3  0.00

ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Consensus pattern (320 bp):   
ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT
CGAAAAAAAATGGAAAACGATATTAGAAGAGTGAAAAACCCTTCAATCTTTTTGGCGTTGAAATA
TATATTTTTTATGACTATTTGTGGAAAATATTGAGAAATAAAATTTTCGGGTCAGTTTTTAGCCG
AAATCGTGTACTAACCATCACGTTTTTGACTAAAAACACGTTCCGGAGCCCCAGCTCAATTTTGC
ATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATACTAACCGAACCAAATCTCAGCCA
Done.