Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007641.1 Corchorus olitorius cultivar O-4 contig07667, 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, 823

Length: 1373
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1091 original size:125 final size:125

Alignment explanation


    Indices: 836--1173  Score: 358
    Period size: 125  Copynumber: 2.7  Consensus size: 125

        826 CCGAAGTTTG

                 *      *                     *                        *     
        836 TAAATATCGGAACAAGTTTTTCACATCAATTGATCTTGACGTATTCCGACATTTGTAAATGTTGG
          1 TAAATGTCGGAATAAGTTTTTCACATCAATTGATTTTGACGTATTCCGACATTTGTAAACGTTGG

             *              *              *             *        * *   
        901 TTTAGATATTATATAGGGACATTTAGTAAACGCCGCTACAAAATACTATACCGTCCCTAA
         66 TATAGATATTATATAGTGACATTTAGTAAACACCGCTACAAAATAATATACCGTACATAA

                                        *                    *        *      
        961 TAAATGTCGGAATAAGTTTTTCACATCAGTTGATTTTGACGTATTCCGATATTTGTAAGCGTTGG
          1 TAAATGTCGGAATAAGTTTTTCACATCAATTGATTTTGACGTATTCCGACATTTGTAAACGTTGG

                                         ** *     *                   **
       1026 TATAGATATTATATAGTGACATTTAGTAAGTATCGCTATAAAATAATATACCG-ACATTT
         66 TATAGATATTATATAGTGACATTTAGTAAACACCGCTACAAAATAATATACCGTACATAA

                       * *  *   *                  *   *           * *     * 
       1085 TCAAATGTCAGCACT-GGTTATTCACAT-AATTTGATTTCGACATATTCCGACATCTATAAACAT
          1 T-AAATGTC-GGAATAAGTTTTTCACATCAA-TTGATTTTGACGTATTCCGACATTTGTAAACGT

                    *        *        
       1148 TGGTATAGCTATTATATCGTGACATT
         63 TGGTATAGATATTATATAGTGACATT

       1174 AATTAAATGT


Statistics
Matches: 177,  Mismatches: 33, Indels: 6
        0.82            0.15        0.03

Matches are distributed among these distances:
 124    4  0.02
 125  170  0.96
 126    3  0.02

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36


Consensus pattern (125 bp):   
TAAATGTCGGAATAAGTTTTTCACATCAATTGATTTTGACGTATTCCGACATTTGTAAACGTTGG
TATAGATATTATATAGTGACATTTAGTAAACACCGCTACAAAATAATATACCGTACATAA

Found at i:1206 original size:125 final size:125

Alignment explanation


    Indices: 980--1215  Score: 274
    Period size: 125  Copynumber: 1.9  Consensus size: 125

        970 GAATAAGTTT

                   *         *   *        *  * *   * *                       
        980 TTCACATCAGTTGATTTTGACGTATTCCGATATTTGTAAGCGTTGGTATAGATATTATATAGTGA
          1 TTCACATAAGTTGATTTCGACATATTCCGACATCTATAAACATTGGTATAGATATTATATAGTGA

                *     *    *             *          *                   
       1045 CATTTAGTAAGTATCGCTATAAAATAATATACCGACATTTTCAAATGTCAGCACTGGTTA
         66 CATTAAGTAAATATCACTATAAAATAATACACCGACATTTACAAATGTCAGCACTGGTTA

                     *                                         *        *    
       1105 TTCACATAATTTGATTTCGACATATTCCGACATCTATAAACATTGGTATAGCTATTATATCGTGA
          1 TTCACATAAGTTGATTTCGACATATTCCGACATCTATAAACATTGGTATAGATATTATATAGTGA

                  *     *     *    *  *    *              
       1170 CATTAATTAAATGTCACTTTAAATTACTACATCGACATTTACAAAT
         66 CATTAAGTAAATATCACTATAAAATAATACACCGACATTTACAAAT

       1216 ATCGGCACAA


Statistics
Matches: 89,  Mismatches: 22, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
 125   89  1.00

ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38


Consensus pattern (125 bp):   
TTCACATAAGTTGATTTCGACATATTCCGACATCTATAAACATTGGTATAGATATTATATAGTGA
CATTAAGTAAATATCACTATAAAATAATACACCGACATTTACAAATGTCAGCACTGGTTA
Done.