Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010816.1 Corchorus olitorius cultivar O-4 contig10848, 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: 1960
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36


Found at i:1492 original size:154 final size:152

Alignment explanation


    Indices: 1176--1960  Score: 1099
    Period size: 154  Copynumber: 5.1  Consensus size: 152

       1166 GTATCACAAA

                       *                                                     
       1176 CCTCAATGCTTCTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
          1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT

                 *                                                     *     
       1241 GTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGTGACGTT
         66 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTA-TTACGTT

                                   
       1306 TTGAATCGTCTTCGATTTGCAAC
        130 TTGAATCGTCTTCGATTTGCAAC

                                              *                             *
       1329 CCTCGAATGCTTTTCTTTCCATTGTTTATGGCCTGACTATAATCATTTTGGTGAGATTAGTCCAA
          1 CCTC-AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC

                           *                       *                         
       1394 TGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTTAAGCCTATCGGGGCCCATTATTGACG
         65 TGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTTGAGCCTATCGGGGCCCATTATT-ACG

               *                     
       1459 TTTGGAATCGTCTTCGATTTGCAAC
        128 TTTTGAATCGTCTTCGATTTGCAAC

                     *       *       *                *                 *    
       1484 CCTCAATGCCTTTCTTTTCATTGTTAATGGCCTAACTATAATAATTTTGGTGAGATTAGTGCACT
          1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT

                                  *           *    *                     *   
       1549 GTGTAA-TTTTTAGCTCATTTGCAACACTTGTTAATTTGGGCCTATCGGGGCCCATTAGTTCCGT
         66 GTG-AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTA-TTACGT

              *  *   *               
       1613 TTAGATTCGCCTTCGATTTGGCAAC
        129 TTTGAATCGTCTTCGATTT-GCAAC

                          *              *                                   
       1638 CCTCAATGC-TTTCATTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACT
          1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT

                        *                *        *       *             *    
       1702 GTGAAGTTTTTAACTCATTTGGAACACTTTTTATTTTGGGCCTATCTGGGCCCATTAGTTCCGTT
         66 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTA-TTACGTT

                              *    *
       1767 TTGAATCGTCTTCGATTAGGCAAA
        130 TTGAATCGTCTTCGATT-TGCAAC

                 *            *                               *            * 
       1791 CCTCAGTGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCAAT
          1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT

                                                *     *      *         *     
       1856 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTCGAGCCAATCGGGCCCCATTAGTAACGTT
         66 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTA-TTACGTT

                                 *  
       1921 TTGAATC-TACTTCGATTTGCGAC
        130 TTGAATCGT-CTTCGATTTGCAAC

                     *       
       1944 CCTCAATGCCTTTCTTT
          1 CCTCAATGCTTTTCTTT


Statistics
Matches: 562,  Mismatches: 60, Indels: 20
        0.88            0.09        0.03

Matches are distributed among these distances:
 152    2  0.00
 153  195  0.35
 154  309  0.55
 155   56  0.10

ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40


Consensus pattern (152 bp):   
CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTATTACGTTT
TGAATCGTCTTCGATTTGCAAC

Found at i:1840 original size:307 final size:304

Alignment explanation


    Indices: 1172--1957  Score: 1110
    Period size: 307  Copynumber: 2.6  Consensus size: 304

       1162 CCCCGTATCA

                           *                                                 
       1172 CAAACCTCAATGCTTCTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
          1 CAAACCTCAATGCTTTTCTTT-CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC

                                                 *                         * 
       1237 CACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGTGA
         65 CACTGTG-AATTTTTAGCTCATTTGGAACACTTGTTAATTTGAGCCTATCGGGGCCCATTAGTAA

                        *                             *              *   *   
       1302 CGTTTTGAATCGTCTTCGATTTGCAACCCTCGAATGCTTTTCTTTCCATTGTTTATGGCCTGACT
        129 CGTTTTGAATCGACTTCGATTTGCAACCCTC-AATGC-TTTCATTCCATTGTTTATGACCTAACT

                                                    *                        
       1367 ATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTT
        192 ATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAACACATTTGGAACACTTGTTATTTT

                                                          * 
       1432 TAAGCCTATCGGGGCCCATTATTGACGTTTGGAATCGTCTTCGATTTG
        257 TAAGCCTATCGGGGCCCATTATTGACGTTTGGAATCGTCTTCGATTGG

               *         *               *                *                 *
       1480 CAACCCTCAATGCCTTTCTTTTCATTGTTAATGGCCTAACTATAATAATTTTGGTGAGATTAGTG
          1 CAAACCTCAATGCTTTTC-TTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC

                                     *                *                    **
       1545 CACTGTGTAATTTTTAGCTCATTTGCAACACTTGTTAATTTGGGCCTATCGGGGCCCATTAGTTC
         65 CACTGTG-AATTTTTAGCTCATTTGGAACACTTGTTAATTTGAGCCTATCGGGGCCCATTAGTAA

                 *  *   *                                                    
       1610 CGTTTAGATTCGCCTTCGATTTGGCAACCCTCAATGCTTTCATTCCATTGTTTATGACCTAACTA
        129 CGTTTTGAATCGACTTCGATTT-GCAACCCTCAATGCTTTCATTCCATTGTTTATGACCTAACTA

                                     *               *              *        
       1675 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTTTTA-TTTT
        193 TAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAACACATTTGGAACACTTGTTATTTTT

            **       *              *     *                  
       1739 GGGCCTATCTGGGCCCATTAGTT-CCGTTTTGAATCGTCTTCGATTAGG
        258 AAGCCTATCGGGGCCCATTA-TTGACGTTTGGAATCGTCTTCGATT-GG

                     *                                            *          
       1787 CAAACCTCAGTGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGCGAGATTAGTC
          1 CAAACCTCAATGCTTTTCTTTC-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC

              *                                            *      *          
       1852 CAATGTGAAGTTTTTAGCTCATTTGGAACACTTGTT-ATTTCGAGCCAATCGGGCCCCATTAGTA
         65 CACTGTGAA-TTTTTAGCTCATTTGGAACACTTGTTAATTT-GAGCCTATCGGGGCCCATTAGTA

                        *            *                
       1916 ACGTTTTGAATCTACTTCGATTTGCGACCCTCAATGCCTTTC
        128 ACGTTTTGAATCGACTTCGATTTGCAACCCTCAATG-CTTTC

       1958 TTT


Statistics
Matches: 423,  Mismatches: 47, Indels: 17
        0.87            0.10        0.03

Matches are distributed among these distances:
 306   63  0.15
 307  210  0.50
 308  138  0.33
 309   12  0.03

ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39


Consensus pattern (304 bp):   
CAAACCTCAATGCTTTTCTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
ACTGTGAATTTTTAGCTCATTTGGAACACTTGTTAATTTGAGCCTATCGGGGCCCATTAGTAACG
TTTTGAATCGACTTCGATTTGCAACCCTCAATGCTTTCATTCCATTGTTTATGACCTAACTATAA
TCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAACACATTTGGAACACTTGTTATTTTTAAG
CCTATCGGGGCCCATTATTGACGTTTGGAATCGTCTTCGATTGG
Done.