Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019919.1 Corchorus olitorius cultivar O-4 contig19952, 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: 12044
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:2388 original size:98 final size:98

Alignment explanation


    Indices: 2203--2381  Score: 256
    Period size: 98  Copynumber: 1.8  Consensus size: 98

       2193 TTTAATTAGT

                                                       *                     
       2203 TTCCACCTTCTCTGTGGGATTCGACCCCTACTTGCCCTAGCTATTAGTTATTGGTTTGTGGGGAT
          1 TTCCACCTTCTCTGTGGGATTCGACCCCTACTTGCCCTAGCTAGTAGTTATT-GTTTGTGGGGAT

                   *                          
       2268 TTATTTTGTGATTGCTCAACGACTCGATCATCTA
         65 TTATTTTATGATTGCTCAACGACTCGATCATCTA

                                         *         *                         
       2302 TTCC-CCTTCTCTGTGGGATTCGACCCCTGCTTGCCCTATCTACGTAGTTAGGTT-TTTGTGGGG
          1 TTCCACCTTCTCTGTGGGATTCGACCCCTACTTGCCCTAGCTA-GTAGTTA--TTGTTTGTGGGG

                              
       2365 A-TTATTTTTATGATTGC
         63 ATTTA-TTTTATGATTGC

       2382 CGACGACCAA


Statistics
Matches: 72,  Mismatches: 4, Indels: 8
        0.86            0.05        0.10

Matches are distributed among these distances:
  98   39  0.54
  99   31  0.43
 101    2  0.03

ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41


Consensus pattern (98 bp):   
TTCCACCTTCTCTGTGGGATTCGACCCCTACTTGCCCTAGCTAGTAGTTATTGTTTGTGGGGATT
TATTTTATGATTGCTCAACGACTCGATCATCTA

Found at i:4174 original size:100 final size:99

Alignment explanation


    Indices: 4001--4353  Score: 327
    Period size: 100  Copynumber: 3.5  Consensus size: 99

       3991 TCTCCCATGT

                              *     *      * *     *          *              
       4001 AATCTTTCAAATTTGTAACCAACGTAAGGATTTGCATATTTAACACTTCTACCGATCTTCGATGT
          1 AATCTTTC-AATTTGTAATCAACGCAAGGATCTCCATATCTAACACTTCTGCCGATCTTCGATGT

                                     *   ** *   
       4066 TGTCGTTCTACC-ATGTTCGGGTTCTACGGTGTTTA
         65 TGTCGTTCT-CCTATGTTCGGGTTCCACGACGATTA

                                                               *             
       4101 AATCTTTCAAGTTTGTAATCAACGCAAGGATCTCCATATCTAACACTTCTGTCGATCTTCGATGT
          1 AATCTTTCAA-TTTGTAATCAACGCAAGGATCTCCATATCTAACACTTCTGCCGATCTTCGATGT

                                                
       4166 T-TCTGTTCTCCTATGTTCGGGTTCCACGACGATTA
         65 TGTC-GTTCTCCTATGTTCGGGTTCCACGACGATTA

                         *     *   *                 *          *     * *    
       4201 AATCTTTCAATTCCGTAATAAACACAAGGATCTCCATATCTGACACTTCTGCTGATCTACAATGT
          1 AATCTTTCAATT-TGTAATCAACGCAAGGATCTCCATATCTAACACTTCTGCCGATCTTCGATGT

                *                    **  *   * * 
       4266 TGTCATTCTCCCT-TGTGT-GGGTTTTACAACGGTAA
         65 TGTCGTTCT-CCTATGT-TCGGGTTCCACGACGATTA

                    *   *        * *        *      * *           
       4301 AATCTTTGTAATCTGTAATCATCACAAGGATCCCCATATGTGACACTTCTGCC
          1 AATCTTT-CAATTTGTAATCAACGCAAGGATCTCCATATCTAACACTTCTGCC

       4354 AGTCGTATAA


Statistics
Matches: 212,  Mismatches: 33, Indels: 16
        0.81            0.13        0.06

Matches are distributed among these distances:
  99    8  0.04
 100  195  0.92
 101    9  0.04

ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36


Consensus pattern (99 bp):   
AATCTTTCAATTTGTAATCAACGCAAGGATCTCCATATCTAACACTTCTGCCGATCTTCGATGTT
GTCGTTCTCCTATGTTCGGGTTCCACGACGATTA
Done.