Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000095.1 Corchorus olitorius cultivar O-4 contig00095, 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: 5956
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33


Found at i:4762 original size:165 final size:167

Alignment explanation


    Indices: 4472--4948  Score: 471
    Period size: 177  Copynumber: 2.8  Consensus size: 167

       4462 GGTTTCCTAA

                               *      **        **                       *   
       4472 AAAAGTTGGAAACTTTGGAGATAAGTTCATGTGGTAAACTGAAATCTCTCTTTCCAGCATCGGTT
          1 AAAAGTTGGAAACTTTGGATATAAGTGAATGTGGTAGCCTGAAATCTCTCTTTCCAGCATCTGTT

             *  *                    * * *                 *     *           
       4537 AGTAGAAATCTTTTGCAATTGAAAAGTCTTAAAGTAGCTGCGTGCGGCATGTTAGAGCAAATCTT
         66 ACTAAAAATCTTTTGCAATTGAAAAATATCAAA-TAGCTGCGTGCGGTATGTTGGAGCAAAT-TT

                                             *     
       4602 TGAGGA-GATAGG-AG-G-TGCTAATGATCAGGTGCTAC
        129 TGAGGAGGATAGGTAGTGCTGCTAATGATCAGGCGCTAC

                 *                         *        *    * *                 
       4637 AAAAGCTGGAAACTTTGGATATAAGTGAATGCGGTAGCCTCAAATATATCTTTCCAGCATCTGTT
          1 AAAAGTTGGAAACTTTGGATATAAGTGAATGTGGTAGCCTGAAATCTCTCTTTCCAGCATCTGTT

                                       *            *   *                    
       4702 ACTAAAAATCTTTTGCAATTGAAAAATGTCAATATAGCTGTGTGTGGTATGTTGGAGCAAATTTG
         66 ACTAAAAATCTTTTGCAATTGAAAAATATCAA-ATAGCTGCGTGCGGTATGTTGGAGCAAATTT-

                               *                           
       4767 TGAGTGTGAGGGGATAGGTGGTGCTACTGCTAATGATCAGGCGCTAC
        129 TGA--G-GA--GGATAGGTAGTG---CTGCTAATGATCAGGCGCTAC

              *               *        *     *    *                     *    
       4814 AAGAGTTGGAAACTTTGGTTATAAGTGGATGTGATAGCTTGAAATCTCTCTTTCCAG--TGTGGA
          1 AAAAGTTGGAAACTTTGGATATAAGTGAATGTGGTAGCCTGAAATCTCTCTTTCCAGCATCT-G-

                                  *                  * *    *                
       4877 TTACTAAAAATCTTTTGCAATTCAAAAATATCAAAATAGCTACCTGCGATATGTTGGAGCAAATT
         64 TTACTAAAAATCTTTTGCAATTGAAAAATATC-AAATAGCTGCGTGCGGTATGTTGGAGCAAA-T

                   
       4942 TTTGAGG
        127 TTTGAGG

       4949 TGGCTGTAGA


Statistics
Matches: 254,  Mismatches: 40, Indels: 27
        0.79            0.12        0.08

Matches are distributed among these distances:
 164    2  0.01
 165  108  0.43
 166    1  0.00
 167    1  0.00
 168    2  0.01
 171    6  0.02
 172    1  0.00
 173    1  0.00
 174    1  0.00
 175    3  0.01
 176    1  0.00
 177  122  0.48
 178    5  0.02

ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31


Consensus pattern (167 bp):   
AAAAGTTGGAAACTTTGGATATAAGTGAATGTGGTAGCCTGAAATCTCTCTTTCCAGCATCTGTT
ACTAAAAATCTTTTGCAATTGAAAAATATCAAATAGCTGCGTGCGGTATGTTGGAGCAAATTTTG
AGGAGGATAGGTAGTGCTGCTAATGATCAGGCGCTAC

Found at i:5299 original size:31 final size:32

Alignment explanation


    Indices: 5261--5320  Score: 95
    Period size: 31  Copynumber: 1.9  Consensus size: 32

       5251 TGTAAAACTT

                      *        *            
       5261 TTGAATCGACTATTATA-CTTTATTTTTCTAA
          1 TTGAATCGACCATTATATCCTTATTTTTCTAA

                                         
       5292 TTGAATCGACCATTATATCCTTATTTTTC
          1 TTGAATCGACCATTATATCCTTATTTTTC

       5321 AAACATATTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  31   16  0.62
  32   10  0.38

ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50


Consensus pattern (32 bp):   
TTGAATCGACCATTATATCCTTATTTTTCTAA
Done.