Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009591.1 Corchorus olitorius cultivar O-4 contig09623, 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: 3605
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31


Found at i:772 original size:40 final size:40

Alignment explanation


    Indices: 719--972  Score: 321
    Period size: 40  Copynumber: 6.4  Consensus size: 40

        709 CGATCACCCG

                    *           *    *           *  
        719 CCGGAAGGAGTTGTTTAAATTCCCAATTTGCCCTTCCTCA
          1 CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

                                       *  *         
        759 CCGGAAGGTGTTGTTTAAATACCCAGTCTGTCCTTCCCCA
          1 CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

            *                          *            
        799 TCGGAAGGTGTTGTTTAAATACCCAGTCTGCCCTTCCCCA
          1 CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

            *                                       
        839 TCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA
          1 CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

                                            *  *  * 
        879 CCGGAAGGTGTTGTTTAAATA-CCAGTTTGCCTTTTCCTA
          1 CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

                  *       *     * **             *  
        918 CCGGAAAGTGTTGTCTAAATTCTTAGTTTGCCCTTCCTCA
          1 CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

            *   *          
        958 TCGGGAGGTGTTGTT
          1 CCGGAAGGTGTTGTT

        973 CCTATTCCCT


Statistics
Matches: 187,  Mismatches: 26, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  39   33  0.18
  40  154  0.82

ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34


Consensus pattern (40 bp):   
CCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCA

Found at i:1464 original size:5 final size:5

Alignment explanation


    Indices: 1454--1489  Score: 56
    Period size: 5  Copynumber: 7.4  Consensus size: 5

       1444 AATGGTTGCC

                           *                            
       1454 TTGTT TTGTT TTGGT TTGTT TTGTT TTG-T TTGTT TT
          1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TT

       1490 AATGTTTTAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   4    4  0.14
   5   24  0.86

ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78


Consensus pattern (5 bp):   
TTGTT

Found at i:1474 original size:15 final size:14

Alignment explanation


    Indices: 1454--1489  Score: 63
    Period size: 15  Copynumber: 2.5  Consensus size: 14

       1444 AATGGTTGCC

                           
       1454 TTGTTTTGTTTTGGT
          1 TTGTTTTGTTTT-GT

                          
       1469 TTGTTTTGTTTTGT
          1 TTGTTTTGTTTTGT

                   
       1483 TTGTTTT
          1 TTGTTTT

       1490 AATGTTTTAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14    9  0.43
  15   12  0.57

ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78


Consensus pattern (14 bp):   
TTGTTTTGTTTTGT
Done.