Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005877.1 Corchorus capsularis cultivar CVL-1 contig05895, 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: 15646
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:1079 original size:13 final size:13

Alignment explanation


    Indices: 1063--1088  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1053 TAATTCAATG

                         
       1063 TTATAAATATTAT
          1 TTATAAATATTAT

                         
       1076 TTATAAATATTAT
          1 TTATAAATATTAT

       1089 CGGGCATTTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (13 bp):   
TTATAAATATTAT

Found at i:1284 original size:30 final size:30

Alignment explanation


    Indices: 1248--1304  Score: 87
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1238 CGATTTCAAT

                                          
       1248 TGTAATTATTGGAAAAAGGGTTCGTTGAGA
          1 TGTAATTATTGGAAAAAGGGTTCGTTGAGA

                   *     *        *    
       1278 TGTAATTGTTGGAGAAAGGGTTTGTTG
          1 TGTAATTATTGGAAAAAGGGTTCGTTG

       1305 GCTCATAAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.28, C:0.02, G:0.33, T:0.37


Consensus pattern (30 bp):   
TGTAATTATTGGAAAAAGGGTTCGTTGAGA

Found at i:7728 original size:52 final size:52

Alignment explanation


    Indices: 7685--7812  Score: 202
    Period size: 52  Copynumber: 2.5  Consensus size: 52

       7675 AAAAATGGTG

                                                *               
       7685 ATTGAATGTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAA
          1 ATTGAATGTTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGACCTAA

                  ***           *                               
       7737 ATTGAACACTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAA
          1 ATTGAATGTTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGACCTAA

                              *     
       7789 ATTGAATGTTTTGAAAACCTGATG
          1 ATTGAATGTTTTGAAAACTTGATG

       7813 AAAATTCTTT


Statistics
Matches: 66,  Mismatches: 10, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  52   66  1.00

ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32


Consensus pattern (52 bp):   
ATTGAATGTTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGACCTAA

Found at i:10827 original size:52 final size:52

Alignment explanation


    Indices: 10771--10897  Score: 200
    Period size: 52  Copynumber: 2.4  Consensus size: 52

      10761 AAAATGGTGT

                                               *                
      10771 TTGAATGTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
          1 TTGAATGTTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGACCTAAA

                 ***           *                                
      10823 TTGAACACTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAA
          1 TTGAATGTTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGACCTAAA

                             *     
      10875 TTGAATGTTTTGAAAACCTGATG
          1 TTGAATGTTTTGAAAACTTGATG

      10898 AAATTTCTTT


Statistics
Matches: 65,  Mismatches: 10, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  52   65  1.00

ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32


Consensus pattern (52 bp):   
TTGAATGTTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGACCTAAA

Found at i:13418 original size:30 final size:30

Alignment explanation


    Indices: 13384--13443  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      13374 CGGAAAAACT

                             *     *       
      13384 GCCTGT-TAATGCTTATGTGGCTTTTTGATG
          1 GCCTGTAT-ATGCTTATATGGCTCTTTGATG

                    *                     
      13414 GCCTGTATTTGCTTATATGGCTCTTTGATG
          1 GCCTGTATATGCTTATATGGCTCTTTGATG

      13444 ACATGTAACT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  30   25  0.96
  31    1  0.04

ACGTcount: A:0.13, C:0.15, G:0.25, T:0.47


Consensus pattern (30 bp):   
GCCTGTATATGCTTATATGGCTCTTTGATG
Done.