Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014187.1 Corchorus capsularis cultivar CVL-1 contig14208, 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: 2469
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:1171 original size:33 final size:33

Alignment explanation


    Indices: 1083--1178  Score: 129
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       1073 GTCTTTTAGA

                                  *  **   *  
       1083 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
          1 TGTTGTTTGCGATGATACTAAATCTGTTTTAAG

                      *    *                 
       1116 TGTTGTTTGCAATGACACTAAATCTGTTTTAAG
          1 TGTTGTTTGCGATGATACTAAATCTGTTTTAAG

                     *                    
       1149 TGTTGTTTGTGATGATACTAAATCTGTTTT
          1 TGTTGTTTGCGATGATACTAAATCTGTTTT

       1179 GGATGCTAAT


Statistics
Matches: 54,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  33   54  1.00

ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45


Consensus pattern (33 bp):   
TGTTGTTTGCGATGATACTAAATCTGTTTTAAG

Found at i:1243 original size:33 final size:33

Alignment explanation


    Indices: 1206--1309  Score: 169
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       1196 AAAACAAATA

                                             
       1206 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
          1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC

                                             
       1239 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
          1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC

                            *      *         
       1272 TGTTTTGGTTG---ATGGCATTGAAAATAATTC
          1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC

                    
       1302 TGTTTTGG
          1 TGTTTTGG

       1310 GTGAAAAGAA


Statistics
Matches: 69,  Mismatches: 2, Indels: 3
        0.93            0.03        0.04

Matches are distributed among these distances:
  30   25  0.36
  33   44  0.64

ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44


Consensus pattern (33 bp):   
TGTTTTGGTTGATCATAGCATTGCAAATAATTC

Found at i:1724 original size:30 final size:30

Alignment explanation


    Indices: 1688--1746  Score: 102
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1678 CAACTGGGAG

                                           
       1688 GGAATGATGCGCCCAAGG-CTTATCATGGAA
          1 GGAATGATGCG-CCAAGGACTTATCATGGAA

                                         
       1718 GGAATGATGCGCCAAGGACTTATCATGGA
          1 GGAATGATGCGCCAAGGACTTATCATGGA

       1747 CTTGAATGAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29    6  0.21
  30   22  0.79

ACGTcount: A:0.31, C:0.19, G:0.31, T:0.20


Consensus pattern (30 bp):   
GGAATGATGCGCCAAGGACTTATCATGGAA
Done.