Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005239.1 Corchorus capsularis cultivar CVL-1 contig05257, 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: 3666
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:390 original size:21 final size:22

Alignment explanation


    Indices: 355--397  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

        345 AAAATTGTCC

                                  
        355 AAAGGAGGGCGGTATCTAGTAA
          1 AAAGGAGGGCGGTATCTAGTAA

                     *     *      
        377 AAAGG-GGGTGGTATTTAGTAA
          1 AAAGGAGGGCGGTATCTAGTAA

        398 TCCCCTATTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.35, C:0.05, G:0.37, T:0.23


Consensus pattern (22 bp):   
AAAGGAGGGCGGTATCTAGTAA

Found at i:3287 original size:63 final size:64

Alignment explanation


    Indices: 3199--3324  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 64

       3189 GCATGCTTTA

                           *              *                                  
       3199 AAATAAAACTAACAAGAAACTTAAACCATGCATA-ATATGGTCTCCAAAATGAGCATCAACTAGG
          1 AAATAAAACTAACAAAAAACTTAAACCA-GAATACATATGGTCTCCAAAATGAGCATCAACTAGG

                       *                                                   
       3263 AAATAAAACT-TCAAAAAACTTAAACCAGAATATGCCATATGGTCTCCAAAATGAGCATCAAC
          1 AAATAAAACTAACAAAAAACTTAAACCAGAATA---CATATGGTCTCCAAAATGAGCATCAAC

       3325 GTCTAGCTGC


Statistics
Matches: 55,  Mismatches: 3, Indels: 6
        0.86            0.05        0.09

Matches are distributed among these distances:
  62    4  0.07
  63   15  0.27
  64   10  0.18
  66   26  0.47

ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21


Consensus pattern (64 bp):   
AAATAAAACTAACAAAAAACTTAAACCAGAATACATATGGTCTCCAAAATGAGCATCAACTAGG
Done.