Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013333.1 Corchorus olitorius cultivar O-4 contig13366, 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: 44004
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:17174 original size:22 final size:23

Alignment explanation


    Indices: 17149--17200  Score: 63
    Period size: 22  Copynumber: 2.3  Consensus size: 23

      17139 TAAATGTTGT

                          *         
      17149 TGATAA-TCTTCTCTTTTATC-TC
          1 TGATAATTC-TCTCATTTATCTTC

                                  *
      17171 TGATAATTCTCTCATTTATCTTT
          1 TGATAATTCTCTCATTTATCTTC

                   
      17194 TGATAAT
          1 TGATAAT

      17201 ATTCGCATGG


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

Matches are distributed among these distances:
  22   16  0.62
  23   10  0.38

ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54


Consensus pattern (23 bp):   
TGATAATTCTCTCATTTATCTTC

Found at i:19328 original size:38 final size:35

Alignment explanation


    Indices: 19241--19313  Score: 146
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      19231 CTCAGTCACC

                                               
      19241 TCAGATCAAGCAAATAATAAATCATGCACATTATG
          1 TCAGATCAAGCAAATAATAAATCATGCACATTATG

                                               
      19276 TCAGATCAAGCAAATAATAAATCATGCACATTATG
          1 TCAGATCAAGCAAATAATAAATCATGCACATTATG

               
      19311 TCA
          1 TCA

      19314 TTTCTCTGCA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   38  1.00

ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26


Consensus pattern (35 bp):   
TCAGATCAAGCAAATAATAAATCATGCACATTATG

Found at i:22954 original size:36 final size:35

Alignment explanation


    Indices: 22907--22981  Score: 141
    Period size: 36  Copynumber: 2.1  Consensus size: 35

      22897 AAGAACAGCA

                                                
      22907 GTTAACTTCTACAAACTAGCGATTTTCTTTTGTCTT
          1 GTTAACTTCTACAAACTAGCGATTTTCTTTTGTC-T

                                               
      22943 GTTAACTTCTACAAACTAGCGATTTTCTTTTGTCT
          1 GTTAACTTCTACAAACTAGCGATTTTCTTTTGTCT

                
      22978 GTTA
          1 GTTA

      22982 TAAGCAATGG


Statistics
Matches: 39,  Mismatches: 0, Indels: 1
        0.98            0.00        0.03

Matches are distributed among these distances:
  35    5  0.13
  36   34  0.87

ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47


Consensus pattern (35 bp):   
GTTAACTTCTACAAACTAGCGATTTTCTTTTGTCT
Done.