Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008326.1 Corchorus capsularis cultivar CVL-1 contig08347, 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: 10887
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:9226 original size:19 final size:18

Alignment explanation


    Indices: 9193--9228  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       9183 TTGAAATAAG

                              
       9193 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       9211 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       9229 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:9681 original size:15 final size:15

Alignment explanation


    Indices: 9661--9690  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       9651 TATCATTCTT

                           
       9661 AAGTAGCTATAATCA
          1 AAGTAGCTATAATCA

                    *      
       9676 AAGTAGCTCTAATCA
          1 AAGTAGCTATAATCA

       9691 CTTACCATCC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27


Consensus pattern (15 bp):   
AAGTAGCTATAATCA

Found at i:10414 original size:16 final size:16

Alignment explanation


    Indices: 10395--10437  Score: 50
    Period size: 17  Copynumber: 2.6  Consensus size: 16

      10385 AAATTTTCAA

                     **   * 
      10395 TTTCAAAAATCAATTT
          1 TTTCAAAAAAAAATCT

                             
      10411 TTTCGAAAAAAAAATCT
          1 TTTC-AAAAAAAAATCT

                      
      10428 TTTCAAAAAA
          1 TTTCAAAAAA

      10438 TTGGAGAAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  16   10  0.43
  17   13  0.57

ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35


Consensus pattern (16 bp):   
TTTCAAAAAAAAATCT
Done.