Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021348.1 Corchorus olitorius cultivar O-4 contig21381, 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: 23129
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30


Found at i:11145 original size:28 final size:28

Alignment explanation


    Indices: 11124--11224  Score: 157
    Period size: 28  Copynumber: 3.6  Consensus size: 28

      11114 CCCTGGATGC

                      *           *     
      11124 GCAAAATGACTAAAATACCCCTAGACAT
          1 GCAAAATGACCAAAATACCCCTGGACAT

               *            *           
      11152 GCAGAATGACCAAAATGCCCCTGGACAT
          1 GCAAAATGACCAAAATACCCCTGGACAT

                            *           
      11180 GCAAAATGACCAAAATGCCCCTGGACAT
          1 GCAAAATGACCAAAATACCCCTGGACAT

                             
      11208 GCAAAATGACCAAAATA
          1 GCAAAATGACCAAAATA

      11225 AGAAATAAAT


Statistics
Matches: 67,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  28   67  1.00

ACGTcount: A:0.44, C:0.26, G:0.16, T:0.15


Consensus pattern (28 bp):   
GCAAAATGACCAAAATACCCCTGGACAT

Found at i:14337 original size:21 final size:21

Alignment explanation


    Indices: 14311--14359  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      14301 ACAACAACTT

                                  
      14311 GCTCCGCGCAAATCAAA-TCAA
          1 GCTCCGCGCAAA-CAAACTCAA

                  *   *           
      14332 GCTCCGTGCATACAAATCTCAA
          1 GCTCCGCGCAAACAAA-CTCAA

                  
      14354 GCTCCG
          1 GCTCCG

      14360 TGCTTTCAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  20    4  0.17
  21   10  0.42
  22   10  0.42

ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18


Consensus pattern (21 bp):   
GCTCCGCGCAAACAAACTCAA

Found at i:19089 original size:183 final size:185

Alignment explanation


    Indices: 18757--19123  Score: 582
    Period size: 183  Copynumber: 2.0  Consensus size: 185

      18747 GGGAGGGATG

                              *   *      *                                   
      18757 GGCATTTTTGAAGTACCGGATCGAAGAATGACCGGAGATCAAAGGGGGATGAGAAACGGTGAAAG
          1 GGCATTTTTGAAGTACCGAATCAAAGAATAACCGGAGATCAAAGGGGGATGAGAAACGGTGAAAG

                    *                       *                                
      18822 GTTAAGGTGGAGAGGGAGGAGAGAAGAGAAGTTGAGAGCTGAGAGGCCGCCCGAGAGAGAGATTA
         66 GTTAAGGTAGAGAGGGAGGAGAGAAGAGAAGTCGAGAGCTGAGAGGCCGCCCGAGAGAGAGATTA

                                                                   
      18887 GAGAAAATTAGG-ATTTTTTTT-TTTTTAGTTTAGGTTTATATATTTTTAAGATT
        131 GAGAAAATTAGGTATTTTTTTTATTTTTAGTTTAGGTTTATATATTTTTAAGATT

                                                                             
      18940 GGCATTTTTGAAGTACCGAATCAAAGAATAACCGGAGATCAGAA-GGGGATGAGAAACGGTGAAA
          1 GGCATTTTTGAAGTACCGAATCAAAGAATAACCGGAGATCA-AAGGGGGATGAGAAACGGTGAAA

                                                *                            
      19004 GGTTAAGGTAGAGAGGGAGGAGAGAAGAGAAGTCGATAGCTGAGAGGCCGCCCGAGAGA-A-ATT
         65 GGTTAAGGTAGAGAGGGAGGAGAGAAGAGAAGTCGAGAGCTGAGAGGCCGCCCGAGAGAGAGATT

                            *                *                       
      19067 AGAGAAAATTAGGGCTTTTTTTTTTAAATTTTTTGTTTAGGTTTATATATTTTTAAG
        130 AGAGAAAATTA-GG-TATTTTTTTT--ATTTTTAGTTTAGGTTTATATATTTTTAAG

      19124 TTAAAAAAAC


Statistics
Matches: 169,  Mismatches: 8, Indels: 10
        0.90            0.04        0.05

Matches are distributed among these distances:
 181   14  0.08
 182    3  0.02
 183  114  0.67
 184   10  0.06
 187   28  0.17

ACGTcount: A:0.34, C:0.08, G:0.31, T:0.27


Consensus pattern (185 bp):   
GGCATTTTTGAAGTACCGAATCAAAGAATAACCGGAGATCAAAGGGGGATGAGAAACGGTGAAAG
GTTAAGGTAGAGAGGGAGGAGAGAAGAGAAGTCGAGAGCTGAGAGGCCGCCCGAGAGAGAGATTA
GAGAAAATTAGGTATTTTTTTTATTTTTAGTTTAGGTTTATATATTTTTAAGATT

Found at i:19165 original size:2 final size:2

Alignment explanation


    Indices: 19160--19189  Score: 51
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      19150 ATTTAATTTA

                                                        
      19160 AT AT AT AT CAT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A

      19190 AACAGTTCAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2   25  0.93
   3    2  0.07

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.