Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012352.1 Corchorus capsularis cultivar CVL-1 contig12373, 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: 44357
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:9318 original size:37 final size:34

Alignment explanation


    Indices: 9236--9306  Score: 124
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       9226 TTCAAAACTT

                     *                *       
       9236 TATTCGTATCTTCTTACTGCATACTAGTATTATA
          1 TATTCGTATTTTCTTACTGCATACTACTATTATA

                                              
       9270 TATTCGTATTTTCTTACTGCATACTACTATTATA
          1 TATTCGTATTTTCTTACTGCATACTACTATTATA

               
       9304 TAT
          1 TAT

       9307 ATGAACGATT


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  34   35  1.00

ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49


Consensus pattern (34 bp):   
TATTCGTATTTTCTTACTGCATACTACTATTATA

Found at i:23462 original size:181 final size:183

Alignment explanation


    Indices: 23152--23512  Score: 627
    Period size: 181  Copynumber: 2.0  Consensus size: 183

      23142 GGTAACCCCT

                            *                                   *            
      23152 AAAATCAGTCCTTAAGTATATTTTCTTCACCAAATGTCATCTAAATTCACCTTTAAGTTCAAAAC
          1 AAAATCAGTCCTTAAGCATATTTTCTTCACCAAATGTCATCTAAATTCACCTCTAAGTTCAAAAC

                                     *                                       
      23217 CAACACTTAACACCAAACTCATCAATTCTATTAAAATTTAAAGCAACACACTTACCCATTACATC
         66 CAACACTTAACACCAAACTCATCAACTCTATTAAAATTTAAAGCAACACACTTACCCATTACATC

                         *         *        *                    
      23282 AAACTCTTAATTTTTTAATCTTCGAAGTGCCCTTTTTAAGCTTCAATTTCTTG
        131 AAACTCTTAATTTCTTAATCTTCCAAGTGCCCGTTTTAAGCTTCAATTTCTTG

                                               *                             
      23335 AAAA-CAGTCCTTAAGCATATTTTCTTCACCAAATTTCATCTAAATTCACC-CTAAGTTCAAAAC
          1 AAAATCAGTCCTTAAGCATATTTTCTTCACCAAATGTCATCTAAATTCACCTCTAAGTTCAAAAC

                                                                   *         
      23398 CAACACTTAACACCAAACTCATCAACTCTATTAAAATTTAAAGCAACACACTTACTCATTACATC
         66 CAACACTTAACACCAAACTCATCAACTCTATTAAAATTTAAAGCAACACACTTACCCATTACATC

                                                    *         
      23463 AAACTCTTAATTTCTTAATCTTCCAAGTGCCCGTTTTAAGGTTCAATTTC
        131 AAACTCTTAATTTCTTAATCTTCCAAGTGCCCGTTTTAAGCTTCAATTTC

      23513 CTTGCGTCAA


Statistics
Matches: 169,  Mismatches: 9, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
 181  121  0.72
 182   44  0.26
 183    4  0.02

ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34


Consensus pattern (183 bp):   
AAAATCAGTCCTTAAGCATATTTTCTTCACCAAATGTCATCTAAATTCACCTCTAAGTTCAAAAC
CAACACTTAACACCAAACTCATCAACTCTATTAAAATTTAAAGCAACACACTTACCCATTACATC
AAACTCTTAATTTCTTAATCTTCCAAGTGCCCGTTTTAAGCTTCAATTTCTTG

Found at i:27804 original size:17 final size:18

Alignment explanation


    Indices: 27771--27804  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

      27761 TTTATTTTAT

                              
      27771 TTTTAATGTTTTGATTTC
          1 TTTTAATGTTTTGATTTC

                        *    
      27789 TTTTAA-GTTTTTATTT
          1 TTTTAATGTTTTGATTT

      27805 AATTAGTGTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.18, C:0.03, G:0.09, T:0.71


Consensus pattern (18 bp):   
TTTTAATGTTTTGATTTC

Found at i:41093 original size:22 final size:22

Alignment explanation


    Indices: 41044--41096  Score: 63
    Period size: 22  Copynumber: 2.4  Consensus size: 22

      41034 ATAAAAAAAG

                                  
      41044 ATTTTCAAAAATCCAAAAATCA
          1 ATTTTCAAAAATCCAAAAATCA

             *             **     
      41066 AATTTCAAAAAT-CAGGAATCA
          1 ATTTTCAAAAATCCAAAAATCA

                      
      41087 AGTTTTCAAA
          1 A-TTTTCAAA

      41097 GTTGTCGAGT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21    8  0.31
  22   18  0.69

ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28


Consensus pattern (22 bp):   
ATTTTCAAAAATCCAAAAATCA

Found at i:44142 original size:2 final size:2

Alignment explanation


    Indices: 44137--44164  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      44127 TGTGTGTGTG

                                                     
      44137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      44165 CACACAAATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:44334 original size:2 final size:2

Alignment explanation


    Indices: 44323--44357  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      44313 TATTGTTTCT

                                                                 
      44323 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.