Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001943.1 Corchorus capsularis cultivar CVL-1 contig01945, 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, 753

Length: 1255
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34


Found at i:78 original size:22 final size:22

Alignment explanation


    Indices: 52--125  Score: 68
    Period size: 22  Copynumber: 3.5  Consensus size: 22

         42 TTTGATAATT

                                  
         52 TACTAATAAATAATAATATATA
          1 TACTAATAAATAATAATATATA

                         *  *     *
         74 TACTAATAAATATTTACTA-ATT
          1 TACTAATAAATA-ATAATATATA

                                  
         96 TACTAAT-AAT-ATAA-ATATA
          1 TACTAATAAATAATAATATATA

              *         
        115 TATTAA-AAATA
          1 TACTAATAAATA

        126 TATATTTTAA


Statistics
Matches: 41,  Mismatches: 7, Indels: 10
        0.71            0.12        0.17

Matches are distributed among these distances:
  18    1  0.02
  19   12  0.29
  21    3  0.07
  22   21  0.51
  23    4  0.10

ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39


Consensus pattern (22 bp):   
TACTAATAAATAATAATATATA

Found at i:91 original size:14 final size:15

Alignment explanation


    Indices: 62--94  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

         52 TACTAATAAA

                           
         62 TAATAATATATATAC
          1 TAATAATATATATAC

                       *   
         77 TAATAA-ATATTTAC
          1 TAATAATATATATAC

                
         91 TAAT
          1 TAAT

         95 TTACTAATAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   11  0.65
  15    6  0.35

ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42


Consensus pattern (15 bp):   
TAATAATATATATAC

Found at i:103 original size:44 final size:40

Alignment explanation


    Indices: 47--126  Score: 115
    Period size: 44  Copynumber: 1.9  Consensus size: 40

         37 TATGTTTTGA

                                                        
         47 TAATTTACTAATAAATAATAATATATATACTAATAAATATTTAC
          1 TAATTTACTAAT-AAT-ATAA-ATATATACTAA-AAATATTTAC

                                      *         
         91 TAATTTACTAATAATATAAATATATATTAAAAATAT
          1 TAATTTACTAATAATATAAATATATACTAAAAATAT

        127 ATATTTTAAC


Statistics
Matches: 35,  Mismatches: 1, Indels: 4
        0.88            0.03        0.10

Matches are distributed among these distances:
  40    6  0.17
  41   10  0.29
  42    4  0.11
  43    3  0.09
  44   12  0.34

ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41


Consensus pattern (40 bp):   
TAATTTACTAATAATATAAATATATACTAAAAATATTTAC

Found at i:1215 original size:2 final size:2

Alignment explanation


    Indices: 1208--1254  Score: 85
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       1198 TTCTACCATG

                                       *                                  
       1208 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                   
       1250 AT AT A
          1 AT AT A

       1255 C


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   43  1.00

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


Consensus pattern (2 bp):   
AT

Done.