Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018100.1 Corchorus olitorius cultivar O-4 contig18133, 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: 4072
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34


Found at i:647 original size:21 final size:21

Alignment explanation


    Indices: 623--672  Score: 91
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        613 TGCTAGGAGA

                                 
        623 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        644 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        665 TCATTGGA
          1 TCATTGGA

        673 ATTGCCTAAG


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:1267 original size:25 final size:24

Alignment explanation


    Indices: 1231--1277  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1221 TCCTTCTATT

                                    
       1231 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       1254 CATCTTATCCATCAAAGTTTTTCA
          1 CATC-TAT-CATCAAAGTTTTTCA

       1278 AATTTTCTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    4  0.19
  24    3  0.14
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Found at i:2924 original size:33 final size:33

Alignment explanation


    Indices: 2823--2927  Score: 115
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2813 TTGCAAAGAG

                    *       *       *      * 
       2823 TGTTTTAGATGTTGTTAGTGATGATACTAAAAC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

             **                      *        
       2856 TAATTT-GAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAG-GTGTTGTTTGTGATGAAACTAAATC

                                              
       2889 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC

                  
       2922 TGTTTT
          1 TGTTTT

       2928 GAATGCTAAT


Statistics
Matches: 60,  Mismatches: 9, Indels: 6
        0.80            0.12        0.08

Matches are distributed among these distances:
  32    4  0.07
  33   55  0.92
  34    1  0.02

ACGTcount: A:0.26, C:0.07, G:0.22, T:0.46


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

Found at i:2929 original size:66 final size:66

Alignment explanation


    Indices: 2823--2960  Score: 145
    Period size: 66  Copynumber: 2.1  Consensus size: 66

       2813 TTGCAAAGAG

                                    *                *  * **          *      
       2823 TGTTTTAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGTGATG-ACACTAAA
          1 TGTTTTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAATGCTAATTGTGATGAAAAC-AAA

              
       2887 TC
         65 TC

                    *       *               *  **                            
       2889 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTGAATGCTAATTGTGATGAAAACAAA
          1 TGTTTTAGATGTTGTTAGTGATGAAACTAAA-ACTAATTTGAATGCTAATTGTGATGAAAACAAA

              
       2953 TC
         65 TC

                  
       2955 TGTTTT
          1 TGTTTT

       2961 GGTATAGCAT


Statistics
Matches: 59,  Mismatches: 11, Indels: 4
        0.80            0.15        0.05

Matches are distributed among these distances:
  65    3  0.05
  66   53  0.90
  67    3  0.05

ACGTcount: A:0.28, C:0.07, G:0.21, T:0.43


Consensus pattern (66 bp):   
TGTTTTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAATGCTAATTGTGATGAAAACAAAT
C
Done.