Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005354.1 Corchorus capsularis cultivar CVL-1 contig05372, 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: 9752
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Found at i:2680 original size:63 final size:63

Alignment explanation


    Indices: 2606--2753  Score: 253
    Period size: 63  Copynumber: 2.4  Consensus size: 63

       2596 CCTTATGGAG

                                                                    *      
       2606 TATAA-TTCAATCAATTAATCAATCAAACACCACTCTAGAACAAAAAATGTTCTTGGCCCTTA
          1 TATAATTTCAATCAATTAATCAATCAAACACCACTCTAGAACAAAAAATGTTCTTGACCCTTA

                                       *                                   
       2668 TATAATTTCAATCAATTAATCAATCAAGCACCACTCTAGAACAAAAAATGTTCTTGACCCTTA
          1 TATAATTTCAATCAATTAATCAATCAAACACCACTCTAGAACAAAAAATGTTCTTGACCCTTA

                          *  *     
       2731 TATAATTTCAATCAGTTCATCAA
          1 TATAATTTCAATCAATTAATCAA

       2754 GCACCACTCT


Statistics
Matches: 81,  Mismatches: 4, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  62    5  0.06
  63   76  0.94

ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31


Consensus pattern (63 bp):   
TATAATTTCAATCAATTAATCAATCAAACACCACTCTAGAACAAAAAATGTTCTTGACCCTTA

Found at i:3095 original size:29 final size:29

Alignment explanation


    Indices: 3049--3109  Score: 72
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       3039 ATTAAAGGCA

                      *       *           
       3049 ATAATATATATATATATATATATAA-TATT
          1 ATAATATATAGATATATAGAT-TAATTATT

                                          
       3078 ATAATATAATAGAT-TATAGATTAATTATT
          1 ATAATAT-ATAGATATATAGATTAATTATT

               
       3107 ATA
          1 ATA

       3110 GTAGTAACTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  28    3  0.11
  29   20  0.71
  30    5  0.18

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (29 bp):   
ATAATATATAGATATATAGATTAATTATT

Found at i:3127 original size:23 final size:23

Alignment explanation


    Indices: 3100--3144  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3090 ATTATAGATT

                          *         
       3100 AATTAT-TATAGTAGTAACTATTC
          1 AATTATATATAGTAATAA-TATTC

                                  
       3123 AATTATATATAGTAATAATATT
          1 AATTATATATAGTAATAATATT

       3145 GTAAAATTAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23   10  0.50
  24   10  0.50

ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44


Consensus pattern (23 bp):   
AATTATATATAGTAATAATATTC

Found at i:4914 original size:2 final size:2

Alignment explanation


    Indices: 4907--4931  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       4897 TTCTGTACGT

                                                 
       4907 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       4932 GCTTTCCCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:9072 original size:20 final size:20

Alignment explanation


    Indices: 9047--9084  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9037 GTTGGTGCAT

                                
       9047 TTCAACAAAGAGATAATTAG
          1 TTCAACAAAGAGATAATTAG

                              
       9067 TTCAACAAAGAGATAATT
          1 TTCAACAAAGAGATAATT

       9085 TGACAACCGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26


Consensus pattern (20 bp):   
TTCAACAAAGAGATAATTAG
Done.