Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013580.1 Corchorus capsularis cultivar CVL-1 contig13601, 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: 9940
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:53 original size:3 final size:3

Alignment explanation


    Indices: 45--89  Score: 90
    Period size: 3  Copynumber: 15.0  Consensus size: 3

         35 TCTAAATTAC

                                                                       
         45 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT

         90 GTTTCCACAC


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   42  1.00

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
CTT

Found at i:2546 original size:3 final size:3

Alignment explanation


    Indices: 2538--2562  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       2528 TTATTTTTCC

                                             
       2538 TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA T

       2563 ATTGATTTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:4480 original size:117 final size:117

Alignment explanation


    Indices: 4351--4562  Score: 343
    Period size: 117  Copynumber: 1.8  Consensus size: 117

       4341 TTTTTTTATA

                                 *                                           
       4351 AATATATAAAAAAAAAGGCACGTGCCAAAAAAGGGGGCGGCATGCCGTGGGTGTTTGCCGCCCTC
          1 AATATATAAAAAAAAAGGCACATGCCAAAAAAGGGGGCGGCATGCCGTGGGTGTTTGCCGCCCTC

                                 *                              
       4416 CTAGGGCGGCTTCACGTGGCACAGCCGCCCCAGGAGGGCGGCTTGCCGTATT
         66 CTAGGGCGGCTTCACGTGGCAAAGCCGCCCCAGGAGGGCGGCTTGCCGTATT

                   *     *            *****                                  
       4468 AATATATTAAAAACAAGGCACATGCCGCCCCAGGGGGCGGCATGCCGTGGGTGTTTGCCGCCCTC
          1 AATATATAAAAAAAAAGGCACATGCCAAAAAAGGGGGCGGCATGCCGTGGGTGTTTGCCGCCCTC

                                          
       4533 CTAGGGCGGCTTCACGTGGCAAAGCCGCCC
         66 CTAGGGCGGCTTCACGTGGCAAAGCCGCCC

       4563 TCCTGGGGCG


Statistics
Matches: 86,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 117   86  1.00

ACGTcount: A:0.23, C:0.29, G:0.32, T:0.17


Consensus pattern (117 bp):   
AATATATAAAAAAAAAGGCACATGCCAAAAAAGGGGGCGGCATGCCGTGGGTGTTTGCCGCCCTC
CTAGGGCGGCTTCACGTGGCAAAGCCGCCCCAGGAGGGCGGCTTGCCGTATT

Found at i:6946 original size:21 final size:19

Alignment explanation


    Indices: 6920--6965  Score: 65
    Period size: 21  Copynumber: 2.3  Consensus size: 19

       6910 CCTCACCAAT

                                
       6920 TTTTTTTTAAAAAAAATATA
          1 TTTTTTTTAAAAAAAAT-TA

                     *          
       6940 TATTTTTTTCAAAAAAATTA
          1 T-TTTTTTTAAAAAAAATTA

                  
       6960 TTTTTT
          1 TTTTTT

       6966 AATCAAAAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  19    5  0.21
  20    4  0.17
  21   15  0.62

ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57


Consensus pattern (19 bp):   
TTTTTTTTAAAAAAAATTA

Found at i:6947 original size:20 final size:19

Alignment explanation


    Indices: 6922--6978  Score: 62
    Period size: 20  Copynumber: 2.9  Consensus size: 19

       6912 TCACCAATTT

                                
       6922 TTTTTTAAAAAAAATATATA
          1 TTTTTTAAAAAAAATAT-TA

                  **           
       6942 TTTTTTTCAAAAAA-ATTA
          1 TTTTTTAAAAAAAATATTA

                               
       6960 TTTTTTAATCAAAAAATAT
          1 TTTTTTAA--AAAAAATAT

       6979 GACGTGGCAT


Statistics
Matches: 30,  Mismatches: 4, Indels: 5
        0.77            0.10        0.13

Matches are distributed among these distances:
  18    8  0.27
  19    2  0.07
  20   18  0.60
  21    2  0.07

ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTTTTTAAAAAAAATATTA

Found at i:9323 original size:2 final size:2

Alignment explanation


    Indices: 9310--9353  Score: 79
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       9300 TATCCAATAC

                   *                                                      
       9310 AT AT AC AT AT AT AT AT AT AT 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

              
       9352 AT
          1 AT

       9354 TTGAACCAGT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.