Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000801.1 Corchorus capsularis cultivar CVL-1 contig00801, 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: 5689
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:254 original size:29 final size:31

Alignment explanation


    Indices: 178--246  Score: 115
    Period size: 31  Copynumber: 2.3  Consensus size: 31

        168 GCTCTAACGG

                                           
        178 GTTATATCCTTAATTGCTCGCTTTTGGTAAC
          1 GTTATATCCTTAATTGCTCGCTTTTGGTAAC

                              *            
        209 GTTATATCCTTAATTGCTTG-TTTT-GTAAC
          1 GTTATATCCTTAATTGCTCGCTTTTGGTAAC

                     
        238 GTTATATCC
          1 GTTATATCC

        247 CAAATTGCAT


Statistics
Matches: 37,  Mismatches: 1, Indels: 2
        0.93            0.03        0.05

Matches are distributed among these distances:
  29   14  0.38
  30    4  0.11
  31   19  0.51

ACGTcount: A:0.20, C:0.17, G:0.14, T:0.48


Consensus pattern (31 bp):   
GTTATATCCTTAATTGCTCGCTTTTGGTAAC

Found at i:489 original size:3 final size:3

Alignment explanation


    Indices: 481--505  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

        471 TAGAACCTTG

                                             
        481 ATC ATC ATC ATC ATC ATC ATC ATC A
          1 ATC ATC ATC ATC ATC ATC ATC ATC A

        506 AAGTGAAGAC


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:0.36, C:0.32, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATC

Found at i:1590 original size:192 final size:192

Alignment explanation


    Indices: 1239--1595  Score: 500
    Period size: 192  Copynumber: 1.9  Consensus size: 192

       1229 ATTTTGTAAT

                        *       *                           *** *        *   
       1239 ATGGGTAATTATTTGATACATCGACGGTGTAAATTTTGGACTCCACAAGTGGGTTCTGCAGTTGA
          1 ATGGGTAATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAACAGATTCTGCAGATGA

            *               *                 *                            * 
       1304 GACATGTCCATTTTTTGAATTAATTAAGTTTTAACTATTTCAATCTAGTCCCTAGACGACACATG
         66 CACATGTCCATTTTTTCAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGACGACACAAG

                                * *                                       
       1369 TCACCCTTCAGGACCCACTTGTGTAGTCTGCTAAACAAACTCCACCAACGGTGTATTGTATA
        131 TCACCCTTCAGGACCCACTTATATAGTCTGCTAAACAAACTCCACCAACGGTGTATTGTATA

                  *                *                   *           *  *      
       1431 ATGGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCTACAAACAGATTGTGGAGATGA
          1 ATGGGTAATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAACAGATTCTGCAGATGA

                                                               *             
       1496 CACATGTCCATTTTTTCAATTAATTAAGTTTTAAATATTTCAATCTAGTCCTTAGGA-GACACAA
         66 CACATGTCCATTTTTTCAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTA-GACGACACAA

                     *       **                 
       1560 GTCACCCTTTAGGACCCGTTTATATAGTCTGCTAAA
        130 GTCACCCTTCAGGACCCACTTATATAGTCTGCTAAA

       1596 TTCCATCGAC


Statistics
Matches: 142,  Mismatches: 22, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
 192  140  0.99
 193    2  0.01

ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34


Consensus pattern (192 bp):   
ATGGGTAATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAACAGATTCTGCAGATGA
CACATGTCCATTTTTTCAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGACGACACAAG
TCACCCTTCAGGACCCACTTATATAGTCTGCTAAACAAACTCCACCAACGGTGTATTGTATA
Done.