Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003938.1 Corchorus capsularis cultivar CVL-1 contig03946, 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: 1960
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32


Found at i:232 original size:29 final size:29

Alignment explanation


    Indices: 180--280  Score: 96
    Period size: 29  Copynumber: 3.4  Consensus size: 29

        170 CATTAGGTTG

                        *      *          
        180 AGGGGGCAAAACATCCCAAAATTGAAGTTC
          1 AGGGGGCAAAACGT-CCAAGATTGAAGTTC

                       *                 
        210 AGGGGGCAAAATGTCCAAGATTGAAGTTC
          1 AGGGGGCAAAACGTCCAAGATTGAAGTTC

                             *    * **      
        239 -GTGGGGCAAAACGTCTAAACGCTACAAGTTC
          1 AG-GGGGCAAAACGTC-CAA-GATTGAAGTTC

                       
        270 AGGGGGCAAAA
          1 AGGGGGCAAAA

        281 TGGTTGTTTA


Statistics
Matches: 59,  Mismatches: 8, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  28    1  0.02
  29   26  0.44
  30   14  0.24
  31   17  0.29
  32    1  0.02

ACGTcount: A:0.37, C:0.18, G:0.29, T:0.17


Consensus pattern (29 bp):   
AGGGGGCAAAACGTCCAAGATTGAAGTTC

Found at i:1386 original size:6 final size:6

Alignment explanation


    Indices: 1375--1409  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       1365 ATATATAGTA

                                                    
       1375 TATATC TATATC TATATC TATATC TATATC TATAT
          1 TATATC TATATC TATATC TATATC TATATC TATAT

       1410 ATTATATAAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51


Consensus pattern (6 bp):   
TATATC

Found at i:1711 original size:3 final size:3

Alignment explanation


    Indices: 1705--1735  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       1695 ATCAAACTTC

                                             *       
       1705 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

       1736 ATCATAAGTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TTA

Done.