Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005122.1 Corchorus capsularis cultivar CVL-1 contig05140, 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: 9755
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34


Found at i:1528 original size:27 final size:26

Alignment explanation


    Indices: 1473--1528  Score: 60
    Period size: 27  Copynumber: 2.1  Consensus size: 26

       1463 ACGTACCCCG

                                   ** 
       1473 ATTTATTGTTTTCAAACTTTTATTCT
          1 ATTTATTGTTTTCAAACTTTTATGAT

                        *               
       1499 ATTTA-TGTTTTGAAATCTTTTTATGAT
          1 ATTTATTGTTTTCAAA-C-TTTTATGAT

               
       1526 ATT
          1 ATT

       1529 GGTGCCTTGT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  25    9  0.36
  26    6  0.24
  27   10  0.40

ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61


Consensus pattern (26 bp):   
ATTTATTGTTTTCAAACTTTTATGAT

Found at i:3265 original size:14 final size:14

Alignment explanation


    Indices: 3228--3270  Score: 56
    Period size: 13  Copynumber: 3.2  Consensus size: 14

       3218 TTTATTACCG

                          
       3228 TTTTATT-AAT-AT
          1 TTTTATTAAATGAT

                           
       3240 GTTTTA-TAAATGAT
          1 -TTTTATTAAATGAT

                          
       3254 TTTTATTAAATGAT
          1 TTTTATTAAATGAT

               
       3268 TTT
          1 TTT

       3271 GGGTGCATGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  12    1  0.04
  13   13  0.48
  14   13  0.48

ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60


Consensus pattern (14 bp):   
TTTTATTAAATGAT

Found at i:6104 original size:3 final size:3

Alignment explanation


    Indices: 6096--6126  Score: 62
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       6086 ATAGTTATAG

                                                     
       6096 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

       6127 ATAATATAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   28  1.00

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


Consensus pattern (3 bp):   
TTA

Done.