DCARv3 SSR Detection with MISA

Resource Type:

File

File Type:

GFF3

Download:


Download File Name	Available at	Size	MD5
12.ssr.gff3.gz	CarrotOmics	8.24MB	4650022d457f936cc02f12805ee6d273

Description:

SSRs were detected in the Daucus carota V.3 assembly using misa, and when possible primers were designed with primer3. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

References:

The following records refer to this file:


Analysis	Daucus carota genome V.3 SSR Detection with MISA
Project	Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot

Project:


Name	Description
Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot	The project goals are to improve the assembly of the genome of cultivated carrot, and improve gene predictions using this improved assembly.

Analysis:

Name	Description
Daucus carota genome V.3 SSR Detection with MISA	SSRs were detected in the Daucus carota V.3 assembly using misa, and when possible primers were designed with primer3. misa detection parameters 2-6 3-4 4-3 5-3 6-3 7-3 8-3 and interruptions 10 This analysis has not been published. RESULTS OF MICROSATELLITE SEARCH ================================ Total number of sequences examined: 11 Total size of examined sequences (bp): 441,119,442 Total number of identified SSRs: 148,264 Number of SSR containing sequences: 11 Number of sequences containing more than 1 SSR: 11 Number of SSRs present in compound formation: 12,941 Distribution to different repeat type classes --------------------------------------------- Unit size Number of SSRs 2 52,385 3 30,622 4 38,281 5 16,265 6 7,217 7 2,622 8 872 128,207 designed primer pairs

Name

Description

Daucus carota genome V.3 SSR Detection with MISA

SSRs were detected in the Daucus carota V.3 assembly using misa, and when possible primers were designed with primer3.

misa detection parameters 2-6 3-4 4-3 5-3 6-3 7-3 8-3 and interruptions 10

This analysis has not been published.

RESULTS OF MICROSATELLITE SEARCH
================================

Total number of sequences examined:                  11
Total size of examined sequences (bp):      441,119,442
Total number of identified SSRs:                148,264
Number of SSR containing sequences:                  11
Number of sequences containing more than 1 SSR:      11
Number of SSRs present in compound formation:    12,941


Distribution to different repeat type classes
---------------------------------------------

Unit size  Number of SSRs
2          52,385
3          30,622
4          38,281
5          16,265
6           7,217
7           2,622
8             872

128,207 designed primer pairs

License:


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