HAU1042, HAU1042 (genetic_marker) gossypium spp

Marker Overview
NameHAU1042
AliasTA24654_3635
Genbank IDN/A
TypeSSR
SpeciesGossypium spp.
Source TypeEST
Repeat Motif(TTCC)5
PCR ConditionAnnealing temperature: 56.8
Primer 1HAU1042_F: TTCACACTCTCTTCGTGCTC
Primer 2HAU1042_R: AAACCAATTTCAACCCAGAA
Product Length178
Publication[view all]
CommentPrimer data obtained in 2012
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D11chromosomeD11:53855039..53855776 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A11chromosomeA11:89447596..89448374 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018225.1chromosomeCM018225.1:51338697..51339434 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018212.1chromosomeCM018212.1:89623764..89624548 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_11chromosomeD5_11:17036740..17037497 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:27748161..27748937 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_11chromosomeD10_11:48423009..48423754 +Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016624.1chromosomeCM016624.1:110217566..110218337 +Gossypium australe (G2) genome CRI_v1.1n/a
At_chr10chromosomeAt_chr10:25771453..25772190 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr1chromosomeAt_chr1:40563149..40563927 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D11chromosomeD11:49008893..49009630 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A11chromosomeA11:70162439..70163217 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D11chromosomeGhir_D11:53906669..53907406 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A11chromosomeGhir_A11:98094149..98094927 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D11chromosomeD11:53362499..53363236 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:96989142..96989920 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D11chromosomeD11:53822184..53822920 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A11chromosomeA11:94206667..94207445 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D11chromosomeD11:51129200..51129937 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A11chromosomeA11:91394751..91395529 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
scaffold16101supercontigscaffold16101:218224..219008 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold11429supercontigscaffold11429:10308..11045 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D11chromosomeGbar_D11:51081727..51082464 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A11chromosomeGbar_A11:87773318..87774102 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D11chromosomeD11:54100562..54101299 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A11chromosomeA11:90981843..90982627 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017633.1chromosomeCM017633.1:53403735..53404472 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017620.1chromosomeCM017620.1:94883647..94884433 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017659.1chromosomeCM017659.1:54673065..54673803 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017646.1chromosomeCM017646.1:101474874..101475657 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017698.1chromosomeCM017698.1:89394898..89395680 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017711.1chromosomeCM017711.1:51020792..51021529 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D11chromosomeD11:53680524..53681261 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A11chromosomeA11:98756422..98757200 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr11chromosomeChr11:102533219..102533994 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr11chromosomeChr11:100794065..100794842 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr11chromosomeChr11:15344357..15345116 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr07chromosomeChr07:51122399..51123160 -Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr07chromosomeChr07:27418771..27419564 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr07chromosomeChr07:33023951..33024694 -Gossypium lobatum (D7) genome ISU_v1n/a
E11chromosomeE11:86924215..86924963 -Gossypium stocksii (E1) genome NSF_v1n/a
Chr11chromosomeChr11:38640440..38641224 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Sequence
>HAU1042 ID=HAU1042; Name=HAU1042; organism=Gossypium spp.; type=genetic_marker; length=178bp
TTCACACTCTCTTCGTGCTCCCGCCGTATTTCACTTCCCCTCTCTTCTCT
CTTCTTTTCCTTCCTTCCTTCCTTCTGTCAACACCACTCTCTAATGGCTT
CCCTTGCTGGTTCATCAATCTCTATGCAACCTCGCCAGACCCTGGCTACA
AGCAGGGTTTCTGGGTTGAAATTGGTTT